diff --git a/_index.db b/_index.db index 74a88d57e..6074f21bb 100644 Binary files a/_index.db and b/_index.db differ diff --git a/data/en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings-0.md b/data/en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings-0.md new file mode 100644 index 000000000..e8fae87d2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings-0.md @@ -0,0 +1,30 @@ +--- +title: "2022 Furuvik Zoo chimpanzee shootings" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:31.986411+00:00" +instance: "kb-cron" +--- + +The 2022 Furuvik Zoo chimpanzee shootings occurred around 12 o'clock noon on Wednesday, 14 December, 2022, when a number of the chimpanzees (Pan troglodytes) kept at Furuvik Zoo (Sw. Furuviksparken) in Furuvik, Gävle Municipality, Sweden, escaped from their enclosure into the chimpanzee building and park and made an attempt to exit the zoo itself, which was closed to the public for the winter season. The zoo staff responded by firing on the escaping apes, killing four of them. +The story gained domestic and international attention, and prompted debate about zoos and the keeping of great apes in captivity. The incident has also been described as "the Massacre in Furuvik", "the Furuvik Bloodbath", and "the Chimpanzee Drama". + +== History == +At around 12 p.m. on Wednesday, 14 December, 2022, two chimpanzees of Furuvik Zoo escaped from their enclosure through an unlocked lattice door and entered the chimpanzee building. An animal keeper attempted to fight one off, but soon fled and warned other employees by yelling and using their radio. Within five minutes, at least two chimps had escaped the building and entered the wider zoo, which was closed to the public for the winter season. +Forty-five minutes later, two chimps were discovered at the park's fairground area. After consulting veterinarians, and excluding the use of anesthesia due to risks involved, the park's CEO and animal manager made the joint decision to shoot the two chimps. Zoo staff opened fire on them using live ammunition, killing Linda and her adoptive infant son Torsten. Later in the afternoon, three chimps escaped the chimpanzee building. Zoo staff again opened fire, wounding Selma, who retreated back inside. Manda and Santino repeatedly entered and exited the building through the windows. Fearing a possible return into the now-dark park, the decision was made to shoot them as well. Santino was killed quickly, whilst Manda was mortally wounded. An unknown time after the shootings, Manda died of her gunshot wounds, while Selma sustained severe injuries to her eye, body, and arm. The remaining two chimpanzees (Maria Magdalena and Tjobbe) remained inside the building. The decision to use lethal force rather than to attempt to use tranquilizers or otherwise recapture the apes resulted in widespread criticism. +Following the deaths of the four chimpanzees, the Swedish Police Authority announce that they had opened an investigation against Furuvik Zoo for possible crimes against the Animal Welfare Act, and the County Administration of Gävleborg County announced that they would make inquiries into conditions at the zoo. + +== List of chimpanzees involved == + +=== Killed chimpanzees === +Santino (born 1978), a male chimpanzee born in captivity at Hellabrunn Zoo in Munich, Germany. He was well known for his proclivity for painting; his paintings, both copies and originals, were previously sold by the zoo for the benefit of the Swedish Chimpanzee Trust. Owners of Santino's paintings include Crown Princess Victoria of Sweden and Princess Madeleine of Sweden. He has been described as "Crown Princess Victoria's favorite chimp". In 2009 Santino gained attention from both news media and scientists when it became known that he had learned to stockpile stone ammunition in anticipation of throwing them at zoo visitors, behaviour which cognitive zoologists suggested indicated that planning and premeditated deception are not uniquely human traits. He was castrated after this incident in an attempt to control his hormone levels and regulate his behaviour. Santino was shot and killed inside the chimpanzee house. +Linda (born c. 1980), a female chimpanzee born in the wild in Liberia and rescued after poachers killed her family. Linda was a Western chimpanzee (Pan troglodytes verus), a critically endangered West African subspecies of the common chimpanzee. According to the European Association of Zoos and Aquaria, Linda's death would not impact Western chimpanzee conservation efforts. Linda was shot and killed in the park's fairground. +Manda (born 2004), a female chimpanzee born in captivity at Kolmården Wildlife Park and transferred to Furuvik Zoo after she was orphaned as an infant. She became well known in Sweden after becoming the focus of the television show Schimpansen Manda , featured in the Bolibompa children's television series soon after the move to Furuvik. Manda was shot and mortally wounded inside the chimpanzee house. +Torsten (born 2019), a male chimpanzee infant born in captivity at Furuvik Zoo, the first born there in 25 years. His parents were Maria Magdalena and Tjobbe, but Linda was seen as his adoptive mother. Torsten was shot and killed in the park's fairground. + +=== Surviving chimpanzees === +Selma (born 2008), a female chimpanzee born in captivity at Kolmården Wildlife Park and transferred to Furuvik Zoo after her mother rejected her. In 2009 she met with King Carl XVI Gustaf and Queen Silvia of Sweden during a royal visit to the zoo. Selma was shot and severely injured outside the chimpanzee house during the incident and suffered damage causing blindness in one eye, embedded shrapnel in her body, and a fracture of one arm, temporarily losing control of it. +Maria Magdalena (born 2000), a female chimpanzee born in captivity at Borås Zoo and transferred to Furuvik Zoo in 2005. She was the biological mother of Torsten (born 2019). +Tjobbe (born 2003), a male chimpanzee born in captivity at Royal Burgers' Zoo in Arnhem, Netherlands. He was transferred from Kittenberger Kálmán Zoo & Botanical Garden in Veszprém, Hungary, to Furuvik Zoo in 2015. He was the father of Torsten (born 2019). \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings-1.md b/data/en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings-1.md new file mode 100644 index 000000000..765a67d3e --- /dev/null +++ b/data/en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings-1.md @@ -0,0 +1,20 @@ +--- +title: "2022 Furuvik Zoo chimpanzee shootings" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/2022_Furuvik_Zoo_chimpanzee_shootings" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:31.986411+00:00" +instance: "kb-cron" +--- + +== Reactions == +The chimpanzee shootings provoked intense media coverage and debate, both domestically in Sweden and abroad. Several political figures commented, including the Green Party politicians Märta Stenevi and Rebecka Le Moine who questioned the state of animal captivity in Sweden, the Sweden Democratic politician Yasmine Eriksson who called for a review of all Swedish zoos, and the Christian Democratic politician Peter Kullgren, Minister for Rural Affairs, who expressed sadness but refrained from commenting on ongoing investigations. Numerous Swedish celebrities and public figures also expressed sadness or condemnation, including Johanna Lind, Jessica Almenäs, Uno Svenningsson, Micael Bindefeld, Thomas Di Leva, Lars-Åke Wilhelmsson, and Linda Lindorff. +The chimpanzee shootings also prompted many reactions from biologists and conservationists. When interviewed about the incident, the noted Dutch primatologist Frans de Waal expressed shock that the 3-year old chimpanzee infant Torsten was among those killed by the zoo, as such a young ape did not pose any physical danger to humans. The Dutch behavioural biologist Patrick van Veen, chair of the Jane Goodall Institute commented on the incident that recapture by non-lethal means, such as tranquilizers, should always be the first priority during chimpanzee escapes, and that lethal force should only be used in the worst-case scenario. The Swedish cognitive zoologist Mathias Osvath, who has spent years researching the chimpanzees at Furuvik Zoo, expressed sorrow over the incident and concern for the trauma experienced by the chimpanzee survivors, further announcing the immediate suspension of the Primate Research Station Furuvik, a joint research programme between the Cognitive Zoology Group of Lund University and Furuvik Zoo. +Camilla Bergvall, chair of the Swedish animal rights organization Djurens Rätt, condemned the actions of Furuvik Zoo and the wider keeping of animals in captivity in Sweden. On the other hand, the zookeeper Jonas Wahlström, director of the Skansen Aquarium, defended the zoological parks of Sweden as necessary and positive forces in society. + +== See also == +Harambe +Kolmården Wildlife Park + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/ARKive-0.md b/data/en.wikipedia.org/wiki/ARKive-0.md new file mode 100644 index 000000000..941cf9535 --- /dev/null +++ b/data/en.wikipedia.org/wiki/ARKive-0.md @@ -0,0 +1,49 @@ +--- +title: "ARKive" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/ARKive" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:54.836385+00:00" +instance: "kb-cron" +--- + +ARKive was a global initiative with the mission of "promoting the conservation of the world's threatened species, through the power of wildlife imagery", which it did by locating and gathering films, photographs and audio recordings of the world's species into a centralised digital archive. Its priority was the completion of audio-visual profiles for the c. 17,000 species on the IUCN Red List of Threatened Species. +The project was an initiative of Wildscreen, a UK-registered educational charity, based in Bristol. The technical platform was created by Hewlett-Packard, as part of the HP Labs' Digital Media Systems research programme. +ARKive had the backing of leading conservation organisations, including BirdLife International, Conservation International, International Union for Conservation of Nature (IUCN), the United Nations' World Conservation Monitoring Centre (UNEP-WCMC), and the World Wide Fund for Nature (WWF), as well as leading academic and research institutions, such as the Natural History Museum; Royal Botanic Gardens, Kew; and the Smithsonian Institution. It was a member of the Institutional Council of the Encyclopedia of Life. +Two ARKive layers for Google Earth, featuring endangered species and species in the Gulf of Mexico were produced by Google Earth Outreach. The first of these was launched in April 2008 by Wildscreen's Patron, Sir David Attenborough. +Due to lack of funding, the website was closed on 15 February 2019 and the media collection taken offline. Its successor, Wildscreen ARK (https://wildscreenark.org/), was launched in February 2024. + + +== History == + +The project formally was launched on 20 May 2003 by its patron, the UK-based natural history presenter, Sir David Attenborough, a long-standing colleague and friend of its chief instigator, the late Christopher Parsons, a former Head of the BBC Natural History Unit. Parsons never lived to see the fruition of the project, succumbing to cancer in November 2002 at the age of 70. +Parsons identified a need to provide a centralised safe haven for wildlife films and photographs after discovering that many such records are held in scattered, non-indexed, collections, often with little or no public access, and sometimes in conditions that could lead to loss or damage. He believed the records could be a powerful force in building environmental awareness by bringing scientific names to life. He also saw their preservation as an important educational resource and conservation tool, not at least because extinction rates and habitat destruction could mean that images and sounds might be the only legacy of some species' existence. +His vision of a permanent, accessible, refuge for audio-visual wildlife material won almost immediate support from many of the world's major broadcasters, including the BBC, Granada, international state broadcasting corporations and National Geographic magazine; leading film and photographic libraries, international conservation organisations and academic institutes such as Cornell University. +The initial feasibility study for creating ARKive was carried out in the late 1980s by conservationist John Burton, but at the time the costs of the technology needed were too far too high, and so it was over a decade later, after the technology had caught up with Christopher Parsons's vision (and the costs dropped), that the project was able to get off the ground. +After capital development funds of £2m were secured from the Heritage Lottery Fund in 1997 and New Opportunities Fund in 2000, work on building ARKive began as part of the UK's Millennium celebrations, using advanced computerised storage and retrieval technology devised for the project by Hewlett-Packard, with an initial capacity of up to 74 terabytes of data, using redundant hardware and multiple copies of media stored at multiple sites. Media was digitised to the highest available quality without compression and encoded to open standards. +A prototype site was online as early as April 1999. There were several design iterations before the formal launch. +By the launch date, the project team had researched, catalogued, copied, described and authenticated image, sound and fact files of 1,000 animals, plants and fungi, many of them critically endangered. More multi-media profiles are added every month, starting with British flora and fauna and with species included on the Red List – that is, species that are believed to be closest to extinction, according to research by the World Conservation Union. By January 2006, the database had grown to 2,000 species, 15,000 still images and more than 50 hours of videos. By 2010, over 5,500 donors had contributed 70,000 film clips and photos of more than 12,000 species. +In February 2019, Wildscreen announced that they "...have had to make the very hard decision to close the Arkive website on 15 February 2019", due to funding issues. On that date the website was replaced with a short statement, concluding: + +The complete Arkive collection of over 100,000 images and videos is now being stored securely offline for future generations. + + +== Recognition == +The site was Sunday Times website of the year for 2005. It was a 2010 Webby Award honouree for its outstanding calibre of work, in the 'Education' category, and a 2010 Association of Educational Publishers 'Distinguished Achievement Award' winner, in the category for websites for 9-to-12-year-olds. + + +== See also == +Catalogue of Life +Encyclopedia of Life +List of online encyclopaedias + + +== References == + + +== External links == + +Official ARKive site +Technical specifications from Hewlett-Packard +Memorandum of Understanding with Encyclopedia of Life \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Animalia_Paradoxa-0.md b/data/en.wikipedia.org/wiki/Animalia_Paradoxa-0.md new file mode 100644 index 000000000..9bcceec3c --- /dev/null +++ b/data/en.wikipedia.org/wiki/Animalia_Paradoxa-0.md @@ -0,0 +1,44 @@ +--- +title: "Animalia Paradoxa" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Animalia_Paradoxa" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:53.676829+00:00" +instance: "kb-cron" +--- + +Animalia Paradoxa (Latin for "contradictory animals"; cf. paradox) are the mythical, magical, or otherwise suspect animals mentioned in the first five editions of Carl Linnaeus's seminal work Systema Naturae under the header Paradoxa. It lists fantastic creatures found in medieval bestiaries and some animals reported by explorers from abroad and explains why they are excluded from Systema Naturae. According to Swedish historian Gunnar Broberg, it was to offer a natural explanation and demystify the world of superstition. Paradoxa was dropped from Linnaeus' classification system as of the 6th edition (1748). + + +== Paradoxa == +These 10 taxa appear in the 1st to 5th editions: + +Hydra: Linnaeus wrote: "Hydra: body of a snake, with two feet, seven necks and the same number of heads, lacking wings, preserved in Hamburg, similar to the description of the Hydra of the Apocalypse of St.John chapters 12 and 13. And it is provided by very many as a true species of animal, but falsely. Nature for itself and always the similar, never naturally makes multiple heads on one body. Fraud and artifice, as we ourselves saw [on it] teeth of a weasel, different from teeth of an Amphibian [or reptile], easily detected." See Carl Linnaeus#Doctorate. (Distinguish from the small real coelenterate Hydra (genus).) +Rana-Piscis: a South American frog which is significantly smaller than its tadpole stage; it was thus (incorrectly) reported to Linnaeus that the metamorphosis in this species went from 'frog to fish'. In the Paradoxa in the 1st edition of Systema Naturae, Linnaeus wrote "Frog-Fish or Frog Changing into Fish: is much against teaching. Frogs, like all Amphibia, delight in lungs and spiny bones. Spiny fish, instead of lungs, are equipped with gills. Therefore the laws of Nature will be against this change. If indeed a fish is equipped with gills, it will be separate from the Frog and Amphibia. If truly [it has] lungs, it will be a Lizard: for under all the sky it differs from Chondropterygii and Plagiuri." In the 10th edition of Systema Naturae, Linnaeus named the species Rana paradoxa, though its genus name was changed in 1830 to Pseudis. +Monoceros (unicorn): Linnaeus wrote: "Monoceros of the older [generations], body of a horse, feet of a "wild animal", horn straight, long, spirally twisted. It is a figment of painters. The Monodon of Artedi [= narwhal] has the same manner of horn, but the other parts of its body are very different." +Pelecanus: Linnaeus wrote "Pelican: The same [sources as for the previous] hand down fabulously [the story] that it inflicts a wound with its beak on its own thigh, to feed its young with the flowing blood. A sack hanging below its throat gave a handle for the story." This source writes: "Linnaeus thought [pelicans] might reflect the over-fervent imaginations of New World explorers." This claim is incorrect; pelicans are widespread in Europe and Linnaeus was merely doubting the legendary behavior. +Satyrus: Linnaeus wrote "with a tail, hairy, bearded, with a manlike body, gesticulating much, very fallacious, is a species of monkey, if ever one has been seen." +Borometz (aka Scythian Lamb): Linnaeus wrote: "Borometz or Scythian Lamb: is reckoned with plants, and is similar to a lamb; whose stalk coming out of the ground enters an umbilicus; and the same is said to be provided with blood from by chance devouring wild animals. But it is put together artificially from roots of American ferns. But naturally it is an allegorical description of an embryo of a sheep, as has all attributed data.". This source says: "Linnaeus [...] had seen a faked vegetable lamb taken from China to Sweden by a traveler." +Phoenix: Linnaeus wrote: "Species of bird, of which only one individual exists in the world, and which when decrepit [arises?] from [its] pyre made of aromatic [plants?] is said fabulously to become again young, to undergo happy former periods of life. In reality it is the date palm, see Kæmpf". +Linnaeus wrote: The Bernicla or Scottish goose & Goose-bearing Seashell: is believed by former generations to be born from rotten wood thrown away in the sea. But the Lepas places seaweed on its featherlike internal parts, and somewhat adhering, as if indeed that goose Bernicla was arising from it. Frederick Edward Hulme noted: "[The] barnacle-goose tree was a great article of faith with our ancestors in the Middle Ages." +Draco: Linnaeus wrote that it has a "snakelike body, two feet, two wings, like a bat, which is a winged lizard or a ray artificially shaped as a monster and dried." See also Jenny Haniver. +Automa Mortis Linnaeus wrote "Death-watch: It produces the sound of a very small clock in walls, is named Pediculus pulsatorius, which perforates wood and lives in it". +The above 10 taxa and the 4 taxa following were in the 2nd (1740) edition and the 4th and 5th editions (total 14 entries): + +Manticora: Linnaeus wrote merely: "face of a decrepit old man, body of a lion, tail starred with sharp points". +Antilope [sic]: Linnaeus wrote merely: "Face of a "wild animal", feet [like those] of cattle, horns like a goat's [but] saw-edged". +Lamia: Linnaeus wrote merely: "Face of a man, breasts of a virgin, body of a four-footed animal [but] scaled, forefeet of a "wild animal", hind[feet] [like those] of cattle". +Siren: Linnaeus wrote: "Art. gen. 81 Syrene Bartol: As long as it is not seen either living or dead, nor faithfully and perfectly described, it is called in doubt". +Linnaeus's reference is to Peter Artedi's writing about the Siren: "Two fins only on all the body, those on the chest. No finned tail. Head and neck and chest to the umbilicus have the human appearance. ... Our or Bartholin's Siren was found and captured in the sea near Massilia in America. From the umbilicus to the extremity of the body was unformed flesh with no sign of a tail. Two pectoral fins on the chest, with five bones or fingers, staying together, by which it swims. Its radius in the forearm is scarcely four fingers' width long. Oh that there could arise a true ichthyologist, who could examine this animal, as to whether it is a fable, or a true fish? About something which has not been seen it is preferable not to judge, than boldly to pronounce something.". Among references and quotations from other authors Artedi quoted that "some say that it is a manatee and others say completely different." + + +== Table == + + +== References == + + +== External links == +Biodiversity Heritage Library – Systema Naturae (10th edition, 1758) by Carl Linnaeus, page 73 ("Animalia Paradoxa") +Gunnar Broberg (2008). "The Dragonslayer". Tijdschrift voor Skandinavistiek. 29 (1): (29)36–37(43). \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Automated_species_identification-0.md b/data/en.wikipedia.org/wiki/Automated_species_identification-0.md new file mode 100644 index 000000000..72f340b34 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Automated_species_identification-0.md @@ -0,0 +1,26 @@ +--- +title: "Automated species identification" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Automated_species_identification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:55.990840+00:00" +instance: "kb-cron" +--- + +Automated species identification is a method of making the expertise of taxonomists available to ecologists, parataxonomists and others via digital technology and artificial intelligence. Today, most automated identification systems rely on images depicting the species for the identification. Based on precisely identified images of a species, a classifier is trained. Once exposed to a sufficient amount of training data, this classifier can then identify the trained species on previously unseen images. + +== Introduction == +The automated identification of biological objects such as insects (individuals) and/or groups (e.g., species, guilds, characters) has been a dream among systematists for centuries. The goal of some of the first multivariate biometric methods was to address the perennial problem of group discrimination and inter-group characterization. Despite much preliminary work in the 1950s and '60s, progress in designing and implementing practical systems for fully automated object biological identification has proven frustratingly slow. As recently as 2004 Dan Janzen + +updated the dream for a new audience: + +The spaceship lands. He steps out. He points it around. It says 'friendly–unfriendly—edible–poisonous—safe– dangerous—living–inanimate'. On the next sweep it says 'Quercus oleoides—Homo sapiens—Spondias mombin—Solanum nigrum—Crotalus durissus—Morpho peleides—serpentine'. This has been in my head since reading science fiction in ninth grade half a century ago. + +== The species identification problem == + +Janzen's preferred solution to this classic problem involved building machines to identify species from their DNA. However, recent developments in computer architectures, as well as innovations in software design, have placed the tools needed to realize Janzen's vision in the hands of the systematics and computer science community not in several years hence, but now; and not just for creating DNA barcodes, but also for identification based on digital images. +A survey published in 2004, studies why automated species identification had not become widely employed at this time and whether it would be a realistic option for the future. The authors found that "a small but growing number of studies sought to develop automated species identification systems based on morphological characters". An overview of 20 studies analyzing species' structures, such as cells, pollen, wings, and genitalia, shows identification success rates between 40% and 100% on training sets with 1 to 72 species. However, they also identified four fundamental problems with these systems: (1) training sets—were too small (5-10 specimens per species) and their extension especially for rare species may be difficult, (2) errors in identification—are not sufficiently studied to handle them and to find systematics, (3) scaling—studies consider only small numbers of species (<200 species), and (4) novel species — systems are restricted to the species they have been trained for and will classify any novel observation as one of the known species. +A survey published in 2017 systematically compares and discusses progress and findings towards automated plant species identification within the last decade (2005–2015). 120 primary studies have been published in high-quality venues within this time, mainly by authors with computer science background. These studies propose a wealth of computer vision approaches, i.e., features reducing the high-dimensionality of the pixel-based image data while preserving the characteristic information as well as classification methods. The vast majority of these studies analyzes leaves for identification, while only 13 studies propose methods for flower-based identification. The reasons being that leaves can easier be collected and imaged and are available for most of the year. Proposed features capture generic object characteristic, i.e., shape, texture, and color as well as leaf-specific characteristics, i.e., venation and margin. The majority of studies still used datasets for evaluation that contained no more than 250 species. However, there is progress in this regard, one study uses a dataset with >2k and another with >20k species. +A system developed in 2022 showed that automated identification achieves accuracy that is sufficiently high for being used in an automated insect surveillance system using electronic traps. By training classifiers on a few hundred images it correctly identified fruit-flies, and can be used for continuous monitoring aimed at detecting species invasion or pest outbreak. Several aspects contribute to the success of this system. Primarily, using e-traps provide a standardized setting, which means that even though they are deployed in different countries and regions, the visual variability, in terms of size view angle and illumination are controlled. This suggests that trap-based systems may be easier to develop than free-view systems for automatic pest identification. +There is a shortage of specialists who can identify the very biodiversity whose preservation has become a global concern. In commenting on this problem in palaeontology in 1993, Roger Kaesler recognized: \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Automated_species_identification-1.md b/data/en.wikipedia.org/wiki/Automated_species_identification-1.md new file mode 100644 index 000000000..664b6b292 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Automated_species_identification-1.md @@ -0,0 +1,45 @@ +--- +title: "Automated species identification" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Automated_species_identification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:55.990840+00:00" +instance: "kb-cron" +--- + +"... we are running out of systematic palaeontologists who have anything approaching synoptic knowledge of a major group of organisms ... Palaeontologists of the next century are unlikely to have the luxury of dealing at length with taxonomic problems ... Palaeontology will have to sustain its level of excitement without the aid of systematists, who have contributed so much to its success."This expertise deficiency cuts as deeply into those commercial industries that rely on accurate identifications (e.g., agriculture, biostratigraphy) as it does into a wide range of pure and applied research programmes (e.g., conservation, biological oceanography, climatology, ecology). It is also commonly, though informally, acknowledged that the technical, taxonomic literature of all organismal groups is littered with examples of inconsistent and incorrect identifications. This is due to a variety of factors, including taxonomists being insufficiently trained and skilled in making identifications (e.g., using different rules-of-thumb in recognizing the boundaries between similar groups), insufficiently detailed original group descriptions and/or illustrations, inadequate access to current monographs and well-curated collections and, of course, taxonomists having different opinions regarding group concepts. Peer review only weeds out the most obvious errors of commission or omission in this area, and then only when an author provides adequate representations (e.g., illustrations, recordings, and gene sequences) of the specimens in question. +Systematics too has much to gain from the further development and use of automated identification systems. In order to attract both personnel and resources, systematics must transform itself into a "large, coordinated, international scientific enterprise". +Many have identified use of the Internet— especially via the World Wide Web — as the medium through which this transformation can be made. While establishment of a virtual, GenBank-like system for accessing morphological data, audio clips, video files and so forth would be a significant step in the right direction, improved access to observational information and/or text-based descriptions alone will not address either the taxonomic impediment or low identification reproducibility issues successfully. Instead, the inevitable subjectivity associated with making critical decisions on the basis of qualitative criteria must be reduced or, at the very least, embedded within a more formally analytic context. + +Properly designed, flexible, and robust, automated identification systems, organized around distributed computing architectures and referenced to authoritatively identified collections of training set data (e.g., images, and gene sequences) can, in principle, provide all systematists with access to the electronic data archives and the necessary analytic tools to handle routine identifications of common taxa. Properly designed systems can also recognize when their algorithms cannot make a reliable identification and refer that image to a specialist (whose address can be accessed from another database). Such systems can also include elements of artificial intelligence and so improve their performance the more they are used. Once morphological (or molecular) models of a species have been developed and demonstrated to be accurate, these models can be queried to determine which aspects of the observed patterns of variation and variation limits are being used to achieve the identification, thus opening the way for the discovery of new and (potentially) more reliable taxonomic characters. + +iNaturalist is a global citizen science project and social network of naturalists that incorporates both human and automatic identification of plants, animals, and other living creatures via browser or mobile apps. +Naturalis Biodiversity Center in the Netherlands develops AI species identification models and service infrastructures, including but not limited to: +A multi-source model trained with expert-validated data and used by 7 European biodiversity portals for citizen scientist projects in different countries across Europe; +A model for analyzing images from insect camera DIOPSIS; +10 AI models for butterflies, cone snails, bird eggs, rays and sharks egg capsules, beach fossils as well as masks from different cultures that are in the collections of 5+ Dutch museums; +(Animal) sound recognition models. +Pl@ntNet is a global citizen science project which provides an app and a website for plant identification through photographs, based on machine-learning +Leaf Snap is an iOS app developed by the Smithsonian Institution that uses visual recognition software to identify North American tree species from photographs of leaves. +Google Photos can automatically identify various species in photographs. +Plant.id is a web application and API made by FlowerChecker company which uses a neural network trained on photos from FlowerChecker mobile app. + +== See also == +Multi-access key +Digital Automated Identification System + +== References cited == + +== External links == +Here are some links to the home pages of species identification systems. The SPIDA and DAISY system are essentially generic and capable of classifying any image material presented. The ABIS and DrawWing system are restricted to insects with membranous wings as they operate by matching a specific set of characters based on wing venation. + +The SPIDA system +ABIS +DAISY +DrawWing +LeafSnap Archived 2013-05-20 at the Wayback Machine +Pl@ntNet +Insect.id by Kindwise recognizes over 6,000 species including beetles, spiders, centipedes, butterflies, ants, bees and other insect-like animals +Mushroom id by Kindwise recognizes over 3,200 species including mushrooms, lichens and slime molds +Plant.id by Kindwise recognizes more than 33,000 taxa, including houseplants, garden plants, trees, weeds, fungi, and lichens; it also recognizes common plant diseases \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-0.md b/data/en.wikipedia.org/wiki/Baltimore_classification-0.md new file mode 100644 index 000000000..2635f5335 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-0.md @@ -0,0 +1,30 @@ +--- +title: "Baltimore classification" +chunk: 1/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +Baltimore classification is a system used to classify viruses by their routes of transferring genetic information from the genome to messenger RNA (mRNA). Seven Baltimore groups, or classes, exist and are numbered in Roman numerals from I to VII. Groups are defined by whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, whether a single-stranded RNA genome is positive-sense (+) or negative-sense (–), and whether the virus makes DNA from RNA (reverse transcription (RT)). Viruses within Baltimore groups typically have the same replication method, but other characteristics such as virion structure are not directly related to Baltimore classification. +The seven Baltimore groups are for double-stranded DNA (dsDNA) viruses, single-stranded DNA (ssDNA) viruses, double-stranded RNA (dsRNA) viruses, positive-sense single-stranded RNA (+ssRNA) viruses, negative-sense single-stranded RNA (–ssRNA) viruses, ssRNA viruses that have a DNA intermediate in their life cycle (ssRNA-RT), and dsDNA viruses that have an RNA intermediate in their life cycle (dsDNA-RT). Only one class exists for ssDNA viruses because their genomes are converted to dsDNA before transcription regardless of sense. Some viruses belong to more than one Baltimore group, such as DNA viruses that have either dsDNA or ssDNA as their genome. +Many virus characteristics do not define which Baltimore group they belong to but do correlate to specific Baltimore groups. This includes the use of RNA editing and alternative splicing, whether the virus's genome is segmented, the size and structure of the virus's genome, the host range of viruses, whether the virus packages replication and transcription machinery into virions, and unorthodox methods of translating mRNA into proteins. Furthermore, while Baltimore groups were not established based on evolutionary relationships, research in the 21st century has found that certain groups, such as dsRNA, +ssRNA, and many –ssRNA viruses, share common ancestry. +Baltimore classification was created in 1971 by virologist David Baltimore and initially only included the first six groups. It was later expanded to include group VII after the discovery of dsDNA-RT viruses. Since then, it has become common among virologists to use Baltimore classification alongside virus taxonomy due to its utility. In 2018 and 2019, Baltimore classification was partially integrated into virus taxonomy based on evidence that certain groups were descended from common ancestors. Various taxa now correspond to specific Baltimore groups. An extension of Baltimore classification has been proposed by virologist Vadim Agol to encompass all possible routes of genetic information transmission. + +== Overview == +Baltimore classification groups viruses together by their routes of transferring genetic information from the genome to messenger RNA (mRNA). Characteristics that determine the Baltimore group of a virus include whether the genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), the strandedness of the genome, which can be either single- or double-stranded, the sense of a single-stranded RNA genome, which can be either positive (+) or negative (–), and whether the virus synthesizes DNA from RNA (reverse transcription (RT)). There are seven Baltimore groups or classes, numbered with Roman numerals, listed hereafter. + +Group I: double-stranded DNA viruses (dsDNA) +Group II: single-stranded DNA viruses (ssDNA) +Group III: double-stranded RNA viruses (dsRNA) +Group IV: positive-sense single-stranded RNA viruses (+ssRNA) +Group V: negative-sense single-stranded RNA viruses (–ssRNA) +Group VI: single-stranded RNA viruses with a DNA intermediate in their life cycle (ssRNA-RT) +Group VII: double-stranded DNA viruses with an RNA intermediate in their life cycle (dsDNA-RT) +Baltimore classification is chiefly based on the path toward transcription of the viral genome, and viruses within each group usually share the manner by which the mRNA synthesis occurs. While not the direct focus of Baltimore classification, groups are organized in such a manner that viruses in each group also typically have the same mechanisms of replicating the viral genome. Structural characteristics of the extracellular virus particle, called a virion, such as the shape of the viral capsid, which stores the genome, and the presence of a viral envelope, a lipid membrane that surrounds the capsid, have no direct relation to Baltimore groups, nor do the groups necessarily show genetic relation based on evolutionary history. + +== Baltimore groups == + +=== Group I: double-stranded DNA viruses === \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-1.md b/data/en.wikipedia.org/wiki/Baltimore_classification-1.md new file mode 100644 index 000000000..f64d04acf --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-1.md @@ -0,0 +1,43 @@ +--- +title: "Baltimore classification" +chunk: 2/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +The first Baltimore group contains viruses that have a double-stranded DNA (dsDNA) genome. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a transcription preinitiation complex binds to the DNA upstream of the transcription site, recruiting a host RNA polymerase enzyme. Once the RNA polymerase is recruited, it uses the negative-sense strand as a template for synthesizing mRNA strands, which are positive sense. The RNA polymerase then terminates transcription upon reaching a specific signal, such as a polyadenylation site. +dsDNA viruses make use of several mechanisms to replicate their genome. A widely used method is bidirectional replication, in which two replication forks are established at a replication origin site and move in opposite directions on a DNA molecule. A rolling circle mechanism that produces linear strands while progressing in a loop around a circular genome is also common. Many dsDNA viruses use a strand displacement method whereby one strand is synthesized from a template strand, and a complementary strand is then synthesized from the previously synthesized strand to form a dsDNA genome. Lastly, some dsDNA viruses are replicated as part of a process called replicative transposition, whereby a viral genome that is integrated into a host cell's genome is replicated to another part of the host cell's genome. +dsDNA viruses can be divided informally into those that replicate in the nucleus, and as such are relatively dependent on host cell machinery for transcription and replication, and those that replicate in cytoplasm, in which case they have obtained their own means of transcription and replication. dsDNA viruses are also sometimes divided between tailed dsDNA viruses, which refers to members of the realm Duplodnaviria, specifically the head-tail of the class Caudoviricetes, and tailless or non-tailed (icosahedral) dsDNA viruses, which refers to viruses in the realms Singelaviria and Varidnaviria. +dsDNA viruses are classified into six realms and many taxa that are unassigned to a realm: + +Viruses in the realms Adnaviria, Duplodnaviria, and Singelaviria are dsDNA viruses. +In the realm Floreoviria, members of the class Papovaviricetes are dsDNA viruses. +The realm Pleomoviria contains both dsDNA viruses and ssDNA viruses. +Viruses in the realm Varidnaviria are dsDNA viruses except for the class Ainoaviricetes, which are ssDNA viruses. +The following taxa that are unassigned to a realm exclusively contain dsDNA viruses: +Classes: Naldaviricetes +Families: Ampullaviridae, Basaltiviridae, Bicaudaviridae, Clavaviridae, Eurekaviridae, Fuselloviridae, Globuloviridae, Guttaviridae, Halspiviridae, Huangdiviridae, Itzamnaviridae, Lomiviridae, Nipumfusiviridae, Ovaliviridae, Plasmaviridae, Portogloboviridae, Thaspiviridae, Xigoviridae, Yamazakiviridae +Genera: Dinodnavirus + +=== Group II: single-stranded DNA viruses === + +The second Baltimore group contains viruses that have a single-stranded DNA (ssDNA) genome. ssDNA viruses have the same manner of transcription as dsDNA viruses. Because the genome is single-stranded, however, it is first made into a double-stranded form by a DNA polymerase enzyme upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replicating the viral genome. +Most ssDNA viruses contain circular genomes that are replicated by rolling circle replication (RCR). ssDNA RCR is initiated by an endonuclease enzyme that bonds to and cleaves the positive-sense strand, which allows a DNA polymerase to use the negative-sense strand as a template for replication. Replication progresses in a loop around the genome by extending the 3′-end ("three prime end") of the positive-sense strand, which displaces the prior positive-sense strand. The endonuclease then cleaves the positive-sense strand again to create a standalone genome that is joined (ligated) into a circular loop. The new ssDNA genome may be packaged into virions or replicated by a DNA polymerase to create a double-stranded form for transcription or additional rounds of replication. +Parvoviruses and bidnaviruses have linear ssDNA genomes that are replicated by rolling hairpin replication (RHR), which is similar to RCR. Their genomes have hairpin loops at each end of the genome that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the linear genome, which produces numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the endonuclease. +Nearly all ssDNA viruses have positive-sense genomes, but a few exceptions and peculiarities exist. Anelloviruses are the only ssDNA viruses that have negative-sense genomes. Parvoviruses may package either the positive- or negative-sense strand into capsids. Lastly, bidnaviruses may package both the positive- and negative-sense strands of their bipartite genome. In any case, the sense of ssDNA viruses, unlike that of ssRNA viruses, is not sufficient to separate ssDNA viruses into two Baltimore groups since all ssDNA viral genomes are converted to dsDNA forms before transcription and replication. +ssDNA viruses are classified into five realms and a couple families that are unassigned to realms: + +Viruses in the realms Efunaviria and Volvereviria are ssDNA viruses. +In the realm Floreoviria, members are ssDNA viruses except for viruses in the class Papovaviricetes, which are dsDNA viruses. +The realm Pleomoviria contains both dsDNA viruses and ssDNA viruses. +In the realm Varidnaviria, viruses of the class Ainoaviricetes are ssDNA viruses. +The unassigned families Obscuriviridae and Spiraviridae are ssDNA virus families. + +=== Group III: double-stranded RNA viruses === + +The third Baltimore group contains viruses that have a double-stranded RNA (dsRNA) genome. After entering a host cell, the viral RNA-dependent RNA polymerase (RdRp) synthesizes a positive-sense strand from the negative-sense strand of the dsRNA genome. This positive-sense strand may be used either as mRNA for translation or as a template for replication to form the dsRNA genome. +dsRNA is not a molecule made by cells, so eukaryotes have evolved antiviral systems to detect and inactivate viral dsRNA. To counter this, many dsRNA viruses replicate their genomes inside of capsids, thereby avoiding detection inside of the host cell's cytoplasm. Positive-sense strands are then forced out from the capsid to be translated or translocated from the mature capsid to a progeny capsid. +dsRNA viruses are classified into two phyla within the kingdom Orthornavirae, realm Riboviria: \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-2.md b/data/en.wikipedia.org/wiki/Baltimore_classification-2.md new file mode 100644 index 000000000..f5a063d8a --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-2.md @@ -0,0 +1,37 @@ +--- +title: "Baltimore classification" +chunk: 3/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +Viruses in the phylum Duplornaviricota are dsRNA viruses. +In the phylum Pisuviricota, members of the class Duplopiviricetes are dsRNA viruses. + +=== Group IV: positive-sense single-stranded RNA viruses === + +The fourth Baltimore group contains viruses that have a positive-sense single-stranded RNA (+ssRNA) genome. For +ssRNA viruses, the genome functions as mRNA, so no transcription is required for translation. +ssRNA viruses will, however, produce positive-sense copies of the genome from negative-sense strands of an intermediate dsRNA genome. This acts as both a transcription and replication process since the replicated +ssRNA is also mRNA. +Many +ssRNA viruses are able to have only a portion of their genome transcribed. Typically, subgenomic RNA (sgRNA) strands are used for the translation of structural and movement proteins needed during intermediate and late stages of infection. sgRNA transcription may occur by commencing RNA synthesis within the genome rather than from the 5′-end ("five prime end"), by stopping RNA synthesis at specific sequences in the genome, or, as a part of both aforementioned methods, by synthesizing leader sequences from viral RNA that are then attached to sgRNA strands. During infection, the viral RdRp is always translated directly from the genome first because replication, performed by the RdRp, is required for sgRNA synthesis. +Because the process of replicating the viral genome produces intermediate dsRNA molecules, +ssRNA viruses can be targeted by the host cell's immune system. To avoid detection, +ssRNA viruses replicate in membrane-associated vesicles that are used as replication factories. From there, only +ssRNA strands enter the main cytoplasmic area of the cell. These strands may be used as mRNA or as progeny genomes. ++ssRNA viruses can be divided informally into those that have polycistronic mRNA, which encodes a polyprotein that is cleaved to form multiple mature proteins, and those that undergo multiple rounds of translation of the genome or subgenomic mRNAs to express proteins. +ssRNA viruses are classified into three phyla in the kingdom Orthornavirae, realm Riboviria: + +Viruses in the phyla Kitrinoviricota and Lenarviricota are +ssRNA viruses. +Viruses in the phylum Pisuviricota are +ssRNA viruses, excluding the class Duplopiviricetes, which contains dsRNA viruses. + +=== Group V: negative-sense single-stranded RNA viruses === + +The fifth Baltimore group contains viruses that have a negative-sense, single-stranded RNA (–ssRNA) genome. At least two lineages of –ssRNA viruses exist, which transcribe and replicate their genomes differently. The first are viruses of the phylum Negarnaviricota in the kingdom Orthornavirae, realm Riboviria. Negarnaviricots transcribe mRNA, which is positive sense, directly from the negative-sense genome. The first process for –ssRNA transcription involves the viral RdRp binding to a leader sequence on the 3′-end of the genome, transcribing a 5′ triphosphate-leader RNA sequence, then stopping and restarting on a transcription signal that is capped, continuing until a stop signal is reached. There, the RdRp synthesizes a polyadenylated tail and releases the mRNA or, for polycistronic genomes, continues transcription. +The second manner is similar, but instead of synthesizing a cap, the RdRp may use its endonuclease activity to snatch a short sequence of nucleotides from host cell mRNA and use it as the 5′ cap of viral mRNA. Genomic –ssRNA is replicated from the positive-sense antigenome in a manner similar to transcription, except in reverse using the antigenome as a template for the genome. The RdRp complex moves from the 3′-end to the 5′-end of the antigenome and ignores all transcription signals when synthesizing genomic –ssRNA. +Various –ssRNA viruses use special mechanisms for transcription. The way of polyadenylating the end of an mRNA sequence may be through polymerase stuttering, during which the RdRp transcribes an adenine from uracil and then moves back in the RNA sequence to transcribe it again, continuing this process until hundreds of adenines have been added to the 3′-end of the mRNA. Some –ssRNA viruses are ambisense, as both the positive- and negative-sense strands separately encode viral proteins. These viruses produce one mRNA strand from the genome and one from a complementary strand. +–ssRNA viruses in Negarnaviricota can be divided informally into those that have non-segmented and segmented genomes. Non-segmented –ssRNA viruses replicate in the cytoplasm, and segmented –ssRNA viruses replicate in the nucleus. For segmented viruses, the RdRp transcribes one monocistronic mRNA strand from each segment of the genome. This distinction is closely followed within Negarnaviricota, as viruses in the subphylum Haploviricotina usually have non-segmented genomes, and viruses in the subphylum Polyploviricotina have segmented genomes. Moreover, –ssRNA viruses that synthesize a cap structure on viral mRNA are assigned to Haploviricotina, whereas –ssRNA viruses that snatch caps from host mRNA belong to Polyploviricotina. + +The second lineage of –ssRNA viruses is the realm Ribozyviria, which includes Hepatitis D virus (HDV) and its relatives. Ribozyvirians have covalently-closed circular –ssRNA genomes that are covered in nucleocapsid proteins to form a ribonucleoprotein (RNP) complex. After entering a cell, the RNP complex migrates from the cytosol to the nucleus, where the genome is replicated by RCR by a host RNA polymerase II enzyme. This process creates a long molecule with many copies of the genome, called a concatemer, that has a series of positive-sense genomic strands. Ribozymes encoded in this antigenome catalyze cleavage of the concatemer to form individual strands that are either translated or ligated for replication through RCR to produce concatemers of –ssRNA antigenomic strands. Ribozymes encoded in the negative-sense strands then catalyze cleavage of the negative-sense concatemer to produce individual genomic –ssRNA strands. +Lastly, there is a group of –ssRNA viruses assigned to the tentative phylum Arctiviricota in the kingdom Orthornavirae. Arctiviricots inhabit the Arctic Ocean and are believed to represent a separate –ssRNA lineage in Orthornavirae from Negarnaviricota. Their mechanisms of replication and transcription have not been described. In summary, –ssRNA viruses belong to the following taxa: + +In the realm Riboviria, viruses in the phyla Arctiviricota (tentative) and Negarnaviricota are –ssRNA viruses. +Viruses in the realm Ribozyviria are –ssRNA viruses. + +=== Group VI: single-stranded RNA viruses with a DNA intermediate === \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-3.md b/data/en.wikipedia.org/wiki/Baltimore_classification-3.md new file mode 100644 index 000000000..d3a62facf --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-3.md @@ -0,0 +1,35 @@ +--- +title: "Baltimore classification" +chunk: 4/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +The sixth Baltimore group contains viruses that have a (positive-sense) single-stranded RNA genome with a DNA intermediate ((+)ssRNA-RT) in their replication cycle. ssRNA-RT viruses are transcribed in the same manner as DNA viruses, but their genomes are first converted to a dsDNA form through a process called reverse transcription (RT). The viral reverse transcriptase enzyme then synthesizes a DNA strand from the +ssRNA strand, and the RNA strand is degraded and replaced with a DNA strand to create a dsDNA copy of the genome. The viral enzyme integrase then integrates the dsDNA molecule into the DNA of the host cell, where it is now called a provirus. The host cell's RNA polymerase II then transcribes RNA in the nucleus from the proviral DNA. Some of this RNA becomes mRNA whereas other strands become copies of the viral genome for replication. +ssRNA-RT viruses are all included in the class Revtraviricetes, the sole class in the kingdom Pararnavirae, realm Riboviria. Excluding the family Caulimoviridae, which belongs to group VII, all members of the Revtraviricetes order Ortervirales are ssRNA-RT viruses. ssRNA-RT viruses are sometimes called retroviruses, a term shared with members of the ssRNA-RT family Retroviridae. + +=== Group VII: double-stranded DNA viruses with an RNA intermediate === + +The seventh Baltimore group contains viruses that have a double-stranded DNA genome with an RNA intermediate (dsDNA-RT) in their replication cycle. dsDNA-RT viruses have gaps in their circular genomes so that parts of the genome are ssDNA. These gaps are repaired to create a complete, covalently-closed circular dsDNA genome before transcription. The host cell's RNA polymerase II then transcribes RNA strands from the genome in the nucleus. The viral enzyme reverse transcriptase then produces dsDNA from pregenomic RNA (pgRNA) strands by the same general mechanism as ssRNA-RT viruses, but with replication occurring in a loop around the circular genome. Replication occurs after pgRNA is packaged into capsids and before capsids bud from the cell. +dsDNA-RT viruses are, like ssRNA-RT viruses, all included in the class Revtraviricetes. Two families of dsDNA-RT viruses are recognized: Caulimoviridae, which belongs to the order Ortervirales, and Hepadnaviridae, which is the sole family in the order Blubervirales. The provisional family Nudnaviridae is considered to be a sister family to hepadnavirids. dsDNA-RT viruses are often called pararetroviruses. + +== Multi-group viruses == +Some viruses can be classified into two Baltimore groups. Pleolipoviruses, for example, encapsidate either ssDNA or dsDNA genomes. For betapleolipoviruses, an encapsidated genome contains ssDNA regions and dsDNA regions. Similarly, bacilladnaviruses are ssDNA viruses with short dsDNA regions in their genomes. Therefore, both pleolipoviruses and bacilladnaviruses can be considered both dsDNA and ssDNA viruses. Ambisense RNA viruses also exist: certain bunyaviruses, such as arenaviruses, contain segmented genomes in which one segment is partly positive sense and partly negative sense. Furthermore, RNA viruses of the phylum Ambiviricota have non-segmented genomes with at least two open reading frames (ORFs). One is encoded on the positive-sense strand and the other on the negative-sense strand. These RNA viruses may constitute a new Baltimore group, or they can be considered both +ssRNA and –ssRNA viruses. + +== Correlates to Baltimore groups == + +Many characteristics of viruses do not define which Baltimore group a virus belongs to but still correspond to specific Baltimore groups. This includes the use of RNA editing, alternative splicing during transcription, whether the virus's genome is segmented, the size and structure of the virus's genome, the host range of viruses, whether the virus packages replication and transcription machinery into virions, and unorthodox methods of translating mRNA. + +=== RNA editing === +RNA editing is used by various ssRNA viruses to produce different proteins from a single gene. This can be done by polymerase slippage during transcription or by post-transcriptional editing. During polymerase slippage, the RNA polymerase slips one nucleotide back during transcription, which adds a nucleotide not included in the template strand to the mRNA strand. Editing of a genomic template would impair gene expression, so RNA editing is only done during and after transcription. For ebola viruses, RNA editing is used to express three different proteins from a single gene, which increases their ability to adapt to their hosts. + +=== Alternative splicing === +Alternative splicing is a mechanism by which different proteins can be produced from a single gene by using alternative splicing sites to produce different mRNA strands. It is used by various DNA, –ssRNA, and reverse transcribing viruses. Viruses may make use of alternative splicing solely to produce multiple proteins from a single pre-mRNA strand or for other specific purposes. For some viruses, such as papillomaviruses, alternative splicing acts as a way to regulate early and late gene expression during different stages of infection. Herpesviruses use it as a potential anti-host defense mechanism to prevent synthesis of specific antiviral proteins. +Alternative splicing differs from RNA editing in that alternative splicing does not change the mRNA sequence like RNA editing but instead changes the coding capacity of an mRNA sequence as a result of alternative splicing sites. The two processes otherwise have the same result: multiple proteins are expressed from a single gene. + +=== Genome segmentation === + +Viral genomes can exist as a single (monopartite) segment, a segmented genome, or a multipartite genome. For monopartite viruses, all genes are on a single genome segment. For segmented viruses, the genome is separated into at least two molecules that are packaged together into one virion. Multipartite viruses are segmented viruses that package their genome segments into separate virions. Monopartite and segmented viruses are found in all cellular life, whereas multipartite viruses mainly infect plants and fungi. By Baltimore group, dsDNA and RT viruses are non-segmented, ssDNA and +ssRNA viruses are mostly non-segmented, dsRNA viruses are mostly segmented, and around half of –ssRNA viruses are segmented. Pleolipoviruses vary as some have monopartite ssDNA genomes while others are bipartite with one ssDNA segment and one dsDNA segment. Viruses in the ssDNA plant virus family Geminiviridae likewise vary between being monopartite and bipartite. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-4.md b/data/en.wikipedia.org/wiki/Baltimore_classification-4.md new file mode 100644 index 000000000..5fae429c4 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-4.md @@ -0,0 +1,31 @@ +--- +title: "Baltimore classification" +chunk: 5/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +=== Genome structure === +Viral genomes may be either linear with ends or circular in a loop. Whether a virus has a linear or circular genome varies from group to group. Most dsDNA and –ssRNA viruses have linear genomes, ssDNA viruses mainly have circular genomes, dsRNA, +ssRNA, and ssRNA-RT viruses have linear genomes, and dsDNA-RT viruses have circular genomes. As all +ssRNA viruses have genomes that can act as mRNA, and circular mRNA does not exist in cellular life, all +ssRNA viruses have linear genomes. Among –ssRNA viruses, those of the phylum Negarnaviricota have linear genomes, and those of the realm Ribozyviria have circular genomes. + +=== Genome size === + +The size, or length, of a genome varies by Baltimore group. dsDNA viruses have genomes ranging from about 5 to 2,500 kilobases (kb) in length, ssDNA viruses 1–25 kb, dsRNA viruses 4–30 kb, +ssRNA viruses 3.5–40 kb, –ssRNA viruses 1.7–20 kb, ssRNA-RT viruses 5–13 kb, and dsDNA-RT viruses 3–10 kb in length. The relatively small genomes of viruses that are not group I are likely due to physical limitations. For example, ssDNA has the potential to form extensive secondary structures, and ssRNA is relatively chemically unstable. dsDNA viruses have much more varied genome sizes, likely because they have the same genomic organization as cells. This enables them to either exploit cellular machinery or encode their own machinery. As such, dsDNA seems to be the only genomic organization that can support genomes that exceed about 50 kb. + +=== Host range === +Different Baltimore groups tend to be found within different branches of cellular life. The vast majority of dsDNA viruses infect prokaryotes, but they also infect protists, animals, and rarely fungi. ssDNA viruses infect bacteria and most eukaryotes but are rare in archaea. dsRNA viruses infect plants, protists, and animals, are rare in bacteria, but are not found in archaea. +ssRNA viruses are found in all eukaryotes, infect many bacteria, but do not infect archaea. –ssRNA viruses infect animals and plants, are rare in fungi, but are not found in prokaryotes. ssRNA-RT viruses infect all eukaryotes but do not infect prokaryotes. Lastly, dsDNA-RT viruses infect animals and plants but not prokaryotes. Whether dsDNA-RT viruses infect protists is unknown. +By host, a large majority of prokaryotic viruses are dsDNA viruses, but a significant minority are ssDNA and +ssRNA viruses. There are a relatively small number of prokaryotic dsRNA viruses and no prokaryotic –ssRNA or RT viruses. Eukaryotic viruses, in contrast, are predominantly RNA viruses, though eukaryotic DNA viruses are common. Well-characterized eukaryotic viromes contain mostly +ssRNA viruses and, in some lineages such as fungi, dsRNA viruses. ssRNA-RT viruses are also common in eukaryotes, especially in animals. +Biological factors influence host range. For example, dsDNA viruses do not infect plants because large dsDNA molecules are unable to pass through plasmodesmata, intercellular channels that connect plant cells. The dominance of DNA viruses in prokaryotes may be because they outcompete RNA viruses. In eukaryotic cells, however, the nucleus is a barrier that requires adaptation by DNA viruses. They either have to evolve means to enter the nucleus to replicate or obtain their own replication and transcription machinery to replicate in virus factories in the cytosol. In contrast, the endomembranes of eukaryotic cells appear to be a beneficial environment for RNA virus replication. + +=== Packaging of replication and transcription machinery === + +Viruses often package into the virion machineries necessary for replication and transcription, varying by Baltimore group. dsDNA viruses sometimes package transcription machinery, ssDNA and +ssRNA viruses do not package either replication or transcription machinery, dsRNA and +ssRNA-RT viruses package both, –ssRNA viruses package almost everything, and dsDNA-RT viruses package most components of their replication and transcription machinery. +dsDNA viruses encode a broad range of proteins involved in replication and transcription. In some cases, they encode nearly complete systems that grant the virus partial autonomy from cells during genome expression and replication. Most ssDNA viruses encode an endonuclease that initiates RCR or RHR while relying on host cell machinery for the rest of replication and transcription. The endonuclease has to be encoded by these viruses because they use a DNA replication method not normally used by cells. Anelloviruses and bidnaviruses are the exceptions: anelloviruses encode proteins that aren't homologous to known proteins, and bidnaviruses encode a protein-primed DNA polymerase. +RNA replication and reverse transcription are usually discouraged by cells, which necessitates that all RNA and RT viruses encode their own RNA-dependent polymerase. Satellite viruses, such as the viruses of Ribozyviria, are the only exception because they depend on other viruses for replication. Almost all RNA and RT viruses incorporate their RNA-dependent polymerase into the virion because the enzyme is required to synthesize viral mRNA in infected cells. The exceptions are +ssRNA viruses and caulimoviruses, which are dsDNA-RT viruses. +ssRNA viruses do not do so because their genomes function as mRNA and are translated upon cell entry. For caulimoviruses, the host enzyme RNA polymerase II transcribes the genome. + +=== Translation === + +Translation is the process by which proteins are synthesized from mRNA by ribosomes. Baltimore groups do not directly pertain to the translation of viral mRNA to proteins, but atypical types of translation used by viruses are usually found within specific Baltimore groups. For example: \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-5.md b/data/en.wikipedia.org/wiki/Baltimore_classification-5.md new file mode 100644 index 000000000..a0d6d2b3c --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-5.md @@ -0,0 +1,27 @@ +--- +title: "Baltimore classification" +chunk: 6/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +Non-canonical translation initiation: +Viral initiation of translation: some viruses have evolved mechanisms to initiate translation. Methods include having internal ribosomal entry sites to allow cap-independent initiation, having downstream hairpin loops that allow for cap-dependent translation without an eIF2 initiation factor, and initiating translation at a CUG codon or other start codon with a leucine amino acid. These methods are used by various +ssRNA and ssRNA-RT viruses. +Ribosomal shunting, also called nonlinear scanning: ribosomes start scanning from a 5′-cap structure then bypass a leader region in the mRNA and initiate translation downstream from the leader sequence. Ribosomal shunting is used by various dsDNA, +ssRNA, –ssRNA, and RT viruses. +Termination-reinitiation, also called stop-start: after termination of translation of an ORF, a proportion of 40S subunits of the ribosome remain attached to the mRNA as a way to reinitiate translation of a subsequent ORF. This is used by various dsRNA and +ssRNA viruses. + +Non-canonical elongation and termination of translation: +Ribosomal frameshifting: ribosomes slip one nucleobase forward or backward during translation. This is used by various dsDNA, dsRNA, +ssRNA, and ssRNA-RT viruses to produce merged proteins from overlapping ORFs. +Suppression of termination, also called stop codon read-through: certain viruses contain codons in their mRNA that would normally signal for termination of translation upon being recognized by a release factor but are instead partially recognized by tRNA during translation, which allows for continued translation up to the next stop codon to produce extended polypeptides at the end of the amino acid sequence. This is used by various dsRNA, +ssRNA, and ssRNA-RT viruses, often to express replicase enzymes. +Ribosomal skipping, also called stop-carry on and stop-go: a viral peptide may prevent a ribosome from covalently linking a newly inserted amino acid, which blocks further translation. The amino acid sequence is then co-translationally cleaved, and a new amino acid sequence is started, which leads to the production of two proteins from one ORF. This is used by various dsRNA and +ssRNA viruses. + +== Evolutionary origins and relations == + +Excluding ribozyvirians, RNA viruses of groups III–V are believed to share common ancestry. +ssRNA viruses form the basal, ancestral lineage of these viruses from which dsRNA viruses and –ssRNA viruses appear to have evolved from on multiple occasions. The two orders of RT viruses in the class Revtraviricetes, Blubervirales and Ortervirales, are believed by virologists to have evolved from two different families of retrotransposons on separate occasions. ssRNA-RT viruses all belong to Ortervirales and thus share common ancestry. dsDNA-RT viruses, on the other hand, are found in both orders and therefore represent two separate lineages of dsDNA-RT viruses. Ribozyvirians constitute a lineage of –ssRNA viruses unrelated to other RNA viruses. +Most ssDNA viruses likely originate from plasmids that, on multiple occasions, recombined with other genomes to obtain the structural proteins needed to form virions. The evolutionary history of dsDNA viruses is the most complex as they appear to have emerged independently on numerous occasions. Two major lineages of dsDNA viruses exist: the realm Duplodnaviria and the realm Varidnaviria, the latter of which also contains ssDNA viruses that are descended from dsDNA viruses. The opposite is true in the realm Floreoviria, which contains dsDNA viruses descended from ssDNA viruses. There are also two minor realms, Adnaviria and Singelaviria, that exclusively contain dsDNA viruses. Lastly, there are dsDNA virus families unassigned to higher taxa that are unique from existing realms and which likely constitute small realms. +Of the replication-expression systems used by viruses, only Baltimore group I (dsDNA) is used by cells. The other groups may be remnants of the primordial stage of life before the emergence of modern-like cells, during which the dsDNA system used by extant cells had not yet become uniform. The ancestors of RNA viruses in particular may have emerged during the time of the RNA world. And although virus realms are evolutionarily independent from each other, the replicative proteins encoded by viruses in the four major realms (Duplodnaviria, Floreoviria, Riboviria, and Varidnaviria) are built on the core RNA recognition motif, one of the most common nucleic acid-binding domains in nature. Therefore, the replication-expression cycles most likely diversified before the separation of large dsDNA replicators, which became the ancestors of cellular life, from other types of replicators, which became selfish genetic elements and gave rise to viruses. + +== History == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Baltimore_classification-6.md b/data/en.wikipedia.org/wiki/Baltimore_classification-6.md new file mode 100644 index 000000000..333e59061 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Baltimore_classification-6.md @@ -0,0 +1,36 @@ +--- +title: "Baltimore classification" +chunk: 7/7 +source: "https://en.wikipedia.org/wiki/Baltimore_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:57.533227+00:00" +instance: "kb-cron" +--- + +Before Baltimore classification was created, a variety of classification systems for viruses had been proposed, classifying viruses by host, structure, biochemical properties, and other characteristics. Baltimore classification was proposed in 1971 by virologist David Baltimore in a paper titled "Expression of Animal Virus Genomes" that was published in the academic journal Bacteriology Reviews (now named Microbiology and Molecular Biology Reviews). Baltimore focused on classifying animal viruses but effectively classified all viruses by their routes of information transmission from genomic nucleic acid to mRNA. The system initially contained the first six groups but was later expanded to include group VII after the discovery of dsDNA-RT viruses. Because of the utility of Baltimore classification, it came to be used alongside standard virus taxonomy, which is based on evolutionary relationships and governed by the International Committee on Taxonomy of Viruses (ICTV). +Over time, the belief that Baltimore groups were monophyletic spread among virologists. This was reflected in taxonomies published by the ICTV and the National Center for Biotechnology Information, which for decades placed the Baltimore groups as informal higher ranks above official taxonomic ranks. From 1991 to 2017, virus taxonomy used a five-rank system ranging from order to species, with Baltimore classification used in conjunction. Outside of official taxonomy, supergroups of viruses joining different taxa were created over time based on increasing evidence of deeper evolutionary relations. The advancement of sequencing methods in the 21st century in particular made it possible to study virus evolution and diversity in greater detail. This enabled virologists to better understand the relationships between Baltimore groups and the evolutionary history of viruses. Consequently, in 2016, the ICTV began to consider establishing ranks higher than order as well as how the Baltimore groups would be treated among higher taxa. +In two votes in 2018 and 2019, the ICTV established a 15-rank system ranging from realm to species. As part of this, the Baltimore groups for ssDNA, dsRNA, +ssRNA, –ssRNA, and RT viruses were incorporated into formal taxa. In 2019, the realm Riboviria was established and initially included all dsRNA, +ssRNA, and –ssRNA viruses. A year later, Riboviria was expanded to also include RT viruses. Within the realm, RT viruses are included in the kingdom Pararnavirae and the three other Baltimore groups in the kingdom Orthornavirae as defining traits of the kingdom's phyla. While –ssRNA viruses of Ribozyviria were initially classified in Riboviria, this was a clerical error that was fixed in 2020. A year later, Ribozyviria was established for HDV and its relatives. For ssDNA viruses, the realm Monodnaviria was established in 2020 to accommodate almost all ssDNA viruses, as well as dsDNA viruses descended from them. In 2026, however, Monodnaviria was split into four realms (Efunaviria, Floreoviria, Pleomoviria, and Volvereviria) based on evidence that its four kingdoms did not share common ancestry. +In 1974, virologist Vadim Agol proposed an extension of Baltimore classification to encompass all possible means of genetic information transmission and describe the hierarchical routes of information transmission, including both expression and replication, rather than solely mRNA synthesis. In the expanded system, there are 35 classes, 17 superclasses, and six types of genetic information transfer. The system was revisited in 2021 by Koonin et al. in light of discoveries made since the 1970s. Known viruses occupy 13 classes, one of which is shared with cells, seven superclasses, and three types. A fourteenth class is occupied by F-like plasmids. Ambisense viruses occupy two classes simultaneously, though separate classes could be made for them. Most unoccupied classes are of DNA-RNA hybrids, which appear to be disfavored by evolution since it may be advantageous to convert such molecules to dsDNA, the molecule most suitable for genome replication. According to Koonin et al., viruses that belong to the unoccupied classes are unlikely to be discovered unless they are rare in nature. + +== Notes == + +== References == + +=== Books cited === +Cann A (6 March 2015). Principles of Molecular Virology. Academic Press. pp. 122–127, 151–156. ISBN 978-0-12-801955-9. +Cotmore SF, Tattersall P (25 November 2005). "A Rolling-Hairpin Strategy: Basic Mechanisms of DNA Replication in the Parvoviruses". In Kerr J, Cotmore S, Bloom ME (eds.). Parvoviruses. CRC Press. pp. 171–185. ISBN 978-1-4441-1478-2. +Fermin G (12 March 2018). "Virion Structure, Genome Organization, and Taxonomy of Viruses". In Tennant P, Fermin G, Foster JE (eds.). Viruses: Molecular Biology, Host Interactions and Applications to Biotechnology. Academic Press. pp. 35–46. doi:10.1016/B978-0-12-811257-1.00002-4. ISBN 978-0-12-811194-9. S2CID 89706800. +Hartl DL (2018). Essential Genetics and Genomics. Jones & Bartlett Learning. p. 8. ISBN 978-1-284-15245-6. +Kuhn JH (1 March 2021). "Virus Taxonomy". In Bamford DH, Zuckerman M (eds.). Encyclopedia of Virology. Academic Press. pp. 28–37. doi:10.1016/B978-0-12-809633-8.21231-4. ISBN 978-0-12-809633-8. PMC 7157452. +Lostroh P (25 March 2024). "The Fundamentals of Molecular and Cellular Virology". Molecular and Cellular Biology of Viruses. CRC Press. pp. 11–13. ISBN 978-1-04-000533-0. +Louten J (28 May 2022). Essential Human Virology. Academic Press. ISBN 978-0-323-91492-5. +Manglik M (24 March 2024). Genomics, Genetic Engineering and Biotechnology Applications. EduGorilla Publication. pp. 17–18. ISBN 978-93-6984-122-6. +Rampersad S, Tennant P (12 March 2018). "Replication and Expression Strategies of Viruses". In Tennant P, Fermin G, Foster JE (eds.). Viruses: Molecular Biology, Host Interactions and Applications to Biotechnology. Academic Press. pp. 55–82. doi:10.1016/B978-0-12-811257-1.00003-6. ISBN 978-0-12-811194-9. S2CID 90170103. + +== Further reading == +Baltimore D (September 1971). "Expression of Animal Virus Genomes". Bacteriol Rev. 35 (3): 235–241. doi:10.1128/MMBR.35.3.235-241.1971. PMC 378387. PMID 4329869. — David Baltimore's original paper in which Baltimore classification was first proposed +Agol VI (October 1974). "Towards the System of Viruses". Biosystems. 6 (2): 113–132. Bibcode:1974BiSys...6..113A. doi:10.1016/0303-2647(74)90003-3. PMID 4613396. — Vadim Agol's paper in which he first proposed an extension of Baltimore classification + +== External links == + Media related to Baltimore classification at Wikimedia Commons \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Circumscriptional_name-0.md b/data/en.wikipedia.org/wiki/Circumscriptional_name-0.md new file mode 100644 index 000000000..48f6746eb --- /dev/null +++ b/data/en.wikipedia.org/wiki/Circumscriptional_name-0.md @@ -0,0 +1,28 @@ +--- +title: "Circumscriptional name" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Circumscriptional_name" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:02.234107+00:00" +instance: "kb-cron" +--- + +In biological classification, circumscriptional names (Latin: nomina circumscribentia) are taxon names that are defined by their circumscription; i.e. the diagnostic feature of the particular set of members included. Such names are not ruled by any nomenclature code and are mainly for taxa above the rank of family (e.g. order or class), but can be used for taxa of any rank or unranked taxa. +Non-typified names other than those of genus or species rank constitute the majority of generally accepted names of taxa higher than superfamily. The standard nomenclature codes regulate names of taxa up to family rank (i.e. superfamily). There are no generally accepted rules for the naming of higher taxa (orders, classes, phyla, etc.). Under the approach of circumscription-based (circumscriptional) nomenclatures, a circumscriptional name is associated with a certain circumscription of a taxon without regard of its rank or position. +In contrast to circumscriptional nomenclature, some authors advocate introducing a mandatory standardized typified nomenclature of higher taxa. They suggest all names of higher taxa to be derived in the same manner as family-group names, by modifying names of type genera with suffixes to reflect the rank. There is no consensus on what such higher rank suffixes should be. A number of established practices exist as to the use of typified names of higher taxa, depending on group of organisms. + + +== See also == +Descriptive botanical name, optional forms still used in botany for ranks above family and for a few family names + + +== References == + +Kluge, N. 2000. "Sovremennaya Sistematika Nasekomyh ..." [Modern Systematics of Insects. Part I. Principles of Systematics of Living Organisms and General System of Insects, with Classification of Primary Wingless and Paleopterous Insects] - S.-Petersburg, Lan', 2000, 333 pp.; (c) N.Ju. Kluge, 2000; (c) "Lan'", 2000. +Kluge N.J. 2010. Circumscriptional names of higher taxa in Hexapoda. // Bionomina, 1: 15–55. https://www.mapress.com/bionomina/content/2010/f/bn00001p055.pdf + + +== External links == +Kluge's PRINCIPLES OF NOMENCLATURE of ZOOLOGICAL TAXA +NOMINA CIRCUMSCRIBENTIA INSECTORUM \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cline_(biology)-0.md b/data/en.wikipedia.org/wiki/Cline_(biology)-0.md new file mode 100644 index 000000000..96908d9b6 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cline_(biology)-0.md @@ -0,0 +1,29 @@ +--- +title: "Cline (biology)" +chunk: 1/4 +source: "https://en.wikipedia.org/wiki/Cline_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:03.435002+00:00" +instance: "kb-cron" +--- + +In biology, a cline is a measurable gradient in a single characteristic (or biological trait) of a species across its geographical range. Clines usually have a genetic (e.g. allele frequency, blood type), or phenotypic (e.g. body size, skin pigmentation) character. They can show either smooth, continuous gradation in a character, or more abrupt changes in the trait from one geographic region to the next. +A cline is a spatial gradient in a single specific trait, rather than in a collection of traits; a single population can therefore have as many clines as it has traits, at least in principle. Additionally, as Julian Huxley recognised, these multiple independent clines may not act in concordance with each other. For example, it has been observed that in Australia, birds generally become smaller the further towards the north of the country they are found. In contrast, the intensity of their plumage colouration follows a different geographical trajectory, being most vibrant where humidity is highest and becoming less vibrant further into the arid centre of the country. +Because of this, Huxley described the notion of clines as an "auxiliary taxonomic principle,” meaning that clinal variation in a species is not awarded taxonomic recognition in the way subspecies or species are. +The term cline was coined by Huxley in 1938 from the Greek κλίνειν klinein, meaning "to lean.” While it and the term ecotype are sometimes used interchangeably, they do in fact differ in that ecotype refers to a population which differs from other populations in a number of characters, rather than the single character that varies amongst populations in a cline. + +== Drivers and the evolution of clines == + +Clines are often cited to be the result of two opposing drivers: selection and gene flow (also known as migration). Selection causes adaptation to the local environment, resulting in different genotypes or phenotypes being favoured in different environments. This diversifying force is countered by gene flow, which has a homogenising effect on populations and prevents speciation through causing genetic admixture and blurring any distinct genetic boundaries. + +=== Development of clines === +Clines are generally thought to arise under one of two conditions: "primary differentiation" (also known as "primary contact" or "primary intergradation"), or "secondary contact" (also known as "secondary introgression", or "secondary intergradation"). + +==== Primary differentiation ==== + +Clines produced through this way are generated by spatial heterogeneity in environmental conditions. The mechanism of selection acting upon organisms is therefore external. Species ranges frequently span environmental gradients (e.g. humidity, rainfall, temperature, or day length) and, according to natural selection, different environments will favour different genotypes or phenotypes. In this way, when previously genetically or phenotypically uniform populations spread into novel environments, they will evolve to be uniquely adapted to the local environment, in the process potentially creating a gradient in a genotypic or phenotypic trait. +Such clines in characters can not be maintained through selection alone if much gene flow occurred between populations, as this would tend to swamp out the effects of local adaptation. However, because species usually tend to have a limited dispersal range (e.g. in an isolation by distance model), restricted gene flow can serve as a type of barrier which encourages geographic differentiation. However, some degree of migration is often required to maintain a cline; without it, speciation is likely to eventually occur, as local adaptation can cause reproductive isolation between populations. +A classic example of the role of environmental gradients in creating clines is that of the peppered moth, Biston betularia, in the UK. During the 19th century, when the industrial sector gained traction, coal emissions blackened vegetation across northwest England and parts of northern Wales. As a result of this, lighter morphs of the moth were more visible to predators against the blackened tree trunks and were therefore more heavily predated relative to the darker morphs. Consequently, the frequency of the more cryptic melanic morph of the peppered moth increased drastically in northern England. This cline in morph colour, from a dominance of lighter morphs in the west of England (which did not suffer as heavily from pollution), to the higher frequency of melanic forms in the north, has slowly been degrading since limitations to sooty emissions were introduced in the 1960s. + +==== Secondary contact ==== \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cline_(biology)-1.md b/data/en.wikipedia.org/wiki/Cline_(biology)-1.md new file mode 100644 index 000000000..c05546288 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cline_(biology)-1.md @@ -0,0 +1,27 @@ +--- +title: "Cline (biology)" +chunk: 2/4 +source: "https://en.wikipedia.org/wiki/Cline_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:03.435002+00:00" +instance: "kb-cron" +--- + + +Clines generated through this mechanism have arisen through the joining of two formerly isolated populations which differentiated in allopatry, creating an intermediate zone. This secondary contact scenario may occur, for example, when climatic conditions change, allowing the ranges of populations to expand and meet. Because over time the effect of gene flow will tend to eventually swamp out any regional differences and cause one large homogenous population, for a stable cline to be maintained when two populations join there must usually be a selective pressure maintaining a degree of differentiation between the two populations. +The mechanism of selection maintaining the clines in this scenario is often intrinsic. This means that the fitness of individuals is independent of the external environment, and selection is instead dependent on the genome of the individual. Intrinsic, or endogenous, selection can give rise to clines in characters through a variety of mechanisms. One way it may act is through heterozygote disadvantage, in which intermediate genotypes have a lower relative fitness than either homozygote genotypes. Because of this disadvantage, one allele will tend to become fixed in a given population, such that populations will consist largely of either AA (homozygous dominant) or aa (homozygous recessive) individuals. The cline of heterozygotes that is created when these respective populations come into contact is then shaped by the opposing forces of selection and gene flow; even if selection against heterozygotes is great, if there is some degree of gene flow between the two populations, then a steep cline may be able to be maintained. +Because instrinsic selection is independent of the external environment, clines generated by selection against hybrids are not fixed to any given geographical area and can move around the geographic landscape. Such hybrid zones where hybrids are a disadvantage relative to their parental lines (but which are nonetheless maintained through selection being counteracted by gene flow) are known as "tension zones". +Another way in which selection can generate clines is through frequency-dependent selection. Characters that could be maintained by such frequency-dependent selective pressures include warning signals (aposematism). For example, aposematic signals in Heliconius butterflies sometimes display steep clines between populations, which are maintained through positive frequency dependence. This is because heterozygosity, mutations and recombination can all produce patterns that deviate from those well-established signals which mark prey as being unpalatable. These individuals are then predated more heavily relative to their counterparts with "normal" markings (i.e. selected against), creating populations dominated by a particular pattern of warning signal. As with heterozygote disadvantage, when these populations join, a narrow cline of intermediate individuals could be produced, maintained by gene flow counteracting selection. +Secondary contact could lead to a cline with a steep gradient if heterozygote disadvantage or frequency-dependent selection exists, as intermediates are heavily selected against. Alternatively, steep clines could exist because the populations have only recently established secondary contact, and the character in the original allopatric populations had a large degree of differentiation. As genetic admixture between the population increases with time however, the steepness of the cline is likely to decrease as the difference in character is eroded. However, if the character in the original allopatric populations was not very differentiated to begin with, the cline between the populations need not display a very steep gradient. Because both primary differentiation and secondary contact can therefore give rise to similar or identical clinal patterns (e.g. gently sloping clines), distinguishing which of these two processes is responsible for generating a cline is difficult and often impossible. However, in some circumstances a cline and a geographic variable (such as humidity) may be very tightly linked, with a change in one corresponding closely to a change in the other. In such cases it may be tentatively concluded that the cline is generated by primary differentiation and therefore moulded by environmental selective pressures. + +==== No selection (drift/migration balance) ==== +While selection can therefore clearly play a key role in creating clines, it is theoretically feasible that they might be generated by genetic drift alone. It is unlikely that large-scale clines in genotype or phenotype frequency will be produced solely by drift. However, across smaller geographical scales and in smaller populations, drift could produce temporary clines. The fact that drift is a weak force upholding the cline however means that clines produced this way are often random (i.e. uncorrelated with environmental variables) and subject to breakdown or reversal over time. Such clines are therefore unstable and sometimes called "transient clines". + +== Clinal structure and terminology == + +The steepness, or gradient, of a cline reflects the extent of the differentiation in the character across a geographic range. For example, a steep cline could indicate large variation in the colour of plumage between adjacent bird populations. It has been previously outlined that such steep clines may be the result of two previously allopatric populations with a large degree of difference in the trait having only recently established gene flow, or where there is strong selection against hybrids. However, it may also reflect a sudden environmental change or boundary. Examples of rapidly changing environmental boundaries like this include abrupt changes in the heavy metal content of soils, and the consequent narrow clines produced between populations of Agrostis that are either adapted to these soils with high metal content, or adapted to "normal" soil. +Conversely, a shallow cline indicates little geographical variation in the character or trait across a given geographical distance. This may have arisen through weak differential environmental selective pressure, or where two populations established secondary contact a long time ago and gene flow has eroded the large character differentiation between the populations. +The gradient of a cline is related to another commonly referred to property, clinal width. A cline with a steep slope is said to have a small, or narrow, width, while shallower clines have larger widths. + +== Types of clines == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cline_(biology)-2.md b/data/en.wikipedia.org/wiki/Cline_(biology)-2.md new file mode 100644 index 000000000..1e353412e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cline_(biology)-2.md @@ -0,0 +1,36 @@ +--- +title: "Cline (biology)" +chunk: 3/4 +source: "https://en.wikipedia.org/wiki/Cline_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:03.435002+00:00" +instance: "kb-cron" +--- + +According to Huxley, clines can be classified into two categories; continuous clines and discontinuous stepped clines. These types of clines characterise the way that a genetic or phenotypic trait transforms from one end of its geographical range of the species to the other. + +=== Continuous clines === +In continuous clines, all populations of the species are able to interbreed and there is gene flow throughout the entire range of the species. In this way, these clines are both biologically (no clear subgroups) and geographically (contiguous distribution) continuous. +Continuous clines can be further sub-divided into smooth and stepped clines. + +Continuous smooth clines are characterised by the lack of any abrupt changes or delineation in the genetic or phenotypic trait across the cline, instead displaying a smooth gradation throughout. Huxley recognised that this type of cline, with its uniform slope throughout, was unlikely to be common. +Continuous stepped clines consist of an overall shallow cline, interspersed by sections of much steeper slope. The shallow slope represents the populations, and the shorter, steeper sections the larger change in character between populations. Stepped clines can be further subdivided into horizontally stepped clines, and obliquely stepped clines. +Horizontally stepped clines show no intra-population variation or gradation in the character, therefore displaying a horizontal gradient. These uniform populations are connected by steeper sections of the cline, characterised by larger changes in the form of the character. However, because in continuous clines all populations exchange genetic material, the intergradation zone between the groups can never have a vertical slope. +In obliquely stepped clines, conversely, each population also demonstrates a cline in the character, albeit of a shallower slope than the clines connecting the populations together. Huxley compared obliquely stepped clines to looking like a "stepped ramp", rather than taking on the formation of a staircase as in the case of horizontally stepped clines. + +=== Discontinuous stepped clines === +Unlike in continuous clines, in discontinuous clines the populations of species are allopatric, meaning there is very little or no gene flow amongst populations. The genetic or phenotypic trait in question always shows a steeper gradient between groups than within groups, as in continuous clines. Discontinuous clines follow the same principles as continuous clines by displaying either + +Horizontally stepped clines, where intra-group variation is very small or non-existent and the geographic space separating groups shows a sharp change in character +Obliquely stepped clines, where there is some intra-group gradation, but this is less than the gradation in the character between populations + +== Clines and speciation == + +It was originally assumed that geographic isolation was a necessary precursor to speciation (allopatric speciation). The possibility that clines may be a precursor to speciation was therefore ignored, as they were assumed to be evidence of the fact that in contiguous populations gene flow was too strong a force of homogenisation, and selection too weak a force of differentiation, for speciation to take place. However, the existence of particular types of clines, such as ring species, in which populations did not differentiate in allopatry but the terminal ends of the cline nonetheless do not interbreed, cast into doubt whether complete geographical isolation of populations is an absolute requirement for speciation. +Because clines can exist in populations connected by some degree of gene flow, the generation of new species from a previously clinal population is termed parapatric speciation. Both extrinsic and intrinsic selection can serve to generate varying degrees of reproductive isolation and thereby instigate the process of speciation. For example, through environmental selection acting on populations and favouring particular allele frequencies, large genetic differences between populations may accumulate (this would be reflected in clinal structure by the presence of numerous very steep clines). If the local genetic differences are great enough, it may lead unfavourable combinations of genotypes and therefore to hybrids being at a decreased fitness relative to the parental lines. When this hybrid disadvantage is great enough, natural selection will select for pre-zygotic traits in the homozygous parental lines that reduce the likelihood of disadvantageous hybridisation - in other words, natural selection will favour traits that promote assortative mating in the parental lines. This is known as reinforcement and plays an important role in parapatric and sympatric speciation. + +== Clinal maps == +Clines can be portrayed graphically on maps using lines that show the transition in character state from one end of the geographic range to the other. Character states can however additionally be represented using isophenes, defined by Ernst Mayr as "lines of equal expression of a clinally varying character". In other words, areas on maps that demonstrate the same biological phenomenon or character will be connected by something that resembles a contour line. When mapping clines therefore, which follow a character gradation from one extreme to the other, isophenes will transect clinal lines at a right angle. + +== Examples of clines == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cline_(biology)-3.md b/data/en.wikipedia.org/wiki/Cline_(biology)-3.md new file mode 100644 index 000000000..c7d2cafe4 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cline_(biology)-3.md @@ -0,0 +1,17 @@ +--- +title: "Cline (biology)" +chunk: 4/4 +source: "https://en.wikipedia.org/wiki/Cline_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:03.435002+00:00" +instance: "kb-cron" +--- + +Although the term "cline" was first officially coined by Huxley in 1938, gradients and geographic variations in the character states of species have been observed for centuries. Indeed, some gradations have been considered so ubiquitous that they have been labelled ecological "rules". One commonly cited example of a gradient in morphology is Gloger's Rule, named after Constantin Gloger, who observed in 1833 that environmental factors and the pigmentation of avian plumage tend to covary with each other, such that birds found in arid areas near the Equator tend to be much darker than those in less arid areas closer to the Poles. Since then, this rule has been extended to include many other animals, including flies, butterflies, and wolves. +Other ecogeographical rules include Bergmann's Rule, coined by Carl Bergmann in 1857, which states that homeotherms closer to the Equator tend to be smaller than their more northerly or southerly conspecifics. One of the proposed reasons for this cline is that larger animals have a relatively smaller surface area to volume ratio and therefore improved heat conservancy – an important advantage in cold climates. The role of the environment in imposing a selective pressure and producing this cline has been heavily implicated due to the fact that Bergmann's Rule has been observed across many independent lineages of species and continents. For example, the house sparrow, which was introduced in the early 1850s to the eastern United States, evolved a north-south gradient in size soon after its introduction. This gradient reflects the gradient that already existed in the house sparrow's native range in Europe. + +Ring species are a distinct type of cline where the geographical distribution in question is circular in shape, so that the two ends of the cline overlap with one another, giving two adjacent populations that rarely interbreed due to the cumulative effect of the many changes in phenotype along the cline. The populations elsewhere along the cline interbreed with their geographically adjacent populations as in a standard cline. In the case of Larus gulls, the habitats of the end populations even overlap, which introduces questions as to what constitutes a species: nowhere along the cline can a line be drawn between the populations, but they are unable to interbreed. +In humans, clines in the frequency of blood types has allowed scientists to infer past population migrations. For example, the Type B blood group reaches its highest frequency in Asia, but become less frequent further west. From this, it has been possible to infer that some Asian populations migrated towards Europe around 2,000 years ago, causing genetic admixture in an isolation by distance model. In contrast to this cline, blood Type A shows the reverse pattern, reaching its highest frequency in Europe and declining in frequency towards Asia. + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Compositional_domain-0.md b/data/en.wikipedia.org/wiki/Compositional_domain-0.md new file mode 100644 index 000000000..4fcf733ef --- /dev/null +++ b/data/en.wikipedia.org/wiki/Compositional_domain-0.md @@ -0,0 +1,24 @@ +--- +title: "Compositional domain" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Compositional_domain" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:04.587158+00:00" +instance: "kb-cron" +--- + +A compositional domain in genetics is a region of DNA with a distinct guanine (G) and cytosine (C) G-C and C-G content (collectively GC content). The homogeneity of compositional domains is compared to that of the chromosome on which they reside. As such, compositional domains can be homogeneous or nonhomogeneous domains. Compositionally homogeneous domains that are sufficiently long (= 300 kb) are termed isochores or isochoric domains. +The compositional domain model was proposed as an alternative to the isochoric model. The isochore model was proposed by Bernardi and colleagues to explain the observed non-uniformity of genomic fragments in the genome. However, recent sequencing of complete genomic data refuted the isochoric model. Its main predictions were: + +GC content of the third codon position (GC3) of protein coding genes is correlated with the GC content of the isochores embedding the corresponding genes. This prediction was found to be incorrect. GC3 could not predict the GC content of nearby sequences. +The genome organization of warm-blooded vertebrates is a mosaic of isochores. This prediction was rejected by many studies that used the complete human genome data. +The genome organization of cold-blooded vertebrates is characterized by low GC content levels and lower compositional heterogeneity. This prediction was disproved by finding high and low GC content domains in fish genomes. +The compositional domain model describes the genome as a mosaic of short and long homogeneous and nonhomogeneous domains. The composition and organization of the domains were shaped by different evolutionary processes that either fused or broke down the domains. This genomic organization model was confirmed in many new genomic studies of cow, honeybee, sea urchin, body louse, Nasonia, beetle, and ant genomes. The human genome was described as consisting of a mixture of compositionally nonhomogeneous domains with numerous short compositionally homogeneous domains and relatively few long ones. + + +== References == + + +== External links == +IsoPlotter — a free, open source program to calculate and visualize isochores in a given genome \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Comstock–Needham_system-0.md b/data/en.wikipedia.org/wiki/Comstock–Needham_system-0.md new file mode 100644 index 000000000..86f24ccfd --- /dev/null +++ b/data/en.wikipedia.org/wiki/Comstock–Needham_system-0.md @@ -0,0 +1,50 @@ +--- +title: "Comstock–Needham system" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Comstock–Needham_system" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:05.728387+00:00" +instance: "kb-cron" +--- + +The Comstock–Needham system is a naming system for insect wing veins, devised by John Comstock and George Needham in 1898. It was an important step in showing the homology of all insect wings. This system was based on Needham's pretracheation theory that was later discredited by Frederic Charles Fraser in 1938. + + +== Vein terminology == + + +=== Longitudinal veins === +The Comstock and Needham system attributes different names to the veins on an insect's wing. From the anterior (leading) edge of the wing towards the posterior (rear), the major longitudinal veins are named: +costa C, meaning rib +subcosta Sc, meaning below the rib +radius R, in analogy with a bone in the forearm, the radius +media M, meaning middle +cubitus Cu, meaning elbow +anal veins A, in reference to its posterior location +Apart from the costal and the anal veins, each vein can be branched, in which case the branches are numbered from anterior to posterior. For example, the two branches of the subcostal vein will be called Sc1 and Sc2. +The radius typically branches once near the base, producing anteriorly the R1 and posteriorly the radial sector Rs. The radial sector may fork twice. +The media may also fork twice, therefore having four branches reaching the wing margin. +According to the Comstock–Needham system, the cubitus forks once, producing the cubital veins Cu1 and Cu2. +According to some other authorities, Cu1 may fork again, producing the Cu1a and Cu1b. +As there are several anal veins, they are called A1, A2, and so on. They are usually unforked. + + +=== Crossveins === +Crossveins link the longitudinal veins, and are named accordingly (for example, the medio-cubital crossvein is termed m-cu). Some crossveins have their own name, like the humeral crossvein h and the sectoral crossvein s. + + +== Cell terminology == +The cells are named after the vein on the anterior side; for instance, the cell between Sc2 and R1 is called Sc2. +In the case where two cells are separated by a crossvein but have the same anterior longitudinal vein, they should have the same name. To avoid this, they are attributed a number. For example, the R1 cell is divided in two by the radial cross vein: the basal cell is termed "first R1", and the distal cell "second R1". +If a cell is bordered anteriorly by a forking vein, such as R2 and R3, the cell is named after the posterior vein, in this case R3. + + +== References == + +Comstock, J.H. & Needham, J.G. (1898) The wings of Insects. IX The Venation of the Wings of Hymenoptera. The American Naturalist, 32:413-424. +Triplehorn, Charles A.; Johnson Norman F. (2005). Borror and DeLong's introduction to the study of insects (7th ed.). Thomson Brooks/Cole. ISBN 0-03-096835-6. + + +== External links == +North–Carolina state University course on insect wings \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Conserved_name-0.md b/data/en.wikipedia.org/wiki/Conserved_name-0.md new file mode 100644 index 000000000..ac98386a2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Conserved_name-0.md @@ -0,0 +1,43 @@ +--- +title: "Conserved name" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Conserved_name" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:06.894682+00:00" +instance: "kb-cron" +--- + +A conserved name or nomen conservandum (plural nomina conservanda, abbreviated as nom. cons.) is a scientific name that has specific nomenclatural protection in that the name is retained, even though it violates one or more rules that would otherwise prevent it from being legitimate. Nomen conservandum is a Latin term, meaning 'a name to be conserved'. While "conserved name" and "nomen conservandum" are often used interchangeably, such as by the International Code of Nomenclature for Algae, Fungi, and Plants (ICN), the International Code of Zoological Nomenclature favors "conserved name". +The process for conserving botanical names is different from that for zoological names. Under the botanical code, names may also be "suppressed", nomen rejiciendum (plural nomina rejicienda or nomina utique rejicienda, abbreviated as nom. rej.), or rejected in favor of a particular conserved name, and combinations based on a suppressed name are also listed as nom. rej. + +== Botany == + +=== Conservation === +In botanical nomenclature, conservation is a nomenclatural procedure governed by Article 14 of the ICN. Its purpose is "to avoid disadvantageous nomenclatural changes entailed by the strict application of the rules, and especially of the principle of priority [...]" (Art. 14.1). It applies only to names at the rank of family, genus or species. +It may effect a change in original spelling, type, or (most commonly) priority. + +Conserved spelling (orthographia conservanda, orth. cons.) allows spelling usage to be preserved even if the name was published with another spelling: Euonymus (not Evonymus), Guaiacum (not Guajacum), etc. (see orthographical variant). +Conserved types (typus conservandus, typ. cons.) are often made when it is found that a type in fact belongs to a different taxon from the description, when a name has subsequently been generally misapplied to a different taxon, or when the type belongs to a small group separate from the monophyletic bulk of a taxon. +Conservation of a name against an earlier taxonomic (heterotypic) synonym (which is termed a rejected name, nomen rejiciendum, nom. rej.) is relevant only if a particular taxonomist includes both types in the same taxon. + +=== Rejection === +Besides conservation of names of certain ranks (Art. 14), the ICN also offers the option of outright rejection of a name (nomen utique rejiciendum) also called suppressed name under Article 56, another way of creating a nomen rejiciendum that cannot be used anymore. Outright rejection is possible for a name at any rank. +Rejection (suppression) of individual names is distinct from suppression of works (opera utique oppressa) under Article 34, which allows for listing certain taxonomic ranks in certain publications that are considered not to include any validly published names. + +=== Effects === +Conflicting conserved names are treated according to the normal rules of priority. Separate proposals (informally referred to as "superconservation" proposals) may be made to protect a conserved name that would be overtaken by another. However, conservation has different consequences depending on the type of name that is conserved: + +A conserved family name is protected against all other family names based on genera that are considered by the taxonomist to be part of the same family. +A conserved genus or species name is conserved against any homonyms, homotypic synonyms, and those specific heterotypic synonyms that are simultaneously declared nomina rejicienda (as well as their own homotypic synonyms). As taxonomic changes are made, other names may require new proposals for conservation and/or rejection. + +=== Documentation === +Conserved and rejected names (and suppressed names) are listed in the appendices to the ICN. As of the 2012 (Melbourne) edition, a separate volume holds the bulk of the appendices (except appendix I, on names of hybrids). The substance of the second volume is generated from a database that also holds a history of published proposals and their outcomes, the binding decisions on whether a name is validly published (article 38.4) and on whether it is a homonym (article 53.5). The database can be queried online. + +=== Procedure === +The procedure starts by submitting a proposal to the journal Taxon (published by the IAPT). This proposal should present the case both for and against conservation of a name. Publication notifies anybody concerned that the matter is being considered and makes it possible for those interested to write in. Publication is the start of the formal procedure: it counts as referring the matter "to the appropriate Committee for study" and Rec 14A.1 comes into effect. The name in question is (somewhat) protected by this Recommendation ("... authors should follow existing usage as far as possible ..."). +After reviewing the matter, judging the merits of the case, "the appropriate Committee" makes a decision either against ("not recommended") or in favor ("recommended"). Then the matter is passed to the General Committee. +After reviewing the matter, mostly from a procedural angle, the General Committee makes a decision, either against ("not recommended") or in favor ("recommended"). At this point Article 14.16 comes into effect. Art 14.16 authorizes all users to indeed use that name. +The General Committee reports to the Nomenclature Section of the International Botanical Congress, stating which names (including types and spellings) it recommends for conservation. Then, by Div.III.1, the Nomenclature Section makes a decision on which names (including types, spellings) are accepted into the Code. At this stage the de facto decision is made to modify the Code. +The Plenary Session of that same International Botanical Congress receives the "resolution moved by the Nomenclature Section of that Congress" and makes a de jure decision to modify the Code. By long tradition this step is ceremonial in nature only. +In the course of time there have been different standards for the majority required for a decision. However, for decades the Nomenclature Section has required a 60% majority for an inclusion in the Code, and the Committees have followed this example, in 1996 adopting a 60% majority for a decision. