butterfly/kb
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Scrape wikipedia-science: 272 new, 2584 updated, 2920 total (kb-cron)

Browse Source
This commit is contained in:
turtle89431 2026-05-05 00:17:18 -07:00
parent cfd651500a
commit ad8f97607b
101 changed files with 8115 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

BIN
_index.db
View File

Binary file not shown.

25
data/en.wikipedia.org/wiki/Actor_analysis-0.md Normal file
View File

@ -0,0 +1,25 @@
---
title: "Actor analysis"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Actor_analysis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:08.242806+00:00"
instance: "kb-cron"
---
Actor analysis can be seen as an approach to environmental management. Environmental issues are often very complex, because many parties are involved. All parties have their own interests, goals and strategies. Actor analysis provides a structured inventory of the parties and their interests to get an overview.
Instead of parties, we speak of actors which comprise both individuals and groups like organizations, administrative authorities or consumer organisations. All these actors can change an existing situation by their priorities or value systems.
There have been many changes of environmental behaviour that can be described via actor analysis. For example, all cars are now equipped with catalytic converters. Environmental organisations, governments, companies, legislators, and customers have all been actors in this process.
== See also ==
Actor–network theory
Stakeholder analysis
== References ==
== External links ==
Communication: a meeting ground for sustainable development

43
data/en.wikipedia.org/wiki/Adventive_plant-0.md Normal file
View File

@ -0,0 +1,43 @@
---
title: "Adventive plant"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Adventive_plant"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:09.478421+00:00"
instance: "kb-cron"
---
Adventive plants, also known as alien plants, foreign plants or casual plants are alien plant species appearing in a place that does not correspond to their area of origin, in contrast to the native species. These plants can arrive by natural means (such as wind or animal) or by human intervention (either intentional or accidental).
Although some alien plants become naturalized, others do not become established, thereby distinguishing them from weeds or an invasive species. Many alien plants have been introduced to aesthetically improve public recreation areas or private properties, or for agricultural purposes. The term "adventive" is derived from the Latin advena, meaning a 'stranger', 'alien' or 'immigrant'.
== Definitions ==
According to Dictionary.com, an adventive plant is "usually not yet well established". According to Collins Dictionary, adventive plants are "introduced to a new area and not yet established there".
In the broadest sense, the term "adventive plants" is used to denote exotic plant species that are alien to the native flora. Though the word has different shades of meaning, as it is also used for species that settle into new environments, and are not self-sufficient or are rarely naturalized, but need an episodic population assistance from their homeland. Less broadly, the term is used for deliberately introduced species, but at times the term only includes species that have arrived on their own or by accident. If, however, an adventive or alien species becomes self-sustaining in its new geographic area, it is then naturalized.
Some adventive species never become established or are usually not yet well established, even though many others can still establish and maintain themselves. Moreover, some adventive plants will stay at the site where they were first introduced, likely finding the conditions meager and missing the means of dispersal to convey them to areas with more approbative conditions for growth. By and large, naturalized alien plants may be viewed as weeds. Though several adventive plant species are in harmony with their adoptive environment, having appearance of their being natives, and are sometimes mistaken for native species.
== Categorization ==
Depending on the question and perspective, adventitious plants are divided into different subcategories:
=== Classification according to establishment history ===
Archaeophytes were introduced before 1492
Neophytes were introduced or immigrated after 1492.
The year 1492 is a conventionally chosen reference point. With the "discovery" of America and the Age of Discovery and colonialism, alien species from other parts of the world came to new areas on a large scale. Most of the archaeophytes immigrated with the introduction of agriculture (in the Neolithic). The status of a species as an archaeophyte is usually deduced (from the location and ecology of the species) and is hardly directly detectable.
=== Classification according to the degree of establishment ===
Agriophytes: Species that have invaded natural or near-natural vegetation and could survive there without human intervention.
Epecophytes: Species that are only naturalized in vegetation units shaped by humans, such as meadows, weed flora or ruderal vegetation, but are firmly naturalized here.
Ephemerophytes: Species that are only introduced inconsistently, that will die out of culture for a short period of time, or that would disappear again without a constant replenishment of seeds.
=== Classification according to immigration route ===
Spontaneous immigrants (sometimes referred to as "acolutophytes") immigrated on their own without direct human assistance, for example when new locations were created through culture or soil changes. Companions (sometimes also "xenophytes") were brought in through human transport. Examples would be seed companions, which were unintentionally sown due to their similarity to cultivated plant seeds, or “wool adventures”, which were dragged into the wool fleece during the transport of sheep's wool.
Feral species or cultural refugees in the narrower sense are those that were originally cultivated, but later escaped from the culture and were able to spread on their own. Such descendants of original cultural clans are subject to natural evolution as they become wild and can more or less quickly differ both from the culture form itself and from the original wild clan that preceded the culture.
== Habitat ==
Adventive plants are often found at freight stations, along railway lines and port areas as well as airports, but also on roads. Seeds of many species were accidentally imported there with the import of goods (so-called agochoria). Occasionally, seed contamination also introduces new plants that could reproduce for a short period of time (so-called speirochory). Agochory and speirochory are sub-forms of hemerochory. The seeds can also hang in wheel arches so that they can be transported and distributed along highways.
The proportion of adventive or alien species in open ruderal corridors at such locations can exceed 30% of the flora of these locations. In natural and near-natural vegetation, alien plants are much rarer. Their share here is between zero and about 5%. Introduced to the United Kingdom in 1616, the horse chestnut has become widely distributed across the country. Though an alien, its leaves attract insects which serve as a food source for populations of native birds.
Alien species have been observed to undergo rapid evolutionary change to adapt to their new environments, with changes in plant height, size, leaf shape, dispersal ability, reproductive output, vegetative reproduction ability, level of dependence on the mycorrhizal network, and level of phenotype plasticity appearing on timescales of decades to centuries.
=== Purpose ===

32
data/en.wikipedia.org/wiki/Adventive_plant-1.md Normal file
View File

@ -0,0 +1,32 @@
---
title: "Adventive plant"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Adventive_plant"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:09.478421+00:00"
instance: "kb-cron"
---
The introduced Norway maple occupies a prominent status in many of Canada's parks. The transport of ornamental plants for landscaping use has and continues to be a source of many introductions. Some of these species have escaped horticultural control and become invasive. Notable examples include water hyacinth, salt cedar, and purple loosestrife.
Peaches originated in China, and have been carried to much of the populated world. Tomatoes are native to the Andes. Squash (pumpkins), maize (corn), and tobacco are native to the Americas, but were introduced to the Old World. Many alien species require continued human intervention to survive in the new environment. Others may become feral, but do not seriously compete with natives, but simply increase the biodiversity of the area. One example would be dandelions in North America, which have become an essential source of early season nectar for both native and introduced pollinators, and do not meaningfully compete with native grasses or flowers.
Many alien plants have been introduced into new territories, initially as either ornamental plants or for erosion control, stock feed, or forestry. Whether an exotic will become an invasive species is seldom understood in the beginning, and many non-native ornamentals languish in the trade for years before suddenly naturalizing and becoming invasive. Studies have shown that introduced species display a greater likeliness of naturalizing when there is an appropriate environmental match, the plant species are short lived herbs or cultivate from seeds.
=== Environmental problems ===
Intentional alien introductions have also been undertaken with the aim of ameliorating environmental problems. A number of fast spreading, alien plants such as kudzu have been introduced as a means of erosion control. Other species have been introduced as biological control agents to control invasive species. This involves the purposeful introduction of a natural enemy of the target species with the intention of reducing its numbers or controlling its spread. Another troublesome alien species is the Phyla canescens, which was intentionally introduced into many countries in North America, Europe, and Africa as an ornamental plant.
A form of unintentional alien introduction is when an intentionally introduced plant carries a parasite or herbivore with it. Some become invasive, for example, the oleander aphid, accidentally introduced with the ornamental plant, oleander.
== See also ==
Introduced species
Invasive species
Hemerochory
Native species
Neophyte
Colonisation
Naturalisation
Escaped plant
== References ==
== Further reading ==
FG Schroeder: On the classification of the anthropochores. In: Vegetatio. 16, pp. 225-238 (1969).

48
data/en.wikipedia.org/wiki/Afghanistanism-0.md Normal file
View File

@ -0,0 +1,48 @@
---
title: "Afghanistanism"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Afghanistanism"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:10.749620+00:00"
instance: "kb-cron"
---
Afghanistanism is a term, first recorded in the United States, for the practice of concentrating on problems in distant parts of the world while ignoring controversial local issues. In other contexts, the term has referred to "hopelessly arcane and irrelevant scholarship",
"fascination with exotic, faraway lands", or "Railing and shaking your fist at an unseen foe who is quite unaware of your existence, much less your fury".
== Origin ==
The Oxford English Dictionary lists Afghanistanism as a U.S. colloquialism; the first written citation it provides is from 1948: J. Lloyd Jones in Probl. Journalism (American Society of Newspaper Editors Convention) 73, "I don't wish to belabor this subject of Afghanistanism, this business of taking forthright stands on elections in Costa Rica, while the uncollected local garbage reeks beneath the editor's window."
Robert H. Stopher and James S. Jackson, writing in their April 1948 column "Behind the Front Page", said the "new term" was coined by Jenkin Lloyd Jones of Oklahoma's Tulsa Tribune at that same convention, in Washington, D.C. They quoted Jones as saying:
The tragic fact is that many an editorial writer can't hit a short-range target. He's hell on distance. He can pontificate about the situation in Afghanistan with perfect safety. It takes more guts to dig up the dirt on the sheriff.
But columnist Joe Klein wrote in Time magazine in 2010 that the term originated in the 19th century when "the British press defined Afghanistanism as the obsession with obscure foreign wars at the expense of domestic priorities", adding that "Afghanistanism seems likely to become a national debate [in the United States] before long: "Is building roads and police stations in Afghanistan more important than doing so at home?"
== Applications ==
The concept earlier came to have several applications. On one hand it was applied in North American journalism to newspaper articles about faraway places that were irrelevant to local readers. Other writers said, though, that Afghanistanism was the tendency of some editors to avoid hard local news by writing opinion pieces about events happening in distant lands. As New York Times writer James Reston put it about journalists, "Like officials in Washington, we suffer from Afghanistanism. If it's far away, it's news, but if it's close to home, it's sociology."
Earlier, educator Robert M. Hutchins used the expression in a speech at the California Institute of Technology in 1955:
Afghanistanism, as you know, is the practice of referring always to some remote country, place, person or problem when there is something that ought to be taken care of near at home that is very acute. So you say to a professor at Caltech, "What about smog?" and he says, "Have you heard about the crisis in Afghanistan?"
In 1973, the concept was adapted to reporting on environmentalism, which was said by journalism researchers Steven E. Hungerford and James B. Lemert to deal with environmental problems of distant communities rather than local ones. This observation was echoed in 2004 by B.A. Taleb, who called it "displacing the [environmental] problems and issues to other places and ignoring their existence in one's own community or country".
== Resurfacing ==
After the attacks on the World Trade Center in New York City on September 11, 2001, the concept resurfaced, with some writers asserting that it was no longer applicable to contemporary events. For example, Stuart H. Loory, chair in Free-Press Studies at the University of Missouri School of Journalism, wrote on December 1, 2001:
A primary mission of the news business is to work as a distant early warning signal of impending problems for the public and those who can deal with those problems. It must work in a convincing way, and that means news organizations must train and educate journalists to work in various parts of the world knowledgably. They cannot fit the image now in vogue — that of parachutists jumping into an area to cover disaster on short notice. That perpetuates "Afghanistanism," a concept that has long since outlived its usefulness, if it ever had any at all.
== See also ==
American exceptionalism
Media bias
Psychological projection
Somebody else's problem
Whataboutism, a more general deflection in American political discourse
== References and notes ==
== Further reading ==