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Conserved_name-1.md b/data/en.wikipedia.org/wiki/Conserved_name-1.md new file mode 100644 index 000000000..ea2562537 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Conserved_name-1.md @@ -0,0 +1,28 @@ +--- +title: "Conserved name" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Conserved_name" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:06.894682+00:00" +instance: "kb-cron" +--- + +== Zoology == +For zoology, the term "conserved name", rather than "nomen conservandum", is used in the International Code of Zoological Nomenclature, although informally both terms are used interchangeably. +In the glossary of the International Code of Zoological Nomenclature (the code for names of animals, one of several nomenclature codes), this definition is given: + +conserved name +A name otherwise unavailable or invalid that the Commission, by the use of its plenary power, has enabled to be used as a valid name by removal of the known obstacles to such use. +This is a more generalized definition than the one for nomen protectum, which is specifically a conserved name that is either a junior synonym or homonym that is in use because the senior synonym or homonym has been made a nomen oblitum ("forgotten name"). +An example of a conserved name is the dinosaur genus name Pachycephalosaurus, which was formally described in 1943. Later, Tylosteus (which was formally described in 1872) was found to be the same genus as Pachycephalosaurus (a synonym). By the usual rules, the genus Tylosteus has precedence and would normally be the correct name. But the International Commission on Zoological Nomenclature (ICZN) ruled that the name Pachycephalosaurus was to be given precedence and treated as the valid name, because it was in more common use and better known to scientists. +The ICZN's procedural details are different from those in botany, but the basic operating principle is the same, with petitions submitted to the commission for review. + +== See also == +Opinion 2027, an example of name conservation as applied by ICZN +Glossary of scientific naming + +== References == + +Crosby, Marshall R. (1972). "An example of a 'nomen rejiciendum et illegitimum'". Taxon. 21 (1): 205–209. doi:10.2307/1219271. JSTOR 1219271. +McVaugh R, Ross R, Stafleu FA (1968). An annotated glossary of botanical nomenclature. Utrecht, Netherlands: International Bureau for Plant Taxonomy and Nomenclature of the International Association for Plant Taxonomy. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cormophyte-0.md b/data/en.wikipedia.org/wiki/Cormophyte-0.md new file mode 100644 index 000000000..1313559d4 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cormophyte-0.md @@ -0,0 +1,15 @@ +--- +title: "Cormophyte" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Cormophyte" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:08.050961+00:00" +instance: "kb-cron" +--- + +Cormophytes (Cormophyta) is a historical term seldom used today for the plants that are differentiated into roots, stems and leaves. These plants differ from thallophytes, whose body is referred to as the thallus, i.e. a simple body not differentiated into leaves and stems. Definitions have varied, notably about whether mosses and liverworts are included. +Stephan Endlicher, a 19th-century Austrian botanist, divided the vegetable kingdom in 1836 into two groups: the thallophytes were only the algae, lichens and fungi, and the cormophytes were the mosses, liverworts, ferns, Equisitaceae, club mosses and seed plants. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Cormus-0.md b/data/en.wikipedia.org/wiki/Cormus-0.md new file mode 100644 index 000000000..311a96d56 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Cormus-0.md @@ -0,0 +1,19 @@ +--- +title: "Cormus" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Cormus" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:09.221911+00:00" +instance: "kb-cron" +--- + +Cormus (pl: cormi) (from ancient Greek: κορμός, kormόs, 'stem') is the appearance of a plant that belong to Cormophyte (Pteridophyte and Spermatophyte). In cormus, the vegetative apparatus is no longer a thallus, such as algae, that cannot be distinctly differentiated. The structure of cormus can be easily differentiated into its roots, stems, and leaves. +In the sense of Ernst Haeckel, cormus is a plant or "colonia" animal made up of a number of individuals which originate by gemmation or budding. As applied to animals, cormus is equivalent to polypidom. + + +== See also == +Thallophyte + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Eocyte_hypothesis-0.md b/data/en.wikipedia.org/wiki/Eocyte_hypothesis-0.md new file mode 100644 index 000000000..a35b88354 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Eocyte_hypothesis-0.md @@ -0,0 +1,34 @@ +--- +title: "Eocyte hypothesis" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Eocyte_hypothesis" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:10.485941+00:00" +instance: "kb-cron" +--- + +The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes (later classified as Thermoproteota, a group of archaea). After his team at the University of California, Los Angeles discovered eocytes in 1984, James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: prokaryotes, which include Bacteria and Archaea, and karyotes, that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria. +Lake's hypothesis was based on an analysis of the structural components of ribosomes. It was largely ignored, being overshadowed by the three-domain system which relied on more precise genetic analysis. In 1990, Carl Woese and his colleagues proposed that cellular life consists of three domains—Eucarya, Bacteria, and Archaea – based on the ribosomal RNA sequences. The three-domain concept was widely accepted in genetics, and became the presumptive classification system for high-level taxonomy, and was promulgated in many textbooks. +Resurgence of archaea research after the 2000s, using advanced genetic techniques, and later discoveries of new groups of archaea revived the eocyte hypothesis; consequently, the two-domain system has found wider acceptance. + +== Description == +In 1984, James A. Lake, Michael W. Clark, Eric Henderson, and Melanie Oakes of the University of California, Los Angeles described a new group of prokaryotic organisms designated as "a group of sulfur-dependent bacteria." Based on the structure and composition of their ribosomal subunits, they found that these organisms were different from other prokaryotes, bacteria and archaea, known at the time. They named them eocytes (for "dawn cells") and proposed a new biological kingdom Eocyta. According to this discovery, the tree of life is represented by four kingdoms, Archaebacteria, Eubacteria, Eukaryote and Eocyta. +Following analyses of the rRNA sequences of the four groups, Lake concluded in 1988 that eukaryotes were closely related to eocytes so that the two groups constitute the same (monophyletic) group, meaning that eukaryotes originated from eocytes and not archaebacteria, as was generally assumed. This was the establishment of the eocyte hypothesis. +In 1988, Lake proposed a systematic classification of all life forms into two taxonomic groups, which he later mentioned as superkingdoms: + +Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes) +Parkaryotes (that consists of eubacteria and two groups of archaea known at the time, halobacteria and methanogens) + +== Development and competition == +Lake's classification was not widely recognised, but the eocyte hypothesis gained considerable attention after its introduction due to the interest in determining the origin of the eukaryotic cell. However, the concept faced a problem because it was not known that eocytes, the main organism group on which the hypothesis was based, were archaea. For example, studies in the late 1980s and early 1990s still treated eocytes as separate group from archaea. As Lake also argued, the rival hypothesis was called archaebacterial tree (as introduced by Carl Woese of the University of Illinois in 1987) or archaebacterial theory, which (supposedly) stated that eukaryotes originated from archaea, and not eocytes. +Due to such confusion, some studies appeared to invalidate the hypothesis. For example, Japanese scientists reported in 1990 their study on the elongation factors Tu(EF-Tu) and G(EF-G) from various organisms that showed that eukaryotes are most closely related to archaea (methanogen and halobacteria), and not eocytes. Other studies also supported the eukaroyte-archaea relationship and rejected the eocyte hypotheses. Ribosomal RNA sequencing in 1989 also opposed the eocyte tree as the origin of eukaryotes. + +=== Three-domain system === +The most important blow to the eocyte hypothesis and Lake's classification was the development of ribosomal RNA sequencing that became a reliable determinant in biological classification. Introduced in 1977 by Carl Woese and George E. Fox in classification, the technique indicated that archaea (with only methanogens known at the time) and bacteria were distinct groups of organisms. Two kingdoms, Archaebacteria (archaea) and Eubacteria (for bacteria) were established. Based on further studies, Woese, Otto Kandler and Mark Wheelis introduced the concept of "domain" in 1990 as the highest level of biological classification, and proposed the three-domain system consisting of Eucarya, Bacteria and Archaea. With it they classified eocytes as archaea under the phylum Crenarchaeota (which was renamed Thermoproteota in 2021). +The classification gradually gained acceptance and was recognised as "arguably the best-developed and most widely-accepted scientific hypotheses [with the five-kingdom classification] regarding the evolutionary history of life." It became a scientific concept and general taxonomy in textbooks. Although Lake continued to advocate his eocyte taxonomy and hypothesis instead of conceding that eocytes were archaea, the hypothesis was largely neglected and support of it waned in favour of the three-domain system. + +== Archaeal studies == +In addition to a Thermoproteota origin of eukaryotes, some studies have suggested that eukaryotes may also have originated in the Nitrososphaerota (formerly Thaumarchaeota). +A superphylum TACK has been proposed that includes the Nitrososphaerota, Thermoproteota, and other groups of archaea, so that this superphylum may be related to the origin of eukaryotes. It is seen that eukaryotes share a large number of proteins with members of the TACK superphylum and that these complex archaea may have had rudimentary phagocytosis abilities to engulf bacteria. +As a result of metagenomic analysis of material found nearby hydrothermal vents, another superphylum — Asgard — has been named and proposed to be more closely related to the original eukaryote and a sister group to TACK more recently. Asgard consists of phyla Lokiarchaeota (found first), Heimdallarchaeota (possibly related closest to eukaryotes) and others. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Eocyte_hypothesis-1.md b/data/en.wikipedia.org/wiki/Eocyte_hypothesis-1.md new file mode 100644 index 000000000..6f20b8539 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Eocyte_hypothesis-1.md @@ -0,0 +1,42 @@ +--- +title: "Eocyte hypothesis" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Eocyte_hypothesis" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:10.485941+00:00" +instance: "kb-cron" +--- + +== Root of the eocyte tree == +The eocyte tree root may be located in the RNA world; that is, the root organism may have been a ribocyte (also known as a ribocell). For cellular DNA and DNA handling, an "out of virus" scenario has been proposed: storing genetic information in DNA may have been an innovation performed by viruses and later handed over to ribocytes twice, once transforming them into bacteria and once transforming them into archaea. +Although archaeal viruses are not as well-studied as bacterial phages, it is thought that dsDNA viruses led to the incorporation of the viral genome into archaeal genomes. The transduction of genetic material through a viral vector led to an increase in complexity in the pre-eukaryotic cells. All these findings do not change the eocyte tree as given here in principle, but examine a higher resolution of it. + +== Arguments against == +Due to the similarities found between eukaryotes and both archaea and bacteria, it is thought that a major source of the genetic variation is through horizontal gene transfer. Horizontal gene transfer explains why archaeal sequences are found in bacteria and bacterial sequences are found in archaea. This could explain why elongation factors found in archaea and eukaryotes are so similar, the data currently out is obscured as horizontal gene transfer, vertical gene transfer, or endosymbiosis and could be behind the gene sequence similarity. The eocyte hypothesis also has troubles due to the endosymbiotic theory, with the archaea being able to phagocytize bacteria for the formation of membrane-bound organelles. It is thought that these ancestral prokaryotes began to have ectosymbiotic relationships with other prokaryotes and gradually engulfed these symbiotes through cell membrane protrusions. +Although more recent data provides evidence in favour of the relationship between eukaryotes and Thermoproteota through the analysis of elongation factors, earlier experimentation with elongation factors provided evidence against such a relationship. Hasegawa et al. uses these elongation factors to show that eukaryotes and archaebacteria are more closely related than archaebacteria and eubacteria than is explained in this two-tree system. + +== Competing hypothesis == +A competing hypothesis is that prokaryotes evolved towards thriving in higher temperatures to evade viruses through the thermoreduction hypothesis, however this does not account for the arising of eukaryotes and only takes into consideration the prokaryotic origins. However decrease in complexity from a more complex origin is the basis of reductive evolution where a commensal relationship occurs, while this reduction explained in the thermoreduction hypothesis uses a parasitic relationship with viruses to explain the movement of complex pre-eukaryotes to a more harsh environment; that being ocean floor hydrothermal vents. + +== Revival == + +=== Molecular studies === +With advancements in genomics, the eocyte hypothesis experienced a revival beginning in the mid-2000s. As more archaeal genomes were sequenced, numerous genes coding for eukaryotic traits have been discovered in various archaean phyla, seemingly providing support for the eocyte hypothesis. Proteomics based research has also found supporting data with the use of elongation factor 1-α (eEF-1), a common housekeeping protein, to compare structural homology between eukaryotic and archaean lineages. Furthermore, other proteins have been sequenced through proteomics with homologous structures in heat shock proteins found in both eukaryotes and archaea. The structure of these heat shock proteins were identified through X-ray crystallography to find the three dimensional structure of the proteins. These proteins however have differing purposes as the eukaryote heat shock protein is a part of the T-complex while the archaeal heat shock protein is a molecular chaperone. This creates an issue with the sequence homology that has been seen between 70 kilodalton heat shock proteins in eukaryotes and Gram-negative bacteria. +Ribosome protein sequencing and phylogenetic analyses in 2004 showed that eukaryotes emerged from archaea. Phylogenomic analysis in 2007 also pointed to the origin of eukaryotes specifically from the Thermoplasmatales. The so-called "eukaryotic signature proteins" actin (cytoskeletal microfilament involved in cell motility), tubulin (component of the large cytoskeleton, microtubule), and the ubiquitin system (protein degradation and recycling), which are thought to be unique to eukaryotes, were found in TACK (comprising the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) archaea but not in other archaea. These indicate that eukaryotes can be merged into archaea. + +=== Discovery of Asgards === +Asgard, described as "eukaryote-like archaea", were discovered in 2012. The first known Asgards called Lokiarchaeota contain more eukaryotic protein-genes than the TACK group that supported the merging of eukaryote–archaea grouping, meaning a single domain of Archaea. Phylogenomic studies indicated that Heimdallarchaeota, another group of Asgards, are the closest relatives of eukaryotes. A new group of Asgard described in 2021, named Wukongarchaeota, are also among the eukaryotic roots. Another new Asgard reported in 2022, named Njordarchaeota, is related to the Heimdallarchaeota–Wukongarchaeota branch and is possibly the origin group for eukaryotes. +The Asgards contain at least 80 genes for eukaryotic signature proteins. In addition to actin, tubulin, ubiquitin and ESCRT proteins found in TACK archaea, Asgards contain functional genes for several other eukaryotic proteins such as profilins, ubiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins), membrane-trafficking systems (such as Sec23/24 and TRAPP domains), variety of small GTPases (including Gtr/Rag family GTPase orthologues), and gelsolins. + +=== Two-domain system === +As more archaea were later discovered and better genetic analyses were available, it was realised that the three-domain concept might not have represented the correct origin of eukaryotes. Ford Doolittle, then at Dalhousie University, wrote in 2020: + +"[The] three-domain tree wrongly represents evolutionary relationships, presenting a misleading view about how eukaryotes evolved from prokaryotes. The three-domain tree does recognize a specific archaeal–eukaryotic affinity, but it would have the latter arising independently, not from within, the former." +This is because research since the early 2000s has revealed two important issues: eukaryotes originated within Archaea, and a new group of archaea called Asgards represent the root of eukaryotes. This led to the rebirth of the eocyte hypothesis and development of the two-domain system. +Discoveries of eukaryotic signature proteins in TACK and Asgard archaea support the notion that eukaryotes evolved from archaea. Discoveries of more Asgards and better understanding of their nature indicate that they are the likely root of eukaryotes and are considered strong "evidence of the Eocyte hypothesis." Although these facts do not completely rule out the three-domain concept, they generally strengthened the two-domain system. + +== See also == +Hydrogen hypothesis + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Evolutionary_taxonomy-0.md b/data/en.wikipedia.org/wiki/Evolutionary_taxonomy-0.md new file mode 100644 index 000000000..39dddc1c5 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Evolutionary_taxonomy-0.md @@ -0,0 +1,29 @@ +--- +title: "Evolutionary taxonomy" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Evolutionary_taxonomy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:11.679071+00:00" +instance: "kb-cron" +--- + +Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s. +Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only) in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, evolutionary taxonomy allows for groups to be excluded from their parent taxa (e.g. dinosaurs are not considered to include birds, but to have given rise to them), thus permitting paraphyletic taxa. + +== Origin of evolutionary taxonomy == + +Evolutionary taxonomy arose as a result of the influence of the theory of evolution on Linnaean taxonomy. The idea of translating Linnaean taxonomy into a sort of dendrogram of the Animal and Plant kingdoms was formulated toward the end of the 18th century, well before Charles Darwin's book On the Origin of Species was published. The first to suggest that organisms had common descent was Pierre-Louis Moreau de Maupertuis in his 1751 Essai de Cosmologie, Transmutation of species entered wider scientific circles with Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's 1809 Philosophie Zoologique. The idea was popularised in the English-speaking world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844. +Following the appearance of On the Origin of Species, Tree of Life representations became popular in scientific works. In On the Origin of Species, the ancestor remained largely a hypothetical species; Darwin was primarily occupied with showing the principle, carefully refraining from speculating on relationships between living or fossil organisms and using theoretical examples only. In contrast, Chambers had proposed specific hypotheses, the evolution of placental mammals from marsupials, for example. +Following Darwin's publication, Thomas Henry Huxley used the fossils of Archaeopteryx and Hesperornis to argue that the birds are descendants of the dinosaurs. Thus, a group of extant animals could be tied to a fossil group. The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, exhibits the essential hallmark of evolutionary taxonomic thinking. +The past three decades have seen a dramatic increase in the use of DNA sequences for reconstructing phylogeny and a parallel shift in emphasis from evolutionary taxonomy towards Hennig's 'phylogenetic systematics'. +Today, with the advent of modern genomics, scientists in every branch of biology make use of molecular phylogeny to guide their research. One common method is multiple sequence alignment. +Thomas Cavalier-Smith, G. G. Simpson and Ernst Mayr are some representative evolutionary taxonomists. + +== New methods in modern evolutionary systematics == + +Efforts in combining modern methods of cladistics, phylogenetics, and DNA analysis with classical views of taxonomy have recently appeared. Certain authors have found that phylogenetic analysis is acceptable scientifically as long as paraphyly at least for certain groups is allowable. Such a stance is promoted in papers by Tod F. Stuessy and others. A particularly strict form of evolutionary systematics has been presented by Richard H. Zander in a number of papers, but summarized in his "Framework for Post-Phylogenetic Systematics". +Briefly, Zander's pluralistic systematics is based on the incompleteness of each of the theories: A method that cannot falsify a hypothesis is as unscientific as a hypothesis that cannot be falsified. Cladistics generates only trees of shared ancestry, not serial ancestry. Taxa evolving seriatim cannot be dealt with by analyzing shared ancestry with cladistic methods. Hypotheses such as adaptive radiation from a single ancestral taxon cannot be falsified with cladistics. Cladistics offers a way to cluster by trait transformations but no evolutionary tree can be entirely dichotomous. Phylogenetics posits shared ancestral taxa as causal agents for dichotomies yet there is no evidence for the existence of such taxa. Molecular systematics uses DNA sequence data for tracking evolutionary changes, thus paraphyly and sometimes phylogenetic polyphyly signal ancestor-descendant transformations at the taxon level, but otherwise molecular phylogenetics makes no provision for extinct paraphyly. Additional transformational analysis is needed to infer serial descent. + +The Besseyan cactus or commagram is the best evolutionary tree for showing both shared and serial ancestry. First, a cladogram or natural key is generated. Generalized ancestral taxa are identified and specialized descendant taxa are noted as coming off the lineage with a line of one color representing the progenitor through time. A Besseyan cactus or commagram is then devised that represents both shared and serial ancestry. Progenitor taxa may have one or more descendant taxa. Support measures in terms of Bayes factors may be given, following Zander's method of transformational analysis using decibans. +Cladistic analysis groups taxa by shared traits but incorporates a dichotomous branching model borrowed from phenetics. It is essentially a simplified dichotomous natural key, although reversals are tolerated. The problem, of course, is that evolution is not necessarily dichotomous. An ancestral taxon generating two or more descendants requires a longer, less parsimonious tree. A cladogram node summarizes all traits distal to it, not of any one taxon, and continuity in a cladogram is from node to node, not taxon to taxon. This is not a model of evolution, but is a variant of hierarchical cluster analysis (trait changes and non-ultrametric branches. This is why a tree based solely on shared traits is not called an evolutionary tree but merely a cladistic tree. This tree reflects to a large extent evolutionary relationships through trait transformations but ignores relationships made by species-level transformation of extant taxa. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Evolutionary_taxonomy-1.md b/data/en.wikipedia.org/wiki/Evolutionary_taxonomy-1.md new file mode 100644 index 000000000..9542bcbc3 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Evolutionary_taxonomy-1.md @@ -0,0 +1,23 @@ +--- +title: "Evolutionary taxonomy" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Evolutionary_taxonomy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:11.679071+00:00" +instance: "kb-cron" +--- + +Phylogenetics attempts to inject a serial element by postulating ad hoc, undemonstrable shared ancestors at each node of a cladistic tree. There are in number, for a fully dichotomous cladogram, one less invisible shared ancestor than the number of terminal taxa. We get, then, in effect a dichotomous natural key with an invisible shared ancestor generating each couplet. This cannot imply a process-based explanation without justification of the dichotomy, and supposition of the shared ancestors as causes. The cladistic form of analysis of evolutionary relationships cannot falsify any genuine evolutionary scenario incorporating serial transformation, according to Zander. +Zander has detailed methods for generating support measures for molecular serial descent and for morphological serial descent using Bayes factors and sequential Bayes analysis through Turing deciban or Shannon informational bit addition. + +== The Tree of Life == + +As more and more fossil groups were found and recognized in the late 19th and early 20th century, palaeontologists worked to understand the history of animals through the ages by linking together known groups. The Tree of life was slowly being mapped out, with fossil groups taking up their position in the tree as understanding increased. +These groups still retained their formal Linnaean taxonomic ranks. Some of them are paraphyletic in that, although every organism in the group is linked to a common ancestor by an unbroken chain of intermediate ancestors within the group, some other descendants of that ancestor lie outside the group. The evolution and distribution of the various taxa through time is commonly shown as a spindle diagram (often called a Romerogram after the American palaeontologist Alfred Romer) where various spindles branch off from each other, with each spindle representing a taxon. The width of the spindles is meant to imply the abundance (often a number of families) plotted against time. +Vertebrate palaeontology had mapped out the evolutionary sequence of vertebrates as currently understood fairly well by the closing of the 19th century, followed by a reasonable understanding of the evolutionary sequence of the plant kingdom by the early 20th century. The tying together of the various trees into a grand Tree of Life only really became possible with advancements in microbiology and biochemistry in the period between the World Wars. + +== Terminological difference == +The two approaches, evolutionary taxonomy and the phylogenetic systematics derived from Willi Hennig, differ in the use of the word "monophyletic". For evolutionary systematicists, "monophyletic" means only that a group is derived from a single common ancestor. In phylogenetic nomenclature, there is an added caveat that the ancestral species and all descendants should be included in the group. The term "holophyletic" has been proposed for the latter meaning. As an example, amphibians are monophyletic under evolutionary taxonomy, since they have arisen from fishes only once. Under phylogenetic taxonomy, amphibians do not constitute a monophyletic group in that the amniotes (reptiles, birds and mammals) have evolved from an amphibian ancestor and yet are not considered amphibians. Such paraphyletic groups are rejected in phylogenetic nomenclature, but are considered a signal of serial descent by evolutionary taxonomists. + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Form_classification-0.md b/data/en.wikipedia.org/wiki/Form_classification-0.md new file mode 100644 index 000000000..2889f9a4a --- /dev/null +++ b/data/en.wikipedia.org/wiki/Form_classification-0.md @@ -0,0 +1,45 @@ +--- +title: "Form classification" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Form_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:12.824213+00:00" +instance: "kb-cron" +--- + +Form classification is the classification of organisms based on their morphology, which does not necessarily reflect their biological relationships. Form classification, generally restricted to palaeontology, reflects uncertainty; the goal of science is to move "form taxa" to biological taxa whose affinity is known. +Form taxonomy is restricted to fossils that preserve too few characters for a conclusive taxonomic definition or assessment of their biological affinity, but whose study is made easier if a binomial name is available by which to identify them. The term "form classification" is preferred to "form taxonomy"; taxonomy suggests that the classification implies a biological affinity, whereas form classification is about giving a name to a group of morphologically-similar organisms that may not be related. +A "parataxon" (not to be confused with parataxonomy), or "sciotaxon" (Gr. "shadow taxon"), is a classification based on incomplete data: for instance, the larval stage of an organism that cannot be matched up with an adult. It reflects a paucity of data that makes biological classification impossible. +A sciotaxon is defined as a taxon thought to be equivalent to a true taxon (orthotaxon), but whose identity cannot be established because the two candidate taxa are of a different nature and thus cannot be compared directly. + + +== Examples == + + +=== In zoology === +Form taxa are groupings that are based on common overall forms. Early attempts at classification of labyrinthodonts was based on skull shape (the heavily armoured skulls often being the only preserved part). The amount of convergent evolution in the many groups led to a number of polyphyletic taxa. Such groups are united by a common mode of life, often one that is generalist, in consequence acquiring generally similar body shapes by convergent evolution. Ediacaran biota — whether they are the precursors of the Cambrian explosion of the fossil record, or are unrelated to any modern phylum — can currently only be grouped in "form taxa". Other examples include the seabirds and the "Graculavidae". The latter were initially described as the earliest family of Neornithes but are nowadays recognized to unite a number of unrelated early neornithine lineages, several of which probably later gave rise to the "seabird" form taxon of today. +Fossil eggs are classified according to the parataxonomic system called Veterovata. There are three broad categories in the scheme, on the pattern of organismal phylogenetic classification, called oofamilies, oogenera and oospecies (collectively known as ootaxa). The names of oogenera and oofamilies conventionally contain the root "oolithus" meaning "stone egg", but this rule is not always followed. They are divided up into several basic types: Testudoid, Geckoid, Crocodiloid, Dinosauroid-spherulitic, Dinosauroid-prismatic, and Ornithoid. + + +=== In botany === + +In paleobotany, two terms were formerly used in the codes of nomenclature, "form genera" and "organ genera", to mean groups of fossils of a particular part of a plant, such as a leaf or seed, whose parent plant is not known because the fossils were preserved unattached to the parent plant. A later term "morphotaxa" also allows for differences in preservational state. These three terms have been replaced as of 2011 by provisions for "fossil-taxa" that are more similar to the provisions for other types of plants. +Names given to organ genera could only be applied to the organs in question, and could not be extended to the entire organism. Fossil-taxon names can cover several parts of an organism, or several preservational states, but do not compete for priority with any names for the same organism that are based on a non-fossil type. +The part of the plant was often, but not universally, indicated by the use of a suffix in the generic name: + +wood fossils may have generic names ending in -xylon +leaf fossils generic names ending in -phyllum +fruit fossils generic names ending in -carpon, -carpum or -carpus +pollen fossils generic names ending in -pollis or -pollenoides. + + +== See also == +Glossary of scientific naming +Folk taxonomy +Phenetics +Taphonomy +Wastebasket taxon + + +== Footnotes == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/GC-content-0.md b/data/en.wikipedia.org/wiki/GC-content-0.md new file mode 100644 index 000000000..c35ae4b79 --- /dev/null +++ b/data/en.wikipedia.org/wiki/GC-content-0.md @@ -0,0 +1,121 @@ +--- +title: "GC-content" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/GC-content" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:14.065445+00:00" +instance: "kb-cron" +--- + +In molecular biology and genetics, GC-content (or G+C content or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of an implied four total bases, also including adenine and thymine in DNA and adenine and uracil in RNA. +GC-content may be given for a certain fragment of DNA or RNA or for an entire genome. When it refers to a fragment, it may denote the GC-content of an individual gene or section of a gene (domain), a group of genes or gene clusters, a non-coding region, or a synthetic oligonucleotide such as a primer. + +== Structure == +Qualitatively, guanine (G) and cytosine (C) undergo a specific hydrogen bonding with each other, whereas adenine (A) bonds specifically with thymine (T) in DNA and with uracil (U) in RNA. Quantitatively, each GC base pair is held together by three hydrogen bonds, while AT and AU base pairs are held together by two hydrogen bonds. To emphasize this difference, the base pairings are often represented as "G≡C" versus "A=T" or "A=U". +DNA with low GC-content is less stable than DNA with high GC-content; however, the hydrogen bonds themselves do not have a particularly significant impact on molecular stability, which is instead caused mainly by molecular interactions of base stacking. Because of the thermostability of GC pairs, it was once presumed that high GC-content in DNA was a necessary adaptation to high temperatures, though this hypothesis was later refuted in 2001 by comparative analysis of over 100 prokaryotes. Furthermore, P. putrefaciens, a species of bacteria with high GC-content DNA, has been observed to undergo autolysis more readily, thereby reducing the overall longevity of the cell. Even so, it has been shown that there is a strong correlation between the optimal growth of prokaryotes at higher temperatures and the GC-content of structural RNAs, such as ribosomal RNA, transfer RNA, and many other non-coding RNAs. The AU base pairs are less stable than the GC base pairs, making high-GC-content RNA structures more resistant to the effects of high temperatures. +More recently, it has been demonstrated that the most important factor contributing to the thermal stability of double-stranded nucleic acids is actually due to the base stackings of adjacent bases rather than the number of hydrogen bonds between the bases. There is more favorable stacking energy for GC pairs than for AT or AU pairs because of the relative positions of exocyclic groups. Additionally, there is a correlation between the order in which the bases stack and the thermal stability of the molecule as a whole. + +== Determination == + +GC-content is usually expressed as a percentage value, but sometimes as a ratio (called G+C ratio or GC-ratio). GC-content percentage is calculated as + + + + + + + + + + + + + G + + + C + + + + + + + + + + A + + + T + + + G + + + C + + + + + + × + 100 + % + + + {\displaystyle {\cfrac {G+C}{A+T+G+C}}\times 100\%} + + +whereas the AT/GC ratio is calculated as + + + + + + + + + + + + + A + + + T + + + + + + + + + + G + + + C + + + + + + + + {\displaystyle {\cfrac {A+T}{G+C}}} + + . +The GC-content percentages as well as GC-ratio can be measured by several means, but one of the simplest methods is to measure the melting temperature of the DNA double helix using spectrophotometry. The absorbance of DNA at a wavelength of 260 nm increases fairly sharply when the double-stranded DNA molecule separates into two single strands when sufficiently heated. The most commonly used protocol for determining GC-ratios uses flow cytometry for large numbers of samples. +In an alternative manner, if the DNA or RNA molecule under investigation has been reliably sequenced, then GC-content can be accurately calculated by simple arithmetic or by using a variety of publicly available software tools, such as the free online GC calculator Archived 26 February 2015 at the Wayback Machine. + +== Genomic content == + +=== Within-genome variation === +The GC-ratio within a genome is found to be markedly variable. These variations in GC-ratio within the genomes of more complex organisms result in a mosaic-like formation with islet regions called isochores. This results in the variations in staining intensity in chromosomes. GC-rich isochores typically include many protein-coding genes within them, and thus determination of GC-ratios of these specific regions contributes to mapping gene-rich regions of the genome. + +=== Coding sequences === +Within a long region of genomic sequence, genes are often characterised by having a higher GC-content in contrast to the background GC-content for the entire genome. There is evidence that the length of the coding region of a gene is directly proportional to higher G+C content. This has been pointed to the fact that the stop codon has a bias towards A and T nucleotides, and, thus, the shorter the sequence the higher the AT bias. +Comparison of more than 1,000 orthologous genes in mammals showed marked within-genome variations of the third-codon position GC content, with a range from less than 30% to more than 80%. + +=== Among-genome variation === +GC content is found to be variable with different organisms, the process of which is envisaged to be contributed to by variation in selection, mutational bias, and biased recombination-associated DNA repair. +The average GC-content in human genomes ranges from 35% to 60% across 100-Kb fragments, with a mean of 41%. The GC-content of Yeast (Saccharomyces cerevisiae) is 38%, and that of another common model organism, thale cress (Arabidopsis thaliana), is 36%. Because of the nature of the genetic code, it is virtually impossible for an organism to have a genome with a GC-content approaching either 0% or 100%. However, a species with an extremely low GC-content is Plasmodium falciparum (GC% = ~20%), and it is usually common to refer to such examples as being AT-rich instead of GC-poor. +Several mammalian species (e.g., shrew, microbat, tenrec, rabbit) have independently undergone a marked increase in the GC-content of their genes. These GC-content changes are correlated with species life-history traits (e.g., body mass or longevity) and genome size, and might be linked to a molecular process called GC-biased gene conversion. + +== Applications == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/GC-content-1.md b/data/en.wikipedia.org/wiki/GC-content-1.md new file mode 100644 index 000000000..b63f9cf90 --- /dev/null +++ b/data/en.wikipedia.org/wiki/GC-content-1.md @@ -0,0 +1,29 @@ +--- +title: "GC-content" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/GC-content" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:14.065445+00:00" +instance: "kb-cron" +--- + +=== Molecular biology === +In polymerase chain reaction (PCR) experiments, the GC-content of short oligonucleotides known as primers is often used to predict their annealing temperature to the template DNA. A higher GC-content level indicates a relatively higher melting temperature. +Many sequencing technologies, such as Illumina sequencing, have trouble reading high-GC-content sequences. Bird genomes are known to have many such parts, causing the problem of "missing genes" expected to be present from evolution and phenotype but never sequenced — until improved methods were used. + +=== Systematics === +The species problem in non-eukaryotic taxonomy has led to various suggestions in classifying bacteria, and the ad hoc committee on reconciliation of approaches to bacterial systematics of 1987 has recommended use of GC-ratios in higher-level hierarchical classification. For example, the Actinomycetota are characterised as "high GC-content bacteria". In Streptomyces coelicolor A3(2), GC-content is 72%. With the use of more reliable, modern methods of molecular systematics, the GC-content definition of Actinomycetota has been abolished and low-GC bacteria of this clade have been found. + +== Software tools == +GCSpeciesSorter and TopSort are software tools for classifying species based on their GC-contents. + +== See also == +Codon usage bias + +== References == + +== External links == +Table with GC-content of all sequenced prokaryotes +Taxonomic browser of bacteria based on GC ratio on NCBI website. +GC ratio in diverse species. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Grading_(tumors)-0.md b/data/en.wikipedia.org/wiki/Grading_(tumors)-0.md new file mode 100644 index 000000000..a1261b009 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Grading_(tumors)-0.md @@ -0,0 +1,48 @@ +--- +title: "Grading (tumors)" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Grading_(tumors)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:16.426978+00:00" +instance: "kb-cron" +--- + +In pathology, grading is a measure of the cell appearance in tumors and other neoplasms. Some pathology grading systems apply only to malignant neoplasms (cancer); others apply also to benign neoplasms. The neoplastic grading is a measure of cell anaplasia (reversion of differentiation) in the sampled tumor and is based on the resemblance of the tumor to the tissue of origin. Grading in cancer is distinguished from staging, which is a measure of the extent to which the cancer has spread. +Pathology grading systems classify the microscopic cell appearance abnormality and deviations in their rate of growth with the goal of predicting developments at tissue level (see also the 4 major histological changes in dysplasia). +Cancer is a disorder of cell life cycle alteration that leads (non-trivially) to excessive cell proliferation rates, typically longer cell lifespans and poor differentiation. The grade score (numerical: G1 up to G4) increases with the lack of cellular differentiation - it reflects how much the tumor cells differ from the cells of the normal tissue they have originated from (see 'Categories' below). Tumors may be graded on four-tier, three-tier, or two-tier scales, depending on the institution and the tumor type. +The histologic tumor grade score along with the metastatic (whole-body-level cancer-spread) staging are used to evaluate each specific cancer patient, develop their individual treatment strategy and to predict their prognosis. A cancer that is very poorly differentiated is called anaplastic. + + +== Categories == +Grading systems are also different for many common types of cancer, though following a similar pattern with grades being increasingly malignant over a range of 1 to 4. If no specific system is used, the following general grades are most commonly used, and recommended by the American Joint Commission on Cancer and other bodies: + +GX Grade cannot be assessed +G1 Well differentiated (Low grade) +G2 Moderately differentiated (Intermediate grade) +G3 Poorly differentiated (High grade) +G4 Undifferentiated (High grade) + + +=== Specific systems === +Of the many cancer-specific schemes, the Gleason system, named after Donald Floyd Gleason, used to grade the adenocarcinoma cells in prostate cancer is the most famous. This system uses a grading score ranging from 2 to 10. Lower Gleason scores describe well-differentiated less aggressive tumors. +Other systems include the Bloom-Richardson grading system for breast cancer and the Fuhrman system for kidney cancer. Invasive-front grading is useful as well in oral squamous cell carcinoma. +For soft-tissue sarcoma two histological grading systems are used : the National Cancer Institute (NCI) system and the French Federation of Cancer Centers Sarcoma Group (FNCLCC) system. + + +== Examples of grading schemes == + + +== See also == +TNM staging system (Other parameters) +Tumor kinds that have their own grading system: +Teratoma +Gleason score + + +== References == + + +== External links == +CancerWeb Archived 2002-04-30 at the Wayback Machine +Atlas Interactif de Neuro-Oncologie \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Herpetarium-0.md b/data/en.wikipedia.org/wiki/Herpetarium-0.md new file mode 100644 index 000000000..47fa83574 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Herpetarium-0.md @@ -0,0 +1,37 @@ +--- +title: "Herpetarium" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Herpetarium" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:33.154295+00:00" +instance: "kb-cron" +--- + +A herpetarium is a zoological exhibition space for reptiles and amphibians, most commonly a dedicated area of a larger zoo. A herpetarium which specializes in snakes is an ophidiarium or serpentarium, which are more common as stand-alone entities also known as snake farms. Many snake farms milk snakes for venom for medical and scientific research. + + +== Notable herpetariums == +Alice Springs Reptile Centre in Alice Springs, Australia +Alligator Bay (zoo) in Beauvoir, France +Armadale Reptile Centre in Perth, Australia +Australian Reptile Park in Somersby, Australia +Chennai Snake Park Trust in Chennai, India +Crocodiles of the World in Brize Norton, UK +Crocosaurus Cove in Darwin, Australia +Clyde Peeling's Reptiland in Allenwood, Pennsylvania +Kentucky Reptile Zoo in Slade, Kentucky +The LAIR at the Los Angeles Zoo in Los Angeles, California +Serpent Safari in Gurnee, Illinois +Saint Louis Zoo Herpetarium in St. Louis, Missouri +Staten Island Zoo Serpentarium in New York City, New York +World of Reptiles at the Bronx Zoo in New York City, New York + + +== See also == +Herpetoculture +Bill Haast (founder of Miami Serpentarium) + + +== References == +Murphy, James B., Herpetological History of the Zoo and Aquarium World, Krieger Publishing Company, Malabar, Florida, 2007. ISBN 1-57524-285-0 \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Human_zoo-0.md b/data/en.wikipedia.org/wiki/Human_zoo-0.md new file mode 100644 index 000000000..e2848b2cd --- /dev/null +++ b/data/en.wikipedia.org/wiki/Human_zoo-0.md @@ -0,0 +1,36 @@ +--- +title: "Human zoo" +chunk: 1/5 +source: "https://en.wikipedia.org/wiki/Human_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:34.331855+00:00" +instance: "kb-cron" +--- + +Human zoos, also known as ethnological expositions, were a colonial practice of publicly displaying people, usually in a so-called "natural" or "primitive" state. They were most prominent during the 19th and 20th centuries. These displays often emphasized the supposed inferiority of the exhibits' culture, and implied the superiority of "Western society", through tropes that depicted marginalized groups as "savage". They then developed into independent displays emphasizing the exhibits' inferiority to western culture and providing further justification for their subjugation. Such displays featured in multiple colonial exhibitions and at temporary exhibitions in animal zoos. + +== Etymology == +The term "human zoo" was not generally used by contemporaries of the shows, and was popularised by the French researcher Pascal Blanchard. The term has been criticised for denying the agency of the shows' non-European performers. +According to Sandra Koutsoukos, the term "human zoos" was likely coined by French historians and anthropologists and first appeared in a 2002 publication. It is widely used in academia to critique the inhumanity and racism of events that displayed people from cultures deemed "exotic" or "savage". + +== Circuses and freak shows == + +The abstract concept of human displays in zoos has been documented throughout the duration of colonial history. In the Western Hemisphere, one of the earliest-known zoos, that of Moctezuma in Mexico, consisted not only of a vast collection of animals, but also exhibited humans, for example, dwarfs, albinos and hunchbacks. +During the Renaissance, the Medici developed a large menagerie in Rome. In the 16th century, Cardinal Hippolytus Medici had a collection of people of different races as well as exotic animals. He is reported as having a troupe of so-called Savages, speaking over twenty languages; there were also Moors, Tartars, Indians, Turks and Africans. In 1691, Englishman William Dampier exhibited a tattooed native of Miangas whom he bought when he was in Mindanao. He also intended to exhibit the man's mother to earn more profit, but the mother died at sea. The man was named Jeoly, falsely branded as "Prince Giolo" to attract more audience, and was exhibited for three months straight until he died of smallpox in London. + +One of the first modern public human exhibitions was P. T. Barnum's exhibition of Joice Heth on 25 February 1835 and, subsequently, the Siamese twins Chang and Eng Bunker. These exhibitions were common in freak shows. Another famous example was that of Saartjie Baartman of the Namaqua, often referred to as the Hottentot Venus, who was displayed in London and France until her death in 1815. +During the 1850s, Maximo and Bartola, two microcephalic children from El Salvador, were exhibited in the US and Europe under the names Aztec Children and Aztec Lilliputians. However, human zoos would become common only in the 1870s in the midst of the New Imperialism period. +From 1936 to 1943, the Canadian province of Ontario displayed five White French Canadian quintuplets, whom the provincial government had removed from their birth family, in a human zoo called Quintland. + +== Start of human exhibits == + +In the 1870s, exhibitions of so-called "exotic populations" became popular throughout the western world. Human zoos could be seen in many of Europe's largest cities, such as Paris, Hamburg, London, and Milan, as well as American cities such as New York City and Chicago. Carl Hagenbeck, an animal trader, was one of the early proponents of this trend, when, in 1874, at the suggestion of Heinrich Leutemann, he decided to exhibit Sami people with the 'Laplander Exhibition'. What differentiated Hagenbeck's exhibit from others, was that he showed these people, with animals and plants, to "re-create", their "natural environment." He sold people the feeling of having travelled to these areas by witnessing his exhibits. These exhibits were a massive success, and only became larger and more elaborate. From this point forward, human exhibitions would lean towards stereotyping and projecting western superiority. Greater feeding into the Imperialist narrative, that these people's culture merited subjugation. It also promoted scientific racism, where they were classified as more or less 'civilized' on a scale, from great apes to western Europeans. +Hagenbeck would go on to launch a Nubian Exhibit in 1876, and an Inuit exhibit in 1880. These were also massively successful. +Aside from Hagenbeck, the Jardin d'Acclimatation was also a hotspot of ethnological exhibits. Geoffroy de Saint-Hilaire, director of the Jardin d'Acclimatation, decided, in 1877, to organize two ethnological exhibits that also presented Nubians and Inuit. That year, the audience of the Jardin d'acclimatation' doubled to one million. Between 1877 and 1912, approximately thirty ethnological exhibitions were presented at the Jardin zoologique d'acclimatation. +These displays were so successful they were incorporated into both the 1878 and the 1889 Parisian World's Fair, which presented a 'Negro Village'. Visited by 28 million people, the 1889 World's Fair displayed 400 indigenous people as the major attraction. +In Amsterdam, the International Colonial and Export Exhibition had a display of people native to Suriname, in 1883. +In 1886, the Spanish displayed natives of the Philippines in an exhibition, as people whom they "civilized". This event added flame to the 1896 Philippine revolution. Queen Consort of Spain, Maria Cristina of Austria, afterwards institutionalized the business of human zoos. By 1887, indigenous Igorot people & animals were sent to Madrid and were exhibited in a human zoo at the newly constructed Palacio de Cristal del Retiro. +At both the 1893 World's Columbian Exposition and the 1901 Pan-American Exposition Little Egypt, a bellydancer, was photographed as a catalogued "type" by Charles Dudley Arnold and Harlow Higginbotha. +At the 1895 African Exhibition in The Crystal Palace, around eighty people from Somalia were displayed in an "exotic" setting. +The Brussels International Exposition (1897) in Tervuren featured a "Congolese Village" that displayed African people in ersatz interpretations of native settings. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Human_zoo-1.md b/data/en.wikipedia.org/wiki/Human_zoo-1.md new file mode 100644 index 000000000..56dbe3078 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Human_zoo-1.md @@ -0,0 +1,26 @@ +--- +title: "Human zoo" +chunk: 2/5 +source: "https://en.wikipedia.org/wiki/Human_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:34.331855+00:00" +instance: "kb-cron" +--- + +=== German ethnographs === +Ethnology studies in Germany took a new approach in the 1870s as human displays were incorporated into zoos. These exhibits were lauded as 'educational' to the general population by the scientific community. Very quickly, the exhibits were used as a way to show that Europeans had "evolved" into a 'superior', 'cosmopolitan' life. +In the late 19th century, German ethnographic museums were seen as an empirical study of human culture. They contained artifacts from cultures around the world organized by continent allowing visitors to see the similarities and differences between the groups and "form their own ideas". + +=== Objectification in human zoos === +Within the history of human zoos, there are patterns of overt sexual representation of displayed peoples, most frequently women. Such objectification often led to treatment that reflected a lack of privacy and respect, including the dissection and display of bodies after death without consent. +An example of the sexualization of ethnically diverse women in Europe is Saartje Baartman, often referred to as her anglicized name Sarah Bartmann. Bartmann was displayed both when she was alive throughout England and Ireland and after her death in the Musée de l'Homme. While alive, she participated in a traveling show depicting her as a "savage female" with a large focus on her body. The clothes she was put in were tight and close to her skin color, and spectators were encouraged to "see for themselves" if Bartmann's body, particularly her buttocks, were real through "poking and pushing". Her living display was financially compensated but there is no record of her consenting to be examined and displayed after death. +Anthropologist Dominika Czarnecka theorizes on the relationship between the radicalization and sexualization of black female bodies in her journal article "Black Female Bodies and the 'White' View." Czarnecka focuses on ethnographic shows that were prominent in Polish territory in the late 19th century. She argues that an essential part of why these shows were so popular is the display of the black female body. Although the women in the shows were meant to be depicting Amazon warriors, their wardrobe was not similar to amazonian dress, and there are several documentations of comments from spectators about their revealing clothes and their bodies. +Although women were most frequently objectified, there are a few instances of "exotic" men being displayed due to their favorable appearance. Angelo Soliman was brought to Italy as a slave from Central Africa in the 18th century, but ended up gaining a reputation in Viennese society for his fighting skills and vast knowledge about language and history. Upon his death in 1796, this positive association did not prevent his body being "stuffed and exhibited in the Viennese Natural History Museum" for almost a decade. + +== Around the turn of the century == +In 1896, to increase the number of visitors, the Cincinnati Zoo invited one hundred Sioux Native Americans to establish a village at the site. The Sioux lived at the zoo for three months. +The 1900 World's Fair presented the famous diorama living in Madagascar, while the Colonial exhibitions in Marseilles (1906 and 1922) and in Paris (1907 and 1931) also displayed humans in cages, often nude or semi-nude. The 1931 exhibition in Paris was so successful that 34 million people attended it in six months, while a smaller counter-exhibition entitled The Truth on the Colonies, organized by the Communist Party, attracted very few visitors—in the first room, it recalled Albert Londres and André Gide's critiques of forced labour in the colonies. Nomadic Senegalese Villages were also presented. + +In 1906, Madison Grant—socialite, eugenicist, amateur anthropologist, and head of the New York Zoological Society—had Congolese pygmy Ota Benga put on display at the Bronx Zoo in New York City alongside apes and other animals. At the behest of Grant, the zoo director William Hornaday placed Benga displayed in a cage with the chimpanzees, then with an orangutan named Dohong, and a parrot, and labeled him The Missing Link, suggesting that in evolutionary terms Africans like Benga were closer to apes than were Europeans. It triggered protests from the city's clergymen, but the public reportedly flocked to see it. +On Monday, 8 September 1906, after just two days, Hornaday decided to close the exhibition, and Benga could be found walking the zoo grounds, often followed by a crowd "howling, jeering and yelling." \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Human_zoo-2.md b/data/en.wikipedia.org/wiki/Human_zoo-2.md new file mode 100644 index 000000000..903ecf6ec --- /dev/null +++ b/data/en.wikipedia.org/wiki/Human_zoo-2.md @@ -0,0 +1,20 @@ +--- +title: "Human zoo" +chunk: 3/5 +source: "https://en.wikipedia.org/wiki/Human_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:34.331855+00:00" +instance: "kb-cron" +--- + +=== First organized backlash === +According to The New York Times, although "few expressed audible objection to the sight of a human being in a cage with monkeys as companions", controversy erupted as black clergymen in the city took great offense. "Our race, we think, is depressed enough, without exhibiting one of us with the apes", said the Reverend James H. Gordon, superintendent of the Howard Colored Orphan Asylum in Brooklyn. "We think we are worthy of being considered human beings, with souls." +New York City Mayor George B. McClellan Jr. refused to meet with the clergymen, drawing the praise of Hornaday, who wrote to him: "When the history of the Zoological Park is written, this incident will form its most amusing passage." +As the controversy continued, Hornaday remained unapologetic, insisting that his only intention was to put on an ethnological exhibition. In another letter, he said that he and Grant—who ten years later would publish the racist tract The Passing of the Great Race—considered it "imperative that the society should not even seem to be dictated to" by the black clergymen. +1903 saw one of the first widespread protests against human zoos, at the "Human Pavilion" of an exposition in Osaka, Japan. The exhibition of Koreans and Okinawans in "primitive" housing incurred protests from the governments of Korea and Okinawa, and a Formosan woman wearing Chinese dress angered a group of Chinese students studying abroad in Tokyo. An Ainu schoolteacher was made to exhibit himself in the zoo to raise money for his schoolhouse, as the Japanese government refused to pay. The fact that the schoolteacher made eloquent speeches and fundraised for his school while wearing traditional dress confused the spectators. An anonymous front-page column in a Japanese magazine condemned these examples and the "Human Pavilion" in total, calling it inhumane to exhibit people as spectacles. + +=== St. Louis World's Fair === +In 1904, over 1,100 Filipinos were displayed at the St. Louis World's Fair in association with the 1904 Summer Olympics. Following the Spanish-American War, the United States had just acquired new territories such as Guam, the Philippines, and Puerto Rico. The organizers of the World's Fair held "Anthropology Days" on August 12 and 13. Since the 1889 Paris Exposition, human zoos, as a key feature of world's fairs, functioned as demonstrations of anthropological notions of race, progress, and civilization. These goals were followed also at the 1904 World's Fair. Fourteen hundred indigenous people from Southeast Asia, the Pacific Islands, East Asia, Africa, the Middle East, South America and North America were displayed in anthropological exhibits that showed them in their natural habitats. Another 1600 indigenous people displayed their culture in other areas of the Louisiana Purchase Exposition (LPE), including on the fairgrounds and at the Model School, where American Indian boarding school students demonstrated their successful assimilation. The sporting event itself took place with the participation of about 100 paid indigenous men (no women participated in Anthropology Days, though some, notably the Fort Shaw Indian School girls basketball team, did compete in other athletic events at the LPE). Contests included "baseball throwing, shot put, running, broad jumping, weight lifting, pole climbing, and tugs-of-war before a crowd of approximately ten thousand". According to theorist Susan Brownell, world's fairs – with their inclusion of human zoos – and the Olympics were a logical fit at this time, as they "were both linked to an underlying cultural logic that gave them a natural affinity". Also, one of the original intentions of Anthropology Days was to create publicity for the official Olympic events. +While Anthropology Days were not officially part of the Olympics program, they were closely associated with each other at the time, and in history—Brownell notes that even today historians still debate as to which of the LPE events were the "real" Olympic Games. Additionally, almost all of the 400 athletic events were referred to as "Olympian," and the opening ceremony was held in May with dignitaries in attendance, though the official Olympic program did not begin until July 1. Also, as previously noted, one of the original intentions of Anthropology Days was to create publicity for the official Olympic events. +The exhibitions of the World's Fair inspired US military officer Truman Hunt to start his own human zoo of "Head-Hunting Igorrotes" in Brooklyn. Reports of questionable living conditions for its Filipino performers led the US Federal government to investigate Hunt's exhibition, and eventually shut it down after Hunt was found guilty of wage theft from the performers. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Human_zoo-3.md b/data/en.wikipedia.org/wiki/Human_zoo-3.md new file mode 100644 index 000000000..c03728355 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Human_zoo-3.md @@ -0,0 +1,33 @@ +--- +title: "Human zoo" +chunk: 4/5 +source: "https://en.wikipedia.org/wiki/Human_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:34.331855+00:00" +instance: "kb-cron" +--- + +=== United Kingdom and France === +Between 1 May and 31 October 1908, the Scottish National Exhibition, opened by one of Queen Victoria's grandsons, Prince Arthur of Connaught, was held in Saughton Park, Edinburgh. One of the attractions was the Senegal Village with its French-speaking Senegalese residents, on show demonstrating their way of life, art and craft while living in beehive huts. +In 1909, the infrastructure of the 1908 Scottish National Exhibition in Edinburgh was used to construct the new Marine Gardens to the coast near Edinburgh at Portobello. A group of Somali men, women, and children were shipped over to be part of the exhibition, living in thatched huts. +In 1924, the British Empire Exhibition had ethnographic displays across the Wembley Park site. Archival records indicate that 273 people from Britain’s colonies took part in this live ethnographic display. The official guide described the arrangement in strikingly clinical terms: "Every section of the empire is represented at Wembley. Many of the colonies have representatives of their local inhabitants at work in local conditions. The following list gives the name of the races and the approximate numbers actually living in the exhibition: Malays 20, Burmans 30, Hong Kong Chinese 160, West Africans 60, and Palestinians 3. In addition there are Indians, Singhalese, West Indians, and natives of British Guiana, who live outside the exhibition, but attend their respective pavilions daily." +In 1925, a display at Belle Vue Zoo in Manchester, England, was entitled "Cannibals" and featured black Africans in supposedly native dress. +In 1931, around 100 other New Caledonian Kanaks were put on display at the Jardin d'Acclimatation in Paris. + +=== Spain === + +Between the end of the 19th century and the beginning of the 20th, several exhibitions of non-Western people were held in Spain, following those held in other areas like the United Kingdom. The first of them was held in 1887 by the Ministry of Overseas, which exhibited a group of between forty and fifty Filipino people (then a Spanish territory) together with local products and plants in the Retiro Park in Madrid. For this exhibition, the Palacio de Cristal del Retiro was built, as well as its pond, which sought to recreate the "natural habitat" of the exposed people. At least four people died during the exhibition. In the following years, private companies organized similar exhibitions in Barcelona and Madrid, including of people who were not from Spanish territories, like the Ashanti or the Inuit. Until 1918, exhibitions of African people were held in the Ronda de la Universitat in Barcelona, which were later taken to other European countries. There are also records of another exhibition in the Ibero-American Exposition of Seville in 1929 and an additional one of Fang people from Equatorial Guinea in Valencia in 1942. Until 1997, the "Negro of Banyoles", an embalmed African man, was exhibited in the Darder Museum in Girona. + +=== Japan === + +In the late 19th and early 20th centuries, Japan, like Western colonial powers, held a "human zoo" (人間動物園, ningen dōbutsuen) exhibiting people from various ethnic groups, including Ryukyuans, Ainu, Chinese, Taiwanese, and Koreans, to show off the inferiority of other Asian peoples and the superiority of the Japanese. + +=== United States (1930s) === +By the 1930s, a new kind of human zoo appeared in America, nude shows masquerading as education. These included the Zoro Garden Nudist Colony at the Pacific International Exposition in San Diego, California (1935–36) and the Sally Rand Nude Ranch at the Golden Gate International Exposition in San Francisco (1939). The former was supposedly a real nudist colony, which used hired performers instead of actual nudists. The latter featured women wearing cowboy hats, gunbelts and boots, and little else. The Golden Gate fair also featured a "Greenwich Village" show, described in the Official Guide Book as "Model artists' colony and revue theatre." + +=== Ethnological expositions during Nazi Germany === +As ethnogenic expositions were discontinued in Germany around 1931, there were many repercussions for the performers. Many of the people brought from their homelands to work in the exhibits had created families in Germany, and there were many children that had been born in Germany. Once they no longer worked in the zoos or for performance acts, these people were stuck living in Germany where they had no rights and were harshly discriminated against. During the rise of the Nazi party, the foreign actors in these stage shows were typically able to stay out of concentration camps because there were so few of them that the Nazis did not see them as a real threat. Although they were able to avoid concentration camps, they were not able to participate in German life as citizens of ethnically German origin could. The Hitler Youth did not allow children of foreign parents to participate, and adults were rejected as German soldiers. Many ended up working in war industry factories or foreign laborer camps. +Hans Massaquoi in his 1999 book Destined to Witness observed a human zoo within the Hamburg zoo Tierpark Hagenbeck during the pre-Nazi Germany period, in which an African family was placed with the animals, openly laughed at, and otherwise treated rudely by the public crowd. And then they turned upon him, a fellow spectator, due to his mixed appearance. The date, according to his book, was approximately 1930. + +== Exhibitions after 1940 == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Human_zoo-4.md b/data/en.wikipedia.org/wiki/Human_zoo-4.md new file mode 100644 index 000000000..6ab451478 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Human_zoo-4.md @@ -0,0 +1,58 @@ +--- +title: "Human zoo" +chunk: 5/5 +source: "https://en.wikipedia.org/wiki/Human_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:34.331855+00:00" +instance: "kb-cron" +--- + +As part of the Portuguese World Exhibition in 1940, members of a tribe from the Bissagos Islands of Guinea-Bissau were displayed on an island in a lake in the Lisbon Tropical Botanical Garden. +A Congolese village was displayed at the Brussels 1958 World's Fair. The Congolese on display were among 598 people—including 273 men, 128 women and 197 children, a total of 183 families. Eight-month-old baby Juste Bonaventure Langa died during Expo 58; he rests in the Tervuren cemetery. In mid-July, the Congolese protested the condescending treatment they were receiving from spectators and demanded to be sent home, abruptly ending the exhibit and eliciting some sympathy from European newspapers. +In April 1994, an example of an Ivory Coast village was presented as part of an African safari in Port-Saint-Père, near Nantes, in France, later called Planète Sauvage. +In July 2005, the Augsburg Zoo in Germany hosted an "African village" featuring African crafts and African cultural performances. The event was subject to widespread criticism. Defenders of the event argued that it was not racist since it did not involve exhibiting Africans in a debasing way, as had been done at zoos in the past. Critics argued that presenting African culture in the context of a zoo contributed to exoticizing and stereotyping Africans, thus laying the ground work for racial discrimination, and that solidarity and mutual understanding with African people were not primary aims of the event. +In August 2005, London Zoo displayed four human volunteers wearing fig leaves (and bathing suits) for four days. +In 2007, Adelaide Zoo ran a Human Zoo exhibition which consisted of a group of people who, as part of a study exercise, had applied to be housed in the former ape enclosure by day, but then returned home by night. The inhabitants took part in several exercises, and spectators were asked for donations towards a new ape enclosure. +In August 2014, as part of the Edinburgh International Festival, South African theatre-maker Brett Bailey's show Exhibit B was performed in the Playfair Library Hall, University of Edinburgh; then in September at The Barbican in London. This explored the nature of Human Zoos and raised much controversy both amongst the performers and the audiences. +With a view to tackling the morality of Human Zoo exhibits, 2018 saw the poster exhibition, Putting People on Display, tour Glasgow School of Art, the University of Edinburgh, the University of Stirling, the University of St Andrews and the University of Aberdeen. Additional posters were added to a selection from the French ACHAC's exhibition, Human Zoos: the Invention of the Savage, in relation to the Scottish dimension in hosting such shows. + +== See also == + +== References == + +== Films == +The Couple in the Cage. 1997. Dir. Coco Fusco and Paula Eredia. 30 min. +Régis Warnier, the film Man to Man. 2005. +"From Bella Coola to Berlin". 2006. Dir. Barbara Hager. 48 minutes. Broadcaster – Bravo! Canada. +"Indianer in Berlin: Hagenbeck's Volkerschau". 2006. Dir. Barbara Hager. Broadcaster – Discovery Germany Geschichte Channel. +Alexander C. T. Geppert, Fleeting Cities. Imperial Expositions in Fin-de-Siècle Europe (Basingstoke: Palgrave Macmillan, 2010). +Sadiah Qureshi, Peoples on Parade: Exhibitions, Empire and Anthropology in Nineteenth-Century Britain (2011). +"Human zoos. The invention of the savage" Archived 18 June 2018 at the Wayback Machine, Dir. Pascal Blanchard, Gilles Boëtsch, Nanette Jacomijn Snoep – exhibition catalogue – Actes Sud (2011) +Sauvages. Au cœur des zoos humains, Dir. Pascal Blanchard, Bruno Victor-Pujebet – 90 minutes – Bonne Pioche production & Archipel (2018) +Human Zoos: America's Forgotten History of Scientific Racism, Dir. John G. West (2019) + +== Bibliography == +Abbattista, Guido, Ethnic Expositions in Italy, 1880 to 1940. Humans on Exhibition (London-New York: Routledge, 2024) +Ankerl, Guy. Coexisting Contemporary Civilizations: Arabo-Muslim, Bharatai, Chinese, and Western, Geneva, INU Press, 2000, ISBN 2881550045. +Conklin, Alice L., and Ian Christopher Fletcher. European Imperialism, 1830–1930: Climax and Contradiction. Boston, MA: Wadsworth Cengage Learning, 1999. ISBN 0395903858 +Dreesbach, Anne. Colonial Exhibitions: 'Völkerschauen' and the Display of the 'Other', European History Online, Mainz: Institute of European History, 2012. +Grant, Kevin. A Civilised Savagery: Britain and the New Slaveries in Africa, 1884–1926. New York; Oxfordshire, England: Routledge, 2005. +Lewis, R. Barry. Understanding humans : introduction to physical anthropology and archaeology. Belmont, Calif. Wadsworth Cengage Learning. 2010. +Oliveira, Cinthya. Human Rights & Exhibitions, 1789–1989, Journal of Museum Ethnography, no. 29, 2016, pp. 71–94. +Penny, H. Glenn. Objects of Culture : Ethnology and Ethnographic Museums in Imperial Germany, The University of North Carolina Press, 2002. +Porter, Louis, Porter, A. N., and Louis, William Roger. The Oxford History of the British Empire. Volume III, The Nineteenth Century. Oxford: Oxford UP, 1999. Oxford History of the British Empire. Web. +Qureshi, Sadiah. Robert Gordon Latham, Displayed Peoples, and the Natural History of Race: 1854–1866, The Historical Journal, vol. 54, no. 1, 2011, pp. 143–166. +Rothfels, Nigel. Savages and Beasts : The Birth of the Modern Zoo, Johns Hopkins University Press, 2002. +Schofield, Hugh. Human Zoos: When Real People Were Exhibits, BBC News, 2011. +India Andaman Jarawa Tribe in 'Shocking' Tourist Video, BBC News, 2012. + +== External links == + Media related to Human zoos at Wikimedia Commons +Human Zoos. The Invention of the Savage +Human Zoos website +Pascal Blanchard; Sandrine Lemaire; Nicolas Bancel (August 2000). "Human zoos – Racist theme parks for Europe's colonialists". Le Monde diplomatique.; +"On A Neglected Aspect Of Western Racism", by Kurt Jonassohn, December 2000 +The Colonial Exposition of May 1931 Archived 15 December 2018 at the Wayback Machine by Michael Vann +"Official site of the Adelaide Human Zoo" +Qureshi, Sadiah (2004), 'Displaying Sara Baartman, the 'Hottentot Venus', History of Science 42:233–257. Available online at Science History Publications. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Ichnotaxon-0.md b/data/en.wikipedia.org/wiki/Ichnotaxon-0.md new file mode 100644 index 000000000..f165b469e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Ichnotaxon-0.md @@ -0,0 +1,37 @@ +--- +title: "Ichnotaxon" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Ichnotaxon" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:17.576577+00:00" +instance: "kb-cron" +--- + +An ichnotaxon (plural ichnotaxa) is "a taxon based on the fossilized work of an organism", i.e. the non-human equivalent of an artifact. Ichnotaxon comes from the Ancient Greek ἴχνος (íchnos) meaning "track" and English taxon, itself derived from Ancient Greek τάξις (táxis) meaning "ordering". +Ichnotaxa are names used to identify and distinguish morphologically distinctive ichnofossils, more commonly known as trace fossils (fossil records of lifeforms' movement, rather than of the lifeforms themselves). They are assigned genus and species ranks by ichnologists, much like organisms in Linnaean taxonomy. These are known as ichnogenera and ichnospecies, respectively. "Ichnogenus" and "ichnospecies" are commonly abbreviated as "igen." and "isp.". The binomial names of ichnospecies and their genera are to be written in italics. +Most researchers classify trace fossils only as far as the ichnogenus rank, based upon trace fossils that resemble each other in morphology but have subtle differences. Some authors have constructed detailed hierarchies up to ichnosuperclass, recognizing such fine detail as to identify ichnosuperorder and ichnoinfraclass, but such attempts are controversial. + + +== Naming == +Due to the chaotic nature of trace fossil classification, several ichnogenera hold names normally affiliated with animal body fossils or plant fossils. For example, many ichnogenera are named with the suffix -phycus due to misidentification as algae. +Edward Hitchcock was the first to use the now common -ichnus suffix in 1858, with Cochlichnus. + + +== History == +Due to ichnofossils' history of being difficult to classify, there have been several attempts to enforce consistency in the naming of ichnotaxa. +The first edition of the International Code of Zoological Nomenclature, published in 1961, ruled that names of taxa published after 1930 should be 'accompanied by a statement that purports to give characters differentiating the taxon'. This had the effect that names for most ichnofossil taxa published after 1930 were unavailable under the code. This restriction was removed for ichnotaxa in the third edition of the code, published in 1985. + + +== See also == +Bird ichnology +Trace fossil classification +Glossary of scientific naming + + +== References == + + +== External links == +Comments on the draft proposal to amend the Code with respect to trace fossils +Trace Fossils - Kansas University Catalogue of Ichnotaxa \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Immersion_exhibit-0.md b/data/en.wikipedia.org/wiki/Immersion_exhibit-0.md new file mode 100644 index 000000000..63d6a84bf --- /dev/null +++ b/data/en.wikipedia.org/wiki/Immersion_exhibit-0.md @@ -0,0 +1,15 @@ +--- +title: "Immersion exhibit" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Immersion_exhibit" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:35.474361+00:00" +instance: "kb-cron" +--- + +An immersion exhibit is a naturalistic zoo environment that gives visitors the sense of being in the animals' habitats. Buildings and barriers are hidden. By recreating sights and other sensorial input from natural environments, immersion exhibits provide an indication about how animals live in the wild. +The landscape immersion term and approach were developed in 1975 through the efforts of David Hancocks at Seattle's Woodland Park Zoo. This led to the zoo's ground-breaking gorilla exhibit, which opened in 1978. The concept became the industry standard by the 1980s, and has since gained widespread acceptance as the best practice for zoological exhibits. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Infraspecific_name-0.md b/data/en.wikipedia.org/wiki/Infraspecific_name-0.md index f0376d2c9..2f378c86a 100644 --- a/data/en.wikipedia.org/wiki/Infraspecific_name-0.md +++ b/data/en.wikipedia.org/wiki/Infraspecific_name-0.md @@ -4,7 +4,7 @@ chunk: 1/2 source: "https://en.wikipedia.org/wiki/Infraspecific_name" category: "reference" tags: "science, encyclopedia" -date_saved: "2026-05-05T07:15:36.651923+00:00" +date_saved: "2026-05-05T09:07:18.794538+00:00" instance: "kb-cron" --- diff --git a/data/en.wikipedia.org/wiki/Infraspecific_name-1.md b/data/en.wikipedia.org/wiki/Infraspecific_name-1.md index 3634d6e16..4673596e3 100644 --- a/data/en.wikipedia.org/wiki/Infraspecific_name-1.md +++ b/data/en.wikipedia.org/wiki/Infraspecific_name-1.md @@ -4,7 +4,7 @@ chunk: 2/2 source: "https://en.wikipedia.org/wiki/Infraspecific_name" category: "reference" tags: "science, encyclopedia" -date_saved: "2026-05-05T07:15:36.651923+00:00" +date_saved: "2026-05-05T09:07:18.794538+00:00" instance: "kb-cron" --- diff --git a/data/en.wikipedia.org/wiki/Institutiones_rei_herbariae-0.md b/data/en.wikipedia.org/wiki/Institutiones_rei_herbariae-0.md new file mode 100644 index 000000000..8717678ee --- /dev/null +++ b/data/en.wikipedia.org/wiki/Institutiones_rei_herbariae-0.md @@ -0,0 +1,46 @@ +--- +title: "Institutiones rei herbariae" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Institutiones_rei_herbariae" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:19.976490+00:00" +instance: "kb-cron" +--- + +Institutiones rei herbariae (transl. The Instruction of Botany), originally published in French as Eléments de botanique, is a 1700 Latin-language botanical compendium. The book was the principal work of Joseph Pitton de Tournefort, a French botanist credited with establishing the modern concept of the genus. + + +== Contents == + +As a part of the book's introduction, Tournefort included what may be the first recorded history of botany, titled Isagoge in rem herbarium. In it, some of the most important botanical authors are noted, and brief biographies are given for each. In the 1694 edition Eléments de botanique, Tournefort argued against John Ray's conception of the genus, to which Ray responded twice in 1696. However, in Institutiones rei herbariae in 1700, criticisms towards Ray were removed and replaced with praise. +The main portion of the book contains an exhaustive list of plant names, organized in a system of "classes", "sections", "genera", and "species". Furthermore, myriad images of plant leaves and flowers are included throughout the volume, engraved on copper-plate. + + +== Publication == +While Institutiones rei herbariae was published in 1700 (and again in 1719), the book was originally written in French in 1694 as Eléments de botanique. Beginning in 1716, an English language version of Institutiones was published monthly under the title Botanical institutions. Rather than being translated from the original French work, Botanical institutions was adapted from the Latin Institutiones rei herbariae. The edition included a direct translation of the original, additional commentary from English contributors, two alphabetical indices, and a brief biography on Tournefort. + + +== Legacy == +Tournefort's central work has been praised for its simplicity of organization, and for its role as a foundational document for later botanists. One biographer of Tournefort noted that the work was highly influenced by the societal thinking of the time. Eléments de botanique was a strictly utilitarian work: it was solely designed to facilitate plant identification in order that those plants may be put to use for their various purposes. As such, every name had to be clearly linked to one species only; there was as little ambiguity as possible. Many French, English, Italian, and German botanists continued to use Tournefort's system throughout the first half of the 18th century, much in the same way that later taxonomists would model their works off the system of Carl Linnaeus. +The book also reached outside of botanical circles. For example, Charles De Geer (who would later become a prominent entomologist) purchased three volumes of the 1719 edition of Institutiones rei herbariae. De Geer used the book to identify plants in his own garden, and also made use of Tournefort's classification system in his publications. +However, some 18th-century naturalists, following the principles of John Locke, argued against the nominalism of Tournefort. Where Tournefort argued that the "essence of the plant" could be tied to specific and generic names, botanists like Georges-Louis Leclerc and Jean-Baptiste Lamarck did not believe an organized science should be burdened by arbitrary nominal distinctions. + + +== Notes == + + +== References == + + +=== Bibliography === +Callot, Émile (1965). "Système et méthode dans l'histoire de la botanique" (PDF). Revue d'histoire des sciences et de leurs applications (in French). 18 (1): 45–53. doi:10.3406/rhs.1965.2392. JSTOR 23903980. +Hamberg, Erik (2023). "The Books of Olof Rudbeck Father and Son at Leufstabruk" (PDF). A Warm Scent of Books: Private Libraries at Leufstabruk and Beyond. Uppsala: Acta Universitatis Upsaliensis. ISSN 0346-7465. +Jacquot, Jean (1953). "Sir Hans Sloane and French men of science". Notes and Records of the Royal Society of London. 10 (2): 85–98. doi:10.1098/rsnr.1953.0004. S2CID 145267005. +Leroy, Jean (1956). "Tournefort (1656–1708)" (PDF). Revue d'histoire des sciences et de leurs applications (in French). 9 (4): 350–354. doi:10.3406/rhs.1956.4372. JSTOR 23903797. +Löve, Áskell (1967). "The Flora of Slovakia" (PDF). Taxon. 16 (2): 133–135. Bibcode:1967Taxon..16..133L. doi:10.2307/1216899. JSTOR 1216899. +von Sachs, Julius (1890). Balfour, Isaak (ed.). History of Botany (1530–1860). Translated by Garnsey, Henry. Oxford: Clarendon Press (published 2020). + + +== External links == +Tournefort, Joseph (1719). Institutiones rei herbariae. doi:10.5962/bhl.title.37642. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Isochore_(genetics)-0.md b/data/en.wikipedia.org/wiki/Isochore_(genetics)-0.md new file mode 100644 index 000000000..7bd77a561 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Isochore_(genetics)-0.md @@ -0,0 +1,50 @@ +--- +title: "Isochore (genetics)" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Isochore_(genetics)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:21.158221+00:00" +instance: "kb-cron" +--- + +In genetics, an isochore is a large region of genomic DNA (greater than 300 kilobases) with a high degree of uniformity in GC content; that is, guanine (G) and cytosine (C) bases. The distribution of bases within a genome is non-random: different regions of the genome have different amounts of G-C base pairs, such that regions can be classified and identified by the proportion of G-C base pairs they contain. +Bernardi and colleagues first noticed the compositional non-uniformity of vertebrate genomes using thermal melting and density gradient centrifugation. + + The DNA fragments extracted by the gradient centrifugation were later termed "isochores", which was subsequently defined as "very long (much greater than 200 KB) DNA segments" that "are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content". Subsequently, the isochores "grew" and were claimed to be ">300 kb in size." + The theory proposed that the isochore composition of genomes varies markedly between "warm-blooded" (homeotherm) vertebrates and "cold-blooded" (poikilotherm) vertebrates and later became known as the isochore theory. + +== The thermodynamic stability hypothesis == +The isochore theory purported that the genome of "warm-blooded" vertebrates (mammals and birds) are mosaics of long isochoric regions of alternating GC-poor and GC-rich composition, as opposed to the genome of "cold-blooded" vertebrates (fishes and amphibians) that were supposed to lack GC-rich isochores. + + These findings were explained by the thermodynamic stability hypothesis, attributing genomic structure to body temperature. GC-rich isochores were purported to be a form of adaptation to environmental pressures, as an increase in genomic GC-content could protect DNA, RNA, and proteins from degradation by heat. + +Despite its attractive simplicity, the thermodynamic stability hypothesis has been repeatedly shown to be in error + +. + + Many authors showed the absence of a relationship between temperature and GC-content in vertebrates, while others showed the existence of GC-rich domains in "cold-blooded" vertebrates such as crocodiles, amphibians, and fish. + +== Principles of the isochore theory == +The isochore theory was the first to identify the nonuniformity of nucleotide composition within vertebrate genomes and predict that the genome of "warm-blooded" vertebrates such as mammals and birds are mosaic of isochores (Bernardi et al. 1985). The human genome, for example, was described as a mosaic of alternating low and high GC content isochores belonging to five compositional families, L1, L2, H1, H2, and H3, whose corresponding ranges of GC contents were said to be <38%, 38%-42%, 42%-47%, 47%-52%, and >52%, respectively. +The main predictions of the isochore theory are that: + +GC content of the third codon position (GC3) of protein coding genes is correlated with the GC content of the isochores embedding the corresponding genes. +The genome organization of warm-blooded vertebrates is a mosaic of mostly GC-rich isochores. +Genome organization of cold-blooded vertebrates is characterized by low GC content levels and lower compositional heterogeneity than warm-blooded vertebrates. Homogeneous domains do not reach the high GC levels attained by the genomes of warm-blooded vertebrates. + +== The neutralist-selectionist controversy == +Two opposite explanations that endeavored to explain the formations of isochores were vigorously debated as part of the neutralist-selectionist controversy. The first view was that isochores reflect variable mutation processes among genomic regions consistent with the neutral model. + Alternatively, isochores were posited as a result of natural selection for certain compositional environment required by certain genes. Several hypotheses derive from the selectionist view, such as the thermodynamic stability hypothesis and the biased gene conversion hypothesis. Thus far, none of the theories provides a comprehensive explanation to the genome structure, and the topic is still under debate. + +== The rise and fall of the isochore theory == +The isochore theory became one of the most useful theories in molecular evolution for many years. It was the first and most comprehensive attempt to explain the long-range compositional heterogeneity of vertebrate genomes within an evolutionary framework. Despite the interest in the early years in the isochore model, in recent years, the theory's methodology, terminology, and predictions have been challenged. +Because this theory was proposed in the 20th century before complete genomes were sequenced, it could not be fully tested for nearly 30 years. In the beginning of the 21st century, when the first genomes were made available it was clear that isochores do not exist in the human genome +nor in other mammalian genomes. When failed to find isochores, many attacked the very existence of isochores. + + The most important predictor of isochores, GC3 was shown to have no predictable power + to the GC content of nearby genomic regions, refuting findings from over 30 years of research, which were the basis for many isochore studies. Isochore-originators replied that the term was misinterpreted + as isochores are not "homogeneous" but rather fairly homogeneous regions with a heterogeneous nature (especially) of GC-rich regions at the 5 kb scale, which only added to the already growing confusion. The reason for this ongoing frustration was the ambiguous definition of isochores as long and homogeneous, allowed some researchers to discover "isochores" and others to dismiss them, although both camps used the same data. +The unfortunate side effect of this controversy was an "arms race" in which isochores are frequently redefined and relabeled following conflicting findings that failed to reveal "mosaic of isochores." The unfortunate outcomes of this controversy and the following terminological-methodological mud were the loss of interest in isochores by the scientific community. When the most important core-concept in isochoric literature, the thermodynamic stability hypothesis, was rejected, the theory lost its appeal. Even today, there is no clear definition to isochores nor is there an algorithm that detects isochores. Isochores are detected manually by visual inspection of GC content curves , however because this approach lacks scientific merit and is difficult to replicate by independent groups, the findings remain disputed. + +== The compositional domain model == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Isochore_(genetics)-1.md b/data/en.wikipedia.org/wiki/Isochore_(genetics)-1.md new file mode 100644 index 000000000..43bf8089e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Isochore_(genetics)-1.md @@ -0,0 +1,17 @@ +--- +title: "Isochore (genetics)" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Isochore_(genetics)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:21.158221+00:00" +instance: "kb-cron" +--- + +As the study of isochores was de facto abandoned by most scientists, an alternative theory was proposed to describe the compositional organization of genomes in accordance with the most recent genomic studies. The Compositional Domain Model depicts genomes as a medley of short and long homogeneous and nonhomogeneous domains. The theory defines "compositional domains" as genomic regions with distinct GC-contents as determined by a computational segmentation algorithm. The homogeneity of compositional domains is compared to that of the chromosome on which they reside using the F-test, which separated them into compositionally homogeneous domains and compositionally nonhomogeneous domains based on the outcome of test. Compositionally homogeneous domains that are sufficiently long (≥ 300 kb) are termed isochores or isochoric domains. These terms are in accordance with the literature as they provide clear distinction between isochoric- and nonisochoric-domains. +A comprehensive study of the human genome unraveled a genomic organization where two-thirds of the genome is a mixture of many short compositionally homogeneous domains and relatively few long ones. The remaining portion of the genome is composed of nonhomogeneous domains. In terms of coverage, only 1% of the total number of compositionally homogeneous domains could be considered "isochores" which covered less than 20% of the genome. +Since its inception the theory received wide attention and was extensively used to explain findings emerging from over dozen new genome sequencing studies. + + However, many important questions remain open, such as which evolutionary forces shaped the structure of compositional domains and the ways they differ between different species. + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Kew_Rule-0.md b/data/en.wikipedia.org/wiki/Kew_Rule-0.md new file mode 100644 index 000000000..9e0e8196f --- /dev/null +++ b/data/en.wikipedia.org/wiki/Kew_Rule-0.md @@ -0,0 +1,31 @@ +--- +title: "Kew Rule" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Kew_Rule" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:22.303608+00:00" +instance: "kb-cron" +--- + +The Kew Rule was used by some authors to determine the application of synonymous names in botanical nomenclature up to about 1906, but was and still is contrary to codes of botanical nomenclature including the International Code of Nomenclature for algae, fungi, and plants. Index Kewensis, a publication that aimed to list all botanical names for seed plants at the ranks of species and genus, used the Kew Rule until its Supplement IV was published in 1913 (prepared 1906–1910). +The Kew Rule applied rules of priority in a more flexible way, so that when transferring a species to a new genus, there was no requirement to retain the epithet of the original species name, and future priority of the new name was counted from the time the species was transferred to the new genus. The effect has been summarized as "nomenclature used by an established monographer or in a major publication should be adopted". This is contrary to the modern article 11.4 of the Code of Nomenclature. + + +== History == + + +=== Beginnings === +The first discussion in print of what was to become known as the Kew Rule appears to have occurred in 1877 between Henry Trimen and Alphonse Pyramus de Candolle. Trimen did not think it was reasonable for older names discovered in the literature to destabilize the nomenclature that had been well accepted:Probably all botanists are agreed that it is very desirable to retain when possible old specific names, but some of the best authors do not certainly consider themselves bound by any generally accepted rule in this matter. Still less will they be inclined to allow that a writer is at liberty, as M. de Candolle thinks, to reject the specific appellations made by an author whose genera are accepted, in favour of older ones in other genera. It will appear to such that to do this is to needlessly create in each case another synonym. + + +=== The end === +The first botanical code of nomenclature that declared itself to be binding was the 1906 publication Règles internationales de la nomenclature botanique adoptées par le Congres International de Botanique de Vienne 1905 that followed from the 1905 International Botanical Congress. The Kew Rule was outlawed by this code. +The end of the Kew Rule brought about considerable upheaval in botanical nomenclature. Many new species names were coined to resurrect older epithets, for example, in 1917 Willis Jepson wrote: + +"The plant so long known as Brodiaea grandiflora Smith ... [was] first published as Hookera coronaria Salisbury (1806). The correct name, then, is Brodiaea coronaria Jepson, n. comb." +Names that had previously been conserved to improve the stability of well-known plant names often now no longer required conservation, and other names that had been formed using the Kew Rule and had become well known, were illegitimate. The entire previous list of conserved and rejected names was consequently replaced in 1959 with a reworked list. +Previously overlooked botanical literature has continued to yield new examples of forgotten older names for more than 100 years since the Kew Rule was banished from the International Code of Nomenclature. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Klepton-0.md b/data/en.wikipedia.org/wiki/Klepton-0.md index 48c7218c0..71665668d 100644 --- a/data/en.wikipedia.org/wiki/Klepton-0.md +++ b/data/en.wikipedia.org/wiki/Klepton-0.md @@ -4,7 +4,7 @@ chunk: 1/1 source: "https://en.wikipedia.org/wiki/Klepton" category: "reference" tags: "science, encyclopedia" -date_saved: "2026-05-05T07:15:37.873011+00:00" +date_saved: "2026-05-05T09:07:23.502386+00:00" instance: "kb-cron" --- diff --git a/data/en.wikipedia.org/wiki/Kyushu_Natural_Animal_Park_African_Safari-0.md b/data/en.wikipedia.org/wiki/Kyushu_Natural_Animal_Park_African_Safari-0.md new file mode 100644 index 000000000..9741e5c53 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Kyushu_Natural_Animal_Park_African_Safari-0.md @@ -0,0 +1,32 @@ +--- +title: "Kyushu Natural Animal Park African Safari" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Kyushu_Natural_Animal_Park_African_Safari" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:36.640314+00:00" +instance: "kb-cron" +--- + +Kyushu Natural Animal Park African Safari (九州自然動物公園アフリカンサファリ, Kyūshū Shizen Dōbutsu Kōen Afurikan Safari), also referred to as simply African Safari, is Japan's largest safari park and is located at the base of the Kunisaki Peninsula in Usa, Ōita Prefecture. + + +== Overview == + + +=== Interaction Zone === +The park is separated into two "zones." In the Fureai Zone, or "Interaction Zone," visitors can interact with and even touch various animals such as rabbits, red kangaroos, and miniature horses while exploring the area on foot. In the area, there are various gift shops and restaurants. There are also both a "dog salon" and a "cat salon" in which visitors can directly interact with the animals. + + +=== Safari Zone === +The Safari Zone is the large safari-style section of the park. This safari is divided into sections, each modeled on a different natural environment. Each animal species is placed in the section which most closely resembles their natural habitat. +The sections within the Safari Zone are each separated by fences and security gates. However, there are no fences separating visitors from the animals during the safari. Visitors can either choose to travel the park in their personal car or ride the park's "Jungle Bus." Visitors are prohibited from exiting their vehicles while in the Safari Zone. + +Visitors who choose to ride Jungle Bus must pay for a bus ticket in addition to the park's admission fee. Tickets are sold on a first-come, first-served basis. During the 50 minute ride through the park, visitors are able to feed some of the animals through the Jungle Bus' cage. Because of this, visitors are able to get closer to the animals by riding the Jungle Bus than by riding in their personal vehicle. + + +=== Safari Zone animals === +Animals in the Safari Zone include American black bears, giraffes, lions, elephants, mouflons, cheetahs, camels, bison, Bengal tigers, white rhinoceroses, spotted hyenas and more. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Limassol_Zoo-0.md b/data/en.wikipedia.org/wiki/Limassol_Zoo-0.md new file mode 100644 index 000000000..01f38113b --- /dev/null +++ b/data/en.wikipedia.org/wiki/Limassol_Zoo-0.md @@ -0,0 +1,25 @@ +--- +title: "Limassol Zoo" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Limassol_Zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:37.815400+00:00" +instance: "kb-cron" +--- + +The Limassol Zoo (Greek: Ζωολογικός Κήπος Λεμεσού, romanized: Zōologikós Kḗpos Lemesoú) is located within the Limassol Public Gardens, is a 15 acres (6.1 ha) zoological garden in Limassol, Cyprus. It was founded by Mayor Kostas Partaside in 1956. After substantial renovations, the Limassol Zoo was reopened in 2012. + + +== See also == +List of zoos by country +Captivity +Botanical garden +Captive animal + + +== References == + + +== External links == + Media related to Limassol zoo at Wikimedia Commons \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/List_of_gene_families-0.md b/data/en.wikipedia.org/wiki/List_of_gene_families-0.md new file mode 100644 index 000000000..1dfb11750 --- /dev/null +++ b/data/en.wikipedia.org/wiki/List_of_gene_families-0.md @@ -0,0 +1,92 @@ +--- +title: "List of gene families" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/List_of_gene_families" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:15.236553+00:00" +instance: "kb-cron" +--- + +This is a list of gene families or gene complexes, i.e. sets of genes which are related ancestrally and often serve similar biological functions. These gene families typically encode functionally related proteins, and sometimes the term gene families is a shorthand for the sets of proteins that the genes encode. They may or may not be physically adjacent on the same chromosome. + + +== Regulatory protein gene families == +14-3-3 protein family +Achaete-scute complex (neuroblast formation) +Cyclins +Cyclin dependent kinases +CDK inhibitors +FOX proteins (forkhead box proteins) +Families containing homeobox domains +DLX gene family +Hox gene family +POU family +GATA transcription factor +General transcription factor +Krüppel-type zinc finger (ZNF) +MADS-box gene family +NF-kB +NOTCH2NL +Nuclear receptor +P300-CBP coactivator family +Transcription factors +SOX gene family + + +== Immune system proteins == +Immunoglobulin superfamily +Killer-cell immunoglobulin-like receptors +Leukocyte immunoglobulin-like receptors +Major histocompatibility complex (MHC) +NOD-like receptors +Pattern recognition receptor +Toll-like receptors +RIG-I like receptors + + +== Motor proteins == +Dynein +Kinesin +Myosin + + +== Signal transducing proteins == +Arf family +G-proteins +Janus kinases +MAP Kinase +Non-receptor tyrosine kinase +Olfactory receptor +Peroxiredoxin +Rab family +Rap family +Ras family +Receptor tyrosine kinases +Rho family +Serine/threonine-specific protein kinase +SRC kinase family + + +== Transporters == +ABC transporters +Antiporter +Aquaporins +Globin +Major facilitator superfamily +Neurotransmitter transporter +GABA transporter +Glutamate transporter +Glycine transporter +Monoamine transporter +Equilibrative nucleoside transporter family +Papain-like protease +Solute carrier family + + +== Other families == + + +== See also == +Protein family +Housekeeping gene \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-0.md b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-0.md new file mode 100644 index 000000000..81969cfb2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-0.md @@ -0,0 +1,200 @@ +--- +title: "List of taxa with candidatus status" +chunk: 1/4 +source: "https://en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:01.046393+00:00" +instance: "kb-cron" +--- + +This is a list of taxa with Candidatus status. For taxa not covered by this list, see also: + +the GenBank taxonomy for "effective" names as published; +the Candidatus Lists and LPSN for latinate names, some sanitized to match the Code. + +== Phyla == + +"Ca. Absconditabacteria" (previously Candidate phylum SR1) +ABY1 aka OD1-ABY1, subgroup of OD1 ("Ca. Parcubacteria") +Candidate phylum AC1 +"Ca. Acetothermia" (previously Candidate phylum OP1) +"Ca. Aerophobetes" (previously Candidate phylum CD12 or BHI80-139) +"Ca. Aminicenantes" (previously Candidate phylum OP8) +aquifer1 +aquifer2 +"Ca. Berkelbacteria" (previously Candidate phylum ACD58) +BRC1 +CAB-I +"Ca. Calescamantes" (previously Candidate phylum EM19) +Candidate phylum CPR2 +Candidate phylum CPR3 +Candidate phylum NC10 +Candidate phylum OP2 +Candidate phylum RF3 +Candidate phylum SAM +Candidate phylum SPAM +Candidate phylum TG2 +Candidate phylum VC2 +Candidate phylum WS1 +Candidate phylum WS2 +Candidate phylum WS4 +Candidate phylum WYO +CKC4 +"Ca. Cloacimonetes" (previously Candidate phylum WWE1) +CPR1 +"Ca. Dependentiae" (previously Candidate phylum TM6) +EM 3 +"Ca. Endomicrobia" Stingl et al. 2005 +"Ca. Fermentibacteria" (Hyd24-12) +"Ca. Fervidibacteria" (previously Candidate phylum OctSpa1-106) +GAL08 +GAL15 +GN01 +GN03 +GN04 +GN05 +GN06 +GN07 +GN08 +GN09 +GN10 +GN11 +GN12 +GN13 +GN14 +GN15 +GOUTA4 +"Ca. Gracilibacteria" (previously Candidate phylum GN02, BD1-5, or BD1-5 group) +Guaymas1 +"Ca. Hydrogenedentes" (previously Candidate phylum NKB19) +JL-ETNP-Z39 +"Ca. Katanobacteria" (previously Candidate phylum WWE3) +Kazan-3B-09 +KD3-62 +kpj58rc +KSA1 +KSA2 +KSB1 +KSB2 +KSB4 +"Ca. Latescibacteria" (previously Candidate phylum WS3) +LCP-89 +LD1-PA38 +"Ca. Marinamargulisbacteria" (previously Candidate division ZB3) +"Ca. Marinimicrobia" (previously Marine Group A or Candidate phylum SAR406) +"Ca. Melainabacteria" +"Ca. Microgenomates" (previously Candidate phylum OP11) +"Ca. Modulibacteria" (previously Candidate phylum KSB3) +MSBL2 +MSBL3 +MSBL4 +MSBL5 +MSBL6 +NPL-UPA2 +NT-B4 +OC31 +"Ca. Omnitrophica" (previously Candidate phylum OP3) +OP4 +OP6 +OP7 +OS-K/OS-K group +"Ca. Parcubacteria" (previously Candidate phylum OD1) +PAUC34f +"Ca. Peregrinibacteria" (previously Candidate phylum PER) +"Ca. Poribacteria" +RsaHF231 +S2R-29 +"Ca. Saccharibacteria" (previously Candidate phylum TM7) +SBR1093 +SBYG-2791 +Candidate phylum SC3 +Candidate phylum SC4 +Sediment-1 +Sediment-2 +Sediment-3 +Sediment-4 +SHA-109 +SM2F11 +TA06 +"Ca. Tectomicrobia" +TG3 ("Ca. Chitinivibrionia") +WCHB1-60 +WD272 +WOR-1 +WOR-3 +WPS-1 +WPS-2 +WS5 +WS6 +ZB2 aka OD1-ZB2 subgroup of OD1 ("Ca. Parcubacteria") +"Ca. Zixibacteria" + +== Classes == + +"Ca. Lambdaproteobacteria" Anantharaman et al. 2016 +"Ca. Muproteobacteria" Anantharaman et al. 2016 +"Ca. Uabimicrobiia" Lodha et al. 2021 +"Ca. Zetaproteobacteria" Emerson et al. 2007 + +== Orders == +"Ca. Nitrosopumilales" Könneke et al. 2005 +"Ca. Uabimicrobiales" Lodha et al. 2021 + +== Families == +"Ca. Midichloriaceae" Montagna et al. 2013 +"Ca. Nitrosopumilaceae" Könneke et al. 2005 +"Ca. Procabacteriaceae" +"Ca. Rhabdochlamydiaceae" +"Ca. Uabimicrobiceae" Lodha et al. 2021 + +== Genera == +"Ca. Accumulibacter" Hesselmann et al. 1999 +"Ca. Allobeggiatoa" Hinck et al. 2011 +"Ca. Arthromitus" Snel et al. 1995 +"Ca. Bacilloplasma" Kostanjšek et al. 2007 +"Ca. Baumannia" Moran et al. 2003 +"Ca. Blochmannia" Sauer et al. 2000 +"Ca. Carsonella" Thao et al. 2000 +"Ca. Chlorothrix" Klappenbach and Pierson 2004 +"Ca. Competibacter" Crocetti et al. 2002 +"Ca. Contubernalis" Zhilina et al. 2005 +"Ca. Desulforudis" +"Ca. Endomicrobium" Stingl et al. 2005 +"Ca. Epixenosoma" +"Ca. Giganthauma" +"Ca. Glomeribacter" Bianciotto et al. 2003 +"Ca. Kleidoceria" Kuechler et al. 2010 +"Ca. Kuenenia" Schmid et al. 2000 +"Ca. Liberibacter" +"Ca. Lokiarchaeum" +"Ca. Lumbricincola" Nechitaylo et al. 2009 +"Ca. Magnetobacterium" Murray and Stackebrandt 1995 +"Ca. Methanoregula" +"Ca. Microthrix" +"Ca. Nardonella" Lefèvre et al. 2004 +"Ca. Nitrosoarchaeum" Blainey et al. 2011 +"Ca. Nitrosopumilus" Könneke et al. 2005 +"Ca. Pelagibacter" Rappe et al. 2002 +"Ca. Photodesmus" Hendry and Dunlap 2011 +"Ca. Phytoplasma" Firrao et al. 2004 +"Ca. Portiera" Thao and Baumann 2004 +"Ca. Procabacter" Horn et al. 2002 +"Ca. Rhabdochlamydia" +"Ca. Riegeria" Gruber-Vodicka et al. 2011 +"Ca. Rohrkolberia" Kuechler et al. 2011 +"Ca. Salinibacter" Antón et al. 2000 +"Ca. Savagella" Thompson et al. 2012 +"Ca. Scalindua" +"Ca. Similichlamydia" Stride et al. 2013 +"Ca. Symbiothrix" Hongoh et al. 2007 +"Ca. Tremblaya" Thao et al. 2002 +"Ca. Uabimicrobium" Shiratori et al. 2019 +"Ca. Xiphinematobacter" Vandekerckhove et al. 2000 + +== Species and subspecies == +Unless otherwise noted (♦), these entries are from LPSN. + +"Ca. Acaryochloris bahamiensis" López-Legentil et al. 2011 +"Ca. Acidianus copahuensis" Giaveno et al. 2013 +"Ca. Aciduliprofundum boonei" Schouten et al. 2008 \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-1.md b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-1.md new file mode 100644 index 000000000..db80b4872 --- /dev/null +++ b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-1.md @@ -0,0 +1,182 @@ +--- +title: "List of taxa with candidatus status" +chunk: 2/4 +source: "https://en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:01.046393+00:00" +instance: "kb-cron" +--- + +"Ca. Accumulibacter phosphatis" Hesselmann et al. 1999 +"Ca. Actinobaculum timonae" Drancourt et al. 2004 +"Ca. Adiaceo aphidicola" Darby et al. 2005 +"Ca. Allobeggiatoa salina" Hinck et al. 2011 +"Ca. Alysiomicrobium bavaricum" Kragelund et al. 2006 +"Ca. Alysiosphaera europaea" Kragelund et al. 2006 +"Ca. Amoebinatus massiliae" Greub et al. 2004 +"Ca. Amoebophilus asiaticus" Horn et al. 2001 +"Ca. Amphibiichlamydia ranarum" Martel et al. 2013 +"Ca. Anadelfobacter veles" Vannini et al. 2010 +"Ca. Ancillula trichonymphae" Strassert et al. 2012 +"Ca. Anammoxoglobus propionicus" Kartal et al. 2007 +"Ca. Anaplasma sparouinense" Duron et al. 2022 +"Ca. Aquiluna rubra" Hahn 2009 +"Ca. Aquirestis calciphila" Hahn and Schauer 2007 +"Ca. Arcobacter sulfidicus" Wirsen et al. 2002 +"Ca. Arsenophonus arthropodicus" Dale et al. 2002 +"Ca. Arsenophonus phytopathogenicus" Bressan et al. 2012 +"Ca. Arsenophonus triatominarum" Hypsa and Dale 1997 +"Ca. Aschnera chinzeii" Hosokawa et al. 2012 +"Ca. Atelocyanobacterium thalassa(♦) +"Ca. Azoamicus ciliaticola" Graf et al. 2021 +"Ca. Bacteroides massiliae" Drancourt et al. 2004 +"Ca. Bartonella ancashi" Blazes et al. 2013 +"Ca. Bartonella antechini" Kaewmongkol et al. 2011 +"Ca. Bartonella breitschwerdtii(♦) +"Ca. Bartonella bandicootii" Kaewmongkol et al. 2011 +"Ca. Bartonella durdenii(♦) +"Ca. Bartonella eldjazairii(♦) +"Ca. Bartonella mayotimonensis" Lin et al. 2010 +"Ca. Bartonella melophagi(♦) +"Ca. Bartonella merieuxii" Chomel et al. 2012 +"Ca. Bartonella monaxi(♦) +"Ca. Bartonella rudakovii(♦) +"Ca. Bartonella thailandensis" Saisongkorh et al. 2009 +"Ca. Bartonella volans(♦) +"Ca. Bartonella woyliei" Kaewmongkol et al. 2011 +"Ca. Baumannia cicadellinicola" Moran et al. 2003 +"Ca. Benitsuchiphilus tojoi" Hosokawa et al. 2010 +"Ca. Berkiella aquae" Mehari et al. 2016 +"Ca. Berkiella cookevillensis" Mehari et al. 2016 +"Ca. Blochmannia floridanus" Sauer et al. 2000 +"Ca. Blochmannia herculeanus" Sauer et al. 2000 +"Ca. Blochmannia rufipes" Sauer et al. 2000 +"Ca. Borrelia tachyglossi" Loh et al. 2017 +"Ca. Borrelia texasensis" Lin et al. 2005 +"Ca. Branchiomonas cysticola" Toenshoff et al. 2012 +"Ca. Brocadia anammoxidans" Jetten et al. 2001 +"Ca. Brocadia caroliniensis" Magrí et al. 2012 +"Ca. Brocadia fulgida" Kartal et al. 2004 +"Ca. Brocadia sinica" Hu et al. 2010 +"Ca. Brownia rhizoecola" Gruwell et al. 2010 +"Ca. Burkholderia andongensis" Lemaire et al. 2011 +"Ca. Burkholderia calva" Van Oevelen et al. 2004 +"Ca. Burkholderia crenata(♦) +"Ca. Burkholderia hispidae" Lemaire et al. 2012 +"Ca. Burkholderia kirkii" Van Oevelen et al. 2002 +"Ca. Burkholderia mamillata(♦) +"Ca. Burkholderia nigropunctata" Van Oevelen et al. 2004 +"Ca. Burkholderia petitii" Lemaire et al. 2011 +"Ca. Burkholderia rigidae" Lemaire et al. 2012 +"Ca. Burkholderia schumannianae" Lemaire et al. 2012 +"Ca. Burkholderia verschuerenii(♦) +"Ca. Burkholderia virens(♦) +"Ca. Caedibacter acanthamoebae" Horn et al. 1999 +"Ca. Caldiarchaeum subterraneum" Nunoura et al. 2011 +"Ca. Campylobacter hominis" Lawson et al. 1998 +"Ca. Captivus acidiprotistae" Baker et al. 2003 +"Ca. Cardinium hertigii" Zchori-Fein et al. 2004 +"Ca. Carsonella ruddii" Thao et al. 2000 +"Ca. Chloracidobacterium thermophilum" Bryant et al. 2007 +"Ca. Chlorothrix halophila" Klappenbach and Pierson 2004 +"Ca. Chryseobacterium massiliae" Greub et al. 2004 +"Ca. Chryseobacterium timonae" Drancourt et al. 2004 +"Ca. Clavochlamydia salmonicola" Karlsen et al. 2008 +"Ca. Cloacamonas acidaminovorans" Pelletier et al. 2008 +"Ca. comitans" Jacobi et al. 1996 +"Ca. Competibacter phosphatis" Crocetti et al. 2002 +"Ca. Consessoris aphidicola" Darby et al. 2005 +"Ca. Contubernalis alkalaceticum" Zhilina et al. 2005 +"Ca. Cryptoprodotis polytropus" Ferrantini et al. 2009 +"Ca. Curculioniphilus buchneri" Toju et al. 2009 +"Ca. Cyrtobacter comes" Vannini et al. 2010 +"Ca. Cyrtobacter zanobii" Boscaro et al. 2013 +"Ca. Defluviella procrastinata" Boscaro et al. 2013 +"Ca. Desulforudis audaxviator" Chivian et al. 2008 +"Ca. Desulfovibrio trichonymphae" Sato et al. 2009 +"Ca. Devosia euplotis" Vannini et al. 2004 +"Ca. Ecksteinia adelgidicola" Toenshoff et al. 2012 +"Ca. Ehrlichia walkerii" Brouqui et al. 2003 +"Ca. Endobugula glebosa" Lim and Haygood 2004 +"Ca. Endobugula sertula" Haygood and Davidson 1997 +"Ca. Endolissoclinum faulkneri" Kwan et al. 2012 +"Ca. Endoecteinascidia frumentensis" Pérez-Matos et al. 2007 +"Ca. Endomicrobium pyrsonymphae" Stingl et al. 2005 +"Ca. Endomicrobium trichonymphae" Stingl et al. 2005 +"Ca. Endonucleobacter bathymodioli" Zielinski et al. 2009 +"Ca. Endoriftia persephone" Robidart et al. 2008 +"Ca. Endowatersipora palomitas" Anderson and Haygood 2007 +"Ca. Endowatersipora rubus" Anderson and Haygood 2007 +"Ca. Entotheonella palauensis" Schmidt et al. 2000 +"Ca. Epiflobacter spp." Xia et al. 2008 +"Ca. Erwinia dacicola" Capuzzo et al. 2005 +"Ca. Evansia muelleri" Kuechler et al. 2013 +"Ca. Flaviluna lacus" Hahn 2009 +"Ca. Fodinabacter communificans" Bertin et al. 2011 +"Ca. Francisella noatunensis subsp. endociliophora" Schrallhammer et al. 2011 +"Ca. Frankia datiscae" Persson et al. 2011 +"Ca. Fritschea bemisiae" Everett et al. 2005 +"Ca. Fritschea eriococci" Everett et al. 2005 +"Ca. Gillettellia cooleyia" Toenshoff et al. 2012 +"Ca. Gilliamella apicola" Martinson et al. 2012 +"Ca. Glomeribacter gigasporarum" Bianciotto et al. 2003 +"Ca. Gortzia infectiva" Boscaro et al. 2012 +"Ca. Haliscomenobacter calcifugiens" Hahn and Schauer 2007 +"Ca. Halomonas phosphatis" Nguyen et al. 2012 +"Ca. Hamiltonella defensa" Moran et al. 2005 +"Ca. Helicobacter bovis" De Groote et al. 1999 +"Ca. Helicobacter heilmannii" O'Rourke et al. 2004 +"Ca. Helicobacter suis" De Groote et al. (includes strains previously known as Helicobacter heilmannii type one) +"Ca. Heliomonas lunata" Asao et al. 2012 +"Ca. Hemipteriphilus asiaticus" Bing et al. 2013 +"Ca. Hemobacterium ranarum" Zhang and Rikihisa 2004 (previously known as Aegyptianella ranarum) +"Ca. Hepatincola porcellionum" Wang et al. 2004 +"Ca. Hepatobacter penaei" Numan et al. 2013 +"Ca. Hepatoplasma crinochetorum" Wang et al. 2004 +"Ca. Hodgkinia cicadicola" McCutcheon et al. 2009 +"Ca. Holdemania massiliensis(♦) +"Ca. Ishikawaella capsulata" Hosokawa et al. 2006 +"Ca. Isobeggiatoa divolgata" Salman et al. 2011 +"Ca. Jettenia asiatica" Quan et al. 2008 +"Ca. Kinetoplastibacterium blastocrithidii" Du et al. 1994 +"Ca. Kinetoplastibacterium crithidii" Du et al. 1994 +"Ca. Kleidoceria schneideri" Kuechler et al. 2010 +"Ca. Kopriimonas aquarianus" Quinn et al. 2012 +"Ca. Korarchaeum cryptofilum" Elkins et al. 2008 +"Ca. Koribacter versatilis" Ward et al. 2009 +"Ca. Kuenenia stuttgartiensis" Schmid et al. 2000 +"Ca. Lariskella arthropodarum" Matsuura et al. 2012 +"Ca. Legionella jeonii" Park et al. 2004 +"Ca. Liberibacter americanus" Teixeira et al. 2005 - one cause of Citrus greening disease +"Ca. Liberibacter africanus" Roberts et al. 2015 - one cause of Citrus greening disease +"Ca. Liberibacter africanus" corrig. Jagoueix et al. 1994 (previously "Ca. Liberobacter africanum) +"Ca. Liberibacter africanus subsp. capensis" Garnier et al. 2000 +"Ca. Liberibacter asiaticus" corrig. Jagoueix et al. 1994 (previously "Ca. Liberobacter asiaticum) - one cause of Citrus greening disease +"Ca. Liberibacter europaeus" Raddadi et al. 2011 +"Ca. Liberibacter psyllaurous" Hansen et al. 2008 +"Ca. Liberibacter solanacearum" Liefting et al. 2009 - cause of Psyllid yellows and Zebra chip +"Ca. Limnoluna rubra" Hahn 2009 +"Ca. Macropleicola appendiculatae" Kölsch et al. 2009 +"Ca. Macropleicola muticae" Kölsch et al. 2009 +"Ca. Magnetobacterium bavaricum" Spring et al. 1993 +"Ca. Magnetoglobus multicellularis" Abreu et al. 2007 +"Ca. Magnospira bakii" Snaidr et al. 1999 +"Ca. Maribeggiatoa vulgaris" Salman et al. 2011 +"Ca. Marispirochaeta associata" Shivani et al. 2016 +"Ca. Marithioploca araucae" Salman et al +"Ca. Marithrix sessilis" Salman et al. 2011 +"Ca. Mesochlamydia elodeae" Corsaro et al. 2013 +"Ca. Metachlamydia lacustris" Corsaro et al. 2010 +"Ca. Methanogranum caenicola" Iino et al. 2013 +"Ca. Methanomethylophilus alvus" Borrel et al. 2012 +"Ca. Methanoregula boonei" Bräuer et al. 2006 +"Ca. Methylacidiphilum infernorum" Hou et al. 2008 +"Ca. Methylomirabilis oxyfera" Ettwig et al. 2010 +"Ca. Micrarchaeum acidiphilum(♦) +"Ca. Microthrix calida" Levantesi et al. 2006 +"Ca. Microthrix parvicella" Blackall et al. 1996 +"Ca. Midichloria mitochondrii" Sassera et al. 2006 +"Ca. Monilibacter batavus" Kragelund et al. 2006 +"Ca. Moranella endobia" McCutcheon and von Dohlen 2011 +"Ca. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-2.md b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-2.md new file mode 100644 index 000000000..31f005318 --- /dev/null +++ b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-2.md @@ -0,0 +1,173 @@ +--- +title: "List of taxa with candidatus status" +chunk: 3/4 +source: "https://en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:01.046393+00:00" +instance: "kb-cron" +--- + +Mycoplasma aoti" Barker et al. 2011 +"Ca. Mycoplasma corallicola" Neulinger et al. 2009 +"Ca. Mycoplasma haematoparvum" Sykes et al. 2005 +"Ca. Mycoplasma haemobos" Tagawa et al. 2008 +"Ca. Mycoplasma haemodidelphidis" Messick et al. 2002 +"Ca. Mycoplasma haemofelis" Neimark et al. 2001 (synonymous with Haemobartonella felis) +"Ca. Mycoplasma haemolamae" Messick et al. 2002 +"Ca. Mycoplasma haemomacaque" Maggi et al. 2013 +"Ca. Mycoplasma haemominutum" Foley and Pedersen 2001 (previously "Haemobartonella felis small form (Hfsm)") +"Ca. Mycoplasma haemomuris" Neimark et al. 2001 (synonymous with Haemobartonella muris) +"Ca. Mycoplasma haemomuris subsp. musculi" Harasawa et al. 2015 +"Ca. Mycoplasma haemomuris subsp. ratti" Harasawa et al. 2015 +"Ca. Mycoplasma haemosuis" Neimark et al. 2001 (synonymous with Eperythrozoon suis and Mycoplasma suis) +"Ca. Mycoplasma haemovis" Hornok et al. 2009 +"Ca. Mycoplasma haemozalophi" Volokhov et al. 2011 +"Ca. Mycoplasma kahanei" Neimark et al. 2002 +"Ca. Mycoplasma ravipulmonis" Neimark et al. 1998 +"Ca. Mycoplasma turicensis" Willi et al. 2006 +"Ca. Mycoplasma wenyonii" Neimark et al. 2001 (synonymous with Eperythrozoon wenyonii) +"Ca. Nebulobacter yamunensis" Boscaro et al. 2012 +"Ca. Neoehrlichia arcana" Gofton et al. 2016 +"Ca. Neoehrlichia australis" Gofton et al. 2016 +"Ca. Neoehrlichia lotoris" Yabsley et al. 2008 +"Ca. Neoehrlichia mikurensis" Kawahara et al. 2004 +"Ca. Nitrosoarchaeum koreensis" Kim et al. 2011 +"Ca. Nitrosoarchaeum limnia" Blainey et al. 2011 +"Ca. Nitrosocaldus yellowstonii" de la Torre et al. 2008 +"Ca. Nitrosopelagicus brevis(♦) +"Ca. Nitrosopumilus koreensis" Park et al. 2012 +"Ca. Nitrosopumilus maritimus" Könneke et al. 2005 +"Ca. Nitrosopumilus salaria" Mosier et al. 2012 +"Ca. Nitrosopumilus sediminis" Park et al. 2012 +"Ca. Nitrososphaera gargensis" Hatzenpichler et al. 2008 +"Ca. Nitrososphaera viennensis" Tourna et al. 2011 +"Ca. Nitrospira bockiana" Lebedeva et al. 2008 +"Ca. Nitrospira defluvii" Spieck et al. 2006 +"Ca. Nitrosotalea devanaterra" Lehtovirta-morley et al. 2011 +"Ca. Nitrotoga arctica" Alawi et al. 2007 +"Ca. Nostocoida limicola" Blackall et al. 2000 (strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 are now Tetrasphaera jenkinsii, strain Ben 70 is Tetrasphaera vanveenii, and strains Ver 1 and Ver 2 are Tetrasphaera veronensis) +"Ca. Odyssella thessalonicensis" Birtles et al. 2000 +"Ca. Ovobacter propellens" Fenchel and Thar 2004 +"Ca. Paenicardinium endonii" Noel and Atibalentja 2006 +"Ca. Parabeggiatoa communis" Salman et al. 2011 +"Ca. Paracaedibacter acanthamoebae" Horn et al. 1999 +"Ca. Paracaedibacter symbiosus" Horn et al. 1999 +"Ca. Paraholospora nucleivisitans" Eschbach et al. 2009 +"Ca. Parilichlamydia carangidicola" Stride et al. 2013 +"Ca. Parvarchaeum acidophilus(♦) +"Ca. Pasteuria aldrichii" Giblin-Davis et al. 2011 +"Ca. Pasteuria usgae" Giblin-Davis et al. 2003 +"Ca. Pelagibacter ubique" Rappe et al. 2002 +"Ca. Peptostreptococcus massiliae" Drancourt et al. 2004 +"Ca. Phlomobacter fragariae" Zreik et al. 1998 +"Ca. Photodesmus katoptron" Hendry and Dunlap 2011 +"Ca. Phytoplasma 16SrII-U" Yang et al. 2016 +"Ca. Phytoplasma allocasuarinae" Marcone et al. 2004 +"Ca. Phytoplasma americanum" Lee et al. 2006 +"Ca. Phytoplasma asteris" Lee et al. 2004 +"Ca. Phytoplasma aurantifolia" Zreik et al. 1995 +"Ca. Phytoplasma australiense" Davis et al. 1997 +"Ca. Phytoplasma balanitae" Win et al. 2013 +"Ca. Phytoplasma brasiliense" Montano et al. 2001 +"Ca. Phytoplasma caricae" Arocha et al. 2005 +"Ca. Phytoplasma castaneae" Jung et al. 2002 +"Ca. Phytoplasma cirsii" Safarova et al. 2016 +"Ca. Phytoplasma convolvuli" Martini et al. 2012 +"Ca. Phytoplasma costaricanum" Lee et al. 2011 +"Ca. Phytoplasma cynodontis" Marcone et al. 2004 +"Ca. Phytoplasma fragariae" Valiunas et al. 2006 +"Ca. Phytoplasma fraxini" Griffiths et al. 1999 - cause of Lilac witches'-broom +"Ca. Phytoplasma graminis" Arocha et al. 2005 +"Ca. Phytoplasma hispanicum" Davis et al. 2016 +"Ca. Phytoplasma japonicum" Sawayanagi et al. 1999 +"Ca. Phytoplasma lycopersici" Arocha et al. 2007 +"Ca. Phytoplasma malaysianum" Nejat et al. 2013 +"Ca. Phytoplasma mali" Seemüller and Schneider 2004 +"Ca. Phytoplasma meliae" Fernandez et al. 2016 +"Ca. Phytoplasma omanense" Al-Saady et al. 2008 +"Ca. Phytoplasma oryzae" Jung et al. 2003 +"Ca. Phytoplasma palmicola" Harrison et al. 2014 +"Ca. Phytoplasma phoenicium" Verdin et al. 2003 +"Ca. Phytoplasma pini" Schneider et al. 2005 +"Ca. Phytoplasma pruni" Davis et al. 2013 +"Ca. Phytoplasma prunorum" Seemüller and Schneider 2004 +"Ca. Phytoplasma pyri" Seemüller and Schneider 2004 +"Ca. Phytoplasma rhamni" Marcone et al. 2004 +"Ca. Phytoplasma rubi" Malembic-Maher et al. 2011 +"Ca. Phytoplasma rubi" Franova et al. 2016 +"Ca. Phytoplasma solani" Quaglino et al. 2013 +"Ca. Phytoplasma spartii" Marcone et al. 2004 +"Ca. Phytoplasma sudamericanum" Davis et al. 2012 +"Ca. Phytoplasma tamaricis" Zhao et al +"Ca. Phytoplasma trifolii" Hiruki and Wang 2004 +"Ca. Phytoplasma ulmi" Lee et al. 2004 +"Ca. Phytoplasma vitis" Marzorati et al. 2006 - cause of Flavescence dorée +"Ca. Phytoplasma ziziphi" Jung et al. 2003 +"Ca. Piscichlamydia salmonis" Draghi et al. 2004 +"Ca. Planktoluna difficilis" Hahn 2009 +"Ca. Planktomarina temperata" Giebel et al. 2011 +"Ca. Planktophila limnetica" Jezbera et al. 2009 +"Ca. Portiera aleyrodidarum" Thao and Baumann 2004 +"Ca. Prevotella massiliensis" Drancourt et al. 2004 +"Ca. Procabacter acanthamoebae" Horn et al. 2002 +"Ca. Profftia tarda" Toenshoff et al. 2012 +"Ca. Profftia virida" Toenshoff et al. 2012 +"Ca. Protochlamydia amoebophila" Collingro et al. 2005 +"Ca. Puchtella pedicinophila" Fukatsu et al. 2009 +"Ca. Puniceispirillum marinum" Oh et al. 2010 +"Ca. Purcelliella pentastirinorum" Bressan et al. 2009 +"Ca. Regiella insecticola" Moran et al. 2005 +"Ca. Renichlamydia lutjani" Corsaro and Work 2012 +"Ca. Rhabdochlamydia crassificans" Corsaro et al. 2006 +"Ca. Rhabdochlamydia porcellionis" Kostanjšek (morphology matches the description of Chlamydia isopodii) +"Ca. Rhizobium massiliae" Greub et al. 2004 +"Ca. Rhodoluna limnophila" Hahn 2009 +"Ca. Rhodoluna planktonica" Hahn 2009 +"Ca. Rickettsia amblyommii" Labruna et al. 2004 +"Ca. Rickettsia andeanae" Jiang et al. 2005 +"Ca. Rickettsia asemboensis" Jiang et al. 2013 +"Ca. Rickettsia barbariae" Mura et al. 2008 +"Ca. Rickettsia hebeiii" Yaxue et al. 2011 +"Ca. Rickettsia hungarica" Hornok et al. 2010 +"Ca. Rickettsia hoogstraalii" Mattila et al. 2007 +"Ca. Rickettsia kellyi" Rolain et al. 2006 +"Ca. Rickettsia kingi" Anstead and Chilton 2013 +"Ca. Rickettsia kotlanii" Sréter-Lancz et al. 2006 +"Ca. Rickettsia liberiensis" Mediannikov et al. 2012 +"Ca. Rickettsia principis" Mediannikov et al. 2006 +"Ca. Rickettsia senegalensis" Mediannikov, Aubadie-Ladrix, and Raoult 2015 +"Ca. Rickettsia tarasevichiae" Shpynov et al. 2003 +"Ca. Rickettsia tasmanensis" Izzard et al. 2009 +"Ca. Rickettsia vini" Palomar et al. 2012 +"Ca. Riegeria galateiae" Gruber-Vodicka et al. 2011 +"Ca. Riesia pediculicola" Sasaki-Fukatsu et al. 2006 +"Ca. Rohrkolberia cinguli" Kuechler et al. 2011 +"Ca. Roseomonas massiliae" Greub et al. 2004 +"Ca. Ruthia magnifica" Newton et al. 2007 +"Ca. Scalindua arabica" Woebken et al. 2008 +"Ca. Scalindua brodae" Schmid et al. 2003 +"Ca. Scalindua pacifica" Dang et al. 2003 +"Ca. Scalindua profunda" Van De Vossenberg et al. 2008 +"Ca. Scalindua richardsii" Fuchsman et al. 2012 +"Ca. Scalindua sorokinii" Kuypers et al. 2003 +"Ca. Scalindua wagneri" Schmid et al. 2003 +"Ca. Serratia symbiotica" Moran et al. 2005 +"Ca. Similichlamydia latridicola" Stride et al. 2013 +"Ca. Snodgrassella alvi" Martinson et al. 2012 +"Ca. Snodgrassella alvi" Martinson et al. 2012 +"Ca. Sodalis melophagi" Chrudimský et al. 2012 +"Ca. Sodalis pierantonius" Oakeson et al. 2014 +"Ca. Sphaeronema italicum" Kragelund et al. 2006 +"Ca. Stammerula tephritidis" Mazzon et al. 2008 +"Ca. Steffania adelgidicola" Toenshoff et al. 2012 +"Ca. Streptomyces philanthi" Kaltenpoth et al. 2006 +"Ca. Sulcia muelleri" Moran et al. 2005 +"Ca. Sulfurovum sediminum" Park et al. 2012 +"Ca. Symbiothrix dinenymphae" Hongoh et al. 2007 +"Ca. Synechococcus spongiarum" Usher et al. 2004 +"Ca. Tammella caduceiae" Hongoh et al. 2007 +"Ca. Tenderia electrophaga" Eddie et al. 2016 +"Ca. Thermochlorobacter aerophilum" Liu et al. 2012 +"Ca. Thiobios zoothamnicoli" Rinke et al. 2006 +"Ca. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-3.md b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-3.md new file mode 100644 index 000000000..442378f2e --- /dev/null +++ b/data/en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status-3.md @@ -0,0 +1,54 @@ +--- +title: "List of taxa with candidatus status" +chunk: 4/4 +source: "https://en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:01.046393+00:00" +instance: "kb-cron" +--- + +Thiodictyon syntrophicum" Peduzzi et al. 2012 +"Ca. Thioglobus singularis" Marshall and Morris 2013 +"Ca. Thiomargarita joergensenii" Salman et al. 2011 +"Ca. Thiomargarita nelsonii" Salman et al. 2011 +"Ca. Thiophysa hinzei" Salman et al. 2011 +"Ca. Thiopilula aggregata" Salman et al. 2011 +"Ca. Thioturbo danicus" Muyzer et al. 2005 +"Ca. Tremblaya phenacola" Gruwell et al. 2010 +"Ca. Tremblaya princeps" Thao et al. 2002 +"Ca. Troglogloea absoloni" Kostanjšek et al. 2013 +"Ca. Uabimicrobium amorphum" Shiratori et al. 2019 +"Ca. Uabimicrobium helgolandensis" Wurzbacher et al. 2024 +"Ca. Uzinura diaspidicola" Gruwell et al. 2007 +"Ca. Vallotia cooleyia" Toenshoff et al. 2012 +"Ca. Vallotia tarda" Toenshoff et al. 2012 +"Ca. Vallotia virida" Toenshoff et al. 2012 +"Ca. Veillonella atypica" Drancourt et al. 2004 +"Ca. Vesicomyosocius okutanii" Kuwahara et al. 2007 +"Ca. Vestibaculum illigatum" Stingl et al. 2004 +"Ca. Vidania fulgoroideae" Gonella et al. 2011 +"Ca. Wolinella africanus" Bohr et al. 2003 +"Ca. Xenohaliotis californiensis" Friedman et al. 2000 +"Ca. Xiphinematobacter americani" Vandekerckhove et al. 2000 +"Ca. Xiphinematobacter brevicolli" Vandekerckhove et al. 2000 +"Ca. Xiphinematobacter rivesi" Vandekerckhove et al. 2000 +"Ca. Zinderia insecticola" McCutcheon and Moran 2010 + +== Former candidatus taxa == +Armatimonadota, formerly Candidate phylum OP10 +Atribacterota (previously Candidate phylum OP9 or JS1) +Caldisericota, formerly Candidate phylum OP5 +Elusimicrobiota, formerly Termite Group 1 +Ignavibacteriota (previously Candidate phylum ZB1) +Lentisphaerota, formerly vadinBE97 +Nitrospinota + +== See also == +Uncultivated bacterial phyla and metagenomics +Open nomenclature, a system of notations used in taxonomy to indicate a taxonomist's judgement about taxon affinities +Glossary of scientific naming +incertae sedis, a taxon of uncertain position in a classification +nomen dubium, a name of unknown or doubtful application + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/MONA_number-0.md b/data/en.wikipedia.org/wiki/MONA_number-0.md new file mode 100644 index 000000000..40fe4ed96 --- /dev/null +++ b/data/en.wikipedia.org/wiki/MONA_number-0.md @@ -0,0 +1,20 @@ +--- +title: "MONA number" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/MONA_number" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:24.654701+00:00" +instance: "kb-cron" +--- + +A MONA number (short for Moths of North America), or Hodges number after Ronald W. Hodges, is part of a numbering system for North American moths found north of Mexico in the Continental United States and Canada, as well as the island of Greenland. Introduced in 1983 by Hodges through the publication of Check List of the Lepidoptera of America North of Mexico, the system began an ongoing numeration process in order to compile a list of the over 12,000 moths of North America north of Mexico. The system numbers moths within the same family close together for identification purposes. For example, the species Epimartyria auricrinella begins the numbering system at 0001 while Epimartyria pardella is numbered 0002. +The system has become somewhat out of date since its inception for several reasons: + +Some numbers no longer exist as the species bearing the number have been reclassified into other species. +Some species have been regrouped into a different family and their MONA numbers are out of order taxonomically. +New species have been discovered since the implementation of the MONA system, resulting in the usage of decimal numbers as to not disrupt the numbering of other species. +Despite the issues above, the MONA system has remained popular with many websites and publications. It is the most popular numbering system used, largely replacing the older McDunnough Numbers system, while some published lists prefer to use other forms of compilation. The Moth Photographer's Group (MPG) at Mississippi State University actively monitors the expansive list of North American moths utilizing the MONA system and updates their checklists in accordance with publishings regarding changes and additions. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Menagerie-0.md b/data/en.wikipedia.org/wiki/Menagerie-0.md new file mode 100644 index 000000000..4cb9ea9ff --- /dev/null +++ b/data/en.wikipedia.org/wiki/Menagerie-0.md @@ -0,0 +1,39 @@ +--- +title: "Menagerie" +chunk: 1/3 +source: "https://en.wikipedia.org/wiki/Menagerie" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:38.997628+00:00" +instance: "kb-cron" +--- + +A menagerie is a collection of captive animals, frequently exotic, kept for display; or the place where such a collection is kept, a precursor to the modern zoo or zoological garden. +The term was first used in 17th-century France, referring to the management of household or domestic stock. Later, it came to be used primarily in reference to aristocratic or royal animal collections. The French-language Methodical Encyclopaedia of 1782 defines a menagerie as an "establishment of luxury and curiosity". Later on, the term referred also to travelling animal collections that exhibited wild animals at fairs across Europe and the Americas. + +== Aristocratic menageries == + +A menagerie was mostly connected with an aristocratic or royal court and was situated within a garden or park of a palace. These aristocrats wanted to illustrate their power and wealth by displaying exotic animals which were uncommon, difficult to acquire, and expensive to maintain in a living and active state. +The aristocratic menageries are distinguished from the later zoological garden (zoos) since they were founded and owned by aristocrats whose intentions were not primarily of scientific and educational interest. + +=== Medieval period and Renaissance === +During the Middle Ages, several sovereigns across Europe maintained menageries at their royal courts. An early example is that of the Emperor Charlemagne in the 8th century. His three menageries, at Aachen, Nijmegen and Ingelheim, located in present-day Netherlands and Germany, housed the first elephants seen in Europe since the Roman Empire, along with monkeys, lions, bears, camels, falcons, and many exotic birds. +Charlemagne received exotic animals for his collection as gifts from rulers of Africa and Asia. +In 797, the caliph of Baghdad, Harun al-Rashid, presented Charlemagne with an Asian elephant named Abul-Abbas. The elephant arrived on July 1, 802 to the Emperor's residence in Aachen. He died in June 810. +William the Conqueror had a small royal menagerie. At his manor, Woodstock, he began a collection of exotic animals. Around the year 1100 his son, Henry I, enclosed Woodstock and enlarged the collection. +At the beginning of the 12th century, Henry I of England is known to have kept a collection of animals at his palace in Woodstock, Oxfordshire, reportedly including lions, leopards, lynxes, camels, owls, and a porcupine. +The most prominent animal collection in medieval England was the Tower Menagerie in London that began as early as 1204. +It was established by King John, who reigned in England from 1199 to 1216 and is known to have held lions and bears. +Henry III received a wedding gift in 1235 of three leopards from Frederick II, Holy Roman Emperor. +The most spectacular arrivals in the early years were a white bear and an elephant, gifts from the kings of Norway and France in 1251 and in 1254 respectively. +In 1264, the animals were moved to the Bulwark, which was renamed the Lion Tower, near the main western entrance of the Tower. +This building was constituted by rows of cages with arched entrances, enclosed behind grilles. They were set in two storeys, and it appears that the animals used the upper cages during the day and were moved to the lower storey at night. +The menagerie was opened to the public during the reign of Elizabeth I in the 16th century. During the 18th century, the price of admission was three half-pence, or the supply of a cat or dog to be fed to the lions. +Animals recorded here at the end of the 18th century included lions, tigers, hyenas, and bears. +Most of the animals were transferred in 1831 to the newly opened London Zoo at Regent's Park, which did not receive all the animals but rather shared them with Dublin Zoo. +The Tower Menagerie was finally closed in 1835, on the orders of the Duke of Wellington. The Tower Menagerie in London can be considered to have been the royal menagerie of England for six centuries. +In the first half of the thirteenth century, Emperor Frederick II had three permanent menageries in Italy, at Melfi in Basilicata, at Lucera in Apulia and at Palermo in Sicily. +In 1235, the Holy Roman Emperor Frederick II established at his court in southern Italy the "first great menagerie" in western Europe. An elephant, a white bear, a giraffe, a leopard, hyenas, lions, cheetahs, camels, and monkeys were all exhibited; but the emperor was particularly interested in birds, and studied them sufficiently to write a number of authoritative books on them. +In the beginning of the 15th century, a royal menagerie was established in the Royal Palace of Lisbon, located nearby the Castle of Saint George. Following the conquest of Ceuta in 1415, King John I of Portugal brought back to Lisbon two Barbary lions, and they were installed in a large room inside his Palace in the Citadel of Lisbon. This area of the palace came to be known as Casa dos Leões (the "Lions' House"); today the area is occupied by a famed restaurant with the same name. Later that century, German humanist Hieronymus Münzer spent five days in Lisbon in 1494, and learned about the lions, claiming to be the most beautiful wild beasts he had ever seen. +Later on, the ménagerie of King Manuel I (1495-1521), inside the Ribeira Palace, in downtown Lisbon, was appreciated in Europe due to its huge elephants that the king ordered to be brought from India. One of his elephants, Hanno, as well as a rhinoceros depicted by Dürer were famous gifts to Pope Leo X. However, the rhinoceros drowned as a result of a shipwreck suffered during the transport trip to Italy. +By the end of the 15th century, the aristocracy of Renaissance Italy began to collect exotic animals at their residences on the outskirts of the cities. The role played by animals within the gardens of Italian villas expanded at the end of the 16th century and the beginning of the seventeenth century, and one prominent example was the Villa Borghese built 1608–1628 in Rome. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Menagerie-1.md b/data/en.wikipedia.org/wiki/Menagerie-1.md new file mode 100644 index 000000000..df3c4203e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Menagerie-1.md @@ -0,0 +1,33 @@ +--- +title: "Menagerie" +chunk: 2/3 +source: "https://en.wikipedia.org/wiki/Menagerie" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:38.997628+00:00" +instance: "kb-cron" +--- + +=== Versailles and its legacy === + +During the seventeenth century, exotic birds and small animals provided diverting ornaments for the court of France; lions and other large animals were kept primarily to be brought out for staged fights. +The collecting grew and attained more permanent lodgings in the 1660s, when Louis XIV constructed two new menageries: one at Vincennes, next to a palace on the eastern edge of Paris, and a more elaborate one, which became a model for menageries throughout Europe, at Versailles, the site of a royal hunting lodge two hours (by carriage) west of Paris. +Around 1661, he had a menagerie of "ferocious" beasts built at Vincennes for the organization of fights. Surrounding a rectangular courtyard, a two-storey building with balconies allowed spectators to view the scene. The animals were housed on the ground floor in cells bordering the courtyard, with small yards on the outside where they could take a bit of exercise. +At Vincennes, lions, tigers, and leopards, as well as polecat, minks, and weasels were kept in cages around an amphitheater where the king could entertain courtiers and visiting dignitaries with bloody battles. +In 1682, for instance, the ambassador of Persia enjoyed the spectacle of a fight to the death between a royal tiger and an elephant. +When the palace of Versailles was built, Louis XIV of France also erected a menagerie within the palace's park. +The menagerie at Versailles was to be something very different from the one at Vincennes. +Most of it was constructed in 1664 when the first animals were introduced, although the interior fittings were not finished until 1668–70. Situated in the south-west of the park, it was Louis XIV's first major project at Versailles and one of several pleasure houses that were gradually assembled around the palace. +It represented the first menagerie according to Baroque style. The prominent feature of Baroque menageries was the circular layout, in the middle of which stood a beautiful pavilion. Around this pavilion was a walking path and outside this path were the enclosures and cages. Each enclosure had a house or stable at the far end for the animals and was bounded on three sides with walls. There were bars only in the direction of the pavilion. +Animal fights were halted at Vincennes around 1700, the site fell into disuse, and the animals were installed at Versailles with the others. +At about this time, the lions, leopards, and tigers from the menagerie at Vincennes were transferred to Versailles, where they were housed in newly built enclosures fronted with iron bars. + +This particular enterprise marked a decisive step in the creation of menageries of curiosities and was imitated to some extent throughout Europe after the late seventeenth century. +Monarchs, princes and important lords built them in France (Chantilly from 1663), England (Kew, Osterley), the United Provinces (Het Loo from 1748), Portugal (Belém in 1726, Queluz around 1780), Spain (Madrid in 1774) and Austria (Belvedere in 1716, Schönbrunn in 1752) as well in the Germanic lands following the ravages of the Thirty Years' War (1618–1648) and the ensuing reconstruction. Frederick William, Elector of Prussia, equipped Potsdam with a menagerie around 1680. The Elector of the Palatinate, the Prince Regent of Westphalia and many others followed suit. +This design was adopted particularly by the Habsburg monarchy in Austria. In 1752 Francis I erected his famous Baroque menagerie in the park of Schönbrunn Palace near Vienna. +Being at first a courtly menagerie with private character it was opened to the general public in 1779. Initially, it was only open for "respectably dressed persons". +Another aristocratic menagerie was founded in 1774 by Charles III of Spain on grounds which were part of the gardens of the Buen Retiro Palace in Madrid. +During two centuries, it was a predecessor institution of the modern facilities of the Madrid Zoo Aquarium, moved in 1972 to the Casa de Campo. +In the nineteenth century the aristocratic menageries were displaced by the modern zoological gardens with their scientific and educational approach. The last menagerie in Europe was the Tiergarten Schönbrunn in Vienna, which was known officially as a "menagerie" until 1924, before evolving into a modern zoological garden with a scientific, educational and conservationist orientation. Due to its local continuity, the former menagerie established in the medieval through baroque tradition of private wild-animal collections of princes and kings, is often seen as the oldest remaining zoo in the world. Although many of the old Baroque enclosures have been changed, one can still obtain a good impression of the symmetrical ensemble of the formerly imperial menagerie. + +== Travelling menageries == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Menagerie-2.md b/data/en.wikipedia.org/wiki/Menagerie-2.md new file mode 100644 index 000000000..fb7e00304 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Menagerie-2.md @@ -0,0 +1,32 @@ +--- +title: "Menagerie" +chunk: 3/3 +source: "https://en.wikipedia.org/wiki/Menagerie" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:38.997628+00:00" +instance: "kb-cron" +--- + +In England travelling menageries had first appeared at around 1700. In contrast to the aristocratic menageries, these travelling animal collections were run by showmen who met the craving for sensation of the ordinary population. These animal shows ranged in size but the largest was George Wombwell's. The earliest record of a fatality at one such travelling menagerie was the death of Hannah Twynnoy in 1703 who was killed by a tiger in Malmesbury, Wiltshire. +Also in North America travelling menageries became even more popular during that time. +The first exotic animal known to have been exhibited in America was a lion, in Boston in 1710, followed a year later in the same city by a camel. +A sailor arrived in Philadelphia in August 1727 with another lion, which he exhibited in the city and surrounding towns for eight years. +The first elephant was imported from India to America by a ship's captain, Jacob Crowninshield, in 1796. It was first displayed in New York City and travelled extensively up and down the East Coast. +In 1834 James and William Howes’ New York Menagerie toured New England with an elephant, a rhinoceros, a camel, two tigers, a polar bear, and several parrots and monkeys. +America's touring menageries slowed to a crawl under the weight of the depression of the 1840s and then to a halt with the outbreak of the Civil War. Only one travelling menagerie of any size existed after the war: The Van Amburgh menagerie travelled the United States for nearly forty years. Unlike their European counterparts, America's menageries and circuses had combined as single travelling shows, with one ticket to see both. This increased the size and the diversity of their collections. Ringling Bros. and Barnum & Bailey Circus advertised their shows as the “World’s Greatest Menagerie”. + +== See also == +Anthrozoology + +== References == +Hahn, Daniel (2003). The Tower Menagerie. London: Simon & Schuster. ISBN 0-7432-2081-1. +Baratay, Eric; Hardouin-Fugier, Elisabeth (2002). Zoo: a History of the Zoological Gardens of the West. London: Reaktion. ISBN 1-86189-111-3. + +== Notes == + +== External links == + +Vienna Zoo +La Ménagerie de Versailles (French) +"Menagerie" . Encyclopædia Britannica (11th ed.). 1911. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Nocturnal_house-0.md b/data/en.wikipedia.org/wiki/Nocturnal_house-0.md new file mode 100644 index 000000000..b7b4f5d5f --- /dev/null +++ b/data/en.wikipedia.org/wiki/Nocturnal_house-0.md @@ -0,0 +1,76 @@ +--- +title: "Nocturnal house" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Nocturnal_house" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:40.149365+00:00" +instance: "kb-cron" +--- + +A nocturnal house, sometimes called a nocturama, is a building in a zoo or research establishment where nocturnal animals are kept and viewable by the public. The unique feature of buildings of this type is that the lighting within is isolated from the outside and reversed; i.e. it is dark during the day and lit at night. This is to enable visitors and researchers to more conveniently study nocturnal animals during daylight hours. +Internally, a building usually consists of several glass-walled enclosures containing a replica of the animals' normal environments. In the case of burrowing animals, often their tunnels are 'half-glassed' so the animals can be observed while underground. + + +== Notable nocturnal houses == + + +=== Current === + + +==== USA ==== +Kingdoms of The Night, Omaha's Henry Doorly Zoo & Aquarium (Nebraska) +Nocturnal Building and Aviary, Columbus Zoo & Aquarium (Ohio) +Animals of The Night, Memphis Zoo (Tennessee) +Bat House in Jaguar Jungle, Audubon Zoo (Louisiana) +Brazos by Night, Cameron Park Zoo (Texas) +Mouse House, Bronx Zoo (New York) +Desert's Edge and Clouded leopard Rain Forest, Brookfield Zoo (Illinois) +Night Hunters, Cincinnati Zoo and Botanical Garden (Ohio) + + +==== Mexico ==== +Guadalajara Zoo + + +==== United Kingdom ==== +Nightlife, ZSL London Zoo +Fruit Bat Forest, Chester Zoo + + +==== Europe ==== +Berlin Zoological Garden +Frankfurt Zoological Garden +Moscow Zoo +Prague Zoo +Plzen Zoo +Budapest Zoological and Botanical Garden + + +==== Australasia ==== +Nguwing Nura, Taronga Zoo +Wild Life Sydney +Adelaide Zoo +Perth Zoo +David Fleay Wildlife Park +Auckland Zoo + + +==== India ==== +Nandankanan Zoological Park + + +=== Former === + + +==== USA ==== +World of Darkness, Bronx Zoo (New York) - closed 2009/reopening 2025 +The Night Exhibit, Woodland Park Zoo (Seattle, WA) - closed 2010 + + +== References == + + +== External links == +Queensland Environmental Protection Agency +Goodzoos.com \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Nomen_novum-0.md b/data/en.wikipedia.org/wiki/Nomen_novum-0.md new file mode 100644 index 000000000..921b89512 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Nomen_novum-0.md @@ -0,0 +1,26 @@ +--- +title: "Nomen novum" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Nomen_novum" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:25.816985+00:00" +instance: "kb-cron" +--- + +In biological nomenclature, a nomen novum (Latin for "new name"), replacement name (or new replacement name, new substitute name, substitute name) is a replacement scientific name that is created when technical, nomenclatural reasons have made it impossible to continue using the previous name (for example because it was discovered to be a homonym – spelled the same as an existing, older name). Nomen novum does not apply when a name is changed for taxonomic reasons alone. It is frequently abbreviated, e.g. nomen nov., nom. nov.. + +== Zoology == +In zoology establishing a new replacement name is a nomenclatural act and it must be expressly proposed to substitute a previously established and available name. +Often, the older name cannot be used because another animal was described earlier with exactly the same name. For example, Lindholm discovered in 1913 that a generic name Jelskia established by Bourguignat in 1877 for a European freshwater snail could not be used because another author Taczanowski had proposed the same name in 1871 for a spider. So Lindholm proposed a new replacement name Borysthenia. This is an objective synonym of Jelskia Bourguignat, 1877, because he has the same type species, and is used today as Borysthenia. +Also, for names of species new replacement names are often necessary. New replacement names have been proposed since more than 100 years ago. In 1859 Bourguignat saw that the name Bulimus cinereus Mortillet, 1851 for an Italian snail could not be used because Reeve had proposed exactly the same name in 1848 for a completely different Bolivian snail. Since it was understood even then that the older name always has priority, Bourguignat proposed a new replacement name Bulimus psarolenus, and also added a note why this was necessary. The Italian snail is known until today under the name Solatopupa psarolena (Bourguignat, 1859). +A new replacement name must obey certain rules; not all of these are well known. +Not every author who proposes a name for a species that already has another name, establishes a new replacement name. An author who writes "The name of the insect species with the green wings shall be named X, this is the one that the other author has named Y", does not establish a new replacement name (but a regular new name). +The International Code of Zoological Nomenclature prescribes that for a new replacement name, an expressed statement must be given by the author, which means an explicit statement concerning the process of replacing the previous name. It is not necessary to employ the term nomen novum, but something must be expressed concerning the act of substituting a name. Implicit evidence ("everybody knows why the author used that new name") is not allowed at this occasion. Many zoologists do not know that this expressed statement is necessary, and therefore a variety of names are regarded as having been established as new replacement names (often including names that were mentioned without any description, which is fundamentally contrary to the rules). +The author who proposes a new replacement name must state exactly which name shall be replaced. It is not possible to mention three available synonyms at once to be replaced. Usually, the author explains why the new replacement name is needed. +Sometimes we read "the species cannot keep this old name P. brasiliensis, because it does not live in Brazil, so I propose a new name P. angolana". Even though this would not justify a new replacement name under the Code's rules, the author believed that a new name was necessary and gave an expressed statement concerning the act of replacing. So the name P. angolana was made available at this occasion, and is an objective synonym of P. brasiliensis. +A new replacement name can only be used for a taxon if the name that it replaces cannot be used, as in the example above with the snail and the spider, or in the other example with the Italian and the Bolivian snail. The animal from Angola must keep its name brasiliensis, because this is the older name. +New replacement names do not occur very frequently, but they are not extremely rare. About 1% of the currently used zoological names might be new replacement names. There are no exact statistics covering all animal groups. In 2,200 names of species and 350 names of genera in European non-marine molluscs, which might be a representative group of animals, 0.7% of the specific and 3.4% of the generic names were correctly established as new replacement names (and a further 0.7% of the specific and 1.7% of the generic names have incorrectly been regarded as new replacement names by some authors). + +== Algae, fungi and plants == +For those taxa whose names are regulated by the International Code of Nomenclature for algae, fungi, and plants (ICNafp), a nomen novum or replacement name is a name published as a substitute for "a legitimate or illegitimate, previously published name, which is its replaced synonym and which, when legitimate, does not provide the final epithet, name, or stem of the replacement name". For species, replacement names may be needed because the specific epithet is not available in the genus for whatever reason. Examples: \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Nomen_novum-1.md b/data/en.wikipedia.org/wiki/Nomen_novum-1.md new file mode 100644 index 000000000..3b908c0d1 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Nomen_novum-1.md @@ -0,0 +1,26 @@ +--- +title: "Nomen novum" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Nomen_novum" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:25.816985+00:00" +instance: "kb-cron" +--- + +Carl Linnaeus gave the herb rosemary the scientific name Rosmarinus officinalis in 1753. It is now regarded as one of many species in the genus Salvia. It cannot be transferred to this genus as "Salvia officinalis" because Linnaeus gave this name to the herb sage. An acceptable name in the genus Salvia was published by Fridolin Spenner in 1835. The replacement name is cited as Salvia rosmarinus Spenn.; the replaced synonym is Rosmarinus officinalis L. The author of the replaced synonym is not included in the citation of the replacement name. +The plant name Polygonum persicaria was published by Linnaeus in 1753. In 1821, Samuel Gray transferred the species to the genus Persicaria. He could not do this using the name "Persicaria persicaria" because the ICNafp does not allow tautonyms. Accordingly, he published the replacement name Persicaria maculosa. The replacement name is Persicaria maculosa Gray; the replaced synonym is Polygonum persicaria L. Again, the author of the replaced synonym is not included in the citation of the replacement name. +The fungus name Marasmius distantifolius was published by Y.S. Tan and Desjardin in 2009. Later it was discovered that this combination had already been used for a different species by William Murrill in 1915, so Tan and Desjardin's name was an illegitimate later homonym. Accordingly, in 2010 Mešić and Tkalčec published the replacement name Marasmius asiaticus for the species. The replacement name is cited as Marasmius asiaticus Mešić & Tkalčec; the replaced synonym as Marasmius distantifolius Y.S. Tan & Desjardin. In this example, the replaced synonym is illegitimate. +The plant name Lycopodium densum was published by Jacques Labillardière in 1807. However, the combination had already been used for a different species by Jean-Baptiste Lamarck in 1779, so Labillardière's name is illegitimate. Werner Rothmaler knew this when in 1944 he transferred the species to the genus Lepidotis, and so explicitly published Lepidotis densa as a new name ("nom. nov.", "neuer Name"). The replacement name is Lepidotis densa Rothm.; the replaced synonym is Lycopodium densum Labill. Even though the specific epithet in Lepidotis appears to be the same, it is nevertheless new. So when in 1983, Josef Holub transferred the species to Pseudolycopodium, the name in that genus is cited as Pseudolycopodium densum (Rothm.) Holub., the basionym being the replacement name Lepidotis densa Rothm. not the illegitimate replaced synonym Lycopodium densum Labill. + +== See also == +Glossary of scientific naming +Nomen dubium +Nomen conservandum +Nomen nudum +Nomen oblitum + +== References == + +== External links == +International Code of Zoological Nomenclature (ICZN) (only English version, the French version is not online) \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Non-cellular_life-0.md b/data/en.wikipedia.org/wiki/Non-cellular_life-0.md new file mode 100644 index 000000000..8b4a45349 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Non-cellular_life-0.md @@ -0,0 +1,40 @@ +--- +title: "Non-cellular life" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Non-cellular_life" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:27.002282+00:00" +instance: "kb-cron" +--- + +Non-cellular life, also known as acellular life, is life that exists without a cellular structure for at least part of its life cycle. Historically, most definitions of life postulated that an organism must be composed of one or more cells, but, for some, this is no longer considered necessary, and modern criteria allow for forms of life based on other structural arrangements. + + +== Nucleic acid-containing infectious agents == + + +=== Viruses === + +Researchers initially described viruses as "poisons" or "toxins", then as "infectious proteins"; but they possess genetic material, a defined structure, and the ability to spontaneously assemble from their constituent parts. This has spurred extensive debate as to whether they should be regarded as fundamentally biotic or abiotic—as very small biological organisms or as very large biochemical molecules. Without their hosts, they are not able to perform any of the functions of life—such as metabolism, growth, or reproduction. Since the 1950s, many scientists have thought of viruses as existing at the border between chemistry and life; a gray area between living and nonliving. + + +=== Viroids === + +If viruses are borderline cases or nonliving, viroids are further from being living organisms. Viroids are some of the smallest infectious agents, consisting solely of short strands of circular, single-stranded RNA without protein coats. They are only known to infect flowering plants, of which some are of commercial importance. Viroid genomes are extremely small in size, ranging from 246 to 467 nucleobases. In comparison, the genome of the smallest viruses capable of causing an infection are around 2,000 nucleobases in size. Viroid RNA does not code for any protein. Its replication mechanism hijacks RNA polymerase II, a host-cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid's RNA as a template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates. +A possible explanation of the origin of viroids sees them as "living relics" from a hypothetical, ancient, and non-cellular RNA world before the evolution of DNA or of protein. This view, first proposed in the 1980s, regained popularity in the 2010s to explain crucial intermediate steps in the evolution of life from inanimate matter (abiogenesis). + + +=== Obelisks === + +In 2024, researchers announced the possible discovery of viroid-like, but distinct, RNA-based elements dubbed obelisks. Obelisks, found in sequence databases of the human microbiome, are possibly hosted in gut bacteria. They differ from viroids in that they code for two distinct proteins, dubbed "oblins", and for the predicted rod-like secondary structure of their RNA. + + +== First universal common ancestor == +The first universal common ancestor (FUCA) is an example of a proposed non-cellular lifeform, as it is the earliest ancestor of the last universal common ancestor, its sister lineages, and every currently living cell. + + +== See also == + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Our_Zoo-0.md b/data/en.wikipedia.org/wiki/Our_Zoo-0.md new file mode 100644 index 000000000..ec06466d9 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Our_Zoo-0.md @@ -0,0 +1,40 @@ +--- +title: "Our Zoo" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Our_Zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:41.344635+00:00" +instance: "kb-cron" +--- + +Our Zoo is a British period drama television series from BBC One, first broadcast on 3 September 2014. +The six-part series, created by Matt Charman, is about George Mottershead, his dreams of creating a cage-free zoo, his family and how their lives changed when they embarked on the creation of Chester Zoo. + + +== Cast == +Lee Ingleby as George Mottershead +Liz White as Lizzie Mottershead +Anne Reid as Lucy Mottershead +Peter Wight as Albert Mottershead +Ralf Little as Billy Atkinson +Sophia Myles as Lady Katherine Longmore +Stephen Campbell Moore as Reverend Aaron Webb +Amelia Clarkson as Muriel Mottershead +Honor Kneafsey as June Mottershead + + +== Production == +Our Zoo was commissioned by Danny Cohen and Ben Stephenson for BBC One. The series was based on an idea introduced to Big Talk Productions by Aenon, the production company headed by Adam Kemp. Filming took place in Liverpool, as well as at Walton Hall in Warrington and at Abney Hall in Cheadle. When BBC said there would be no second series of Our Zoo, many fans were left surprised by the decision. On 10 December 2014 the Chester Chronicle created an online petition in the hopes of renewing the show for another series, and by the next day more than 1000 fans had signed it. In spite of these efforts, however, the BBC reiterated that they would not be producing a second series. + + +== Episode list == + + +== References == + + +== External links == + +Our Zoo at BBC Online +Our Zoo at IMDb \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Pathovar-0.md b/data/en.wikipedia.org/wiki/Pathovar-0.md new file mode 100644 index 000000000..76d8b2582 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Pathovar-0.md @@ -0,0 +1,23 @@ +--- +title: "Pathovar" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Pathovar" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:28.151461+00:00" +instance: "kb-cron" +--- + +A pathovar is a bacterial strain or set of strains with the same or similar characteristics, that is differentiated at infrasubspecific level from other strains of the same species or subspecies on the basis of distinctive pathogenicity to one or more plant hosts. + +Pathovars are named as a ternary or quaternary addition to the species binomial name, for example the bacterium that causes citrus canker Xanthomonas axonopodis, has several pathovars with different host ranges, X. axonopodis pv. citri is one of them; the abbreviation 'pv.' means pathovar. +The type strains of pathovars are pathotypes, which are distinguished from the types (holotype, neotype, etc.) of the species to which the pathovar belongs. + + +== See also == +Infraspecific names in botany +Phytopathology +Trinomen, infraspecific names in zoology (subspecies only) + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Petting_zoo-0.md b/data/en.wikipedia.org/wiki/Petting_zoo-0.md new file mode 100644 index 000000000..8785a44ec --- /dev/null +++ b/data/en.wikipedia.org/wiki/Petting_zoo-0.md @@ -0,0 +1,40 @@ +--- +title: "Petting zoo" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Petting_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:42.494466+00:00" +instance: "kb-cron" +--- + +A petting zoo (also called a children's zoo, children's farm, or petting farm) features a combination of domesticated animals and some wild species that are docile enough to touch and feed. In addition to independent petting zoos, many general zoos contain a petting zoo. +Most petting zoos are designed to provide only relatively placid, herbivorous domesticated animals, such as sheep, goats, rabbits, ponies and donkeys to feed and interact physically with safety. This is in contrast to the usual zoo experience, where normally wild animals are viewed from behind safe enclosures where no contact is possible. A few provide wild species (such as pythons or big cat cubs) to interact with, but these are rare and usually found outside Western nations. Petting zoos are categorized as part of the agritourism sector. +Concerns have been raised about the welfare of animals in petting zoos, particularly due to interactions with large numbers of visitors, which can be stressful. Under appropriate conditions, where animals have access to refuge and can avoid visitors, friendly species such as goats may be unaffected, while more sensitive animals, such as pigs, may alter their behavior, especially under high visitor density. Highly sensitive animals, including rabbits, experience persistent stress from human contact, even during calm petting, as indicated by hormonal and behavioral responses such as eye closure and pressed back. In contrast, some animals, such as horses, may find gentle petting in preferred areas positive. The Environmental Literacy Council recommends that petting zoos provide rest periods and areas inaccessible to visitors, adequate space and enrichment, veterinary care, and clear guidelines for interaction. Such guidelines are particularly important for young children, whose behavior may be unpredictable and stressful for animals. + + +== History == +In 1938, the London Zoo included the first children's zoo in Europe and the Philadelphia Zoo was the first in North America to open a special zoo just for children. +During the 1990s, Dutch cities began building petting zoos in many neighbourhoods, so that urban children could interact with animals. + + +== Animals and food == +Petting zoos feature a variety of domestic animals. Common animals include cattle, zebu, yaks, sheep, goats, rabbits, guinea pigs, ponies, alpacas, llamas, pigs, miniature donkeys, miniature horses, ducks, geese, chickens, and turkeys. They occasionally contain several exotic animals such as kangaroos, wallabies, emus, swans, deer, zebras, parrots, porcupines, camels, ostriches, bison, water buffaloes, rheas, peafowl, guinea fowl, antelopes, capybaras, lemurs, tortoises and many others. +Petting zoos are popular with small children, who will often feed the animals. In order to ensure the animals' health, the food is supplied by the zoo, either from vending machines or a kiosk. Food often fed to animals includes grass or hay, pellets, or crackers. Such feeding is an exception to the usual rule about not feeding animals. + + +== Mobile petting zoos == +Some petting zoos are also mobile and will travel to a home for a children's party or event. Many areas have a qualified mobile petting zoo. One of the first mobile petting zoos in Australia (begun in 1992), was Kindifarm. As a result of its popularity, many Australians use the term kindy farms to describe petting zoos. In Australia, mobile petting zoos are allowed in schools, child care centres and even shopping centres. For many children, a mobile petting zoo is their first opportunity to see and touch an animal. American mobile petting zoos have gained popularity in the southern states. + + +== Health effects == +Touching animals can result in the transmission of diseases between animals and humans (zoonosis) so it is recommended that people should thoroughly wash their hands before and after touching the animals. There have been several outbreaks of E. coli etc. Another threat is salmonella specifically from chicks handled by children. Petting zoo attendees under the age of 5 are at a higher risk of contracting these diseases and they are a major target audience of these petting zoos. + + +== See also == + +Cat café +Pet rental + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Pheasantry-0.md b/data/en.wikipedia.org/wiki/Pheasantry-0.md new file mode 100644 index 000000000..cfa6050d3 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Pheasantry-0.md @@ -0,0 +1,21 @@ +--- +title: "Pheasantry" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Pheasantry" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:43.655744+00:00" +instance: "kb-cron" +--- + +A pheasantry is a place or facility used for captive breeding and rearing pheasants, peafowls and other related birds, which may or may not be confined with enclosures such as aviaries. The pheasants may be sold or displayed to public as ornamental animals, or used as game birds. Pheasantries may also be used for conservation and research purposes. + + +== See also == +Aviculture +Falconry +Poultry +Hatchery + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Phenetics-0.md b/data/en.wikipedia.org/wiki/Phenetics-0.md new file mode 100644 index 000000000..0cb1b6e26 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Phenetics-0.md @@ -0,0 +1,42 @@ +--- +title: "Phenetics" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Phenetics" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:29.294813+00:00" +instance: "kb-cron" +--- + +In biology, phenetics (; from Ancient Greek φαίνειν (phainein) 'to appear'), also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually with respect to morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is related closely to numerical taxonomy which is concerned with the use of numerical methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath and Robert R. Sokal. Their books are still primary references for this sub-discipline, although now out of print. +Phenetics has been largely superseded by cladistics for research into evolutionary relationships among species. However, certain phenetic methods, such as neighbor-joining, are used for phylogenetics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference) are too expensive computationally. +Phenetic techniques include various forms of clustering and ordination. These are sophisticated methods of reducing the variation displayed by organisms to a manageable degree. In practice this means measuring dozens of variables, and then presenting them as two- or three-dimensional graphs. Much of the technical challenge of phenetics concerns balancing the loss of information due to such a reduction against the ease of interpreting the resulting graphs. +The method can be traced back to 1763 and Michel Adanson (in his Familles des plantes) because of two shared basic principles – overall similarity and equal weighting – and modern pheneticists are sometimes termed neo-Adansonians. + + +== Difference from cladistics == +Phenetic analyses are "unrooted", that is, they do not distinguish between plesiomorphies, traits that are inherited from an ancestor, and apomorphies, traits that evolved anew in one or several lineages. A common problem with phenetic analysis is that basal evolutionary grades, which retain many plesiomorphies compared to more advanced lineages, seem to be monophyletic. Phenetic analyses are also liable to be rendered inaccurate by convergent evolution and adaptive radiation. Cladistic methods attempt to solve those problems. +Consider for example songbirds. These can be divided into two groups – Corvida, which retains ancient characteristics of phenotype and genotype, and Passerida, which has more modern traits. But only the latter are a group of closest relatives; the former are numerous independent and ancient lineages which are related about as distantly to each other as each single one of them is to the Passerida. For a phenetic analysis, the large degree of overall similarity found among the Corvida will make them seem to be monophyletic too, but their shared traits were present in the ancestors of all songbirds already. It is the loss of these ancestral traits rather than their presence that signifies which songbirds are more closely related to each other than to other songbirds. However, the requirement that taxa be monophyletic – rather than paraphyletic as for the case of the Corvida – is itself part of the cladistic method of taxonomy, not necessarily obeyed absolutely by other methods. +The two methods are not mutually exclusive. There is no reason why, e.g., species identified using phenetics cannot subsequently be subjected to cladistic analysis, to determine their evolutionary relationships. Phenetic methods can also be superior to cladistics when only the distinctness of related taxa is important, as the computational requirements are less. +The history of pheneticism and cladism as rival taxonomic systems is analysed in David Hull's 1988 book Science as a Process. + + +== Current usage == +Traditionally there was much debate between pheneticists and cladists, as both methods were proposed initially to resolve evolutionary relationships. One of the most noteworthy applications of phenetics were the DNA–DNA hybridization studies by Charles G. Sibley, Jon E. Ahlquist and Burt L. Monroe Jr., from which resulted the 1990 Sibley-Ahlquist taxonomy for birds. Controversial at its time, some of its findings (e.g. the Galloanserae) have been vindicated, while others (e.g. the all-inclusive "Ciconiiformes" or the "Corvida") have been rejected. However, with computers growing increasingly powerful and widespread, more refined cladistic algorithms became available which could test the suggestions of Willi Hennig. The results of cladistic analyses were proven superior to those of phenetic methods, at least for resolving phylogenies. +Many systematists continue to use phenetic methods, particularly to address species-level questions. While a major goal of taxonomy remains describing the 'tree of life' – the evolutionary relationships of all species – for fieldwork one needs to be able to separate one taxon from another. Classifying diverse groups of closely related organisms that differ very subtly is difficult using a cladistic method. Phenetics provides numerical methods for examining patterns of variation, allowing researchers to identify discrete groups that can be classified as species. +Modern applications of phenetics are common for botany, and some examples can be found in most issues of the journal Systematic Botany. Indeed, due to the effects of horizontal gene transfer, polyploid complexes and other peculiarities of plant genomics, phenetic techniques of botany – though less informative altogether – may, for these special cases, be less prone to errors compared with cladistic analysis of DNA sequences. +In addition, many of the techniques developed by phenetic taxonomists have been adopted and extended by community ecologists, due to a similar need to deal with large amounts of data. + + +== See also == +Distance matrices in phylogeny +Folk taxonomy +Form classification +Linnaean taxonomy +Phenomics +Taxonomy +Dendrogram +Operational taxonomic unit + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Quinarian_system-0.md b/data/en.wikipedia.org/wiki/Quinarian_system-0.md new file mode 100644 index 000000000..5da38ede7 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Quinarian_system-0.md @@ -0,0 +1,26 @@ +--- +title: "Quinarian system" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Quinarian_system" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:30.436793+00:00" +instance: "kb-cron" +--- + +The quinarian system was a method of zoological classification which was popular in the mid 19th century, especially among British naturalists. It was largely developed by the entomologist William Sharp Macleay in 1819. The system was further promoted in the works of Nicholas Aylward Vigors, William Swainson and Johann Jakob Kaup. Swainson's work on ornithology gave wide publicity to the idea. The system had opponents even before the publication of Charles Darwin's On the Origin of Species (1859), which paved the way for evolutionary trees. + + +== Classification approach == + +Quinarianism gets its name from the emphasis on the number five: it proposed that all taxa are divisible into five subgroups, and if fewer than five subgroups were known, quinarians believed that a missing subgroup remained to be found. + +Presumably this arose as a chance observation of some accidental analogies between different groups, but it was erected into a guiding principle by the quinarians. It became increasingly elaborate, proposing that each group of five classes could be arranged in a circle, with those closer together having greater affinities. Typically they were depicted with relatively advanced groups at the top, and supposedly degenerate forms towards the bottom. Each circle could touch or overlap with adjacent circles; the equivalent overlapping of actual groups in nature was called osculation. + +Another aspect of the system was the identification of analogies across groups: + +[W]e shall consider that to be a natural system which endeavours to explain the multifarious relations which one object bears to another, not simply in their direct affinity, by which they follow each other like the links of a vast chain, but in their more remote relations [analogies], whereby they typify or represent other objects totally distinct in structure and organization from themselves +Quinarianism was not widely popular outside the United Kingdom (some followers like William Hincks persisted in Canada); it became unfashionable by the 1840s, during which time more complex "maps" were made by Hugh Edwin Strickland and Alfred Russel Wallace. Strickland and others specifically rejected the use of relations of "analogy" in constructing natural classifications. These systems were eventually discarded in favour of principles of genuinely natural classification, namely based on evolutionary relationship. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Reptile_centre-0.md b/data/en.wikipedia.org/wiki/Reptile_centre-0.md new file mode 100644 index 000000000..06d21d6f9 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Reptile_centre-0.md @@ -0,0 +1,24 @@ +--- +title: "Reptile centre" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Reptile_centre" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:44.830421+00:00" +instance: "kb-cron" +--- + +A reptile center is typically a facility devoted to keeping living reptiles, educating the public about reptiles, and serving as a control center for collecting reptiles that turn up in populated areas, where they will then help to rehabilitate some reptiles before returning them to the wild. Most are public-access, run as private businesses, or are state-sponsored. Some centers work with venomous reptiles as venom research labs. Others are simply privately run zoos devoted solely to reptiles, or are incorporated into larger zoos or organizations. +One example is the reptile center in Alice Springs, Australia devoted to indigenous reptiles. Many are collected from local homes, yards, or from areas about to be burned under the controlled burning program to keep summer grass fires from threatening the local homes. Most of the reptiles end up being relocated to uninhabited areas. The Alice Springs center also doubles as a snake call centre, with the owner and staff coming out to homes to remove venomous snakes from inconvenient places. +The United States of America has the world's largest collection of reptiles and reptile centers, with a lot of the states in the South hosting the majority of them. In Punta Gorda, Florida, Iguanaland is the nation's largest collection of reptiles and amphibians, with over two hundred fifty species. It first opened in 2022. A close second is Black Hills Reptile Gardens located in Rapid City, South Dakota. Founded in 1937, it is located in the heart of the Black Hills and has over two hundred twenty-five species. The St. Augustine Alligator Farm Zoological Park is the only complete collection of the world's crocodilians. In 1893, the park started as a small facility, displaying the American Alligator. It was accredited with the AZA (Association of Zoos and Aquariums) in 1989. +A renowned privately-owned reptile center is located in Fountain Valley, California called the Reptile Zoo. It has a significant social media following, as well as over a hundred species housed within its facility, which includes amphibians, fish, and arachnids. +The United States also holds some of the world's records for which specific species can be found in reptile centers, as well as particular feats that those reptiles have achieved. For example, a Burmese python at the reptile center Serpent Safari in Gurnee, Illinois was billed as the heaviest living snake in captivity. In 2005, it weighed 183 kilograms (403 lb) at a length of 8.2 metres (27 ft). The snake was named Baby. Zoo Atlanta in Atlanta, Georgia is home to one of the rarest breeds of lizards on the planet called the Guatemalan beaded lizard. Outside of Guatemala, Zoo Atlanta is the only organization in the entire world that breeds them. +Outside of the United States, the largest reptile centers are notably Reptiland in Martel, France and Reptilia in Vaughan, Canada. Reptilland features a large collection of venomous snakes and foreign species, such as crocodiles, cobras, and chameleons. It was opened in 1990. Reptilia opened in 1996 and began as a small reptile pet store, then later expanded into a major zoo. A facility within the United States that deals with venomous snakes is the Reptile Discovery Center in Volusia County, Florida, where they put on venom extraction presentations and house both local and exotic snakes. + + +== See also == +Herpetarium + Reptiles portal + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Safari_park-0.md b/data/en.wikipedia.org/wiki/Safari_park-0.md new file mode 100644 index 000000000..4cca99a80 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Safari_park-0.md @@ -0,0 +1,29 @@ +--- +title: "Safari park" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Safari_park" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:46.021271+00:00" +instance: "kb-cron" +--- + +A safari park, sometimes known as a wildlife park, is a zoo-like commercial drive-in tourist attraction where visitors can drive their own vehicles or ride in vehicles provided by the facility to observe freely roaming animals. +A safari park is larger than a zoo and smaller than a game reserve. For example, African Lion Safari in Hamilton, Ontario, Canada is 750 acres (3.0 km2). For comparison, Lake Nakuru in the Great Rift Valley, Kenya, is 168 square kilometres (65 sq mi), and a typical large game reserve is Tsavo East, also in Kenya, which encompasses 11,747 square kilometres (4,536 sq mi). +Many parks have conservation programmes with endangered animals like: elephants, white rhinos, giraffes, lions, tigers, cheetahs and wild dogs. + +== General overview of a safari park == + +The main attractions are frequently large animals from Africa which people can see in wildlife reserves such as: giraffes, lions (including white lions), white rhinos, African bush elephants, hippopotamuses, zebras, ostriches, lesser and greater flamingos, ground hornbills, guineafowl, African buffaloes, sometimes dromedary camels, great white and pink-backed pelicans, African sacred ibises, Ankole cattle, cheetahs, leopards, hyenas, chimpanzees, baboons, African wild dogs, Barbary sheep, crowned cranes, Egyptian geese, saddle-billed, yellow-billed and marabou storks, Nile crocodiles (in a side paddock), Nubian ibexes, and many antelope species including- wildebeest, hartebeest, topi, gazelles, elands, lechwe, addaxes, oryxes, bongos, kudus, nyalas, impalas, springbok, blesbok, sitatunga, duikers, waterbucks, sable antelopes, and roan antelopes, just to name a few. +Also in the reserves there are animals that are not from Africa: Asian species include: Asian elephants, Indian and Sumatran rhinoceroses, gaur, water buffaloes, nilgais, blackbucks, banteng, markhor, Malayan tapirs, wild asses, sambar deer, Indian hog deer, yaks, gibbons, tigers (including white tigers), Asian black bears, Eld's deer, babirusas, chital, dholes, barasinghas, painted storks, peafowl, and Bactrian camels; North American species include: American black bears, brown bears, wolves (including Arctic wolves), American bison, elk, and white-tailed deer; South American species include: llamas, alpacas, jaguars, capybaras, anteaters, South American tapirs, rheas, and black-necked swans; Australian species include kangaroos, wallabies, emus, and black swans; European species include: European bisons, Eurasian wolves, mute swans, fallow deer, red deer, and moose. +Most safari parks have a "walk-around" area with animals too small or too dangerous to roam freely in the reserves, like: small birds, squirrel monkeys, penguins, marmosets, tamarins, mongooses, meerkats, lemurs, gorillas, reptiles, hornbills, red pandas, snow leopards, otters and warthogs. Some also have: children's zoos, aquariums, butterfly houses and reptile and insect houses. Besides animals, in the walk-round area, there are public facilities like toilets, snack bars and cafés, play areas and sometimes amusement rides. There can be walk-through exhibits with animals like kangaroos, lemurs and wallabies. The Knowsley Safari in England keeps Siberian tigers and giraffes in their walking area. +Safari parks often have other associated tourist attractions: golf courses, carnival rides, cafés/restaurants, ridable miniature railways, boat trips to see aquatic animals like sea lions, life-sized recreations of dinosaurs and other prehistoric animals, plant mazes, playgrounds, monorails, cable cars and gift shops. These are commonly found in the walk-around area. On river safari areas, there may be islands with primates; Longleat keeps gorillas and black-and-white colobus on their islands, which are used to house chimpanzees and siamangs; African Lion Safari in Canada has black-and-white ruffed lemurs, ring-tailed lemurs, lar gibbons, siamangs, Colombian spider monkeys, Geoffroy's spider monkeys, pink-backed pelicans and black swans in the waters. + +== History and list of parks == + +The predecessor of safari parks is Africa U.S.A. Park (1953–1961) in Florida. +The first lion drive-through opened in 1963 in Tama Zoological Park in Tokyo. In double-glazed buses, visitors made a tour through a one-hectare enclosure with twelve African lions. +The first drive-through safari park outside of Africa opened in 1966 at Longleat in Wiltshire, England. Longleat, Windsor, Woburn and arguably the whole concept of safari parks were the brainchild of Jimmy Chipperfield (1912–1990), former co-director of Chipperfield's Circus, although a similar concept is explored as a plot device in Angus Wilson's "The Old Men at the Zoo" which was published five years before Chipperfield set up Longleat. Longleat's Marquess of Bath agreed to Chipperfield's proposition to fence off 40 hectares (100 acres) of his vast Wiltshire estate to house 50 lions. Knowsley, the Earl of Derby's estate outside Liverpool, and the Duke of Bedford's Woburn estate in Bedfordshire both established their own safari parks with Chipperfield's partnership. Another circus family, the Smart Brothers, joined the safari park business by opening a park at Windsor for visitors from London. The former Windsor Safari Park was in Berkshire, England, but closed in 1992 and has since been made into a Legoland theme park. There is also Chipperfield's "Scotland Safari Park" established on Baronet Sir John Muir's estate at Blair Drummond near Stirling, and the American-run "West Midland Safari and Leisure Park" near Birmingham. One park, along with Jimmy Chipperfield at Lambton Castle in North East England, has closed. +Between 1967 and 1974, Lion Country Safari, Inc. opened 6 animal parks, one near each of the following American cities: West Palm Beach, Florida; Los Angeles, California; Grand Prairie, Texas; Atlanta, Georgia; Cincinnati, Ohio, and Richmond, Virginia. The first park, in South Florida, is the only Lion Country Safari still in operation. +Royal Burgers' Zoo at Arnhem, opened a "safari park" in 1968 within a traditional zoo. In 1995, Burgers' Safari modified this to a walking safari with a 250-metre (820 ft) boardwalk. Another safari park in the Netherlands is Safaripark Beekse Bergen. +Most safari parks were established in a short period of ten years, between 1966 and 1975. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Safari_park-1.md b/data/en.wikipedia.org/wiki/Safari_park-1.md new file mode 100644 index 000000000..f92f24ef6 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Safari_park-1.md @@ -0,0 +1,80 @@ +--- +title: "Safari park" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Safari_park" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:46.021271+00:00" +instance: "kb-cron" +--- + +Africa +Egypt: Alexandria (Africa Safari Park, 2004) +Americas +Brazil: São Paulo (Zoo Safári, 2001 - this park was formerly known as Simba Safari from 1972 to 2001) +Canada: +Ontario: Hamilton (African Lion Safari, 1969) +Quebec: Hemmingford (Parc Safari, 1972), Montebello (Parc Omega, 1985) +Chile: Rancagua (Safari Park Rancagua, 2009) +Guatemala: Escuintla (Auto Safari Chapin, 1980) +Mexico: +Amacuzac (Zoofari, 1984), Puebla (Africam Safari, 1972) +United States: +Alabama: Hope Hull, Alabama (Alabama Safari Park, 2018) +Arizona: Camp Verde (Out of Africa Wildlife Park, 1988) +Arkansas: Gentry (Wild Wilderness Drive-Through Safari, 1970) +California: Escondido (San Diego Zoo Safari Park, formerly San Diego Wild Animal Park, 1972) +Florida: Loxahatchee (Lion Country Safari, 1967) +Georgia: Pine Mountain (Wild Animal Safari, 1991), Cleveland, Georgia (North Georgia Wildlife and Safari Park, 2018), Metter, Georgia (Wild Georgia Safari Park, 2018), Hartwell, Georgia (Lake Hartwell Wildlife Safari, 2021), Atlanta (Atlanta Safari Park, 2023), Madison, Georgia (Georgia Safari Conservation Park, 2024) +Louisiana: Delhi (High Delta Safari Park, 2009) +Nebraska: Ashland (Lee G. Simmons Conservation Park and Wildlife Safari, 1998) +New Jersey: Jackson Township (Great Adventure, 1974, now Six Flags Great Adventure) +New York: Chittenango (Wild Animal Park, 2010) +Ohio: Port Clinton (African Safari Wildlife Park, 1973) +Oregon: Winston (Wildlife Safari, 1973) +Texas: San Antonio (Natural Bridge Wildlife Ranch, 1984), Glen Rose (Fossil Rim Wildlife Ranch, 1984), near Dallas (Texas Zoosafari Park, 2023) +Virginia: Natural Bridge (Virginia Safari Park, 2000) +Asia +Bangladesh: Gazipur (Gazipur Safari Park, 2013), Cox's Bazar (Dulahazara Safari Park, 1999) +China: Shenzhen (Safari Park, 1993), Shanghai (Wild Animal Park, 1995), Qinhuangdao (Qinhuangdao Wildlife Park, 1995), Guangzhou (Xiangjiang Safari Park, 1997), Jinan (Safari Park, 1999), Badaling (Safari World, 2001) +India: Etawah (Etawah Safari Park, formerly Lion Safari Etawah, 2019), Rajgir (Rajgir Zoo Safari, 2022) +Indonesia: Cisarua, Prigen and Bali (in Bali includes a Marine Park too) (Taman Safari, 1990) +Israel: Ramat Gan (Ramat Gan Safari, 1974) +Japan: Miyazaki (Phoenix Zoo, 1975), Usa (Kyushu Natural Animal Park African Safari, 1976), Mine (Akiyoshidai Safari Land, 1977), Tomioka (Gunma Safari Park, 1979), Susono (Fuji Safari Park, 1980), Himeji (Central Park, 1984) +Malaysia: Alor Gajah (A'Famosa Resort, 2001), Gambang (Bukit Gambang Safari Park) +Pakistan: Lahore (Lahore Zoo Safari, 2009, formerly Lahore Wildlife Park, 1982) +Philippines: Busuanga (Calauit Safari Park, 1975), Morong (Zoobic Safari, 2003), Carmen (Cebu Safari and Adventure Park, 2018) +Singapore: (Night Safari, 1994) +Taiwan: Guanxi (Leofoo Village Theme Park, 1979) +Thailand: Bangkok (Safari World, 1988) +United Arab Emirates: Dubai (Dubai Safari Park, 2017) +Vietnam: Phú Quốc (Vinpearl Safari, 2015) +Europe +Belgium: Aywaille (Le Monde Sauvage, 1975) +Denmark: Givskud (Løveparken, 1969), Knuthenborg (Knuthenborg Safaripark, 1969), Ebeltoft (Ree Park – Ebeltoft Safari, 1991) +France: Thoiry (Wow Safari Thoiry, 1968), Peaugres (Safari de Peaugres, 1974), Sigean (Réserve africaine de Sigean, 1974), Obterre (Haute Touche Zoological Park, 1980) owned by the National Museum of Natural History, Port-Saint-Père (Planète Sauvage, 1992) +Germany: Gelsenkirchen (ZOOM Erlebniswelt Gelsenkirchen, 1949), Stuckenbrock (Safariland Stukenbrock, 1969), Hodenhagen (Serengeti Park, 1974) +Great Britain: Longleat (1966), Woburn (1970), Knowsley (1971), Bewdley (West Midlands Safari Park, 1973), Blair Drummond (1970), Highland Wildlife Park (1972) +Italy: Bussolengo (Parco Natura Viva, 1969), Fasano (Zoosafari Fasanolandia, 1973), Pombia (Pombia Safari Park, 1976), Murazzano (Parco Safari delle Langhe, 1976), Ravenna (Safari Ravenna, 2012) +Netherlands: Hilvarenbeek (Safaripark Beekse Bergen, 1968) +Portugal: Santo André (Badoca Safari Park, 1999) +Russia: near Kamenka (Kudykina Gora, 2009) +Spain: Penagos (Cabarceno Natural Park, 1990) +Sweden: Smålandet (Markaryds Älg & Bison Safari) +Oceania +Australia +South Australia: Monarto (Monarto Safari Park, 1983) +Victoria: Werribee (Werribee Open Range Zoo, 1983) + +== See also == + +SimSafari: a computer game simulating the management of a safari park +Effects of the car on societies + +== References == + +== Further reading == +Copperfield, Jimmy (1975). My Wild Life. Macmillan. London. 219 p. ISBN 0-333-18044-5. + +== External links == + Media related to Safari parks at Wikimedia Commons \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Serotype-0.md b/data/en.wikipedia.org/wiki/Serotype-0.md new file mode 100644 index 000000000..12c54003d --- /dev/null +++ b/data/en.wikipedia.org/wiki/Serotype-0.md @@ -0,0 +1,78 @@ +--- +title: "Serotype" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Serotype" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:31.676673+00:00" +instance: "kb-cron" +--- + +A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their shared reactivity between their surface antigens and a particular antiserum, allowing the classification of organisms to a level below the species. A group of serovars with common antigens is called a serogroup or sometimes serocomplex. +Serotyping often plays an essential role in determining species and subspecies. The Salmonella genus of bacteria, for example, has been determined to have over 2600 serotypes. Vibrio cholerae, the species of bacteria that causes cholera, has over 200 serotypes, based on cell antigens. Only two of them have been observed to produce the potent enterotoxin that results in cholera: O1 and O139. +Serotypes were discovered in hemolytic streptococci by the American microbiologist Rebecca Lancefield in 1933. + + +== Procedure == +Serotyping is the process of determining the serotype of an organism, using prepared antisera that bind to a set of known antigens. Some antisera detect multiple known antigens and are known as polyvalent or broad; others are monovalent. For example, what was once described as HLA-A9 is now subdivided into two more specific serotypes ("split antigens"), HLA-A23 and HLA-A24. As a result, A9 is now known as a "broad" serotype. For organisms with many possible serotypes, first obtaining a polyvalent match can reduce the number of tests required. +The binding between a surface antigen and the antiserum can be experimentally observed in many forms. A number of bacteria species, including Streptococcus pneumoniae, display the Quellung reaction visible under a microscope. Others such as Shigella (and E. coli) and Salmonella are traditionally detected using a slide agglutination test. HLA types are originally determined with the complement fixation test. Newer procedures include the latex fixation test and various other immunoassays. +"Molecular serotyping" refers to methods that replace the antibody-based test with a test based on the nucleic acid sequence – therefore actually a kind of genotyping. By analyzing which surface antigen-defining allele(s) are present, these methods can produce faster results. However, their results may not always agree with traditional serotyping, as they can fail to account for factors that affect the expression of antigen-determining genes. + + +== Role in organ transplantation == + +The immune system is capable of discerning a cell as being 'self' or 'non-self' according to that cell's serotype. In humans, that serotype is largely determined by human leukocyte antigen (HLA), the human version of the major histocompatibility complex. Cells determined to be non-self are usually recognized by the immune system as foreign, causing an immune response, such as hemagglutination. Serotypes differ widely between individuals; therefore, if cells from one human (or animal) are introduced into another random human, those cells are often determined to be non-self because they do not match the self-serotype. For this reason, transplants between genetically non-identical humans often induce a problematic immune response in the recipient, leading to transplant rejection. In some situations, this effect can be reduced by serotyping both recipient and potential donors to determine the closest HLA match. + + +=== Human leukocyte antigens === + + +== Bacteria == +Most bacteria produce antigenic substances on the outer surface that can be distinguished by serotyping. + +Almost all species of Gram-negative bacteria produce a layer of lipopolysaccharide on the outer membrane. The outermost portion of the LPS accessible to antibodies is the O antigen. Variation in the O antigen can be caused by genetic differences in the biosynthetic pathway or the transporter used to move the building-blocks to the outside of the cell. +The flagella on motile bacteria is called the H antigen in serotyping. Minute genetic differences in the components of the flagella lead to variations detectable by antibodies. +Some bacteria produce a polysaccharide capsule, called the K antigen in serotyping. +The LPS (O) and capsule (K) antigens are themselves important pathogenicity factors. +Some antigens are invariant among a taxonomic group. Presence of these antigens would not be useful for classification lower than the species level, but may inform identification. One example is the enterobacterial common antigen (ECA), universal to all Enterobacterales. + + +=== E. coli === +E. coli have 187 possible O antigens (6 later removed from list, 3 actually producing no LPS), 53 H antigens, and at least 72 K antigens. Among these three, the O antigen has the best correlation with lineages; as a result, the O antigen is used to define the "serogroup" and is also used to define strains in taxonomy and epidemiology. + + +=== Shigella === +Shigella are only classified by their O antigen, as they are non-motile and produce no flagella. Across the four "species", there are 15 + 11 + 20 + 2 = 48 serotypes. Some of these O antigens have equivalents in E. coli, which also cladistically include Shigella. + + +=== Salmonella === +The Kauffman–White classification scheme is the basis for naming the manifold serovars of Salmonella. To date, more than 2600 different serotypes have been identified. A Salmonella serotype is determined by the unique combination of reactions of cell surface antigens. For Salmonella, the O and H antigens are used. +There are two species of Salmonella: Salmonella bongori and Salmonella enterica. Salmonella enterica can be subdivided into six subspecies. +The process to identify the serovar of the bacterium consists of finding the formula of surface antigens which represent the variations of the bacteria. The traditional method for determining the antigen formula is agglutination reactions on slides. The agglutination between the antigen and the antibody is made with a specific antisera, which reacts with the antigen to produce a mass. The antigen O is tested with a bacterial suspension from an agar plate, whereas the antigen H is tested with a bacterial suspension from a broth culture. The scheme classifies the serovar depending on its antigen formula obtained via the agglutination reactions. Additional serotyping methods and alternative subtyping methodologies have been reviewed by Wattiau et al. + + +=== Streptococcus === +Streptococcus pneumoniae has 93 capsular serotypes. 91 of these serotypes use the Wzy enzyme pathway. The Wzy pathway is used by almost all gram-positive bacteria, by lactococci and streptococci (exopolysacchide), and is also responsible for group 1 and 4 Gram-negative capsules. + + +== Viruses == + + +== Other organisms == +Many other organisms can be classified using recognition by antibodies. + +The malaria pathogen Plasmodium falciparum is notorious for its many surface antigen variants. A certain vaccine candidate is designed to cover all of these serotypes. +Toxoplasma gondii can be classified into serotypes. +Trypanosoma cruzi, which causes Chagas disease, can be serotyped using whole parasites. + + +== See also == +Biovar +Morphovar + + +== References == + + +== External links == +HLA Allele and Haplotype Frequency Database \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Sister_group-0.md b/data/en.wikipedia.org/wiki/Sister_group-0.md new file mode 100644 index 000000000..f8fb38776 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Sister_group-0.md @@ -0,0 +1,33 @@ +--- +title: "Sister group" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Sister_group" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:32.832221+00:00" +instance: "kb-cron" +--- + +In phylogenetics, a sister group or sister taxon, also called an adelphotaxon, comprises the closest relative(s) of another given unit in an evolutionary tree. + + +== Definition == +The expression is most easily illustrated by a cladogram: + +Taxon A and taxon B are sister groups to each other. Taxa A and B, together with any other extant or extinct descendants of their most recent common ancestor (MRCA), form a monophyletic group, the clade AB. Clade AB and taxon C are also sister groups. Taxa A, B, and C, together with all other descendants of their MRCA form the clade ABC. +The whole clade ABC is itself a subtree of a larger tree which offers yet more sister group relationships, both among the leaves and among larger, more deeply rooted clades. The tree structure shown connects through its root to the rest of the universal tree of life. +In cladistic standards, taxa A, B, and C may represent specimens, species, genera, or any other taxonomic units. If A and B are at the same taxonomic level, terminology such as sister species or sister genera can be used. + + +== Example == + +The term sister group is used in phylogenetic analysis; however, only groups identified in the analysis are labeled as "sister groups". +An example is birds, whose commonly cited living sister group is the crocodiles, but that is true only when discussing extant organisms; when other, extinct groups are considered, the relationship between birds and crocodiles appears distant. +Although the bird family tree is rooted in the dinosaurs, there were a number of other, earlier groups, such as the pterosaurs, that branched off the line leading to the dinosaurs after the last common ancestor of birds and crocodiles. +The term sister group must thus be seen as a relative term, with the caveat that the sister group is only the closest relative among the groups/species/specimens that are included in the analysis. + + +== Notes == + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Soft-bodied_organism-0.md b/data/en.wikipedia.org/wiki/Soft-bodied_organism-0.md new file mode 100644 index 000000000..0029f5a11 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Soft-bodied_organism-0.md @@ -0,0 +1,31 @@ +--- +title: "Soft-bodied organism" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Soft-bodied_organism" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:35.060590+00:00" +instance: "kb-cron" +--- + +Soft-bodied organisms are organisms that lack rigid physical skeletons or frame, roughly corresponds to the group Vermes as proposed by Carl von Linné. The term typically refers to non-panarthropod invertebrates from the kingdom Animalia, although many non-vascular plants (mosses and algae), fungi (such as jelly fungus), lichens and slime molds can also be seen as soft-bodied organisms by definition. +All animals have a muscular system of some sort but, since myocytes are tensile actuator units that can only contract and pull but never push, some animals evolved rigid body parts upon which the muscles can attach and act as levers/cantilevers to redirect force and produce locomotive propulsion. These rigid parts also serve as structural elements to resist gravity and ambient pressure, as well as sometimes provide protective surfaces shielding internal structures from trauma and exposure to external thermal, chemical and pathogenic insults. Such physical structures are the commonly referred "skeletons", which may be internal (as in vertebrates, echinoderms and sponges) or external (as in arthropods and non-coleoid molluscs). However, many soft-bodied animals do still have a functional skeleton maintained by body fluid hydrostatics known as a hydroskeleton, such as that of earthworms, jellyfish, tapeworms, squids and an enormous variety of invertebrates from almost every phyla of the animal kingdom; and many have hardened teeth that allow them to chew, bite and burrow despite the rest of body being soft. + + +== Commonality == +Most soft-bodied animals are small, but they do make up the majority of the animal biomass. If we were to weigh up all animals on Earth with hard parts against soft-bodied ones, estimates indicate that the biomass of soft-bodied animals would be at least twice that of animals with hard parts, quite possibly much larger. Particularly the roundworms are extremely numerous. The nematodologist Nathan Cobb described the ubiquitous presence of nematodes on Earth as follows: + +"In short, if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable, and if, as disembodied spirits, we could then investigate it, we should find its mountains, hills, vales, rivers, lakes, and oceans represented by a film of nematodes. The location of towns would be decipherable, since for every massing of human beings there would be a corresponding massing of certain nematodes. Trees would still stand in ghostly rows representing our streets and highways. The location of the various plants and animals would still be decipherable, and, had we sufficient knowledge, in many cases even their species could be determined by an examination of their erstwhile nematode parasites." + + +== Anatomy == +Being a morphological grouping rather than a true phylogenetic group, soft-bodied organisms vary enormously in anatomy. Cnidarians and flatworms have a single opening to the gut and a diffuse nerve system. The roundworms, annelids, molluscs, the various lophoporate phyla and non-vertebrate chordates have a tubular gut open at both ends. While the majority of the soft-bodied animals typically don't have any kind of skeleton, some do, mainly in the form of stiff cuticles (roundworms, water bears) or hydrostatic skeletons (annelids). +While lack of a skeleton typically restricts the body size of soft-bodied animals on land, marine representatives can grow to very large sizes. The heaviest soft-bodied organisms are likely the giant squids, with maximum weight estimated at 275 kilograms (606 lb) for females, while arctic lion's mane jellyfish may reach comparable sizes. The longest animal on record is also thought to be a soft-bodied organism, a 55 metres (180 ft) long thread-like bootlace worm, Lineus longissimus found on a Scottish beach 1864. Siphonophores may grow to considerable sizes too, though they are colonial organisms, and each single animal is small. Most soft-bodied organisms are as small or smaller, even microscopic. The various organisms grouped as mesozoans and the curious Placozoa are typically composed of just a few hundred cells. + + +== Fossil record == + +The lack of hard parts in soft-bodied organisms makes them extremely rare in the fossil record. Accordingly, the evolutionary histories of many of the soft-bodied groups are poorly known. The first major find of fossil soft-bodied animals was from the Burgess Shale in Canada. Today, several sites with Burgess Shale type preservation are known, but the history of many groups of soft-bodied animals is still poorly understood. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Species_Survival_Plan-0.md b/data/en.wikipedia.org/wiki/Species_Survival_Plan-0.md new file mode 100644 index 000000000..28c147c43 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Species_Survival_Plan-0.md @@ -0,0 +1,37 @@ +--- +title: "Species Survival Plan" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Species_Survival_Plan" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:48.446007+00:00" +instance: "kb-cron" +--- + +The American Species Survival Plan or SSP program was developed in 1981 by the (American) Association of Zoos and Aquariums to help ensure the survival of selected species in zoos and aquariums, most of which are threatened or endangered in the wild. + + +== SSP program == +SSP programs focus on animals that are near threatened, threatened, endangered, or otherwise in danger of extinction in the wild, when zoo and zoology conservationists believe captive breeding programs will aid in their chances of survival. These programs help maintain healthy and genetically diverse animal populations within the Association of Zoos and Aquariums-accredited zoo community. AZA accredited zoos and AZA conservation partners that are involved in SSP programs engage in cooperative population management and conservation efforts that include research, conservation genetics, public education, reintroduction, and in situ or field conservation projects. The process for selecting recommended species is guided by Taxon Advisory Groups, whose sole objective is to curate Regional Collection Plans for the conservation needs of a species and how AZA institutions will cooperate to reach those needs. Today, there are almost 300 existing SSP programs. The SSP has been met with widespread success in ensuring that, should a species population become functionally extinct in its natural habitat, a viable population still exists within a zoological setting. This has also led to AZA species reintroduction programs, examples of which include the black-footed ferret, the California condor, the northern riffleshell, the golden lion tamarin, the Karner blue butterfly, the Oregon spotted frog, the palila finch, the red wolf, and the Wyoming toad. + + +== SSP master plan == +An SSP master plan is a document produced by the SSP coordinator (generally a zoo professional under the guidance of an elected management committee) for a certain species. This document sets ex situ population goals and other management recommendations to achieve the maximum genetic diversity and demographic stability for a species, given transfer and space constraints. + + +== See also == +European Endangered Species Programme + + +== List of SSP programs == +As of 2025, there are 295 species that are a part of the Species Survival Plan program. + + +== Notes == + + +== References == + + +== External links == +AZA website \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Superorganism-0.md b/data/en.wikipedia.org/wiki/Superorganism-0.md new file mode 100644 index 000000000..9c2ea00b5 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Superorganism-0.md @@ -0,0 +1,56 @@ +--- +title: "Superorganism" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Superorganism" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:36.277495+00:00" +instance: "kb-cron" +--- + +A superorganism, or supraorganism, is a group of synergetically interacting organisms of the same species. A community of synergetically interacting organisms of different species is called a holobiont. + + +== Concept == +The term superorganism is used most often to describe a social unit of eusocial animals in which division of labour is highly specialised and individuals cannot survive by themselves for extended periods. Ants are the best-known example of such a superorganism. A superorganism can be defined as "a collection of agents which can act in concert to produce phenomena governed by the collective", phenomena being any activity "the hive wants" such as ants collecting food and avoiding predators, or bees choosing a new nest site. In challenging environments, micro organisms collaborate and evolve together to process unlikely sources of nutrients such as methane. This process called syntrophy ("eating together") might be linked to the evolution of eukaryote cells and involved in the emergence or maintenance of life forms in challenging environments on Earth and possibly other planets. Superorganisms tend to exhibit homeostasis, power law scaling, persistent disequilibrium and emergent behaviours. +The term was coined in 1789 by James Hutton, the "father of geology", to refer to Earth in the context of geophysiology. The Gaia hypothesis of James Lovelock, and Lynn Margulis as well as the work of Hutton, Vladimir Vernadsky and Guy Murchie, have suggested that the biosphere itself can be considered a superorganism, but that has been disputed. This view relates to systems theory and the dynamics of a complex system. +The concept of a superorganism raises the question of what is to be considered an individual. Toby Tyrrell's critique of the Gaia hypothesis argues that Earth's climate system does not resemble an animal's physiological system. Planetary biospheres are not tightly regulated in the same way that animal bodies are: "planets, unlike animals, are not products of evolution. Therefore we are entitled to be highly skeptical (or even outright dismissive) about whether to expect something akin to a 'superorganism'". He concludes that "the superorganism analogy is unwarranted". +Some scientists have suggested that individual human beings can be thought of as "superorganisms"; as a typical human digestive system contains 1013 to 1014 microorganisms whose collective genome, the microbiome studied by the Human Microbiome Project, contains at least 100 times as many genes as the human genome itself. Salvucci wrote that superorganism is another level of integration that is observed in nature. These levels include the genomic, the organismal and the ecological levels. The genomic structure of organisms reveals the fundamental role of integration and gene shuffling along evolution. + + +== In social theory == +The 19th-century thinker Herbert Spencer coined the term super-organic to focus on social organization (the first chapter of his Principles of Sociology is entitled "Super-organic Evolution"), though this was apparently a distinction between the organic and the social, not an identity: Spencer explored the holistic nature of society as a social organism while distinguishing the ways in which society did not behave like an organism. For Spencer, the super-organic was an emergent property of interacting organisms, that is, human beings. And, as has been argued by D. C. Phillips, there is a "difference between emergence and reductionism". +The economist Carl Menger expanded upon the evolutionary nature of much social growth but never abandoned methodological individualism. Many social institutions arose, Menger argued, not as "the result of socially teleological causes, but the unintended result of innumerable efforts of economic subjects pursuing 'individual' interests". +Both Spencer and Menger argued that because individuals choose and act, any social whole should be considered less than an organism, but Menger emphasized that more strongly. Spencer used the organistic idea to engage in extended analysis of social structure and conceded that it was primarily an analogy. For Spencer, the idea of the super-organic best designated a distinct level of social reality above that of biology and psychology, not a one-to-one identity with an organism. Nevertheless, Spencer maintained that "every organism of appreciable size is a society", which has suggested to some that the issue may be terminological. +The term superorganic was adopted by the anthropologist Alfred L. Kroeber in 1917. Social aspects of the superorganism concept are analysed by Alan Marshall in his 2002 book "The Unity of Nature". Finally, recent work in social psychology has offered the superorganism metaphor as a unifying framework to understand diverse aspects of human sociality, such as religion, conformity, and social identity processes. + + +== In cybernetics == +Superorganisms are important in cybernetics, particularly biocybernetics, since they are capable of the so-called "distributed intelligence", a system composed of individual agents that have limited intelligence and information. They can pool resources and so can complete goals that are beyond reach of the individuals on their own. Existence of such behavior in organisms has many implications for military and management applications and is being actively researched. +Superorganisms are also considered dependent upon cybernetic governance and processes. This is based on the idea that a biological system – in order to be effective – needs a sub-system of cybernetic communications and control. This is demonstrated in the way a mole rat colony uses functional synergy and cybernetic processes together. +Joël de Rosnay also introduced a concept called "cybionte" to describe cybernetic superorganism. The notion associates superorganism with chaos theory, multimedia technology, and other new developments. + + +== See also == +Collective intelligence +Gaia hypothesis +Group mind (science fiction) +Holobiont +Organismic computing +Quorum sensing, collective behaviour of bacteria +Stigmergy +Siphonophore + + +== References == + + +== Literature == +Jürgen Tautz, Helga R. Heilmann: The Buzz about Bees – Biology of a Superorganism, Springer-Verlag 2008. ISBN 978-3-540-78727-3 +Bert Hölldobler, E. O. Wilson: "The Superorganism: The Beauty, Elegance, and Strangeness of Insect Societies", W.W. Norton, 2008. ISBN 978-0-393-06704-0 +Selin Kesebir (2012). "The Superorganism Account of Human Sociality How and When Human Groups Are Like Beehives". Personality and Social Psychology Review. 