155
data/en.wikipedia.org/wiki/Astroecology-0.md Normal file
View File

@ -0,0 +1,155 @@
---
title: "Astroecology"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Astroecology"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:12.052454+00:00"
instance: "kb-cron"
---
Astroecology concerns the interactions of biota with space environments. It studies resources for life on planets, asteroids and comets, around various stars, in galaxies, and in the universe. The results allow estimating the future prospects for life, from planetary to galactic and cosmological scales.
Available energy, and microgravity, radiation, pressure and temperature are physical factors that affect astroecology. The ways by which life can reach space environments, including natural panspermia and directed panspermia are also considered. Further, for human expansion in space and directed panspermia, motivation by life-centered biotic ethics, panbiotic ethics and planetary bioethics are also relevant.
== Overview ==
The term "astroecology" was first applied in the context of performing studies in actual meteorites to evaluate their potential resources favorable to sustaining life. Early results showed that meteorite/asteroid materials can support microorganisms, algae and plant cultures under Earth's atmosphere and supplemented with water.
Several observations suggest that diverse planetary materials, similar to meteorites collected on Earth, could be used as agricultural soils, as they provide nutrients to support microscopic life when supplemented with water and an atmosphere. Experimental astroecology has been proposed to rate planetary materials as targets for astrobiology exploration and as potential biological in-situ resources. The biological fertilities of planetary materials can be assessed by measuring water-extractable electrolyte nutrients. The results suggest that carbonaceous asteroids and Martian basalts can serve as potential future resources for substantial biological populations in the Solar System.
Analysis of the essential nutrients (C, N, P, K) in meteorites yielded information for calculating the amount of biomass that can be constructed from asteroid resources. For example, carbonaceous asteroids are estimated to contain about 1022 kg potential resource materials, and laboratory results suggest that they could yield a biomass on the order of 6·1020 kg, about 100,000 times more than biological matter presently on Earth.
== Cultures on simulated asteroid/meteorite materials ==
To quantify the potential amounts of life in biospheres, theoretical astroecology attempts to estimate the amount of biomass over the duration of a biosphere. The resources, and the potential time-integrated biomass were estimated for planetary systems, for habitable zones around stars, and for the galaxy and the universe. Such astroecology calculations suggest that the limiting elements nitrogen and phosphorus in the estimated 1022 kg carbonaceous asteroids could support 6·1020 kg biomass for the expected five billion future years of the Sun, yielding a future time-integrated BIOTA (BIOTA, Biomass Integrated Over Times Available, measured in kilogram-years) of 3·1030 kg-years in the Solar System, a hundred thousand times more than life on Earth to date. Considering biological requirements of 100 W kg−1 biomass, radiated energy about red giant stars and white and red dwarf stars could support a time-integrated BIOTA up to 1046 kg-years in the galaxy and 1057 kg-years in the universe.
Such astroecology considerations quantify the immense potentials of future life in space, with commensurate biodiversity and possibly, intelligence. Chemical analysis of carbonaceous chondrite meteorites show that they contain extractable bioavailable water, organic carbon, and essential phosphate, nitrate and potassium nutrients. The results allow assessing the soil fertilities of the parent asteroids and planets, and the amounts of biomass that they can sustain.
Laboratory experiments showed that material from the Murchison meteorite, when ground into a fine powder and combined with Earth's water and air, can provide the nutrients to support a variety of organisms including bacteria (Nocardia asteroides), algae, and plant cultures such as potato and asparagus. The microorganisms used organics in the carbonaceous meteorites as the carbon source. Algae and plant cultures grew well also on Mars meteorites because of their high bio-available phosphate contents. The Martian materials achieved soil fertility ratings comparable to productive agricultural soils. This offers some data relating to terraforming of Mars.
Terrestrial analogues of planetary materials are also used in such experiments for comparison, and to test the effects of space conditions on microorganisms.
The biomass that can be constructed from resources can be calculated by comparing the concentration of elements in the resource materials and in biomass (Equation 1). A given mass of resource materials (mresource) can support mbiomass, X of biomass containing element X (considering X as the limiting nutrient), where cresource, X is the concentration (mass per unit mass) of element X in the resource material and cbiomass, X is its concentration in the biomass.
m
b
i
o
m
a
s
s
,
X
=
m
r
e
s
o
u
r
c
e
,
X
c
r
e
s
o
u
r
c
e
,
X
c
b
i
o
m
a
s
s
,
X
{\displaystyle m_{biomass,\,X}=m_{resource,\,X}{\frac {c_{resource,\,X}}{c_{biomass,\,X}}}}
(1)
Assuming that 100,000 kg biomass supports one human, the asteroids may then sustain about 6e15 (six million billion) people, equal to a million Earths (a million times the present population). Similar materials in the comets could support biomass and populations about one hundred times larger. Solar energy can sustain these populations for the predicted further five billion years of the Sun. These considerations yield a maximum time-integrated BIOTA of 3e30 kg-years in the Solar System. After the Sun becomes a white dwarf star, and other white dwarf stars, can provide energy for life much longer, for trillions of eons. (Table 2)
== Effects of wastage ==
Astroecology also concerns wastage, such as the leakage of biological matter into space. This will cause an exponential decay of space-based biomass as given by Equation (2), where M (biomass 0) is the mass of the original biomass, k is its rate of decay (the fraction lost in a unit time) and biomass t is the remaining biomass after time t.
Equation 2:
M
b
i
o
m
a
s
s
(
t
)
=
M
b
i
o
m
a
s
s
(
0
)
e
−
k
t
{\displaystyle M_{biomass}(t)=M_{biomass}(0)e^{-kt}\,}
Integration from time zero to infinity yields Equation (3) for the total time-integrated biomass (BIOTA) contributed by this biomass:

94
data/en.wikipedia.org/wiki/Astroecology-1.md Normal file
View File

@ -0,0 +1,94 @@
---
title: "Astroecology"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Astroecology"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:12.052454+00:00"
instance: "kb-cron"
---
Equation 3:
B
I
O
T
A
=
M
b
i
o
m
a
s
s
(
0
)
k
{\displaystyle BIOTA={\frac {M_{biomass}(0)}{k}}}
For example, if 0.01% of the biomass is lost per year, then the time-integrated BIOTA will be 10,000
M
b
i
o
m
a
s
s
(
0
)
{\displaystyle M_{biomass}(0)}
. For the 6·1020 kg biomass constructed from asteroid resources, this yields 6·1024 kg-years of BIOTA in the Solar System. Even with this small rate of loss, life in the Solar System would disappear in a few hundred thousand years, and the potential total time-integrated BIOTA of 3·1030 kg-years under the main-sequence Sun would decrease by a factor of 5·105, although a still substantial population of 1.2·1012 biomass-supported humans could exist through the habitable lifespan of the Sun.
The integrated biomass can be maximized by minimizing its rate of dissipation. If this rate can be reduced sufficiently, all the constructed biomass can last for the duration of the habitat and it pays to construct the biomass as fast as possible. However, if the rate of dissipation is significant, the construction rate of the biomass and its steady-state amounts may be reduced allowing a steady-state biomass and population that lasts throughout the lifetime of the habitat.
An issue that arises is whether we should build immense amounts of life that decays fast, or smaller, but still large, populations that last longer. Life-centered biotic ethics suggests that life should last as long as possible.
== Galactic ecology ==
If life reaches galactic proportions, technology should be able to access all of the materials resources, and sustainable life will be defined by the available energy. The maximum amount of biomass about any star is then determined by the energy requirements of the biomass and by the luminosity of the star. For example, if 1 kg biomass needs 100 Watts, we can calculate the steady-state amounts of biomass that can be sustained by stars with various energy outputs. These amounts are multiplied by the life-time of the star to calculate the time-integrated BIOTA over the life-time of the star. Using similar projections, the potential amounts of future life can then be quantified.
For the Solar System from its origins to the present, the current 1015 kg biomass over the past four billion years gives a time-integrated biomass (BIOTA) of 4·1024 kg-years. In comparison, carbon, nitrogen, phosphorus and water in the 1022 kg asteroids allows 6·1020 kg biomass that can be sustained with energy for the 5 billion future years of the Sun, giving a BIOTA of 3·1030 kg-years in the Solar System and 3·1039 kg-years about 1011 stars in the galaxy. Materials in comets could give biomass and time-integrated BIOTA a hundred times larger.
The Sun will then become a white dwarf star, radiating 1015 Watts that sustains 1e13 kg biomass for an immense hundred million trillion (1020) years, contributing a time-integrated BIOTA of 1033 years. The 1012 white dwarfs that may exist in the galaxy during this time can then contribute a time-integrated BIOTA of 1045 kg-years. Red dwarf stars with luminosities of 1023 Watts and life-times of 1013 years can contribute 1034 kg-years each, and 1012 red dwarfs can contribute 1046 kg-years, while brown dwarfs can contribute 1039 kg-years of time-integrated biomass (BIOTA) in the galaxy. In total, the energy output of stars during 1020 years can sustain a time-integrated biomass of about 1045 kg-years in the galaxy. This is one billion trillion (1020) times more life than has existed on the Earth to date. In the universe, stars in 1011 galaxies could then sustain 1057 kg-years of life.
== Directed panspermia ==
The astroecology results above suggest that humans can expand life in the galaxy through space travel or directed panspermia. The amounts of possible life that can be established in the galaxy, as projected by astroecology, are immense. These projections are based on information about 15 billion past years since the Big Bang, but the habitable future is much longer, spanning trillions of eons. Therefore, physics, astroeclogy resources, and some cosmological scenarios may allow organized life to last, albeit at an ever slowing rate, indefinitely. These prospects may be addressed by the long-term extension of astroecology as cosmoecology.
== See also ==
Cosmology
Meteorites
== References ==
== External links ==
Astro-Ecology / Science of expanding life in space
AstroEthics / Ethics of expanding life in space
Panspermia-Society / Science and ethics of expanding life in space

29
data/en.wikipedia.org/wiki/Biogeography-0.md Normal file
View File

@ -0,0 +1,29 @@
---
title: "Biogeography"
chunk: 1/4
source: "https://en.wikipedia.org/wiki/Biogeography"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:13.296244+00:00"
instance: "kb-cron"
---
Biogeography is the study of the distribution of species and ecosystems in geographic space and through geological time. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, isolation and habitat area. Phytogeography is the branch of biogeography that studies the distribution of plants, Zoogeography is the branch that studies distribution of animals, while Mycogeography is the branch that studies distribution of fungi, such as mushrooms.
Knowledge of spatial variation in the numbers and types of organisms is as vital to us today as it was to our early human ancestors, as we adapt to heterogeneous but geographically predictable environments. Biogeography is an integrative field of inquiry that unites concepts and information from ecology, evolutionary biology, taxonomy, geology, physical geography, palaeontology, and climatology.
Modern biogeographic research combines information and ideas from many fields, from the physiological and ecological constraints on organismal dispersal to geological and climatological phenomena operating at global spatial scales and evolutionary time frames.
The short-term interactions within a habitat and species of organisms describe the ecological application of biogeography. Historical biogeography describes the long-term, evolutionary periods of time for broader classifications of organisms. Early scientists, beginning with Carl Linnaeus, contributed to the development of biogeography as a science.
The scientific theory of biogeography grows out of the work of Alexander von Humboldt (1769–1859), Francisco Jose de Caldas (1768–1816), Hewett Cottrell Watson (1804–1881), Alphonse de Candolle (1806–1893), Alfred Russel Wallace (1823–1913), Philip Lutley Sclater (1829–1913) and other biologists and explorers.
== Introduction ==
The patterns of species distribution across geographical areas can usually be explained through a combination of historical factors such as: speciation, extinction, continental drift, and glaciation. Through observing the geographic distribution of species, we can see associated variations in sea level, river routes, habitat, and river capture. Additionally, this science considers the geographic constraints of landmass areas and isolation, as well as the available ecosystem energy supplies.
Over periods of ecological changes, biogeography includes the study of plant and animal species in: their past and/or present living refugium habitat; their interim living sites; and/or their survival locales. As David Quammen put it, "...biogeography does more than ask Which species? and Where. It also asks Why? and, what is sometimes more crucial, Why not?."
Modern biogeography often employs the use of Geographic Information Systems (GIS), to understand the factors affecting organism distribution, and to predict future trends in organism distribution.
Often mathematical models and GIS are employed to solve ecological problems that have a spatial aspect to them.
Biogeography is most keenly observed on the world's islands. These habitats are often much more manageable areas of study because they are more condensed than larger ecosystems on the mainland. Islands are also ideal locations because they allow scientists to look at habitats that new invasive species have only recently colonized and can observe how they disperse throughout the island and change it. They can then apply their understanding to similar but more complex mainland habitats. Islands are very diverse in their biomes, ranging from the tropical to arctic climates. This diversity in habitat allows for a wide range of species study in different parts of the world.
Charles Darwin recognized the importance of these geographic locations, and remarked in his journal that "the Zoology of Archipelagoes will be well worth examination". Two chapters in On the Origin of Species were devoted to geographical distribution.
== History ==
=== 18th century ===
The first discoveries that contributed to the development of biogeography as a science began in the mid-18th century, as Europeans explored the world and described the biodiversity of life. During the 18th century most views on the world were shaped around religion and for many natural theologists, the bible. Carl Linnaeus, in the mid-18th century, improved our classifications of organisms through the exploration of undiscovered territories by his students and disciples. When he noticed that species were not as perpetual as he believed, he developed the Mountain Explanation to explain the distribution of biodiversity; when Noah's ark landed on Mount Ararat and the waters receded, the animals dispersed throughout different elevations on the mountain. This showed that different species in different climates proved the fact that species are not constant. Linnaeus' findings set a basis for ecological biogeography. Through his strong beliefs in Christianity, he was inspired to classify the living world, which then gave way to additional accounts of secular views on geographical distribution. He argued that the structure of an animal was very closely related to its physical surroundings.
Closely after Linnaeus, Georges-Louis Leclerc, Comte de Buffon observed shifts in climate and how species spread across the globe as a result. Buffon believed there was a single species creation event, and he was the first to theorize different groups of organisms coming from different regions of the world. Buffon saw similarities between some regions which led him to believe that at one point continents were connected and then water separated them and caused differences in species. His hypotheses were described in his work, the 36 volume Histoire Naturelle, générale et particulière, in which he argued that varying geographical regions would have different forms of life, inspired by his observations comparing the Old and New World. He noted that similar environments in different regions of the world held separate and distinct species, a concept later known as Buffon's Law, which eventually became a major principle of biogeography. Buffon also studied fossils which led him to believe that the Earth was over tens of thousands of years old, and that humans had not lived there long in comparison to the age of the Earth.

21
data/en.wikipedia.org/wiki/Biogeography-1.md Normal file
View File

@ -0,0 +1,21 @@
---
title: "Biogeography"
chunk: 2/4
source: "https://en.wikipedia.org/wiki/Biogeography"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:13.296244+00:00"
instance: "kb-cron"
---
=== 19th century ===
Following the period of exploration came the Age of Enlightenment in Europe, which attempted to explain the patterns of biodiversity observed by Buffon and Linnaeus. At the birth of the 19th century, Alexander von Humboldt, known as the "founder of plant geography", developed the concept of "physique generale" to demonstrate the unity of science and how species fit together. As one of the first to contribute empirical data to the science of biogeography through his travel as an explorer, he observed differences in climate and vegetation. The Earth was divided into regions which he defined as tropical, temperate, and arctic and within these regions there were similar forms of vegetation. This ultimately enabled him to create the isotherm (temperature lines on a map), which allowed scientists to see patterns of life within different climates. He contributed his observations to findings of botanical geography by previous scientists, and sketched this description of both the biotic and abiotic features of the Earth in his book, Cosmos.
Augustin de Candolle contributed to the field of biogeography as he observed species competition and the several differences that influenced the discovery of the diversity of life. He was a Swiss botanist and created the first Laws of Botanical Nomenclature in his work, Prodromus. He discussed plant distribution and his theories eventually had a great impact on Charles Darwin, who was inspired to consider species adaptations and evolution after learning about botanical geography. De Candolle was the first to describe the differences between the small-scale and large-scale distribution patterns of organisms around the globe.
Several additional scientists contributed new theories to further develop the concept of biogeography. Charles Lyell developed the Theory of Uniformitarianism after studying fossils. This theory explained how the world was not created by one sole catastrophic event, but instead from numerous creation events and locations. Uniformitarianism also introduced the idea that the Earth was actually significantly older than was previously accepted. Using this knowledge, Lyell concluded that it was possible for species to go extinct. Since he noted that Earth's climate changes, he realized that species distribution must also change accordingly. Lyell argued that climate changes complemented vegetation changes, thus connecting the environmental surroundings to varying species. This largely influenced Charles Darwin in his development of the theory of evolution.
Charles Darwin was a natural theologist who studied around the world, and most importantly in the Galapagos Islands. Darwin introduced the idea of natural selection, as he theorized against previously accepted ideas that species were static or unchanging. His contributions to biogeography and the theory of evolution were different from those of other explorers of his time, because he developed a mechanism to describe the ways that species changed. His influential ideas include the development of theories regarding the struggle for existence and natural selection. Darwin's theories started a biological segment to biogeography and empirical studies, which enabled future scientists to develop ideas about the geographical distribution of organisms around the globe.
Alfred Russel Wallace studied the distribution of flora and fauna in the Amazon Basin and the Malay Archipelago in the mid-19th century. His research was essential to the further development of biogeography, and he was later nicknamed the "father of Biogeography". Wallace conducted fieldwork researching the habits, breeding and migration tendencies, and feeding behavior of thousands of species. He studied butterfly and bird distributions in comparison to the presence or absence of geographical barriers. His observations led him to conclude that the number of organisms present in a community was dependent on the amount of food resources in the particular habitat. Wallace believed species were dynamic by responding to biotic and abiotic factors. He and Philip Sclater saw biogeography as a source of support for the theory of evolution as they used Darwin's conclusion to explain how biogeography was similar to a record of species inheritance. Key findings, such as the sharp difference in fauna either side of the Wallace Line, and the sharp difference that existed between North and South America prior to their relatively recent faunal interchange, can only be understood in this light. Otherwise, the field of biogeography would be seen as a purely descriptive one.
=== 20th and 21st century ===
Moving on to the 20th century, Alfred Wegener introduced the Theory of Continental Drift in 1912, though it was not widely accepted until the 1960s. This theory was revolutionary because it changed the way that everyone thought about species and their distribution around the globe. The theory explained how continents were formerly joined in one large landmass, Pangea, and slowly drifted apart due to the movement of the plates below Earth's surface. The evidence for this theory is in the geological similarities between varying locations around the globe, the geographic distribution of some fossils (including the mesosaurs) on various continents, and the jigsaw puzzle shape of the landmasses on Earth. Though Wegener did not know the mechanism of this concept of Continental Drift, this contribution to the study of biogeography was significant in the way that it shed light on the importance of environmental and geographic similarities or differences as a result of climate and other pressures on the planet. Importantly, late in his career Wegener recognised that testing his theory required measurement of continental movement rather than inference from fossils species distributions.
In 1958 paleontologist Paul S. Martin published A Biogeography of Reptiles and Amphibians in the Gómez Farias Region, Tamaulipas, Mexico, which has been described as "ground-breaking" and "a classic treatise in historical biogeography". Martin applied several disciplines including ecology, botany, climatology, geology, and Pleistocene dispersal routes to examine the herpetofauna of a relatively small and largely undisturbed area, but ecologically complex, situated on the threshold of temperate – tropical (nearctic and neotropical) regions, including semiarid lowlands at 70 meters elevation and the northernmost cloud forest in the western hemisphere at over 2200 meters.