16 (3): 233–261. doi:10.1177/1088868311430834. PMID 22202149. S2CID 9530301. SSRN 1933734. + + +== External links == +People Are Human-Bacteria Hybrid, Wired Magazine, October 11, 2004 +First Bees and Ants, and Now People: This Evolutionary Transition Might Be Coming for Humanity, Haaretz Magazine, November 19, 2022 \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Svenska_Spindlar-0.md b/data/en.wikipedia.org/wiki/Svenska_Spindlar-0.md new file mode 100644 index 000000000..1740f8628 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Svenska_Spindlar-0.md @@ -0,0 +1,37 @@ +--- +title: "Svenska Spindlar" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Svenska_Spindlar" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:37.480194+00:00" +instance: "kb-cron" +--- + +The book Svenska Spindlar or Aranei Svecici (Swedish and Latin, respectively, for "Swedish spiders") is one of the major works of the Swedish arachnologist and entomologist Carl Alexander Clerck and was first published in Stockholm in the year 1757. It was the first comprehensive book on the spiders of Sweden and one of the first regional monographs of a group of animals worldwide. The full title of the work is Svenska Spindlar uti sina hufvud-slägter indelte samt under några och sextio särskildte arter beskrefne och med illuminerade figurer uplyste – Aranei Svecici, descriptionibus et figuris æneis illustrati, ad genera subalterna redacti, speciebus ultra LX determinati, ("Swedish spiders into their main genera separated, and as sixty and a few particular species described and with illuminated figures illustrated") and included 162 pages of text (eight pages were unpaginated) and six colour plates. It was published in Swedish, with a Latin translation printed in a slightly smaller font below the Swedish text. +Clerck described in detail 67 species of Swedish spiders, and for the first time in a zoological work consistently applied binomial nomenclature as proposed by Carl Linnaeus. Linnaeus had originally invented this system for botanical names in his 1753 work Species Plantarum, and presented it again in 1758 in the 10th edition of Systema Naturae for more than 4,000 animal species. Svenska Spindlar is the only pre-Linnaean source to be recognised as a taxonomic authority for such names. + + +== Presentation of the spiders == + +Clerck explained in the last (9th of the 2nd part) chapter of his work that in contrast to previous authors he used the term "spider" in the strict sense, for animals possessing eight eyes and separated prosoma and opisthosoma, and that his concept of this group of animals did not include Opiliones (because they had two eyes and a broadly joined prosoma and opisthosoma) and other groups of arachnids. +For all spiders Clerck used a single generic name (Araneus), to which was added a specific name which consisted of only one word. Each species was presented in the Swedish text with their Latin scientific names, followed by detailed information containing the exact dates when he had found the animals, and a detailed description of eyes, legs and body. The differences between the sexes were also described. Each species was illustrated in impressively accurate drawings printed on coloured copper plates which were bound at the end of the volume. + + +== Impact and importance of the work == +Because of the exceptionally thorough treatment of the spider species, the scientific names proposed by Clerck (which were adopted by Carl Linnaeus in his Systema Naturae in 1758 with only minor modifications) had traditionally been recognized by arachnologists as binomial and available. In 1959 the ICZN Commission decided that Clerck's work should be available for zoological nomenclature, but the International Code of Zoological Nomenclature did not mention Clerck's work. Only after 1999 was this officially recognized in the Code. This means that in case of doubt the spelling of a spider name as from Clerck's 1757 work has priority over that proposed by Linnaeus in 1758 (an example is Araneus instead of Aranea), and that Clerck's spiders were the first animals in modern zoology to have obtained an available scientific name in the Linnean system. + + +== Year 1757 or 1758? == +In the late 19th century, Clerck's 1757 work was commonly accepted as the first application of binomial nomenclature to spiders. In 1959 the ICZN Commission ruled that the date 1758 should be used for Clerck's names, this date 1758 was repeated to apply to Clerck's names in the 4th edition of the International Code of Zoological Nomenclature in 1999. +In a complete binomial name with author and year, the year corresponds to the year of publication of the original source. Since 2000, the ICZN Code includes an exception of this very basic rule. From the beginning on the new provision in the Code has been misunderstood by many researchers who believed that by setting the date for Clerck's work to 1758 (overriding its true date 1757) and the date for Systema Naturae to 1 January 1758, the priority was changed. In 2007, a case was even brought before the Commission because the researchers were no longer sure whether the generic name should be Araneus Clerck or Aranea Linnaeus. In their judgement the year 1758 for Clerck's Svenska Spindlar could be interpreted in a way that the Linnean work from 1 January 1758 should have priority. In 2009 the Commission saw itself forced to repeat once more, although this was already explicit in the Code's Article 3.1, that the name Araneus established by Clerck shall have priority and be used for the genus. + + +== Species == +Svenska Spindlar lists the following 67 species of spider; their current identities follow Platnick (2000–2010). + + +== Footnotes == + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Systema_Naturae-0.md b/data/en.wikipedia.org/wiki/Systema_Naturae-0.md new file mode 100644 index 000000000..c580e4baf --- /dev/null +++ b/data/en.wikipedia.org/wiki/Systema_Naturae-0.md @@ -0,0 +1,24 @@ +--- +title: "Systema Naturae" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Systema_Naturae" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:38.632255+00:00" +instance: "kb-cron" +--- + +Systema Naturae (originally in Latin written Systema Naturæ with the ligature æ) is one of the major works of Swedish botanist, zoologist, and physician Carl Linnaeus (1707–1778) and introduced the Linnaean taxonomy. Although the system, now known as binomial nomenclature, was partially developed by the Bauhin brothers, Gaspard and Johann, Linnaeus was the first to use it consistently throughout his book. The first edition was published in 1735. The full title of the 10th edition (1758), which was the most important one, was Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, which appeared in English in 1806 with the title: "A General System of Nature, Through the Three Grand Kingdoms of Animals, Vegetables, and Minerals, Systematically Divided Into their Several Classes, Orders, Genera, Species, and Varieties, with their Habitations, Manners, Economy, Structure and Peculiarities". +The tenth edition of this book (1758), published in Stockholm, is considered the starting point of zoological nomenclature. In 1766–1768 Linnaeus published the much enhanced 12th edition, the last under his authorship. Another again enhanced work in the same style titled "Systema Naturae" was published by Johann Friedrich Gmelin between 1788 and 1793. Since at least the early 20th century, zoologists have commonly recognized this as the last edition belonging to this series. + +== Overview == +Linnaeus (later known as "Carl von Linné", after his ennoblement in 1761) published the first edition of Systema Naturae in 1735, during his stay in the Netherlands. As was customary for the scientific literature of its day, the book was published in Latin. In it, he outlined his ideas for the hierarchical classification of the natural world, dividing it into the animal kingdom (regnum animale), the plant kingdom (regnum vegetabile), and the "mineral kingdom" (regnum lapideum). +Linnaeus's Systema Naturae lists only about 10,000 species of organisms, of which about 6,000 are plants and 4,236 are animals. According to the historian of botany William T. Stearn, "Even in 1753, he believed that the number of species of plants in the whole world would hardly reach 10,000; in his whole career, he named about 7,700 species of flowering plants." +Linnaeus developed his classification of the plant kingdom in an attempt to describe and understand the natural world as a reflection of the logic of God's creation. His sexual system, where species with the same number of stamens were treated in the same group, was convenient, but in his view artificial. Linnaeus believed in God's creation and that no deeper relationships were to be expressed. The classification of animals was more natural than for plants. For instance, humans were for the first time placed together with other primates, as Anthropomorpha. They were also divided into four varieties, as distinguished by skin color and corresponding with the four known continents and temperaments. The tenth edition expanded on these varieties with behavioral and cultural traits that the Linnean Society acknowledges as having cemented colonial stereotypes and provided one of the foundations for scientific racism. +As a result of the popularity of the work, and the number of new specimens sent to him from around the world, Linnaeus kept publishing new and ever-expanding editions of his work. It grew from 11 very large pages in the first edition (1735) to 2,400 pages in the 12th edition (1766–1768). Also, as the work progressed, he made changes; in the first edition, whales were classified as fishes, following the work of Linnaeus' friend and "father of ichthyology" Peter Artedi; in the 10th edition, published in 1758, whales were moved into the mammal class. In this same edition, he introduced two-part names (see binomen) for animal species, which he had done for plant species (see binary name) in the 1753 publication of Species Plantarum. The system eventually developed into modern Linnaean taxonomy, a hierarchically organized biological classification. +After Linnaeus' health declined in the early 1770s, publication of editions of Systema Naturae went in two directions. Another Swedish scientist, Johan Andreas Murray, issued the Regnum Vegetabile section separately in 1774 as the Systema Vegetabilium, confusingly labelled the 13th edition. Meanwhile, a 13th edition of the entire Systema appeared in parts between 1788 and 1793. It was as the Systema Vegetabilium that Linnaeus' work became widely known in England following translation from the Latin by the Lichfield Botanical Society, as A System of Vegetables (1783–1785). + +== Taxonomy == +In his Imperium Naturæ, Linnaeus established three kingdoms, namely Regnum Animale, Regnum Vegetabile, and Regnum Lapideum. This approach, the Animal, Vegetable, and Mineral Kingdoms, survives until today in the popular mind, notably in the form of parlour games: "Is it animal, vegetable or mineral?" The classification was based on five levels: kingdom, class, order, genus, and species. While species and genus were seen as God-given (or "natural"), the three higher levels were seen by Linnaeus as constructs. The concept behind the set ranks being applied to all groups was to make a system that was easy to remember and navigate, a task in which most say he succeeded. + +Linnaeus's work had a huge impact on science; it was indispensable as a foundation for biological nomenclature, now regulated by the Nomenclature Codes. Two of his works, the first edition of the Species Plantarum (1753) for plants and the 10th edition of the Systema Naturæ (1758), are accepted to be among the starting points of nomenclature. Most of his names for species and genera were published at very early dates and thus take priority over those of other, later authors. Zoology has one exception, which is a monograph on Swedish spiders, Svenska Spindlar, published by Carl Clerck in 1757, so the names established there take priority over the Linnean names. His exceptional importance to science was less in the value of his taxonomy, but more in his deployment of skillful young students abroad to collect specimens. At the close of the 18th century, his system had effectively become the standard for biological classification. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Systema_Naturae-1.md b/data/en.wikipedia.org/wiki/Systema_Naturae-1.md new file mode 100644 index 000000000..ca364adb5 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Systema_Naturae-1.md @@ -0,0 +1,64 @@ +--- +title: "Systema Naturae" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Systema_Naturae" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:38.632255+00:00" +instance: "kb-cron" +--- + +=== Animals === +Only in the animal kingdom is the higher taxonomy of Linnaeus still more or less recognizable and some of these names are still in use, but usually not quite for the same groups as used by Linnaeus. He divided the Animal Kingdom into six classes; in the tenth edition (1758), these were: + +Mammalia comprised the mammals. In the first edition, whales and the West Indian manatee were classified among the fishes. +Aves comprised the birds. Linnaeus was the first to remove bats from the birds and classify them under mammals. +Amphibia comprised amphibians, reptiles, and assorted fishes that are not of Osteichthyes. +Pisces comprised the bony fishes. These included the spiny-finned fishes (Perciformes) as a separate order. +Insecta comprised all arthropods. Crustaceans, arachnids and myriapods were included as the order "Aptera". +Vermes comprised the remaining invertebrates, roughly divided into "worms", molluscs, and hard-shelled organisms such as echinoderms. + +==== Humans ==== +Linnaeus was one of the first scientists to classify humans as primates (originally Anthropomorpha for "manlike"), eliciting some controversy for placing people among animals, thus not ruling over nature. He distinguished humans (Homo sapiens) from Homo troglodytes, a species of human-like creatures with exaggerated or non-human characteristics, despite finding limited evidence. He divided Homo sapiens into four varieties, corresponding with the four known continents and four temperaments (some editions also classify Ferus wild children and Monstrosus monstrous to accommodate adaptations to extreme environments). The first edition included Europæus albescens (whitish Europeans), Americanus rubescens (reddish Americans), Asiaticus fuscus (tawny Asians), and Africanus nigriculus (blackish Africans). The 10th edition solidified these descriptions by removing the "ish" qualifiers (e.g. albus "white" instead of albescens "whitish") and revising the characterization of Asiaticus from fuscus (tawny) to luridus (pale yellow). It also incorporates behavioral and cultural traits that the Linnean Society recognizes as having cemented colonial stereotypes and provided one of the foundations for scientific racism. + +=== Plants === + +The orders and classes of plants, according to his Systema Sexuale, were never intended to represent natural groups (as opposed to his ordines naturales in his Philosophia Botanica), but only for use in identification. They were used in that sense well into the 19th century. +The Linnaean classes for plants, in the Sexual System, were: + +=== Minerals === +Linnaeus's taxonomy of minerals has long since fallen out of use. In the 10th edition, 1758, of the Systema Naturæ, the Linnaean classes were: + +Classis 1. Petræ (rocks) +Classis 2. Mineræ (minerals and ores) +Classis 3. Fossilia (fossils and aggregates) + +== Editions == +Gmelin's 13th (decima tertia) edition of Systema Naturae (1788–1793) should be carefully distinguished from the more limited Systema Vegetabilium first prepared and published by Johan Andreas Murray in 1774 (but labelled as "thirteenth edition"). + +The dates of publication for Gmelin's edition were the following: + +Part 1: pp. [1–12], 1–500 (25 July 1788) +Part 2: pp. 501–1032 (20 April 1789) +Part 3: pp. 1033–1516 (20 November 1789) +Part 4: pp. 1517–2224 (21 May 1790) +Part 5: pp. 2225–3020 (6 December 1790) +Part 6: pp. 3021–3910 (14 May 1791) +Part 7: pp. 3911–4120 (2 July 1792) + +== See also == +Supplementum Plantarum +Animalia Paradoxa +10th edition of Systema Naturae +12th edition of Systema Naturae +Systema Vegetabilium +English edition by William Turton, translated from Gmelin's last edition. https://doi.org/10.5962/bhl.title.37018 + +== References == + +== Bibliography == + +== External links == + +Linné online +Systema Naturae is available for free viewing and download at the Internet Archive \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Systematics-0.md b/data/en.wikipedia.org/wiki/Systematics-0.md new file mode 100644 index 000000000..76e30a3b1 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Systematics-0.md @@ -0,0 +1,68 @@ +--- +title: "Systematics" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Systematics" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:39.775331+00:00" +instance: "kb-cron" +--- + +Systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: phylogenetic trees, phylogenies). Phylogenies have two components: branching order (showing group relationships, graphically represented in cladograms) and branch length (showing amount of evolution). Phylogenetic trees of species and higher taxa are used to study the evolution of traits (e.g., anatomical or molecular characteristics) and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth. +The word systematics is derived from the Latin word of Ancient Greek origin systema, which means systematic arrangement of organisms. Carl Linnaeus used 'Systema Naturae' as the title of his book. + + +== Branches and applications == +In the study of biological systematics, researchers use the different branches to further understand the relationships between differing organisms. These branches are used to determine the applications and uses for modern day systematics. +Biological systematics classifies species by using three specific branches. Numerical systematics, or biometry, uses biological statistics to identify and classify animals. Biochemical systematics classifies and identifies animals based on the analysis of the material that makes up the living part of a cell—such as the nucleus, organelles, and cytoplasm. Experimental systematics identifies and classifies animals based on the evolutionary units that comprise a species, as well as their importance in evolution itself. Factors such as mutations, genetic divergence, and hybridization all are considered evolutionary units. +With the specific branches, researchers are able to determine the applications and uses for modern-day systematics. These applications include: + +Studying the diversity of organisms and the differentiation between extinct and living creatures. Biologists study the well-understood relationships by making many different diagrams and "trees" (cladograms, phylogenetic trees, phylogenies, etc.). +Including the scientific names of organisms, species descriptions and overviews, taxonomic orders, and classifications of evolutionary and organism histories. +Explaining the biodiversity of the planet and its organisms. The systematic study is that of conservation. +Manipulating and controlling the natural world. This includes the practice of 'biological control', the intentional introduction of natural predators and disease. + + +== Definition and relation with taxonomy == +John Lindley provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics". +In 1970 Michener et al. defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relationship to one another as follows: + +Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above. + +The term "taxonomy" was coined by Augustin Pyramus de Candolle while the term "systematic" was coined by Carl Linnaeus the father of taxonomy. +Taxonomy, systematic biology, systematics, biosystematics, scientific classification, biological classification, phylogenetics: At various times in history, all these words have had overlapping, related meanings. However, in modern usage, they can all be considered synonyms of each other. +Europeans tend to use the terms "systematics" and "biosystematics" for the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. However, taxonomy, and in particular alpha taxonomy, is more specifically the identification, description, and naming (i.e. nomenclature) of organisms, while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms. All of these biological disciplines can deal with both extinct and extant organisms. +Systematics uses taxonomy as a primary tool in understanding, as nothing about an organism's relationships with other living things can be understood without it first being properly studied and described in sufficient detail to identify and classify it correctly. Scientific classifications are aids in recording and reporting information to other scientists and to laymen. The systematist, a scientist who specializes in systematics, must, therefore, be able to use existing classification systems, or at least know them well enough to skillfully justify not using them. +Phenetics was an attempt to determine the relationships of organisms through a measure of overall similarity, making no distinction between plesiomorphies (shared ancestral traits) and apomorphies (derived traits). From the late-20th century onwards, it was superseded by cladistics, which rejects plesiomorphies in attempting to resolve the phylogeny of Earth's various organisms through time. Today's systematists generally make extensive use of molecular biology and of computer programs to study organisms. + + +== Taxonomic characters == +Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the phylogeny) between taxa are inferred. Kinds of taxonomic characters include: + + +== See also == +Evolutionary systematics – a school of systematics +Global biodiversity +16S ribosomal RNA – an intensively studied nucleic acid that has been useful in phylogenetics +Phylogenetic comparative methods – use of evolutionary trees in other studies, such as biodiversity, comparative biology. adaptation, or evolutionary mechanisms +Lichen systematics + + +== References == + + +=== Notes === + + +=== Further reading === +Brower, Andrew V. Z. and Randall T. Schuh. 2021. Biological Systematics: Principles and Applications, 3rd edn. ISBN 978-1-5017-5277-3 +Simpson, Michael G. 2005. Plant Systematics. ISBN 978-0-12-644460-5 +Wiley, Edward O. and Bruce S. Lieberman. 2011. "Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd edn." ISBN 978-0-470-90596-8 + + +== External links == +Society of Australian Systematic Biologists +Society of Systematic Biologists +The Willi Hennig Society + +. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taphotaxon-0.md b/data/en.wikipedia.org/wiki/Taphotaxon-0.md new file mode 100644 index 000000000..dff310656 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taphotaxon-0.md @@ -0,0 +1,15 @@ +--- +title: "Taphotaxon" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Taphotaxon" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:40.917370+00:00" +instance: "kb-cron" +--- + +A taphotaxon (from the Greek ταφος, taphos meaning burial and ταξις, taxis meaning ordering) is an invalid taxon based on fossils remains that have been altered in a characteristic way during burial and diagenesis. The fossils so altered have distinctive characteristics that make them appear to be a new taxon, but these characteristics are spurious and do not reflect any significant taxonomic distinction from an existing fossil taxon. The term was first proposed by Spencer G. Lucas in 2001, who particularly applied it to spurious ichnotaxons, but it has since been applied to body fossils such as Nuia (interpreted as cylindrical oncolites formed around filamentous cyanobacteria) or Ivanovia (thought to be a taphotaxon of Anchicondium or Eugonophyllum); conulariids, and crustaceans. +In his original definition of the term, Lucas emphasized that he was not seeking to create a new field of taphotaxonomy. The term is intended simply as a useful description of a particular type of invalid taxon. It should not be used indiscriminately, particularly with ichnotaxons, where the fact that an ichnotaxon derives part of its morphology from taphonomic processes may not always render it an invalid ichnotaxon. + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taronga b/data/en.wikipedia.org/wiki/Taronga new file mode 100644 index 000000000..e69de29bb diff --git a/data/en.wikipedia.org/wiki/Taxon-0.md b/data/en.wikipedia.org/wiki/Taxon-0.md new file mode 100644 index 000000000..8d0f8a5ab --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxon-0.md @@ -0,0 +1,73 @@ +--- +title: "Taxon" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Taxon" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:42.075698+00:00" +instance: "kb-cron" +--- + +In biology, a taxon is a group of one or more populations of an organism, or organisms, as seen by taxonomists to form a biological unit; (taxon: back-formation from taxonomy; pl.: taxa). Although neither is required, a taxon, once its description has become established, is usually known by a particular name and is given a particular ranking. + + +== Methods == +Taxonomists consider: + +which organisms belong to a given taxon +which criteria are to be used for deciding inclusion. This is especially the case in context of rank-based nomenclature (Linnaean taxonomy). +Once a taxon is given a formal scientific name, its use is governed by one of the nomenclature codes that specify the correct scientific name for a particular grouping. +Initial attempts at preserving human knowledge of plants and animals were presumably made in prehistoric times by hunter-gatherers, as suggested by folk taxonomies interpreted from archeological and anthropological studies. Much later, as of Aristotle's teachings, and later still—as of the published works of Magnol, Tournefort, and Carl Linnaeus, (his Systema Naturae, 10th edition (1758)), and as of the unpublished works of Bernard and Antoine Laurent de Jussieu—then did European naturalists and scientists begin documenting this new field of human knowledge. +The idea of a unit-based system to classify the characteristics of plants and animals (later known as biological classification) was first made widely available in 1805 via Augustin Pyramus de Candolle's Principes élémentaires de botanique, published as the introduction to Jean-Baptiste Lamarck's Flore françoise, 3rd ed. (1805), which treatise presented a system for the "natural classification" of plants. From that time forward systematists have competed, collaborated, and published—while providing for organizing and classifying human knowledge of the life forms on planet Earth. +In modern biology studies, a "good" or "useful" taxon is commonly taken to be one that reflects evolutionary relationships. Many modern systematists are advocates of phylogenetic nomenclature; they use cladistic methods that require taxa to be monophyletic (i.e., show all the descendants of a common ancestor). Their basic unit, the clade, is equivalent to the taxon, and their using the clade implies that taxa should reflect evolutionary relationships. Similarly, among those contemporary taxonomists working with the traditional Linnean (binomial) nomenclature, only a few still propose taxa they know to be paraphyletic. +An example of a long-established taxon that is paraphyletic—meaning not also a clade—is the class Reptilia: the reptiles. Birds and mammals are descendants of animals long classed as reptiles; but traditionally, neither was placed in class Reptilia. Instead, birds are found in the class Aves, and mammals in the class Mammalia. + + +== History == +The term taxon was first used in 1926 by Adolf Meyer-Abich for animal groups, as a back-formation from the word taxonomy; the word taxonomy had been coined a century before from the Greek components τάξις (táxis), meaning "arrangement", and νόμος (nómos), meaning "method". For plants, it was proposed by Herman Johannes Lam in 1948, and it was adopted at the VII International Botanical Congress, held in 1950. + + +== Definition == +The glossary of the International Code of Zoological Nomenclature (1999) defines a + +"taxon, (pl. taxa), n. +A taxonomic unit, whether named or not: i.e. a population, or group of populations of organisms which are usually inferred to be phylogenetically related and which have characters in common which differentiate (q.v.) the unit (e.g. a geographic population, a genus, a family, an order) from other such units. A taxon encompasses all included taxa of lower rank (q.v.) and individual organisms. [...]" + + +== Ranks == + +A taxon can be assigned a taxonomic rank, usually (but not necessarily) when it is given a formal description, though it is common to place a taxon as an unranked group called a clade. +"Phylum" applies formally to any biological domain, but traditionally it was always used for animals, whereas "division" was traditionally often used for plants, fungi, etc. +The prefix super- indicates a rank above, the prefix sub- indicates a rank below. In zoology, the prefix infra- indicates a rank below sub-. For instance, among the additional ranks of class are superclass, subclass and infraclass. +Rank is relative, and restricted to a particular systematic schema. For example, liverworts have been grouped, in various systems of classification, as a family, order, class, or division (phylum). The use of a narrow set of ranks is challenged by users of cladistics; for example, the mere 10 ranks traditionally used between animal families (governed by the International Code of Zoological Nomenclature [ICZN]) and animal phyla (usually the highest relevant rank in taxonomic work) often cannot adequately represent the evolutionary history as more about a lineage's phylogeny becomes known. +In addition, the class rank is quite often not an evolutionary but a phenetic or paraphyletic group and as opposed to those ranks governed by the ICZN (family-level, genus-level and species-level taxa), can usually not be made monophyletic by exchanging the taxa contained therein. This has given rise to phylogenetic taxonomy and the ongoing development of the PhyloCode, which has been proposed as a new alternative to replace Linnean classification and govern the application of names to clades. Many cladists do not see any need to depart from traditional nomenclature as governed by the ICZN, International Code of Nomenclature for algae, fungi, and plants, etc. + + +== See also == + +ABCD Schema +Alpha taxonomy +Chresonym +Cladistics +Folk taxonomy +Ichnotaxon +International Code of Nomenclature for algae, fungi, and plants +International Code of Nomenclature of Prokaryotes +International Code of Phylogenetic Nomenclature +International Code of Zoological Nomenclature (ICZN) +List of taxa named by anagrams +Rank (botany) +Rank (zoology) +Segregate (taxonomy) +Virus classification +Wastebasket taxon + + +== Notes == + + +== References == + + +== External links == + The dictionary definition of taxon at Wiktionary \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxon_in_disguise-0.md b/data/en.wikipedia.org/wiki/Taxon_in_disguise-0.md new file mode 100644 index 000000000..5a99117b2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxon_in_disguise-0.md @@ -0,0 +1,47 @@ +--- +title: "Taxon in disguise" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Taxon_in_disguise" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:43.257317+00:00" +instance: "kb-cron" +--- + +In bacteriology, a taxon in disguise is a species, genus or higher unit of biological classification whose evolutionary history reveals that it has evolved from another unit of a similar or lower rank, making the parent unit paraphyletic. That happens when rapid evolution makes a new species appear so radically different from the ancestral group that it is not (initially) recognised as belonging to the parent phylogenetic group, which is left as an evolutionary grade. +While the term is from bacteriology, parallel examples are found throughout the tree of life. For example, four-footed animals have evolved from piscine ancestors but since they are not generally considered fish, they can be said to be "fish in disguise". +In many cases, the paraphyly can be resolved by reclassifying the taxon in question under the parent group. However, in bacteriology, since renaming groups may have serious consequences by causing confusion over the identity of pathogens, it is generally avoided for some groups. + + +== Examples == + + +=== Shigella === +The bacterial genus Shigella is the cause of bacillary dysentery, a potentially-severe infection that kills over a million people every year. The genus (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) have evolved from the common intestinal bacterium Escherichia coli, which renders that species paraphyletic. E. coli itself can also cause serious dysentery, but differences in genetic makeup between E. coli and Shigella cause different medical conditions and symptoms. +Escherichia coli is a poorly-classified species as some strains share only 20% of their genome. The species has proven to be quite diversive and should ideally be subdivided into further taxonomic groups. However, medical conditions associated with E. coli and Shigella complicate reclassification in an attempt to avoid causing confusion in medical contexts. As such, Shigella and several sub-branches of E. coli remain undivided despite genomic evidence suggesting otherwise. + + +=== B. cereus-group === +Similarly, the Bacillus species of the B. cereus-group (B. anthracis, B. cereus, B . thuringiensis, B. mycoides, B. pseudomycoides, B. weihenstephanensis and B. medusa) have 99-100% similar 16S rRNA sequence (97% is a commonly-cited adequate species limit) and should be considered a single species. Some members of the group appear to have arisen from other Bacillus strains by acquiring a protein coding plasmid and so the group may thus be polyphyletic. For medical reasons, such as anthrax, the current arrangement of separate species has remained intact. + + +=== Large genera of microbes === +The bacterial genus Pseudomonas has enlarged through several generations of taxonomic methods, bringing the species count to alarming proportions, with around 800 species recognized by the mid-20th century. The nitrogen-fixing bacteria of the genus Azotobacter and the species Azomonas macrocytogenes have evolved from a species in the genus Pseudomonas. Its nitrogen-fixing capabilities and deviant features have caused Azotobacter to be described as "Pseudomonas in disguise". +The genus Bacillus was described early in the history of microbiology and so is a large genus that is very genetically diverse, 266 species. The genera Paenibacillus and Brevibacillus are clades that are nested within Bacillus. Since Bacillus is highly medically relevant and Paenibacillus is a model organism that is used in research, renaming them to reflect phylogeny would result in confusion. + + +== See also == +Monophyly +Paraphyly +Polyphyly +Species problem +Evolutionary grade +Cryptic species complex +Synonym (taxonomy) +Taxonomy +LPSN, a list of accepted bacterial and archaeal names +Bacterial phyla, a complex classification scheme +Cyanobacteria, a phylum of common bacteria that remain poorly classified + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomic_boundary_paradox-0.md b/data/en.wikipedia.org/wiki/Taxonomic_boundary_paradox-0.md new file mode 100644 index 000000000..bf9d93719 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomic_boundary_paradox-0.md @@ -0,0 +1,35 @@ +--- +title: "Taxonomic boundary paradox" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Taxonomic_boundary_paradox" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:44.398378+00:00" +instance: "kb-cron" +--- + +The term boundary paradox refers to the conflict between traditional, rank-based classification of life and evolutionary thinking. In the hierarchy of ranked categories it is implicitly assumed that the morphological gap is growing along with increasing ranks: two species from the same genus are more similar than other two species from different genera in the same family, these latter two species are more similar than any two species from different families of the same order, and so on. However, this requirement may only satisfy for the classification of contemporary organisms; difficulties arise if we wish to classify descendants together with their ancestors. Theoretically, such a classification necessarily involves segmentation of the spatio-temporal continuum of populations into groups with crisp boundaries. However, the problem is not only that many parent populations would separate at species level from their offspring. The truly paradoxical situation is that some between-species boundaries would necessarily coincide with between-genus boundaries, and a few between-genus boundaries with borders between families, and so on. This apparent ambiguity cannot be resolved in Linnaean systems; resolution is only possible if classification is cladistic (see below). + +== Historical background == +Jean-Baptiste Lamarck, in Philosophie zoologique (1809), was the first who questioned the objectivity of rank-based classification of life, by saying: + +…classes, orders, families, genera and nomenclatures are weapons of our own invention. We could not do without them, but we must use them with discretion. …among her productions nature has not really formed either classes, orders, families, genera or constant species, but only individuals who succeed one another and resemble those from which they sprung. +Half a century later, Charles Darwin explained that sharp separation of groups of organisms observed at present becomes less obvious if we go back into the past: + +The most common case, especially with respect to very distinct groups, such as fish and reptiles, seems to be, that supposing them to be distinguished at the present day from each other by a dozen characters, the ancient members of the same two groups would be distinguished by a somewhat lesser number of characters, so that the two groups, though formerly quite distinct, at that period made some small approach to each other. +In his book on orchids, Darwin also warned that the system of ranks would not work if we knew more details about past life: + +To make a perfect gradation, all the extinct forms which have ever existed, along many lines of descent converging to the common progenitor of the order, would have to be called into life. It is due to their absence, and to the consequent wide gaps in the series, that we are enabled to divide the existing species into definable groups, such as genera, families, and tribes. +Finally, Richard Dawkins has argued recently thatIf we assume, as almost every anthropologist today accepts, that all members of the genus Homo are descended from ancestors belonging to the genus we call Australopithecus, it necessarily follows that, somewhere along the chain of descent from one species to the other, there must have been at least one individual who sat exactly on the borderline. +and + +Indeed, on the evolutionary view, the conferring of discrete names should actually become impossible if only the fossil record were more complete. In one way, it is fortunate that fossils are so rare. If we had a continuous and unbroken fossil record, the granting of distinct names to species and genera would become impossible, or at least very problematical. +with the following conclusion: + +The [Linnaean] system works, as long as we don’t try to classify the dead antecedents. But as soon as we include our hypothetically complete fossil record, all the neat separations break down. + +== Illustrative models == +The paradox may be best illustrated by model diagrams similar to Darwin’s single evolutionary tree in On the Origin of Species. In these tree graphs, dots represent populations and edges correspond to parent-offspring relations. The trees are placed into a coordinate system which is one-dimensional (time) for a single lineage, and two-dimensional (differentiation vs. time) for cladogenesis or evolution with divergence. + + +In the single lineage model we now consider a sequence of populations along an extremely long time axis, say several hundred million years, with the last dot representing an extant population. In the figure there is space for a few dots even though edges between adjacent populations are hidden. We could use a second axis to express differentiation, but it is not necessary for our purposes. Here we assume that there is no extinction and all branching events are disregarded (if there were no branches at all, then the changes would correspond to a typical anagenesis. Classification of organisms along this sequence into species is shown by small ellipses. If the differences between certain species are judged to be large enough to justify classification into distinct genera, then generic separators must each coincide with a between-species boundary. If differences reach family-level differentiation, which is easy to imagine over the very long time we consider here, the consequence is that a family-level border must overlap with a between-genus and, in turn, a between-species border (gray arrow in the figure). One cannot imagine, however, that a parent and its offspring are so distinct that they should be classified to different families, or even genera – that would be paradoxical. This illustrates Dawkins’ above argumentation on human ancestry at the level of genera, Homo and Australopithecus. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomic_boundary_paradox-1.md b/data/en.wikipedia.org/wiki/Taxonomic_boundary_paradox-1.md new file mode 100644 index 000000000..d2f6a7219 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomic_boundary_paradox-1.md @@ -0,0 +1,26 @@ +--- +title: "Taxonomic boundary paradox" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Taxonomic_boundary_paradox" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:44.398378+00:00" +instance: "kb-cron" +--- + + +Darwin placed emphasis on divergence, that is, when a parent population splits and these offspring populations diverge gradually, each following their own anagenetic sequence potentially with further divergence events. In this case, evolutionary (say morphological) divergence is expressed on a new, horizontal, axis and time becomes the vertical axis. At time point 1 an imaginary taxonomist judges populations A and B to belong to different species, but within the same genus. Their respective descendants, C and D are observed at time 2, and considered to represent two separate genera because their morphological difference is large. The paradox is that while A and C, as well as B and D remain within generic limits but C and D do not, so that ancestors cannot be classified together with their descendants meaningfully in a Linnaean system. This figure illustrates the problem Darwin has discussed in the fish and reptile example. + + +Let us consider a hypothetical evolutionary tree with four recent species, A to D, classified into two genera that are fairly distant from each other morphologically. We assume, further, that from the fossil record we only know their common ancestor, E, representing yet another genus for a taxonomist because it takes “intermediate” position between the other two – yet considerably different from both. All other forms went extinct; therefore we have classification of these five species into three genera, which would be illogical if more fossils were known. This illustrates Darwin’s and Dawkins’ examples on the role of gaps in the fossil record in classification – and nomenclature. + +== Resolution == + +As demonstrated, given a Darwinian evolutionary model, descendants and their ancestors cannot be classified together within the system of Linnean ranks. Solution is provided by cladistic classification in which each group is composed of an ancestor and all of its descendant populations, a condition called monophyly. In the above models monophyletic groups may be obtained by cutting a branch (subtree) from the tree at places where, for instance, new apomorphic (evolutionary derived) characters appear. For these groups there is no need to consider how much change occurred between members of one group as compared to those of the other. + +== See also == +Clade +Sister group +Temporal paradox (paleontology) + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomic_vandalism-0.md b/data/en.wikipedia.org/wiki/Taxonomic_vandalism-0.md new file mode 100644 index 000000000..8b40de59e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomic_vandalism-0.md @@ -0,0 +1,23 @@ +--- +title: "Taxonomic vandalism" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Taxonomic_vandalism" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:46.713738+00:00" +instance: "kb-cron" +--- + +Taxonomic vandalism is a term used in biology to describe the practice of publishing numerous scientifically unfounded or poorly-justified taxonomic names, often without adequate research or peer review. This phenomenon has been observed across various fields of taxonomy, but has been particularly prevalent in herpetology. + + +== See also == +Mihi itch +Taxonomic inflation + + +== References == + + +== External links == +Why Do Taxonomists Write the Meanest Obituaries? \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomy_(biology)-0.md b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-0.md new file mode 100644 index 000000000..cc15400e4 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-0.md @@ -0,0 +1,48 @@ +--- +title: "Taxonomy (biology)" +chunk: 1/5 +source: "https://en.wikipedia.org/wiki/Taxonomy_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:47.872113+00:00" +instance: "kb-cron" +--- + +In biology, taxonomy (from Ancient Greek τάξις (taxis) 'arrangement' and -νομία (-nomia) 'method') is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Modern approaches prioritize common ancestory and evolutionary relationships. Organisms are grouped into taxa (singular: taxon), and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, having developed a ranked system known as Linnaean taxonomy for categorizing organisms. +With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolutionary relationships among organisms, both living and extinct. + +== Definition == +The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of groups of organisms. As points of reference, recent definitions of taxonomy are presented below: + +Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification. +A field of science (and a major component of systematics) that encompasses description, identification, nomenclature, and classification +The science of classification, in biology the arrangement of organisms into a classification +"The science of classification as applied to living organisms, including the study of means of formation of species, etc." +"The analysis of an organism's characteristics for the purpose of classification" +"Systematics studies phylogeny to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" (listed as a desirable but unusual definition) +The varied definitions either place taxonomy as a sub-area of systematics (definition 2), invert that relationship (definition 6), or appear to consider the two terms synonymous. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy. For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy: + +Systematics: "The study of the identification, taxonomy, and nomenclature of organisms, including the classification of living things with regard to their natural relationships and the study of variation and the evolution of taxa". +In 1970, Michener et al. defined "systematic biology" and "taxonomy" in relation to one another as follows: + +Systematic biology (hereafter called simply systematics) is the field that + +(a) provides scientific names for organisms, +(b) describes them, +(c) preserves collections of them, +(d) provides classifications for the organisms, keys for their identification, and data on their distributions, +(e) investigates their evolutionary histories, and +(f) considers their environmental adaptations. +This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above. + +A whole set of terms including taxonomy, systematic biology, systematics, scientific classification, biological classification, and phylogenetics have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting. The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by de Candolle, in his Théorie élémentaire de la botanique. John Lindley provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics". Europeans tend to use the terms "systematics" and "biosystematics" for the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. However, taxonomy, and in particular alpha taxonomy, is more specifically the identification, description, and naming (i.e., nomenclature) of organisms, while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms. + +=== Monograph and taxonomic revision === +A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular taxon. This analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological, anatomical, palynological, biochemical and genetic. A monograph or complete revision is a revision that is comprehensive for a taxon for the information given at a particular time, and for the entire world. Other (partial) revisions may be restricted in the sense that they may only use some of the available character sets or have a limited spatial scope. A revision results in a conformation of or new insights in the relationships between the subtaxa within the taxon under study, which may lead to a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa. + +=== Taxonomic characters === +Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the phylogeny) between taxa are inferred. Kinds of taxonomic characters include: + +=== Alpha and beta taxonomy === + +The term "alpha taxonomy" is primarily used to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, and the products of research through the end of the 19th century. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomy_(biology)-1.md b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-1.md new file mode 100644 index 000000000..1d735675d --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-1.md @@ -0,0 +1,36 @@ +--- +title: "Taxonomy (biology)" +chunk: 2/5 +source: "https://en.wikipedia.org/wiki/Taxonomy_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:47.872113+00:00" +instance: "kb-cron" +--- + +William Bertram Turrill introduced the term "alpha taxonomy" in a series of papers published in 1935 and 1937 in which he discussed the philosophy and possible future directions of the discipline of taxonomy. ... there is an increasing desire amongst taxonomists to consider their problems from wider viewpoints, to investigate the possibilities of closer co-operation with their cytological, ecological and genetics colleagues and to acknowledge that some revision or expansion, perhaps of a drastic nature, of their aims and methods, may be desirable ... Turrill (1935) has suggested that while accepting the older invaluable taxonomy, based on structure, and conveniently designated "alpha", it is possible to glimpse a far-distant taxonomy built upon as wide a basis of morphological and physiological facts as possible, and one in which "place is found for all observational and experimental data relating, even if indirectly, to the constitution, subdivision, origin, and behaviour of species and other taxonomic groups". Ideals can, it may be said, never be completely realized. They have, however, a great value of acting as permanent stimulants, and if we have some, even vague, ideal of an "omega" taxonomy we may progress a little way down the Greek alphabet. Some of us please ourselves by thinking we are now groping in a "beta" taxonomy. +Turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy. + +Later authors have used the term in a different sense, to mean the delimitation of species (not subspecies or taxa of other ranks), using whatever investigative techniques are available, and including sophisticated computational or laboratory techniques. Thus, Ernst Mayr in 1968 defined "beta taxonomy" as the classification of ranks higher than species.An understanding of the biological meaning of variation and of the evolutionary origin of groups of related species is even more important for the second stage of taxonomic activity, the sorting of species into groups of relatives ("taxa") and their arrangement in a hierarchy of higher categories. This activity is what the term classification denotes; it is also referred to as "beta taxonomy". + +=== Microtaxonomy and macrotaxonomy === + +How species should be defined in a particular group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy. By extension, macrotaxonomy is the study of groups at the higher taxonomic ranks subgenus and above, or simply in clades that include more than one taxon considered a species, expressed in terms of phylogenetic nomenclature. + +== History == +While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, a truly scientific attempt to classify organisms did not occur until the 18th century, with the possible exception of Aristotle, whose works hint at a taxonomy. Earlier works were primarily descriptive and focused on plants that were useful in agriculture or medicine. +There are a number of stages in this scientific thinking. Early taxonomy was based on arbitrary criteria, the so-called "artificial systems", including Linnaeus's system of sexual classification for plants (Linnaeus's 1735 classification of animals was entitled "Systema Naturae" ("the System of Nature"), implying that he, at least, believed that it was more than an "artificial system"). +Later came systems based on a more complete consideration of the characteristics of taxa, referred to as "natural systems", such as those of de Jussieu (1789), de Candolle (1813) and Bentham and Hooker (1862–1863). These classifications described empirical patterns and were pre-evolutionary in thinking. +The publication of Charles Darwin's On the Origin of Species (1859) led to a new explanation for classifications, based on evolutionary relationships. This was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler (1883) and Engler (1886–1892). +The advent of cladistic methodology in the 1970s led to classifications based on the sole criterion of monophyly, supported by the presence of synapomorphies. Since then, the evidentiary basis has been expanded with data from molecular genetics that for the most part complements traditional morphology. + +=== Pre-Linnaean === + +==== Early taxonomists ==== +Naming and classifying human surroundings likely began with the onset of language. Distinguishing poisonous plants from edible plants is integral to the survival of human communities. Medicinal plant illustrations show up in Egyptian wall paintings from c. 1500 BC, indicating that the uses of different species were understood and that a basic taxonomy was in place. + +==== Ancient times ==== + +Organisms were first classified by Aristotle (Ancient Greece, 384–322 BC) during his stay on the island of Lesbos. He classified beings by their parts, or in modern terms attributes, such as having live birth, having four legs, laying eggs, having blood, or being warm-bodied. He divided all living things into two groups: plants and animals. +Some of his groups of animals, such as Anhaima (animals without blood, translated as invertebrates) and Enhaima (animals with blood, roughly the vertebrates), as well as groups like the sharks and cetaceans, are commonly used. +His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Several plant genera can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomy_(biology)-2.md b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-2.md new file mode 100644 index 000000000..114aadbfe --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-2.md @@ -0,0 +1,27 @@ +--- +title: "Taxonomy (biology)" +chunk: 3/5 +source: "https://en.wikipedia.org/wiki/Taxonomy_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:47.872113+00:00" +instance: "kb-cron" +--- + +==== Medieval ==== +Taxonomy in the Middle Ages was largely based on the Aristotelian system, with additions concerning the philosophical and existential order of creatures. This included concepts such as the great chain of being in the Western scholastic tradition, again deriving ultimately from Aristotle. +The Aristotelian system did not classify plants or fungi, due to the lack of microscopes at the time, as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder). This, as well, was taken into consideration in the great chain of being. +Advances were made by scholars such as Procopius, Timotheus of Gaza, Demetrios Pepagomenos, and Thomas Aquinas. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy. In the Muslim world, Al-Damiri (d. 1405) wrote an influential work called Life of Animals (Ḥayāt al-ḥayawān al-kubrā, c.1371) which treats in alphabetic order of 931 animals mentioned in the Quran, the traditions and the poetic and proverbial literature of the Arabs. + +==== Renaissance and early modern ==== +During the Renaissance and the Age of Enlightenment, categorizing organisms became more prevalent, and taxonomic works became ambitious enough to replace the ancient texts. This is sometimes credited to the development of sophisticated optical lenses, which allowed the morphology of organisms to be studied in much greater detail. +One of the earliest authors to take advantage of this leap in technology was the Italian physician Andrea Cesalpino (1519–1603), who has been called "the first taxonomist". His magnum opus De Plantis came out in 1583, and described more than 1,500 plant species. Two large plant families that he first recognized are in use: the Asteraceae and Brassicaceae. +In the 17th century, John Ray (England, 1627–1705) wrote many important taxonomic works. Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), in which he published details of over 18,000 plant species. At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. +The next major taxonomic works were produced by Joseph Pitton de Tournefort (France, 1656–1708). His work from 1700, Institutiones Rei Herbariae, included more than 9,000 species in 698 genera, which directly influenced Linnaeus, as it was the text he used as a young student. + +=== Linnaean era === + +The Swedish botanist Carl Linnaeus (1707–1778) ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735, Species Plantarum in 1753, and Systema Naturae 10th Edition, he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species, which proved to be an elegant solution to a chaotic and disorganized taxonomic literature. He not only introduced the standard of class, order, genus, and species, but also made it possible to identify plants and animals from his book, by using the smaller parts of the flower (known as the Linnaean system). +Plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively). Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean. + +== Modern system of classification == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomy_(biology)-3.md b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-3.md new file mode 100644 index 000000000..104083ac1 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-3.md @@ -0,0 +1,31 @@ +--- +title: "Taxonomy (biology)" +chunk: 4/5 +source: "https://en.wikipedia.org/wiki/Taxonomy_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:47.872113+00:00" +instance: "kb-cron" +--- + +A pattern of groups nested within groups was specified by Linnaeus' classifications of plants and animals, and these patterns began to be represented as dendrograms of the animal and plant kingdoms toward the end of the 18th century, well before Charles Darwin's On the Origin of Species was published. The pattern of the "Natural System" did not entail a generating process, such as evolution, but may have implied it, inspiring early transmutationist thinkers. Among early works exploring the idea of a transmutation of species were Zoonomia in 1796 by Erasmus Darwin (Charles Darwin's grandfather), and Jean-Baptiste Lamarck's Philosophie zoologique of 1809. The idea was popularized in the Anglophone world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844. +With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. Tree of life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds. Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842. The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, palaeontologists worked to understand the history of animals through the ages by linking together known groups. With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place. As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use. +The cladistic method has emerged since the 1960s. In 1958, Julian Huxley used the term clade. Later, in 1960, Cain and Harrison introduced the term cladistic. The salient feature is arranging taxa in a hierarchical evolutionary tree, with the desired objective of all named taxa being monophyletic. A taxon is called monophyletic if it includes all the descendants of an ancestral form. Groups that have descendant groups removed from them are termed paraphyletic, while groups representing more than one branch from the tree of life are called polyphyletic. Monophyletic groups are recognized and diagnosed on the basis of synapomorphies, shared derived character states. +Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes of Zoological and Botanical nomenclature, to a certain extent. An alternative system of nomenclature, the International Code of Phylogenetic Nomenclature or PhyloCode has been proposed, which regulates the formal naming of clades. Linnaean ranks are optional and have no formal standing under the PhyloCode, which is intended to coexist with the current, rank-based codes. While popularity of phylogenetic nomenclature has grown steadily in the last few decades, it remains to be seen whether a majority of systematists will eventually adopt the PhyloCode or continue using the current systems of nomenclature that have been employed (and modified, but arguably not as much as some systematists wish) for over 250 years. + +== Kingdoms and domains == + +Domains are a relatively new grouping. First proposed in 1977, Carl Woese's three-domain system was not generally accepted until later. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera), with the Eukaryota for all organisms whose cells contain a nucleus. A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method. +Thomas Cavalier-Smith, who published extensively on the classification of protists, in 2002 proposed that the Neomura, the clade that groups together the Archaea and Eucarya, would have evolved from Bacteria, more precisely from Actinomycetota. His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely. Stefan Luketa in 2012 proposed a five "dominion" system, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains. + +=== Recent comprehensive classifications === +Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available; however, comprehensive, published treatments of most or all life are rarer; recent examples are that of Adl et al., 2012 and 2019, which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015, covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives. A separate compilation (Ruggiero, 2014) covers extant taxa to the rank of Family. Other, database-driven treatments include the Encyclopedia of Life, the Global Biodiversity Information Facility, the NCBI taxonomy database, the Interim Register of Marine and Nonmarine Genera, the Open Tree of Life, and the Catalogue of Life. The Paleobiology Database is a resource for fossils. + +== Application == +Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists known as "taxonomists", although enthusiastic naturalists are also frequently involved in the publication of new taxa. Because taxonomy aims to describe and organize life, the work conducted by taxonomists is essential for the study of biodiversity and the resulting field of conservation biology. + +=== Classifying organisms === + +Biological classification is a critical component of the taxonomic process. As a result, it informs the user as to what the relatives of the taxon are hypothesized to be. Biological classification uses taxonomic ranks, including among others (in order from most inclusive to least inclusive): domain, kingdom, phylum, class, order, family, genus, species, and strain. + +=== Taxonomic descriptions === \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Taxonomy_(biology)-4.md b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-4.md new file mode 100644 index 000000000..3aa2bdff8 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Taxonomy_(biology)-4.md @@ -0,0 +1,73 @@ +--- +title: "Taxonomy (biology)" +chunk: 5/5 +source: "https://en.wikipedia.org/wiki/Taxonomy_(biology)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:47.872113+00:00" +instance: "kb-cron" +--- + +The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined. There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules. In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code). In the fields of phycology, mycology, and botany, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN). +The initial description of a taxon involves five main requirements: + +The taxon must be given a name based on the 26 letters of the Latin alphabet (a binomial for new species, or uninomial for other ranks). +The name must be unique (i.e. not a homonym). +The description must be based on at least one name-bearing type specimen. +It should include statements about appropriate attributes either to describe (define) the taxon or to differentiate it from other taxa (the diagnosis, ICZN Code, Article 13.1.1, ICN, Article 38, which may or may not be based on morphology). Both codes deliberately separate defining the content of a taxon (its circumscription) from defining its name. +These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record. +However, often much more information is included, like the geographic range of the taxon, ecological notes, chemistry, behavior, etc. How researchers arrive at their taxa varies: depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence data. + +=== Author citation === + +An "authority" may be placed after a scientific name. The authority is the name of the scientist or scientists who first validly published the name. For example, in 1758, Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758". The names of authors are often abbreviated: the abbreviation L., for Linnaeus, is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (see list of botanists by author abbreviation). The system for assigning authorities differs slightly between botany and zoology. However, it is standard that if the genus of a species has been changed since the original description, the original authority's name is placed in parentheses. + +== Phenetics == + +In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships. It results in a measure of hypergeometric "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish shared ancestral (or plesiomorphic) traits from shared derived (or apomorphic) traits. However, certain phenetic methods, such as neighbor joining, have persisted, as rapid estimators of relationships when more advanced methods (such as Bayesian inference) are too computationally expensive. + +== Databases == + +Modern taxonomy uses database technologies to search and catalogue classifications and their documentation. While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species. The catalogue listed 1.64 million species for all kingdoms as of April 2016, claiming coverage of more than three-quarters of the estimated species known to modern science. + +== See also == +Automated species identification – Taxonomic AI processes +Bacterial taxonomy – Rank based classification of bacteria +Cladogram – Diagram used to show relations among groups of organisms with common origins +Classification – Putting things into categories +Cluster analysis – Grouping a set of objects by similarity +Consortium for the Barcode of Life – Organization for DNA barcoding as a global standard for species identification +Consortium of European Taxonomic Facilities – European research network +Dendrogram – Diagram with a treelike structure +Family resemblance – Philosophical idea popularized by Ludwig Wittgenstein +Folk taxonomy – Vernacular, as opposed to scientific, naming system +Genetypes – Concept in genetic science +Glossary of scientific naming +Identification (biology) – Process of taking existing name to single organisms +Incertae sedis – Term to indicate an uncertain taxonomic position +Numerical taxonomy – Classification system in biological systematics +Open Tree of Life – Online phylogenetic tree of life +Parataxonomy +Phenetics (or Taximetrics) – Attempt to classify organisms based on overall similarity +Phenogram +Prototype theory – Theory of categorization in psychology +Set theory – Branch of mathematics that studies sets +Systema Naturae – Major work by botanist Carolus Linnaeus +Taximetrics (or Phenetics) – Attempt to classify organisms based on overall similarity +Taxonomy (general) – Development of classes and classifications +Virus classification – Organisation of viruses into a taxonomic system + +== Notes == + +== References == + +== Bibliography == + +== External links == +What is taxonomy? at the Natural History Museum London +Taxonomy at NCBI the National Center for Biotechnology Information +Taxonomy at UniProt the Universal Protein Resource +ITIS the Integrated Taxonomic Information System +CETaF the Consortium of European Taxonomic Facilities +Wikispecies free species directory +Biological classification. Archived 13 August 2020 at the Wayback Machine \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/The_Secret_Life_of_the_Zoo-0.md b/data/en.wikipedia.org/wiki/The_Secret_Life_of_the_Zoo-0.md new file mode 100644 index 000000000..1d0da1e60 --- /dev/null +++ b/data/en.wikipedia.org/wiki/The_Secret_Life_of_the_Zoo-0.md @@ -0,0 +1,76 @@ +--- +title: "The Secret Life of the Zoo" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/The_Secret_Life_of_the_Zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:47.251792+00:00" +instance: "kb-cron" +--- + +The Secret Life of the Zoo is a British documentary programme produced by Blast! Films on behalf of Channel 4. The series is filmed on location at Chester Zoo in the North West of England, and focuses on the behaviour of the animals at the zoo and their relationships with the keepers. The first five series were narrated by Olivia Colman. Actress Tamsin Greig took over narration from the sixth series. + + +== Production == +The series gives viewers behind the scenes access to Chester Zoo's 21,000 animals and the people who work there. The zoo's keepers are interviewed in each episode about the various animals and incidents. Head of programmes at Blast!, Nick Hornby explained that as they wanted to tell the story from the animals' perspectives, they did not want the bars of the cages to be in shot, so they placed fixed cameras in the various enclosures. The first series was filmed over 10 months. The series was originally narrated by Olivia Colman. Tamsin Greig took over from October 2018. Ten series have aired between 2016 and 2021. The 8th series started airing in the UK on Channel 4 from 31 October 2019. The ninth series began on 13 February 2020. The tenth and final series began on 10 August 2021. + + +== Episodes == + + +=== Season 1 (2016) === + + +=== Season 2 (2016) === + + +=== Season 3 (2017) === + + +=== Season 4 (2017–2018) === + + +=== Season 5 (2018) === + + +=== Season 6 (2018) === + + +=== Season 7 (2019) === + + +=== Special (2019) === + + +=== Season 8 (2019) === + + +=== Season 9 (2020) === + + +=== Compilation Series (2020) === +This series looks back at Chester Zoo over the last five years. + + +=== Series 10 (2021) === + + +== Reception == +In 2018, The Secret Life of the Zoo received a nomination for the British Academy Television Award for Best Feature. However, it lost out to Cruising with Jane McDonald. +Gerard O'Donovan of The Daily Telegraph stated "For those who like their nature full of cute oohs and aahs, rather than red in tooth and claw, The Secret Life of the Zoo gently ticked all the boxes." O'Donovan's colleague Michael Hogan gave the opening episode of the fourth series a positive review, saying that it made him "emotionally invested as the devoted zookeepers." He found the "gently joyful documentary" was made all the more "uplifting" thanks to Colman's narration. He concluded, "it might have been no Blue Planet II but The Secret Life of the Zoo was equally enchanting in its own, more modest way." + + +== References == + +https://www.express.co.uk/life-style/life/637748/Channel-4-The-Secret-Life-Of-The-Zoo +http://www.radiotimes.com/tv-programme/e/dy6jfn/the-secret-life-of-the-zoo-episode-guide/ +https://www.cheshire-live.co.uk/news/chester-cheshire-news/chesters-secret-life-zoo-misses-14653634 +http://www.chesterzoo.org/global/press-and-media/press-releases/2017/11/secret-life-of-the-zoo-is-back?page=7 +http://www.chesterzoo.org/global/press-and-media/press-releases/2018/04/the-secret-life-of-the-zoo-series-five +http://www.thenational.scot/news/16242957.Tonight__39_s_TV__The_Secret_Life_of_the_Zoo__and_The_Doctor_Who_Gave_Up_Drugs/ + + +== External links == + +Official website +The Secret Life of the Zoo at IMDb \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Three-domain_system-0.md b/data/en.wikipedia.org/wiki/Three-domain_system-0.md new file mode 100644 index 000000000..67ca6bb68 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Three-domain_system-0.md @@ -0,0 +1,69 @@ +--- +title: "Three-domain system" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Three-domain_system" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:49.037834+00:00" +instance: "kb-cron" +--- + +The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of Archaea (previously named "archaebacteria") from Bacteria as completely different organisms. +The three-domain system has been contested by some scientists who believe that eukaryotes do not form a separate domain of life, but instead represent a clade alongside the Archaea, in a single shared domain. + + +== Background == +Woese argued, on the basis of differences in 16S rRNA genes, that bacteria, archaea, and eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Originally his split of the prokaryotes was into Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990. +Acceptance of the validity of Woese's phylogenetically valid classification was a slow process. Prominent biologists including Salvador Luria and Ernst Mayr objected to his division of the prokaryotes. Not all criticism of him was restricted to the scientific level. A decade of labor-intensive oligonucleotide cataloging left him with a reputation as "a crank", and Woese would go on to be dubbed "Microbiology's Scarred Revolutionary" by a news article printed in the journal Science in 1997. The growing amount of supporting data led the scientific community to accept the Archaea by the mid-1980s. Today, very few scientists still accept the concept of a unified Prokarya. + + +== Classification == + +The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the previously used five- or six-kingdom systems. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to eukaryotes than they are to other prokaryotes – bacteria-like organisms with no cell nucleus. The three-domain system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya. + + +=== Domain Archaea === +The Archaea are prokaryotic, with no nuclear membrane, but with biochemistry and RNA markers that are distinct from bacteria. The archaeans possess unique, ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth, most notably their diverse, exotic metabolisms. +Some examples of archaeal organisms are: + +methanogens – which produce the gas methane +halophiles – which live in very salty water +thermoacidophiles – which thrive in acidic high-temperature water + + +=== Domain Bacteria === +The Bacteria are also prokaryotic; their domain consists of cells with bacterial rRNA, no nuclear membrane, and whose membranes possess primarily diacyl glycerol diester lipids. Traditionally classified as bacteria, many thrive in the same environments favored by humans, and were the first prokaryotes discovered; they were briefly called the Eubacteria or "true" bacteria when the Archaea were first recognized as a distinct clade. +Most known pathogenic prokaryotic organisms belong to bacteria (see for exceptions). For that reason, and because the Archaea are typically difficult to grow in laboratories, Bacteria are currently studied more extensively than Archaea. +Some examples of bacteria include: + +"Cyanobacteria" – photosynthesizing bacteria that are related to the chloroplasts of eukaryotic plants and algae +Spirochaetota – Gram-negative bacteria that include those causing syphilis and Lyme disease +Actinomycetota – Gram-positive bacteria including Bifidobacterium animalis which is present in the human large intestine + + +=== Domain Eukarya === +Eukaryota are organisms whose cells contain a membrane-bound nucleus. They include many large single-celled organisms and all known non-microscopic organisms. The domain contains, for example: + +Holomycota – mushrooms and allies +Viridiplantae – green plants +Holozoa – animals and allies +Stramenopiles – includes brown algae +Amoebozoa – solitary and social amoebae +Discoba – includes euglenoids + + +== Niches == +Each of the three cell types tends to fit into recurring specialities or roles. Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans. In fact, the structure of a eukaryote is likely to have derived from a joining of different cell types, forming organelles. +Parakaryon myojinensis (incertae sedis) is a single-celled organism known to be a unique example. "This organism appears to be a life form distinct from prokaryotes and eukaryotes", with features of both. + + +== Alternatives == + +Parts of the three-domain theory have been challenged by scientists including Ernst Mayr, Thomas Cavalier-Smith, and Radhey S. Gupta. +Recent work has proposed that Eukaryota may have actually branched off from the domain Archaea. According to Spang et al., Lokiarchaeota forms a monophyletic group with eukaryotes in phylogenomic analyses. The associated genomes also encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. This work suggests a two-domain system as opposed to the three-domain system. Exactly how and when Archaea, Bacteria, and Eucarya developed and how they are related continues to be debated. + + +== See also == + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Trace_fossil_classification-0.md b/data/en.wikipedia.org/wiki/Trace_fossil_classification-0.md new file mode 100644 index 000000000..2e20324da --- /dev/null +++ b/data/en.wikipedia.org/wiki/Trace_fossil_classification-0.md @@ -0,0 +1,51 @@ +--- +title: "Trace fossil classification" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Trace_fossil_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:50.156876+00:00" +instance: "kb-cron" +--- + +Trace fossils are classified in various ways for different purposes. Traces can be classified taxonomically (by morphology), ethologically (by behavior), and toponomically, that is, according to their relationship to the surrounding sedimentary layers. Except in the rare cases where the original maker of a trace fossil can be identified with confidence, phylogenetic classification of trace fossils is an unreasonable proposition. + +== Taxonomic classification == +The taxonomic classification of trace fossils parallels the taxonomic classification of organisms under the International Code of Zoological Nomenclature. In trace fossil nomenclature a Latin binomial name is used, just as in animal and plant taxonomy, with a genus and specific epithet. However, the binomial names are not linked to an organism, but rather just a trace fossil. This is due to the rarity of association between a trace fossil and a specific organism or group of organisms. Trace fossils are therefore included in an ichnotaxon separate from Linnaean taxonomy. When referring to trace fossils, the terms ichnogenus and ichnospecies parallel genus and species respectively. +The most promising cases of phylogenetic classification are those in which similar trace fossils show details complex enough to deduce the makers, such as bryozoan borings, large trilobite trace fossils such as Cruziana, and vertebrate footprints. However, most trace fossils lack sufficiently complex details to allow such classification. + +== Ethologic classification == + +=== The Seilacherian System === + +Adolf Seilacher was the first to propose a broadly accepted ethological basis for trace fossil classification. He recognized that most trace fossils are created by animals in one of five main behavioural activities, and named them accordingly: + +Cubichnia are the traces of organisms left on the surface of a soft sediment. This behaviour may simply be resting as in the case of a starfish, but might also evidence the hiding place of prey, or even the ambush position of a predator. +Domichnia are dwelling structures that reflect the life positions of organisms, for example the burrows or borings of suspension feeders, and are perhaps the most common of the established ethological classes. +Fodinichnia are feeding traces which are formed as a result of organisms disturbing the sediment in their search for food. They are normally created by deposit feeders as they tunnel through soft sediments, usually producing a 3D structure. +Pascichnia are a different type of feeding trace for which the trophic guild responsible are grazers. They create 2D features as they scour the surface of a hard or soft substrate in order to obtain nutriment. +Repichnia are locomotory tracks that show evidence of organisms moving from one station to another, usually in a near-straight to slightly curved line. Most of the very few traces to be verifiably assigned to a specific organism are in this category, such as various arthropod and vertebrate trackways. + +=== Other ethological classes === +Since the inception of behavioural categorization, several other ethological classes have been suggested and accepted, as follows: + +Aedificichnia: evidence of organisms building structures outside of the infaunal realm, such as termite mounds or wasp nests. +Agrichnia: so called "gardening traces", which are systematic burrow networks designed to capture migrating meiofauna or perhaps even to culture bacteria. The organism would have continually inspected this burrow system to prey on any smaller organisms that strayed into it. +Calichnia: structures that were created by organisms specifically for breeding purposes, e.g. bee cells. +Equilibrichnia: burrows within the sediment that show evidence for organisms' responses to variations in sedimentation rate (i.e. the burrow moves upwards to avoid burial, or downwards to avoid exposure). Typically this evidence will be in the form of spreiten, which are small laminations in the sediment that reflect previous positions the organisms were in. +Fugichnia: "escape traces" that are formed as a result of organisms' attempts to escape burial in sudden high-sedimentation events like turbidity currents. The burrows are often marked with chevron patterns showing the upward direction the organisms were tunnelling. +Praedichnia: trace fossils that show evidence of predatory behaviour, such as the drill holes (borings) left in shells by carnivorous gastropods, or more dramatically, the bite marks found on some vertebrate bones. +Over the years several other behavioural groups have been proposed, but in general they have been quickly discarded by the ichnological community. Some of the failed proposals are listed below, with a brief description. + +Chemichnia: a type of agrichnia applied specifically to those instances of bacterial harvesting. +Cecidoichnia: a plant trace in which a gall is left on the plant as a result of interaction with animals, bacteria, or other plants. +Corrosichnia: traces that are left by plant roots as a result of their corrosive action on the sediments. +Cursichnia: a subgroup of the repichnia, created by a crawling or walking habit. +Fixichnia: traces left by sessile organisms that anchored themselves to a hard substrate. +Mordichnia: a praedichnial subgroup that shows evidence of the prey's death as a result of the attack. +Natichnia: a type of repichnia caused by disturbances to a soft sediment by a swimming organism, e.g. a benthic fish. +Polychresichnia: traces that show an origin in the combination of two or more established trace-producing behaviours, e.g. domichnia that served as the feeding position of the organisms. +Sphenoichnia: a plant trace created by the bioturbational action of roots. +Taphichnia: fugichnia in which the organism failed to escape and was buried, often resulting in its body fossil being found in association with the trace. +Volichnia: traces that show the position a flying organism (usually an insect) landed on a soft sediment. +Fixichnia is perhaps the group with the most weight as a candidate for the next accepted ethological class, being not fully described by any of the eleven currently accepted categories. There is also potential for the three plant traces (cecidoichnia, corrosichnia and sphenoichnia) to gain recognition in coming years, with little attention having been paid to them since their proposal. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Trace_fossil_classification-1.md b/data/en.wikipedia.org/wiki/Trace_fossil_classification-1.md new file mode 100644 index 000000000..58d5ef934 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Trace_fossil_classification-1.md @@ -0,0 +1,31 @@ +--- +title: "Trace fossil classification" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Trace_fossil_classification" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:50.156876+00:00" +instance: "kb-cron" +--- + +== Toponomic classification == +Another way to classify trace fossils is to look at their relation to the sediment of origin. Martinsson has provided the most widely accepted of such systems, identifying four distinct classes for traces to be separated in this regard: + +Endichnia are those traces that are found wholly within the casting medium, and therefore can only have been made by an infaunal organism. +Epichnia are found on the tops of the strata of origin, being those ridges and grooves that were formed by benthic organisms or infaunal burrows that have been exposed by erosion. +Exichnia are traces that are made of material that is different from the surrounding medium, having either been actively filled by an organism or eroded out and re-covered by an alien sediment. +Hypichnia are ridges and grooves found on the soles of the beds of origin at their interfaces with other strata, representing the opposite of epichnia. +Other classifications have been proposed, but none stray far from the above. + +== History == +Early paleontologists originally classified many burrow fossils as the remains of marine algae, as is apparent in ichnogenera named with the -phycus suffix. Alfred Gabriel Nathorst and Joseph F. James both controversially challenged this incorrect classification, suggesting the reinterpretation of many "algae" as marine invertebrate trace fossils. +Several attempts to classify trace fossils have been made throughout the history of paleontology. In 1844, Edward Hitchcock proposed two orders: Apodichnites, including footless trails, and Polypodichnites, including trails of organisms with more than four feet. + +== See also == +Ichnology +Trace fossil + +== References == + +== External links == +"Trace Fossils" by Kristian Saether & Christopher Clowes \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Travelling_menagerie-0.md b/data/en.wikipedia.org/wiki/Travelling_menagerie-0.md new file mode 100644 index 000000000..7fede2f38 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Travelling_menagerie-0.md @@ -0,0 +1,34 @@ +--- +title: "Travelling menagerie" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Travelling_menagerie" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:50.795343+00:00" +instance: "kb-cron" +--- + +A travelling menagerie was a touring group of showmen and animal handlers who visited towns and cities with common and exotic animals. The term "menagerie", first used in seventeenth century France, was primarily used to refer to aristocratic or royal animal collections. Most visitors to travelling menageries would never have the opportunity to see such animals under other circumstances and their arrival in a town would catalyse great excitement. The shows were both entertaining and educational; in 1872 The Scotsman described George Wombwell's travelling menagerie as "[having] done more to familiarise the minds of the masses of our people with the denizens of the forest than all the books of natural history ever printed during its wandering existence." + + +== Europe == +In England travelling menageries had first appeared at the turn of the eighteenth century, but did not gain widespread popularity until closer to the beginning of the nineteenth century. In contrast to the aristocratic menageries, these travelling animal collections were run by showmen who met the craving for sensation of the ordinary population. These animal shows ranged in size but the largest was George Wombwell's which, by 1839, totalled fifteen wagons. By 1880 Bostock and Wombwell's Royal National Menagerie had eighteen ″huge and spacious carriages″ and over six hundred beasts to take on the annual tour. + + +== North America == +The first exotic animal known to have been exhibited in America was a lion, in Boston in 1710, followed five years later in the same city by a camel. A sailor arrived in Philadelphia in August 1727 with another lion, which he exhibited in the city and surrounding towns for eight years. +The first elephant was imported from India to America by a ship’s captain, Jacob Crowninshield, in 1796. It was first displayed in New York City and travelled extensively up and down the East Coast. In 1834 James and William Howes’ New York Menagerie toured New England with an elephant, a rhinoceros, a camel, a zebra, a wildebeest, two tigers, a polar bear, and several parrots and monkeys. +America's touring menageries slowed to a crawl under the weight of the depression of the 1840s and then to a halt with the outbreak of the Civil War. Only one travelling menagerie of any size existed after the war: Isaac A. Van Amburgh's menagerie travelled the United States for nearly forty years. Unlike their European counterparts, America's menageries and circuses had combined as single travelling shows, with one ticket to see both. This increased the size and the diversity of their collections. Ringling Bros. and Barnum & Bailey Circus advertised their shows as the "World's Greatest Menagerie". + + +== See also == +Lion taming + + +== References == + + +== External links == + +Travelling Menageries, National Fairground Archive +The development of circus acts, Victoria and Albert Museum \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Two-domain_system-0.md b/data/en.wikipedia.org/wiki/Two-domain_system-0.md new file mode 100644 index 000000000..cfbc499ee --- /dev/null +++ b/data/en.wikipedia.org/wiki/Two-domain_system-0.md @@ -0,0 +1,30 @@ +--- +title: "Two-domain system" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Two-domain_system" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:51.348037+00:00" +instance: "kb-cron" +--- + +The two-domain system is a biological classification of all organisms in the tree of life into two domains: Archaea, which includes eukaryotes in this classification, and Bacteria. +It emerged from development of knowledge of archaea diversity and challenges the widely accepted three-domain system that classifies life into Bacteria, Archaea, and Eukarya. It was preceded by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system, due to evidence at the time. Better understanding of archaea, especially of their roles in the origin of eukaryotes through symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became more widely accepted after the discovery of a large kingdom of archaea called Promethearchaeati in 2017, which evidence suggests to be the evolutionary root of eukaryotes, thereby making eukaryotes members of the domain Archaea. +While the features of promethearchaea do not completely rule out the three-domain system, the notion that eukaryotes originated within Archaea has been strengthened by genetic and proteomic studies. Under the three-domain system, Eukarya is mainly distinguished by the presence of "eukaryotic signature proteins" that are not found in Archaea and Bacteria. However, promethearchaea contain genes that code for multiple such proteins. + +== Background == +Classification of life into two main divisions is not a new concept, with the first such proposal by French biologist Édouard Chatton in 1938. Chatton distinguished organisms into: + +Procaryotes (including bacteria) +Eucaryotes (including protozoans) +While he coined the terms in 1925, his detailed classification was published in a limited circulation format in 1938, titled Titres et Travaux Scientifiques (1906–1937) de Edouard Chatton. +These were later named empires, and Chatton's classification as the two-empire system. Chatton used the name Eucaryotes only for protozoans, excluded other eukaryotes, and published in limited circulation so that his work was not recognised. His classification was rediscovered by Canadian bacteriologist Roger Yates Stanier of the University of California in Berkeley in 1961 while at the Pasteur Institute in Paris. The next year, Stanier and his colleague Cornelis Bernardus van Niel published in Archiv für Mikrobiologie (now Archives of Microbiology) Chatton's classification with Eucaryotes eloborated to include higher algae, protozoans, fungi, plants, and animals. It became a popular system of classification, as John O. Corliss wrote in 1986: "[The] Chatton-Stanier concept of a kingdom (better, superkingdom) Prokaryota for bacteria (in the broadest sense) and a second superkingdom Eukaryota for all other organisms has been widely accepted with enthusiasm." +In 1977, Carl Woese and George E. Fox classified prokaryotes into two groups (kingdoms), Archaebacteria (for methanogens, the first known archaea) and Eubacteria, based on their 16S ribosomal RNA (16S rRNA) genes. In 1984, James A. Lake, Michael W. Clark, Eric Henderson, and Melanie Oakes of the University of California, Los Angeles described what was known as "a group of sulfur-dependent bacteria" as a new group of organisms called eocytes (for "dawn cells") and created a new kingdom Eocyta. With it they proposed the existence of four kingdoms, based on the structure and composition of the ribosomal subunits, namely Archaebacteria, Eubacteria, Eukaryote and Eocyta Lake further analysed the rRNA sequences of the four groups and suggested that eukaryotes originated from eocytes, and not archaebacteria, as was generally assumed. This was the basis of the eocyte hypothesis. In 1988, he proposed the division of all life forms into two taxonomic groups: + +Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes) +Parkaryotes (that consist of eubacteria and archaea such as halobacteria and methanogens) +In 1990, Woese, Otto Kandler, and Mark Wheelis showed that archaea are a distinct group of organisms and that eocytes (renamed Crenarchaeota as a phylum of Archaea but corrected as Thermoproteota in 2021) are Archaea. They introduced the major division of life into the three-domain system comprising domain Eucarya, domain Bacteria, and domain Archaea. With a number of revisions of details and discoveries of several new archaea lineages, Woese's classification gradually gained acceptance as "arguably the best-developed and most widely-accepted scientific hypotheses [with the five-kingdom classification] regarding the evolutionary history of life." +The three-domain concept did not, however, resolve the issues with the relationship between Archaea and eukaryotes. As Ford Doolittle, then at the Dalhousie University, put it in 2020: "[The] three-domain tree wrongly represents evolutionary relationships, presenting a misleading view about how eukaryotes evolved from prokaryotes. The three-domain tree does recognize a specific archaeal–eukaryotic affinity, but it would have the latter arising independently, not from within, the former." + +== Concept == +The two-domain system relies mainly on two key concepts that define eukaryotes as members of the domain Archaea and not as a separate domain: eukaryotes originated within Archaea, and promethearchaea represent the origin of eukaryotes. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Two-domain_system-1.md b/data/en.wikipedia.org/wiki/Two-domain_system-1.md new file mode 100644 index 000000000..d1a7a5220 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Two-domain_system-1.md @@ -0,0 +1,57 @@ +--- +title: "Two-domain system" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Two-domain_system" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:07:51.348037+00:00" +instance: "kb-cron" +--- + +=== Eukaryotes evolved from archaea === +The three-domain system presumes that eukaryotes are more closely related to archaea than to Bacteria and are sister group to Archaea, thus, it treats them as separate domain. As more new archaea were discovered in the early 2000s, this distinction became doubtful as eukaryotes became deeply nested within Archaea. The origin of eukaryotes from Archaea, meaning the two are of the same larger group, came to be supported by studies based on ribosome protein sequencing and phylogenetic analyses in 2004. Phylogenomic analysis of about 6000 gene sets from 185 bacterial, archaeal, and eukaryotic genomes in 2007 also suggested the origin of eukaryotes from Methanobacteriota (specifically the Thermoplasmatales). +In 2008, researchers from Natural History Museum, London and Newcastle University reported a comprehensive analysis of 53 genes from archaea, bacteria, and eukaryotes that included essential components of the nucleic acid replication, transcription, and translation machineries. The conclusion was that eukaryotes evolved from archaea, specifically Crenarchaeota (eocytes) and the results "favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life." A study around the same time also found several genes common to eukaryotes and Crenarchaeota. These accumulating evidences support the two-domain system. +In 2019, research led by Gergely J. Szöllősi assistant professor at ELTE has also concluded that two domains are the correct system. The studies conducted used simulations of more than 3,000 gene families. The study concluded that eukaryotes probably evolved from a bacterium entering an Promethearchaeati host (probably from the phylum Heimdallarchaeota). +One of the distinctions of the domain Eukarya in the three-domain system is that eukaryotes have unique proteins such as actin (cytoskeletal microfilament involved in cell motility), tubulin (component of the large cytoskeleton, microtubule), and the ubiquitin system (protein degradation and recycling) that are not found in prokaryotes. However, these so-called "eukaryotic signature proteins" are encoded in genomes of Thermoproteati (comprising the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) archaea, but not encoded in other archaea genomes. The first eukaryotic proteins identified in Crenarchaeota were actin and actin-related proteins (Arp) 2 and 3, perhaps explaining the origin of eukaryotes by symbiogenic phagocytosis, in which an ancient archaeal host had an actin-based mechanism by which to envelop other cells, like protomitochondrial bacteria. +Tubulin-like proteins named artubulins are found in the genomes of several ammonium-oxidising Thaumarchaeota. Homologs for a unique class of endosomal sorting complexes required for transport (ESCRT) involved in eukaryotic cell division, known as ESCRT-III, are found in all Thermoproteati groups. The ESCRT-III-like proteins constitute the primary cell division system in these archaea. Genes encoding the ubiquitin system are known from multiple genomes of Aigarchaeota. Ubiquitin-related protein called Urm1 is also present in Crenarchaeota. DNA replication system (GINS proteins) in Crenarchaeota and Halobacteria are similar to the CMG (CDC45, MCM, GINS) complex of eukaryotes. The presence of these eukaryotic proteins in Archaea indicates their direct relationship and that eukaryotes emerged from Archaea. + +=== Promethearchaea are the last eukaryotic common ancestor === +The discovery of Promethearchaeati, described as "eukaryote-like archaea", in 2012 and the following phylogenetic analyses have strengthened the two-domain view of life. Promethearchaea called Lokiarchaeota contain even more eukaryotic protein-genes than the Thermoproteati kingdom. Initial genetic analysis and later reanalysis showed that out of over 31 selected eukaryotic genes in the archaea, 75% of them directly support eukaryote-archaea grouping, meaning a single domain of Archaea including eukaryotes; although the findings did not completely rule out the three-domain system. +As more Promethearchaeati groups were subsequently discovered including Thorarchaeota, Odinarchaeota, and Heimdallarchaeota, their relationships with eukaryotes became better established. Phylogenetic analyses using ribosomal RNA genes indicated that eukaryotes stemmed from promethearchaea, and that Heimdallarchaeota are the closest relatives of eukaryotes. Eukaryotic origin from Heimdallarchaeota is also supported by phylogenomic study in 2020. A new group of Promethearchaeati found in 2021 (provisionally named Wukongarchaeota) also indicated a deep root for eukaryotic origin. A report in 2022 of another Promethearchaeati, named Njordarchaeota, indicates that Heimdallarchaeota-Wukongarchaeota branch is possibly the origin group for eukaryotes. +The promethearchaea contain at least 80 genes for eukaryotic signature proteins. In addition to actin, tubulin, ubiquitin, and ESCRT proteins found in Thermoproteati archaea, promethearchaea contain functional genes for several other eukaryotic proteins such as profilins, ubiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins), membrane-trafficking systems (such as Sec23/24 and TRAPP domains), a variety of small GTPases (including Gtr/Rag family GTPase orthologues), and gelsolins. Although this information do not completely resolve the three-domain and two-domain controversies, they are generally considered to favour the two-domain system. + +== Classification == +The two-domain system defines classification of all known cellular life forms into two domains: Bacteria and Archaea. It overrides the domain Eukaryota recognised in the three-domain classification as one of the main domains. In contrast to the eocyte hypothesis, which proposed two major groups of life (similar to domains) and posited that Archaea could be divided to both bacterial and eukaryotic groups, it merged Archaea and eukaryotes into a single domain, Bacteria entirely in a separate domain. + +=== Domain Bacteria === +It consists of all bacteria, which are prokaryotes (lacking nucleus), thus, Domain Bacteria is made up solely of prokaryotic organisms. Some examples are: + +Cyanobacteriota – photosynthesising bacteria related to the plastids of eukaryotes. +Spirochaetota – Gram-negative bacteria involved in human diseases like syphilis and lyme disease. +Actinomycetota – Gram-positive bacteria including Streptomyces species from which several antibiotics are derived including streptomycin, neomycin, bottromycins and chloramphenicol. + +=== Domain Archaea === +It comprises both prokaryotic and eukaryotic organisms. + +Archaea +Archaea are prokaryotic organisms, some examples are: + +All methanogens – which produce the gas methane. +Most halophiles – which live in very salty water. +Most thermoacidophiles – which live in acidic high-temperature water. +Eukarya +Eukaryotes have a nucleus in their cells, and include: + +Protists – many unicellular eukaryotes including malarial parasites, amoeba, and diatoms. +Kingdom Fungi – eukaryotes such as mushroom, yeast, and mould; all fungi. +Kingdom Plantae – all plants. +Kingdom Animalia – all animals. + +== See also == +Two-empire system +Three-domain system +Domain (biology) + +== Notes == + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Virtual_zoo-0.md b/data/en.wikipedia.org/wiki/Virtual_zoo-0.md new file mode 100644 index 000000000..bde6d93c2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Virtual_zoo-0.md @@ -0,0 +1,43 @@ +--- +title: "Virtual zoo" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Virtual_zoo" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T09:06:51.974926+00:00" +instance: "kb-cron" +--- + +A virtual zoo is an exploration of the zoo model of interacting with animals, but in a virtual environment such as a web page, a collection of videos, or virtual reality. +Many virtual zoos are websites that are created to simulate a visit to a zoo, and the visitors to these sites can view exhibits about animals and their habitats. Many zoos as well as schools have developed virtual zoos offering educational articles and media as exhibits. + + +== History == +The first virtual zoo was created in 1994 by Ken Boschert, DVM. Boschert created his site as a way of informing people about animals and how to care for them. His site has been recognized by Education World and "Web 100". +In 2017, Hari Kunduru founded Zoptiks, a virtual zoo offering zoologist-backed information about animals and dinosaurs, and an augmented reality interface. + +During the COVID-19 pandemic, families and children were unable to attend zoos due to nationwide lockdowns. Some groups such as Zoos Victoria offered a 24/7 livestream of animals including otters, lions and penguins. + + +== Purpose == +The validity of virtual zoos has met with some resistance. However, many view virtual zoos as the way of the future for conservation. Zoos have faced ethical issues surrounding the capture and keeping of wild animals. Virtual zoos can provide information and experience without any disturbance to habits or ecosystems. According to Zoos Victoria, the stated purpose of a zoo is to be centers for wildlife experience, education, conservation and research. Virtual Zoos can contribute to these stated purposes, such as education and research, with little impact to animal life. + + +== References == + + +== External links == +Animal Photos: + +"Lawrence Goes To The Zoo" +Educational Virtual Zoos: + +[3] +"The Electronic Zoo" +Zoobooks, Virtual Zoo +"The Virtual Zoo" +"The Wild Ones" +"Mr. Crean's Virtual Zoo" Archived 2016-05-27 at the Wayback Machine +Selling Animal Products: + +"The Big Zoo" \ No newline at end of file