22
data/en.wikipedia.org/wiki/Biogeography-2.md Normal file
View File

@ -0,0 +1,22 @@
---
title: "Biogeography"
chunk: 3/4
source: "https://en.wikipedia.org/wiki/Biogeography"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:13.296244+00:00"
instance: "kb-cron"
---
The publication of The Theory of Island Biogeography by Robert MacArthur and E.O. Wilson in 1967 showed that the species richness of an area could be predicted in terms of such factors as habitat area, immigration rate and extinction rate. This added to the long-standing interest in island biogeography. The application of island biogeography theory to habitat fragments spurred the development of the fields of conservation biology and landscape ecology.
Classic biogeography has been expanded by the development of molecular systematics, creating a new discipline known as phylogeography. This development allowed scientists to test theories about the origin and dispersal of populations, such as island endemics. For example, while classic biogeographers were able to speculate about the origins of species in the Hawaiian Islands, phylogeography allows them to test theories of relatedness between these populations and putative source populations on various continents, notably in Asia and North America.
Biogeography continues as a point of study for many life sciences and geography students worldwide, however it may be under different broader titles within institutions such as ecology or evolutionary biology.
In recent years, one of the most important and consequential developments in biogeography has been to show how multiple organisms, including mammals like monkeys and reptiles like squamates, overcame barriers such as large oceans that many biogeographers formerly believed were impossible to cross. See also Oceanic dispersal.
== Modern applications ==
Biogeography now incorporates many different fields including, but not limited to, physical geography, geology, plant biology, zoology, general biology, and modelling. A biogeographer's main focus is on how the environment and humans affect the distribution of species and genetic diversity. Biogeography is being applied to biodiversity conservation and planning, projecting global environmental changes on species and biomes, projecting the spread of infectious diseases, invasive species, and for supporting planning for the establishment of crops. Technological evolution and advances in knowledge have generated a suite of predictor variables for biogeographic analysis, including global satellite imaging and image processing of the Earth. Two main types of satellite imaging that are important within modern biogeography are Global Production Efficiency Model (GLO-PEM) and Geographic Information Systems (GIS). GLO-PEM uses satellite-imaging gives "repetitive, spatially contiguous, and time specific observations of vegetation". These observations are on a global scale. GIS can show certain processes on the earth's surface like whale locations, sea surface temperatures, and bathymetry. Current scientists also use coral reefs to delve into the history of biogeography through the fossilized reefs.
Two global information systems are either dedicated to, or have strong focus on, biogeography (in the form of the spatial location of observations of organisms), namely the Global Biodiversity Information Facility (GBIF: 2.57 billion species occurrence records reported as at August 2023) and, for marine species only, the Ocean Biodiversity Information System (OBIS, originally the Ocean Biogeographic Information System: 116 million species occurrence records reported as at August 2023), while at a national scale, similar compilations of species occurrence records also exist such as the U.K. National Biodiversity Network, the Atlas of Living Australia, and many others. In the case of the oceans, in 2017 Costello et al. analyzed the distribution of 65,000 species of marine animals and plants as then documented in OBIS, and used the results to distinguish 30 distinct marine realms, split between continental-shelf and offshore deep-sea areas.
Since it is self evident that compilations of species occurrence records cannot cover with any completeness, areas that have received either limited or no sampling, a number of methods have been developed to produce arguably more complete "predictive" or "modelled" distributions for species based on their associated environmental or other preferences (such as availability of food or other habitat requirements); this approach is known as either Environmental niche modelling (ENM) or Species distribution modelling (SDM). Depending on the reliability of the source data and the nature of the models employed (including the scales for which data are available), maps generated from such models may then provide better representations of the "real" biogeographic distributions of either individual species, groups of species, or biodiversity as a whole, however it should also be borne in mind that historic or recent human activities (such as hunting of great whales, or other human-induced exterminations) may have altered present-day species distributions from their potential "full" ecological footprint. Examples of predictive maps produced by niche modelling methods based on either GBIF (terrestrial) or OBIS (marine, plus some freshwater) data are the former Lifemapper project at the University of Kansas (now continued as a part of BiotaPhy) and AquaMaps, which as at 2023 contain modelled distributions for around 200,000 terrestrial, and 33,000 species of teleosts, marine mammals, and invertebrates. One advantage of ENM/SDM is that in addition to showing current (or even past) modelled distributions, insertion of changed parameters such as the anticipated effects of climate change can also be used to show potential changes in species distributions that may occur in the future based on such scenarios.
== Paleobiogeography ==

67
data/en.wikipedia.org/wiki/Biogeography-3.md Normal file
View File

@ -0,0 +1,67 @@
---
title: "Biogeography"
chunk: 4/4
source: "https://en.wikipedia.org/wiki/Biogeography"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:13.296244+00:00"
instance: "kb-cron"
---
Paleobiogeography goes one step further to include paleogeographic data and considerations of plate tectonics. Using molecular analyses and corroborated by fossils, it has been possible to demonstrate that perching birds evolved first in the region of Australia or the adjacent Antarctic (which at that time lay somewhat further north and had a temperate climate). From there, they spread to the other Gondwanan continents and Southeast Asia – the part of Laurasia then closest to their origin of dispersal – in the late Paleogene, before achieving a global distribution in the early Neogene. Not knowing that at the time of dispersal, the Indian Ocean was much narrower than it is today, and that South America was closer to the Antarctic, one would be hard pressed to explain the presence of many "ancient" lineages of perching birds in Africa, as well as the mainly South American distribution of the suboscines.
Paleobiogeography also helps constrain hypotheses on the timing of biogeographic events such as vicariance and geodispersal, and provides unique information on the formation of regional biotas. For example, data from species-level phylogenetic and biogeographic studies tell us that the Amazonian teleost fauna accumulated in increments over a period of tens of millions of years, principally by means of allopatric speciation, and in an arena extending over most of the area of tropical South America. In other words, unlike some of the well-known insular faunas (Galapagos finches, Hawaiian drosophilid flies, African rift lake cichlids), the species-rich Amazonian ichthyofauna is not the result of recent adaptive radiations.
For freshwater organisms, landscapes are divided naturally into discrete drainage basins by watersheds, episodically isolated and reunited by erosional processes. In regions like the Amazon Basin (or more generally Greater Amazonia, the Amazon basin, Orinoco basin, and Guianas) with an exceptionally low (flat) topographic relief, the many waterways have had a highly reticulated history over geological time. In such a context, stream capture is an important factor affecting the evolution and distribution of freshwater organisms. Stream capture occurs when an upstream portion of one river drainage is diverted to the downstream portion of an adjacent basin. This can happen as a result of tectonic uplift (or subsidence), natural damming created by a landslide, or headward or lateral erosion of the watershed between adjacent basins.
== Concepts and fields ==
Biogeography is a synthetic science, related to geography, biology, soil science, geology, climatology, ecology and evolution.
Some fundamental concepts in biogeography include:
allopatric speciation – the splitting of a species by evolution of geographically isolated populations
evolution – change in genetic composition of a population
extinction – disappearance of a species
dispersal – movement of populations away from their point of origin, related to migration
endemic areas
geodispersal – the erosion of barriers to biotic dispersal and gene flow, that permit range expansion and the merging of previously isolated biotas
range and distribution
vicariance – the formation of barriers to biotic dispersal and gene flow, that tend to subdivide species and biotas, leading to speciation and extinction; vicariance biogeography is the field that studies these patterns
=== Comparative biogeography ===
The study of comparative biogeography can follow two main lines of investigation:
Systematic biogeography, the study of biotic area relationships, their distribution, and hierarchical classification
Evolutionary biogeography, the proposal of evolutionary mechanisms responsible for organismal distributions. Possible mechanisms include widespread taxa disrupted by continental break-up or individual episodes of long-distance movement.
== Biogeographic units ==
There are many types of biogeographic units used in biogeographic regionalisation schemes, as there are many criteria (species composition, physiognomy, ecological aspects) and hierarchization schemes: biogeographic realms (ecozones), bioregions (sensu stricto), ecoregions, zoogeographical regions, floristic regions, vegetation types, biomes, etc.
The terms biogeographic unit or biogeographic area can be used for these regions, regardless of where they fall in any hierarchy.
In 2008, an International Code of Area Nomenclature was proposed for biogeography. It achieved limited success; some studies commented favorably on it, but others were much more critical, and it "has not yet gained a significant following". Similarly, a set of rules for paleobiogeography has achieved limited success. In 2000, Westermann suggested that the difficulties in getting formal nomenclatural rules established in this field might be related to "the curious fact that neither paleo- nor neobiogeographers are organized in any formal groupings or societies, nationally (so far as I know) or internationally — an exception among active disciplines."
== See also ==
== Notes and references ==
== Further reading ==
Albert, J.S.; Crampton, W.G.R. (2010). "The geography and ecology of diversification in Neotropical freshwaters". Nature Education. 1 (10): 3.
Cox, CB (2001). "The biogeographic regions reconsidered" (PDF). Journal of Biogeography. 28 (4): 511–523. Bibcode:2001JBiog..28..511B. doi:10.1046/j.1365-2699.2001.00566.x. Archived from the original (PDF) on 4 March 2016.
Ebach, MC (2015). Origins of biogeography. The role of biological classification in early plant and animal geography. Dordrecht: Springer. ISBN 978-94-017-9999-7.
Lieberman, BS (2001). Paleobiogeography: using fossils to study global change, plate tectonics, and evolution. Kluwer Academic, Plenum Publishing. ISBN 978-0-306-46277-1.
Lomolino, MV; Brown, JH (2004). Foundations of biogeography: classic papers with commentaries. University of Chicago Press. ISBN 978-0-226-49236-0.
MacArthur, Robert H. (1972). Geographic Ecology. New York: Harper & Row.
McCarthy, Dennis (2009). Here be dragons: how the study of animal and plant distributions revolutionized our views of life and Earth. Oxford & New York: Oxford University Press. ISBN 978-0-19-954246-8.
Millington, A; Blumler, M; Schickhoff, eds. (2011). The SAGE handbook of biogeography. London: Sage. ISBN 978-1-4462-5445-5.
Nelson, GJ (1978). "From Candolle to Croizat: Comments on the history of biogeography" (PDF). Journal of the History of Biology. 11 (2): 269–305. doi:10.1007/BF00389302. PMID 11610435.
Udvardy, MDF (1975). "A classification of the biogeographical provinces of the world" (PDF). IUCN Occasional Paper (18). Morges, Switzerland: IUCN. Archived from the original (PDF) on 11 August 2011.
== External links ==
The International Biogeography Society
Systematic & Evolutionary Biogeographical Society (archived 5 December 2008)
Early Classics in Biogeography, Distribution, and Diversity Studies: To 1950
Early Classics in Biogeography, Distribution, and Diversity Studies: 1951–1975
Some Biogeographers, Evolutionists and Ecologists: Chrono-Biographical Sketches
Major journals
Journal of Biogeography homepage (archived 15 December 2004)
Global Ecology and Biogeography homepage. Archived 2012-07-28 at the Wayback Machine.
Ecography homepage.

41
data/en.wikipedia.org/wiki/Biological_pollution-0.md Normal file
View File

@ -0,0 +1,41 @@
---
title: "Biological pollution"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Biological_pollution"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:14.514866+00:00"
instance: "kb-cron"
---
Biological pollution (impacts or bio pollution) is the impact of humanity's actions on the quality of aquatic and terrestrial environment. Specifically, biological pollution is the introduction of non-indigenous and invasive species, otherwise known as Invasive Alien Species (IAS). When the biological pollution is introduced to an aquatic environment, it contributes to water pollution.
Biopollution may cause adverse effects at several levels of biological organization:
an individual organism (internal pollution by parasites or pathogens),
a population (by genetic change, i.e. hybridization of IAS with a native species),
a community or biocoenosis (by structural shifts, i.e. dominance of IAS, replacement or elimination of native species),
a habitat (by modification of physical-chemical conditions),
an ecosystem (by alteration of energy and organic material flow).
Biopollution may also cause decline in naturalness of nature conservation areas, adverse economic consequences and impacts on human health. The notion of "biological pollution" and "biological pollutants" described by Elliott (2000) is generally accepted in invasion biology; it was used to develop the concept of biopollution level assessment (Olenin et al., 2007) and criteria for a Good Ecological Status descriptor in the European Marine Strategy Framework Directive (Olenin et al., 2010)
The magnitude of the bioinvasion impact or biopollution level (Olenin et al., 2007) may be quantified using a free online service BINPAS.
In 1991 The Indiana Academy of Science held a national cross disciplinary conference in Indianapolis (McKnight 1993), the first of its find dealing with the issue.
== Biopollution level ==
"Biopollution Level (BPL)" is a quantitative measure of the magnitude of the biological invasion impact, ranging from "no impact" (BPL=0) through "weak" (BPL=1), "moderate" (BPL=2), "strong" (BPL=3) and "massive" (BPL=4) impact.
Initially the method of calculation involves assessing the abundance and distribution range of a non-indigenous species (NIS) for a specific area (this can be, for example, an entire regional sea, bay, inlet, lagoon, pond, lake, marina, a sand bank, an aquaculture site etc.). Abundance of a NIS may be ranked as "low", "moderate" or "high"; and the distribution may be scored as "one locality" (when a NIS was found only at one locality within the assessment area), "several localities", "many localities" or "all localities" (found at all localities). Combination of the abundance and distribution scores gives five classes of the abundance and distribution range. Once obtained this value aids in calculating an impact on 1) native communities, 2) habitats and, 3) ecosystem functioning. The calculation is based on ecological concepts, e.g. "key species", "type specific communities", "habitat alteration, fragmentation and loss", "functional groups", "food web shift", etc. Calculations are for a stated time period to enable assessment of temporal changes.
The method can be used for a single species or for several species for a specific (assessment) area. The method was designed for species in aquatic ecosystems (Olenin et al., 2007) but is currently being tested for terrestrial environments and there is a free on-line service BINPAS.
The biopollution level enables quantification of an impact in a robust manner in a standard and repeatable way. It makes it possible for comparison between different regions and taxonomic groups at different time intervals. The most impacting biota can be readily distinguished for a given region. It does not evaluate whether an impact effect is either good or bad, it states the change in an ecosystem due to an alien species invasion and measures the magnitude of this change. However, the method requires adequate information in order to obtain the magnitude of the impact, assessed at three levels of confidence (low, medium and high) according to the quality of the data available.
The method is simple to undertake and provide a means of quantifying impacts within any world region. Some assessments have been published (Olenina et al., 2010).
== Biological Invasion Impact / Biopollution Assessment System (BINPAS) ==
This is a free online system that calculates the magnitude of the biological invasion impact or biopollution level (Narščius et al., 2012).
BINPAS translates the existing data on miscellaneous invasive alien species impacts on population, community, habitat or ecosystem into uniform biopollution measurement units. The service is free of charge and available at for anyone interested in biological invasions. Experts willing to perform the assessment for their studied regions are welcome to register and compile the information as contributors.
== References ==
== External links ==
BINPAS (Biological Invasion Impact / Biopollution Assessment System)

35
data/en.wikipedia.org/wiki/Biomass_(ecology)-0.md Normal file
View File

@ -0,0 +1,35 @@
---
title: "Biomass (ecology)"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Biomass_(ecology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:15.767962+00:00"
instance: "kb-cron"
---
Biomass is the total mass of living biological organisms in a given area or ecosystem at a specific time. Biomass may refer to the species biomass, which is the mass of one or more species, or to community biomass, which is the mass of all species in the community. It encompasses microorganisms, plants, and animals, and is typically expressed as total mass or average mass per unit area.
The method used to measure biomass depends on the context. In some cases, biomass refers to the wet weight of organisms as they exist in nature. For example, in a salmon fishery, the salmon biomass might be regarded as the total wet weight the salmon would have if they were taken out of the water. In other contexts, biomass can be measured in terms of the dried organic mass, so perhaps only 30% of the actual weight might count, the rest being water. In other contexts, it may refer to dry weight (excluding water content), or to the mass of organic carbon, excluding inorganic components such as bones, shells, or teeth.
In 2018, Bar-On et al. estimated Earth's total live biomass at approximately 550 billion tonnes of carbon, the majority of which is found in plants. A 1998 study by Field et al. estimated global annual net primary production at just over 100 billion tonnes of carbon per year. While bacteria were once believed to account for a biomass comparable to that of plants, more recent research indicates they represent a much smaller proportion. The total number of DNA base pairs on Earth – sometimes used as a possible approximation of global biodiversity – has been estimated at (5.3±3.6)×1037, with a mass of around 50 billion tonnes. By the year 2020, the mass of human-made materials or anthropogenic mass, defined as "the mass embedded in inanimate solid objects made by humans (that have not yet been demolished or taken out of service)", was projected to surpass that of all living biomass on Earth.
== Ecological pyramids ==
An ecological pyramid is a graphical representation that shows, for a given ecosystem, the relationship between biomass or biological productivity and trophic levels.
A biomass pyramid shows the amount of biomass at each trophic level.
A productivity pyramid shows the production or turn-over in biomass at each trophic level.
An ecological pyramid provides a snapshot in time of an ecological community.
The bottom of the pyramid represents the primary producers (autotrophs). The primary producers take energy from the environment in the form of sunlight or inorganic chemicals and use it to create energy-rich molecules such as carbohydrates. This mechanism is called primary production. The pyramid then proceeds through the various trophic levels to the apex predators at the top.
When energy is transferred from one trophic level to the next, typically only ten percent is used to build new biomass. The remaining ninety percent goes to metabolic processes or is dissipated as heat. This energy loss means that productivity pyramids are never inverted, and generally limits food chains to about six levels. However, in oceans, biomass pyramids can be wholly or partially inverted, with more biomass at higher levels.
== Terrestrial biomass ==
Terrestrial biomass generally decreases markedly at each higher trophic level (plants, herbivores, carnivores). Examples of terrestrial producers are grasses, trees and shrubs. These have a much higher biomass than the animals that consume them, such as deer, zebras and insects. The level with the least biomass are the highest predators in the food chain, such as foxes and eagles.
In a temperate grassland, grasses and other plants are the primary producers at the bottom of the pyramid. Then come the primary consumers, such as grasshoppers, voles and bison, followed by the secondary consumers, shrews, hawks and small cats. Finally the tertiary consumers, large cats and wolves. The biomass pyramid decreases markedly at each higher level.
Changes in plant species in the terrestrial ecosystem can result in changes in the biomass of soil decomposer communities. Biomass in C3 and C4 plant species can change in response to altered concentrations of CO2. C3 plant species have been observed to increase in biomass in response to increasing concentrations of CO2 of up to 900 ppm.
== Ocean biomass ==
Ocean or marine biomass, in a reversal of terrestrial biomass, can increase at higher trophic levels. In the ocean, the food chain typically starts with phytoplankton, and follows the course:
Phytoplankton → zooplankton → predatory zooplankton → filter feeders → predatory fish

28
data/en.wikipedia.org/wiki/Biomass_(ecology)-1.md Normal file
View File

@ -0,0 +1,28 @@
---
title: "Biomass (ecology)"
chunk: 2/3
source: "https://en.wikipedia.org/wiki/Biomass_(ecology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:15.767962+00:00"
instance: "kb-cron"
---
Phytoplankton are the main primary producers at the bottom of the marine food chain. Phytoplankton use photosynthesis to convert inorganic carbon into protoplasm. They are then consumed by zooplankton that range in size from a few micrometers in diameter in the case of protistan microzooplankton to macroscopic gelatinous and crustacean zooplankton.
Zooplankton comprise the second level in the food chain, and includes small crustaceans, such as copepods and krill, and the larva of fish, squid, lobsters and crabs.
In turn, small zooplankton are consumed by both larger predatory zooplankters, such as krill, and by forage fish, which are small, schooling, filter-feeding fish. This makes up the third level in the food chain.
A fourth trophic level can consist of predatory fish, marine mammals and seabirds that consume forage fish. Examples are swordfish, seals and gannets.
Apex predators, such as orcas, which can consume seals, and shortfin mako sharks, which can consume swordfish, make up a fifth trophic level. Baleen whales can consume zooplankton and krill directly, leading to a food chain with only three or four trophic levels.
Marine environments can have inverted biomass pyramids. In particular, the biomass of consumers (copepods, krill, shrimp, forage fish) is larger than the biomass of primary producers. This happens because the ocean's primary producers are tiny phytoplankton which are r-strategists that grow and reproduce rapidly, so a small mass can have a fast rate of primary production. In contrast, terrestrial primary producers, such as forests, are K-strategists that grow and reproduce slowly, so a much larger mass is needed to achieve the same rate of primary production.
Among the phytoplankton at the base of the marine food web are members from a phylum of bacteria called cyanobacteria. Marine cyanobacteria include the smallest known photosynthetic organisms. The smallest of all, Prochlorococcus, is approximately 0.5 to 0.8 micrometres across. In terms of individual numbers, Prochlorococcus is possibly the most plentiful species on Earth: a single millilitre of surface seawater can contain 100,000 cells or more. Worldwide, there are estimated to be several octillion (1027) individuals. Prochlorococcus is ubiquitous between 40°N and 40°S and dominates in the oligotrophic (nutrient poor) regions of the oceans. The bacterium accounts for an estimated 20% of the oxygen in the Earth's atmosphere, and forms part of the base of the ocean food chain.
== Bacterial biomass ==
Bacteria and archaea are both classified as prokaryotes, and their biomass is commonly estimated together. The global biomass of prokaryotes is estimated at 30 billion tonnes C, dominated by bacteria.
The estimates for the global biomass of prokaryotes had changed significantly over recent decades, as more data became available. A much-cited study from 1998 collected data on abundances (number of cells) of bacteria and archaea in different natural environments, and estimated their total biomass at 350 to 550 billion tonnes C. This vast amount is similar to the biomass of carbon in all plants. The vast majority of bacteria and archaea were estimated to be in sediments deep below the seafloor or in the deep terrestrial biosphere (in deep continental aquifers). However, updated measurements reported in a 2012 study reduced the calculated prokaryotic biomass in deep subseafloor sediments from the original ≈300 billion tonnes C to ≈4 billion tonnes C (range 1.5–22 billion tonnes). This update originates from much lower estimates of both the prokaryotic abundance and their average weight.
A census published in PNAS in May 2018 estimated global bacterial biomass at ≈70 billion tonnes C, of which ≈60 billion tonnes are in the terrestrial deep subsurface. It also estimated the global biomass of archaea at ≈7 billion tonnes C. A later study by the Deep Carbon Observatory published in 2018 reported a much larger dataset of measurements, and updated the total biomass estimate in the deep terrestrial biosphere. It used this new knowledge and previous estimates to update the global biomass of bacteria and archaea to 23–31 billion tonnes C. Roughly 70% of the global prokaryotic biomass was estimated to be found in the deep subsurface. The estimated number of prokaryotic cells globally was estimated to be 11–15 × 1029. With this information, the authors of the May 2018 PNAS article revised their estimate for the global biomass of prokaryotes to ≈30 billion tonnes C, similar to the Deep Carbon Observatory estimate.
These estimates convert global abundance of prokaryotes into global biomass using average cellular biomass figures that are based on limited data. Recent estimates used an average cellular biomass of about 20–30 femtogram carbon (fgC) per cell in the subsurface and terrestrial habitats.
== Global biomass ==
The total global biomass has been estimated at 550 billion tonnes C. A breakdown of the global biomass is given by kingdom in the table below, based on a 2018 study by Bar-On et. al.

35
data/en.wikipedia.org/wiki/Biomass_(ecology)-2.md Normal file
View File

@ -0,0 +1,35 @@
---
title: "Biomass (ecology)"
chunk: 3/3
source: "https://en.wikipedia.org/wiki/Biomass_(ecology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:15.767962+00:00"
instance: "kb-cron"
---
Animals represent less than 0.5% of the total biomass on Earth, with about 2 billion tonnes C in total. Most animal biomass is found in the oceans, where arthropods, such as copepods, account for about 1 billion tonnes C and fish for another 0.7 billion tonnes C. Roughly half of the biomass of fish in the world are mesopelagic, such as lanternfish, spending most of the day in the deep, dark waters. Marine mammals such as whales and dolphins account for about 0.006 billion tonnes C.
Land animals account for about 500 million tonnes C, or about 20% of the biomass of animals on Earth. Terrestrial arthropods account for about 150 million tonnes C, most of which is found in the topsoil. Land mammals account for about 180 million tonnes C, most of which are humans (about 80 million tonnes C) and domesticated mammals (about 90 million tonnes C). Wild terrestrial mammals account for only about 3 million tonnes C, less than 2% of the total mammalian biomass on land.
Most of the global biomass is found on land, with only 5 to 10 billion tonnes C found in the oceans. On land, there is about 1,000 times more plant biomass (phytomass) than animal biomass (zoomass). About 18% of this plant biomass is eaten by the land animals. However, marine animals eat most of the marine autotrophs, and the biomass of marine animals is greater than that of marine autotrophs.
According to a 2020 study published in Nature, human-made materials, or technomass, outweigh all living biomass on earth, with plastic alone exceeding the mass of all land and marine animals combined.
== Global rate of production ==
Net primary production is the rate at which new biomass is generated, mainly due to photosynthesis. Global primary production can be estimated from satellite observations. Satellites scan the normalised difference vegetation index (NDVI) over terrestrial habitats and scan sea-surface chlorophyll levels over oceans. This results in 56.4 billion tonnes C/yr (53.8%) for terrestrial primary production and 48.5 billion tonnes C/yr for oceanic primary production. Thus, the total photoautotrophic primary production for the Earth is about 104.9 billion tonnes C/yr. This translates to about 426 gC/m2/yr for land production (excluding areas with permanent ice cover) and 140 gC/m2/yr for the oceans.
However, there is a much more significant difference in standing stocks—while accounting for almost half of the total annual production, oceanic autotrophs account for only about 0.2% of the total biomass.
Terrestrial freshwater ecosystems generate about 1.5% of the global net primary production.
Some global producers of biomass, in order of productivity rates, are
== See also ==
== References ==
== Further reading ==
== External links ==
Biocubes: a visualization of biomass and technomass
The mass of all life on Earth is staggering — until you consider how much we've lost
Counting bacteria Archived 12 December 2013 at the Wayback Machine
Trophic levels
Biomass distributions for high trophic-level fishes in the North Atlantic, 1900–2000

25
data/en.wikipedia.org/wiki/Bioremediation-0.md Normal file
View File

@ -0,0 +1,25 @@
---
title: "Bioremediation"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Bioremediation"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:17.028374+00:00"
instance: "kb-cron"
---
Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, water, soil, fuel gasses, industrial effluents etc., in natural or artificial settings. The natural ability of organisms to adsorb, accumulate, and degrade common and emerging pollutants has attracted the use of biological resources in treatment of contaminated environment. In comparison to conventional physicochemical treatment methods bioremediation may offer advantages as it aims to be sustainable, eco-friendly, cheap, and scalable.
Most bioremediation is inadvertent, involving native organisms. Research on bioremediation is heavily focused on stimulating the process by inoculation of a polluted site with organisms or supplying nutrients to promote their growth. Environmental remediation is an alternative to bioremediation.
While organic pollutants are susceptible to biodegradation, heavy metals cannot be degraded, but rather oxidized or reduced. Typical bioremediations involves oxidations. Oxidations enhance the water-solubility of organic compounds and their susceptibility to further degradation by further oxidation and hydrolysis. Ultimately biodegradation converts hydrocarbons to carbon dioxide and water. For heavy metals, bioremediation offers few solutions. Metal-containing pollutant can be removed, at least partially, with varying bioremediation techniques. The main challenge to bioremediations is rate: the processes are slow.
Bioremediation techniques can be classified as (i) in situ techniques, which treat polluted sites directly, vs (ii) ex situ techniques which are applied to excavated materials. In both these approaches, additional nutrients, vitamins, minerals, and pH buffers are added to enhance the growth and metabolism of the microorganisms. In some cases, specialized microbial cultures are added (biostimulation). Some examples of bioremediation related technologies are phytoremediation, bioventing, bioattenuation, biosparging, composting (biopiles and windrows), and landfarming. Other remediation techniques include thermal desorption, vitrification, air stripping, bioleaching, rhizofiltration, and soil washing. Biological treatment, bioremediation, is a similar approach used to treat wastes including wastewater, industrial waste and solid waste. The end goal of bioremediation is to remove harmful compounds to improve soil and water quality.
== Techniques ==
=== In situ techniques ===
==== Bioventing ====
Bioventing is a process that increases the oxygen or air flow into the unsaturated zone of the soil, this in turn increases the rate of natural in situ degradation of the targeted hydrocarbon contaminant. Bioventing, an aerobic bioremediation, is the most common form of oxidative bioremediation process where oxygen is provided as the electron acceptor for oxidation of petroleum, polyaromatic hydrocarbons (PAHs), phenols, and other reduced pollutants. Oxygen is generally the preferred electron acceptor because of the higher energy yield and because oxygen is required for some enzyme systems to initiate the degradation process. Microorganisms can degrade a wide variety of hydrocarbons, including components of gasoline, kerosene, diesel, and jet fuel. Under ideal aerobic conditions, the biodegradation rates of the low- to moderate-weight aliphatic, alicyclic, and aromatic compounds can be very high. As molecular weight of the compound increases, the resistance to biodegradation increases simultaneously. This results in higher contaminated volatile compounds due to their high molecular weight and an increased difficulty to remove from the environment.
Most bioremediation processes involve oxidation-reduction reactions where either an electron acceptor (commonly oxygen) is added to stimulate oxidation of a reduced pollutant (e.g. hydrocarbons) or an electron donor (commonly an organic substrate) is added to reduce oxidized pollutants (nitrate, perchlorate, oxidized metals, chlorinated solvents, explosives and propellants). In both these approaches, additional nutrients, vitamins, minerals, and pH buffers may be added to optimize conditions for the microorganisms. In some cases, specialized microbial cultures are added (bioaugmentation) to further enhance biodegradation.
Approaches for oxygen addition below the water table include recirculating aerated water through the treatment zone, addition of pure oxygen or peroxides, and air sparging. Recirculation systems typically consist of a combination of injection wells or galleries and one or more recovery wells where the extracted groundwater is treated, oxygenated, amended with nutrients and re-injected. However, the amount of oxygen that can be provided by this method is limited by the low solubility of oxygen in water (8 to 10 mg/L for water in equilibrium with air at typical temperatures). Greater amounts of oxygen can be provided by contacting the water with pure oxygen or addition of hydrogen peroxide (H2O2) to the water. In some cases, slurries of solid calcium or magnesium peroxide are injected under pressure through soil borings. These solid peroxides react with water releasing H2O2 which then decomposes releasing oxygen. Air sparging involves the injection of air under pressure below the water table. The air injection pressure must be great enough to overcome the hydrostatic pressure of the water and resistance to air flow through the soil.
==== Biostimulation ====

41
data/en.wikipedia.org/wiki/Bioremediation-1.md Normal file
View File

@ -0,0 +1,41 @@
---
title: "Bioremediation"
chunk: 2/3
source: "https://en.wikipedia.org/wiki/Bioremediation"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:17.028374+00:00"
instance: "kb-cron"
---
Bioremediation can be carried out by bacteria that are naturally present. In biostimulation, the population of these helpful bacteria can be increased by adding nutrients.
Bacteria can in principle be used to degrade hydrocarbons. Specific to marine oil spills, nitrogen and phosphorus have been key nutrients in biodegradation. The bioremediation of hydrocarbons suffers from low rates.
Bioremediation can involve the action of microbial consortium. Within the consortium, the product of one species could be the substrate for another species.
Anaerobic bioremediation can in principle be employed to treat a range of oxidized contaminants including PCE, TCE, DCE, VC), chlorinated ethanes (TCA, DCA), chloromethanes (CT, CF), chlorinated cyclic hydrocarbons, various energetics (e.g., perchlorate, RDX, TNT), and nitrate. This process involves the addition of an electron donor to: 1) deplete background electron acceptors including oxygen, nitrate, oxidized iron and manganese and sulfate; and 2) stimulate the biological and/or chemical reduction of the oxidized pollutants. The choice of substrate and the method of injection depend on the contaminant type and distribution in the aquifer, hydrogeology, and remediation objectives. Substrate can be added using conventional well installations, by direct-push technology, or by excavation and backfill such as permeable reactive barriers (PRB) or biowalls. Slow-release products composed of edible oils or solid substrates tend to stay in place for an extended treatment period. Soluble substrates or soluble fermentation products of slow-release substrates can potentially migrate via advection and diffusion, providing broader but shorter-lived treatment zones. The added organic substrates are first fermented to hydrogen (H2) and volatile fatty acids (VFAs). The VFAs, including acetate, lactate, propionate and butyrate, provide carbon and energy for bacterial metabolism.
Bioremediation is not specific to metals. In 2010 there was a massive oil spill in the Gulf of Mexico. Populations of bacteria and archaea were used to rejuvenate the coast after the oil spill. These microorganisms over time have developed metabolic networks that can utilize hydrocarbons such as oil and petroleum as a source of carbon and energy. Microbial bioremediation is a very effective modern technique for restoring natural systems by removing toxins from the environment.
==== Bioattenuation ====
During bioattenuation, biodegradation occurs naturally with the addition of nutrients or bacteria. The indigenous microbes present will determine the metabolic activity and act as a natural attenuation. While there is no anthropogenic involvement in bioattenuation, the contaminated site must still be monitored.
==== Biosparging ====
Biosparging is the process of groundwater remediation as oxygen, and possible nutrients, is injected. When oxygen is injected, indigenous bacteria are stimulated to increase rate of degradation. However, biosparging focuses on saturated contaminated zones, specifically related to ground water remediation.
UNICEF, power producers, bulk water suppliers, and local governments are early adopters of low cost bioremediation, such as aerobic bacteria tablets which are simply dropped into water.
=== Ex situ techniques ===
Ex situ techniques are often more expensive because of excavation and transportation costs to the treatment facility, while in situ techniques are performed at the site of contamination so they only have installation costs. While there is less cost there is also less of an ability to determine the scale and spread of the pollutant. The pollutant ultimately determines which bioremediation method to use. The depth and spread of the pollutant are other important factors.
==== Biopiles ====
Biopiles, similar to bioventing, are used to remove petroleum pollutants by increasing aerobic degradation to contaminated soils. However, the soil is excavated and piled with an aeration system. This aeration system enhances microbial activity by introducing oxygen under positive pressure or removes oxygen under negative pressure.
==== Windrows ====
Windrow systems are similar to compost techniques where soil is periodically turned in order to enhance aeration. This periodic turning also allows contaminants present in the soil to be uniformly distributed which accelerates the process of bioremediation.
==== Landfarming ====
Landfarming, or land treatment, is a method commonly used for sludge spills. This method disperses contaminated soil and aerates the soil by cyclically rotating. This process is an above land application and contaminated soils are required to be shallow in order for microbial activity to be stimulated. However, if the contamination is deeper than 5 feet, then the soil is required to be excavated to above ground. While it is an ex situ technique, it can also be considered an in situ technique as Landfarming can be performed at the site of contamination.
== Targetted pollutants ==
=== Heavy metals ===
Heavy metals are introduced into the environment by both anthropogenic activities and natural factors. Unlike organic pollutants, metals (or more properly, metal ions and metal compounds) cannot be degraded. Hyperaccumulating plants could in principle extract metals from soil, but this technology remains impractical. The mobility of the metals could be decreased, resulting in their immobilization. For example, reduction of the more mobile U(VI) species affords the less mobile U(IV) derivatives. Again, this approach remains more conceptual than practical.

33
data/en.wikipedia.org/wiki/Bioremediation-2.md Normal file
View File

@ -0,0 +1,33 @@
---
title: "Bioremediation"
chunk: 3/3
source: "https://en.wikipedia.org/wiki/Bioremediation"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:17.028374+00:00"
instance: "kb-cron"
---
=== Pesticides ===
Of the many ways to deal with pesticide contamination, bioremediation promises to be more effective. Many sites around the world are contaminated with agrichemicals. These agrichemicals often resist biodegradation, by design. Harming all manners of organic life with long term health issues such as cancer, rashes, blindness, paralysis, and mental illness. An example is Lindane which was a commonly used insecticide in the 20th century. Long time exposure poses a serious threat to humans and the surrounding ecosystem. Lindane reduces the potential of beneficial bacteria in the soil such as nitrogen fixation cyanobacteria. As well as causing central nervous system issues in smaller mammals such as seizures, dizziness, and even death. What makes it so harmful to these organisms is how quickly distributed it gets through the brain and fatty tissues. While Lindane has been mostly limited to specific use, it is still produced and used around the world.
Actinobacteria has been a promising candidate in situ technique specifically for removing pesticides. When certain strains of Actinobacteria have been grouped together, their efficiency in degrading pesticides has enhanced. As well as being a reusable technique that strengthens through further use by limiting the migration space of these cells to target specific areas and not fully consume their cleansing abilities. Despite encouraging results, Actinobacteria has only been used in controlled lab settings and will need further development in finding the cost effectiveness and scalability of use.
== Limitations of bioremediation ==
Bioremediation is rarely employed to remediate pollutants. Heavy metals and radionuclides simply do not biodegrade, although in some cases, these metals can be immobilized. In some cases, microbes do not fully mineralize the pollutant, potentially producing a more toxic compound. For example, under anaerobic conditions, the reductive dehalogenation of TCE may produce dichloroethylene (DCE) and vinyl chloride (VC), which are suspected or known carcinogens. However, the microorganism Dehalococcoides can further reduce DCE and VC to the non-toxic product ethene. The molecular pathways for bioremediation are of considerable interest. In addition, knowing these pathways will help develop new technologies that can deal with sites that have uneven distributions of a mixture of contaminants.
Biodegradation requires microbial population with the metabolic capacity to degrade the pollutant in a suitable timeframe. The biological processes used by these microbes are highly specific, therefore, many environmental factors must be taken into account and regulated as well. It can be difficult to extrapolate the results from the small-scale test studies into big field operations. In many cases, bioremediation takes more time than other alternatives such as land filling and incineration. Another example is bioventing, which is inexpensive to bioremediate contaminated sites, however, this process is extensive and can take a few years to decontaminate a site.
Another major challeng is invasive species: indigenous species are preferred. The organism must be sufficiently plentiful to clean the site.
Pesticides are a top contributor to soil contamination and runoff contamination. Pesticides are difficult to biodegrade.
== Genetic engineering ==
The use of genetic engineering to create organisms specifically designed for bioremediation is under preliminary research. Two category of genes can be inserted in the organism: degradative genes, which encode proteins required for the degradation of pollutants, and reporter genes, which encode proteins able to monitor pollution levels. Numerous members of Pseudomonas have been modified with the lux gene for the detection of the polyaromatic hydrocarbon naphthalene. A field test for the release of the modified organism has been successful on a moderately large scale.
There are concerns surrounding release and containment of genetically modified organisms into the environment due to the potential of horizontal gene transfer. Genetically modified organisms are classified and controlled under the Toxic Substances Control Act of 1976 under United States Environmental Protection Agency. Measures have been created to address these concerns. Organisms can be modified such that they can only survive and grow under specific sets of environmental conditions. In addition, the tracking of modified organisms can be made easier with the insertion of bioluminescence genes for visual identification.
Genetically modified organisms have been created to treat oil spills and break down certain plastics (PET).
== See also ==
== References ==
== External links ==
Phytoremediation, hosted by the Missouri Botanical Garden
To remediate or to not remediate?
Anaerobic Bioremediation

41
data/en.wikipedia.org/wiki/Matriphagy-0.md Normal file
View File

@ -0,0 +1,41 @@
---
title: "Matriphagy"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Matriphagy"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:55.810435+00:00"
instance: "kb-cron"
---
Matriphagy is the consumption of the mother by her offspring. The behavior generally takes place within the first few weeks of life and has been documented in some species of insects, nematode worms, pseudoscorpions, and other arachnids as well as in caecilian amphibians.
The specifics of how matriphagy occurs varies among different species. However, the process is best-described in the desert spider (Stegodyphus lineatus), where the mother harbors nutritional resources for her young through food consumption. The mother can regurgitate small portions of food for her growing offspring, but between 1–2 weeks after hatching, the progeny capitalize on this food source by eating her alive. Typically, offspring only feed on their biological mother as opposed to other females in the population. In other arachnid species, matriphagy occurs after the ingestion of nutritional eggs known as trophic eggs (e.g. Black lace-weaver Amaurobius ferox, crab spider Australomisidia ergandros). It involves different techniques for killing the mother, such as transfer of poison via biting and sucking to cause a quick death (e.g. Black lace-weaver) or continuous sucking of the hemolymph, resulting in a more gradual death (e.g. Crab spider). The behavior is less well described but follows a similar pattern in species such as the Hump earwig, pseudoscorpions, and caecilians.
Spiders that engage in matriphagy produce offspring with higher weights, shorter and earlier moulting time, larger body mass at dispersal, and higher survival rates than clutches deprived of matriphagy. In some species, matriphagous offspring were also more successful at capturing large prey items and had a higher survival rate at dispersal. These benefits to offspring outweigh the cost of survival to the mothers and help ensure that her genetic traits are passed to the next generation, thus perpetuating the behavior.
Overall, matriphagy is an extreme form of parental care but is highly related to extended care in the funnel-web spider, parental investment in caecilians, and gerontophagy in social spiders. The uniqueness of this phenomenon has led to several expanded analogies in human culture and contributed to the pervasive fear of spiders throughout society.
== Etymology ==
Matriphagy can be broken down into two components:
matri- (mother)
-phagy (to feed on)
== Description of behavior ==
Matriphagy generally consists of offspring consuming their mother; however, different species exhibit different variations of this behavior.
=== Spiders ===
==== Black lace-weaver: Amaurobius ferox ====
In many black lace-weavers, Amaurobius ferox, offspring do not immediately consume their mother. A day after offspring emerge from their eggs, their mother lays a set of trophic eggs, which contain nutrition for the offspring to consume. Matriphagy commences days later when the mother begins communicating with her offspring through web vibrations, drumming, and jumping. Through these behaviors, offspring are able to detect when and where they can consume their mother. They migrate towards her and a couple of the spiderlings jump onto her back to consume her. In response, the mother jumps and drums more frequently to keep her offspring off of her, however, they relentlessly continue attempting to get onto her back. When the mother feels ready, she presses her body onto her offspring and allows them to consume her via sucking on her insides. As they consume her, they also release poison into her body, causing a quick death. The mother's body is kept for a few weeks as a nutritional reserve.
Matriphagy in this species is dependent on the developmental stage that the offspring are currently at. If offspring, older than four days, are given to an unrelated mother, they refuse to consume her. However, if younger offspring are given to an unrelated mother, they readily consume her. Additionally, if a mother loses her offspring, she is able to produce another clutch of offspring.
==== Crab spider: Australomisidia ergandros ====
Mothers of one particular Australian species of the crab spider, Australomisidia ergandros (formerly in genus Diaea), are only able to lay one clutch, unlike the black lace-weaver. They invest a significant amount of time and energy into storing nutrients and food into large oocytes, known as trophic eggs, similar to the black lace-weaver. However, these trophic eggs are too large to physically leave her body. Some of the nutrients from the trophic eggs are liquefied into haemolymph, which can be consumed through the mother's leg joints by her offspring. She gradually shrinks until she becomes immobile and dies.
In this species, it has been shown that this behavior may contribute to reducing cannibalism by siblings.
==== Desert Spider: Stegodyphus lineatus ====
Right after hatching, the hatchlings of the desert spider Stegodyphus lineatus rely solely upon their mother to provide them with food and nutrients. Their mother does this by regurgitating her bodily fluids, which contain a mixture of nutrients for them to feed on.
This behavior begins during mating. Mating causes an increase in the mother's production of digestive enzymes to better digest her prey. Consequently, she is able to retain more nutrients for her offspring to consume later. The mother's midgut tissues start to slowly degrade during the incubation period of her eggs. After her offspring hatch, she regurgitates food for them to feed on with the help of her already-liquefied midgut tissues. Meanwhile, her midgut tissues continue to degrade into a liquid state to maximize the amount of nutrients from the mother's body that her offspring will be able to obtain. As degradation continues, nutritional vacuoles form within her abdomen to amass all of the nutrients. Consumption begins when her offspring puncture her abdomen to suck up the nutritional vacuoles. After approximately 2–3 hours, the mother's bodily fluids are completely consumed, and only her exoskeleton remains.
This species is only able to have one clutch, which might explain why so much time and energy is spent on taking care of offspring. Furthermore, matriphagy can also occur between offspring and mothers who have recently laid eggs that are not related.
=== Hump earwig ===

51
data/en.wikipedia.org/wiki/Matriphagy-1.md Normal file
View File

@ -0,0 +1,51 @@
---
title: "Matriphagy"
chunk: 2/3
source: "https://en.wikipedia.org/wiki/Matriphagy"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:55.810435+00:00"
instance: "kb-cron"
---
==== Anechura harmandi ====
Anechura harmandi is the only species of earwigs that has been currently documented to exhibit matriphagy. Mothers in this particular species of earwigs have been found to reproduce during colder temperatures. This is mainly for the purpose of avoiding predation and maximizing their offspring's survival, since females are unable to produce a second clutch. Due to the cold temperature, there is a scarcity of available nutrients when the offspring hatch, which is why the offspring end up consuming their mother.
=== Pseudoscorpions ===
==== Paratemnoides nidificator ====
Matriphagy in this species of pseudoscorpions is usually observed during times of food scarcity. After their offspring hatch, mothers exit their nests and wait to be consumed. Offspring follow their mothers out of the nest where they grab onto her legs and proceed to feed through her leg joints, similar to that of Australomisidia ergandros.
Females of this species are able to produce more than one clutch of offspring if their first clutch was unsuccessful.
Matriphagy in this species has been predicted to prevent cannibalism between siblings as well.
== Evolution ==
The adaptive value of matriphagy is based on the benefits provided to the offspring and the costs borne by the mother. Functionally analyzing matriphagy in this manner sheds light on why this unusual and extreme form of care has evolved and been selected for.
=== Benefits to offspring ===
Consuming the mother is a source of nutrition which is important for growth and development.
The body mass and opisthosoma length of spiderlings increases after matriphagy compared to before (opisthosoma is the posterior part of the body in spiders, analogous to the abdomen). Additionally, body mass tends to be higher for spiderlings that engage in matriphagy as compared to those that do not.
Matriphagy advances molting time. Molting is the growing of a larger exoskeleton and shedding the old one. Advancement of molting time means that the spiders are able to grow at a faster rate.
Matriphagous spiderlings tend to experience significantly greater survival rates and fitness compared to non-matriphagous offspring at dispersal.
Matriphagous spiderlings hunt larger prey and show much more complete prey consumption than non-matriphagous spiderlings.
Matriphagy improves sociality in spiders, primarily by reducing sibling cannibalism.
=== Costs and benefits to the mother ===
Unlike other milder forms of parental care, matriphagy necessarily costs the mother her life. Nevertheless, matriphagy may serve the mother's reproductive fitness, considering reproductive output, egg sac development, and number of young reared. The key question is whether the mother would produce more surviving offspring by evading matriphagy and reproducing again or by engaging in matriphagy and producing only one clutch.
In the black lace-weaver (Amaurobius ferox) around 80% of females separated prior to matriphagy produce second egg sacs and only approximately 40% of these develop completely (compared to the >90% development of egg sacs in the first brood).
Additionally, the number of spiderlings in the second brood tends to be significantly lower than in the first brood. These individuals are also smaller than the spiders in the first brood.
Females that successively lay two egg sacs have a lower expected output of dispersing offspring than females that are victims of matriphagy and produce only a single clutch.
== Forms of parental care similar to matriphagy ==
Matriphagy is one of the most extreme forms of parental care observed in the animal kingdom. However, in some species such as the Funnel-web spider Coelotes terrestris, matriphagy is only observed under certain conditions and extended maternal protection is the main method by which offspring receive care. In other organisms such as the African social velvet spider, Stegodyphus mimosarum and Caecilian amphibians, parental behavior closely related in form and function to matriphagy is used.
=== Extended care in a Funnel-web spider: Coelotes terrestris ===
The ‘maternal social’ spider, Coelotes terrestris (Funnel-web spider) uses extended maternal care as a reproductive model for its offspring. Upon laying the egg sac, a C. terrestris mother stands guard and incubates the sac for 3 to 4 weeks. She stays with her young from the time of their emergence until dispersal approximately 5 to 6 weeks later. During the offsprings’ development, mothers will provide the spiderlings prey based on their levels of gregariousness.
Protecting the egg sacs from predation and parasites yields a high benefit to cost ratio for the mothers. Fitness of the mother is highly correlated to offspring developmental state—a mother in better condition yields larger young that are better at surviving predation. The presence of the mother also protects the offspring against parasitism. In addition, the mother can keep feeding while guarding her progeny without any weight loss, allowing her to collect sufficient food for both herself and her offspring.
Overall, costs of protecting the egg sac are low. Upon separation from egg sacs, 90% of females have the energy sustenance to lay new sacs, although it does induce a time loss of several weeks that could potentially affect reproductive success.
In experimental conditions, costs arose if maternal care was not provided, with egg sacs drying out and developing molds, thus illustrating that maternal care is essential for survival. Experimental food-deprived broods reared by the mother induced matriphagy, where 77% of offspring consumed their mother upon birth. This suggests that matriphagy can exist under nutrient-limited conditions, but the costs generally outweigh the benefits when mothers have sufficient access to resources.
=== Parental investment by skin-feeding in Caecilian amphibians ===
Caecilian amphibians are worm-like in appearance, and mothers have thick epithelial skin layers. The skin on a caecilian mother is used for a form of parent-offspring nutrient transfer. In at least two species, Boulengerula taitana and Siphonops annulatus, the young feed on the mother's skin by tearing it off with their teeth. Because these two are not closely related, either this behaviour is more common than currently observed or it evolved independently. The consumed skin then regenerates within a few days.

47
data/en.wikipedia.org/wiki/Matriphagy-2.md Normal file
View File

@ -0,0 +1,47 @@
---
title: "Matriphagy"
chunk: 3/3
source: "https://en.wikipedia.org/wiki/Matriphagy"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:55.810435+00:00"
instance: "kb-cron"
---
The Taita African caecilian Boulengerula taitana is an oviparous (egg-laying) caecilian whose skin transforms in brooding females to supply nutrients to growing offspring. The offspring are born with specific dentition that they can use to peel and eat the outer epidermal layer of their mother's skin. Young move around their mother's bodies, using their lower jaws to lift and peel the mother's skin while vigorously pressing their heads against her abdomen. To account for this, the epidermis of brooding females can be up to twice the thickness of non-brooding females.
Viviparous (developing in the mother) caecilians on the other hand, have specialized fetal dentition which can be used for scraping lipid-rich secretions and cellular materials from the maternal oviduct lining. The ringed caecilian Siphonops annulatus, an oviparous caecilian, exhibits characteristics similar to viviparous caecilians. Mothers have paler skin tones than non-attending females, suggesting that offspring feed on glandular secretions on the mother's skin—a process that resembles mammalian lactation. This scraping method is different from the peeling actions performed by oviparous caecilians.
For both oviparous and viviparous caecilians, delayed investment is a common benefit. Providing nutrition through the skin allows for redirection of nutrients, yielding fewer and larger offspring than caecilians who only provide their offspring with yolk nutrients. Rather than the mother sacrificing herself and solely being used for the offspring's nutrition, caecilian mothers supplement their offspring's growth; they provide enough nutrients for the offspring to survive, but not at the cost of their own life.
=== Gerontophagy in social spiders, Genus Stegodyphus ===
Stegodyphus mothers liquefy their inner organs and maternal tissue into food deposits. The African social velvet spider Stegodyphus mimosarum and the African social spider Stegodyphus dumicola are two social spider species that eat their mothers and other adult females, which is unique since social spiders do not tend to exhibit cannibalistic life history traits. In these specific spiders, deceased females are often found shriveled with shrunken abdomens. Offspring suck nutrients primarily from the dorsal part of the adult female's abdomen, and she may still be alive during this process.
This behavior is not quite the same as matriphagy because Stegodyphus spiderlings are perfectly tolerant to other offspring, healthy conspecifics, and members of other species, suggesting that ordinary cannibalism is suppressed. Instead, the parental care exhibited is known as "gerontophagy", or the "consumption of old individuals" (geron = old person, phagy = to feed on). Gerontophagy is the final act of care for the offspring, and some offspring are found larger than others. This implies that some young spiders are already able to feed on prey by themselves and gerontophagy as a source of nutrition is supplemental rather than necessary. Thus, there exists the ‘cannibal's kin-dilemma’, which reveals a form of kin selection in social spiders. In this scenario, kin selection should counteract cannibalism of related individuals in social spiders, but any designated victim should prefer to be eaten by available close relatives.
== Cultural significance ==
Those who have been exposed to matriphagy may be frightened by such a seemingly strange and bizarre natural behavior, especially since it is mainly observed in already feared organisms. Thus, matriphagy is often posed as perpetuation of a long held fear of arachnids in human society.
In contrast, others may look to matriphagy as a leading example of purity, as it represents an instinctive form of altruism. Altruism in this case refers to an "intentional action ultimately for the welfare of others that entails at least the possibility of either no benefit or a loss to the actor," and is a highly popularized and desirable concept in many human cultures. Matriphagy can be viewed as altruism, insofar as participating mothers "sacrifice" their survival for the welfare of their offspring. Although participation in matriphagy is not truly an intentional action, mothers are nevertheless driven by natural selection pressures based on offspring fitness to engage in such behavior. This in turn creates a cycle that perpetuates altruistic matriphagous behavior through generations. Such an example of altruism on a purely biological level differs severely from human standards of altruism, which are influenced by moral virtues such as rationality, trust, and reciprocity.
== List of species that engage in matriphagy ==
=== Spiders ===
Agelena labyrinthica
Amaurobius ferox
Cheiracanthium japonicum
Seothyra
Stegodyphus lineatus
Stegodyphus sarasinorum
Eresus sandaliatus
=== Earwigs ===
Anechura harmandi
=== Strepsiptera ===
The order Strepsiptera is known for hemocoelous vivipary, where the offspring lives in the female's hemocoel and feed on her hemolymph, consuming her from within.
=== Pseudoscorpions ===
Paratemnoides nidificator
=== Vertebrates ===
Caecilian
== References ==

43
data/en.wikipedia.org/wiki/Modularity_(biology)-0.md Normal file
View File

@ -0,0 +1,43 @@
---
title: "Modularity (biology)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Modularity_(biology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:56.996480+00:00"
instance: "kb-cron"
---
Modularity refers to the ability of a system to organize discrete, individual units that can overall increase the efficiency of network activity and, in a biological sense, facilitates selective forces upon the network. Modularity is observed in all model systems, and can be studied at nearly every scale of biological organization, from molecular interactions all the way up to the whole organism.
== Evolution of Modularity ==
The exact evolutionary origins of biological modularity has been debated since the 1990s. In the mid 1990s, Günter Wagner argued that modularity could have arisen and been maintained through the interaction of four evolutionary modes of action:
[1] Selection for the rate of adaptation: If different complexes evolve at different rates, then those evolving more quickly reach fixation in a population faster than other complexes. Thus, common evolutionary rates could be forcing the genes for certain proteins to evolve together while preventing other genes from being co-opted unless there is a shift in evolutionary rate.
[2] Constructional selection: When a gene exists in many duplicated copies, it may be maintained because of the many connections it has (also termed pleiotropy). There is evidence that this is so following whole genome duplication, or duplication at a single locus. However, the direct relationship that duplication processes have with modularity has yet to be directly examined.
[3] Stabilizing selection: While seeming antithetical to forming novel modules, Wagner maintains that it is important to consider the effects of stabilizing selection as it may be "an important counter force against the evolution of modularity". Stabilizing selection, if ubiquitously spread across the network, could then be a "wall" that makes the formation of novel interactions more difficult and maintains previously established interactions. Against such strong positive selection, other evolutionary forces acting on the network must exist, with gaps of relaxed selection, to allow focused reorganization to occur.
[4] Compounded effect of stabilizing and directional selection: This is the explanation seemingly favored by Wagner and his contemporaries as it provides a model through which modularity is constricted, but still able to unidirectionally explore different evolutionary outcomes. The semi-antagonistic relationship is best illustrated using the corridor model, whereby stabilizing selection forms barriers in phenotype space that only allow the system to move towards the optimum along a single path. This allows directional selection to act and inch the system closer to optimum through this evolutionary corridor.
For over a decade, researchers examined the dynamics of selection on network modularity. However, in 2013 Clune and colleagues challenged the sole focus on selective forces, and instead provided evidence that there are inherent "connectivity costs" that limit the number of connections between nodes to maximize efficiency of transmission. This hypothesis originated from neurological studies that found that there is an inverse relationship between the number of neural connections and the overall efficiency (more connections seemed to limit the overall performance speed/precision of the network). This connectivity cost had yet to be applied to evolutionary analyses. Clune et al. created a series of models that compared the efficiency of various evolved network topologies in an environment where performance, their only metric for selection, was taken into account, and another treatment where performance as well as the connectivity cost were factored together. The results show not only that modularity formed ubiquitously in the models that factored in connection cost, but that these models also outperformed the performance-only based counterparts in every task. This suggests a potential model for module evolution whereby modules form from a system’s tendency to resist maximizing connections to create more efficient and compartmentalized network topologies.
== References ==
== Sources ==
SF Gilbert, JM Opitz, and RA Raff. 1996. "Resynthesizing Evolutionary and Developmental Biology". Developmental Biology. 173:357-372
G von Dassow and E Munro. "Modularity in Animal Development and Evolution: Elements of a Conceptual Framework for EvoDevo". J. Exp. Zool. 285:307-325.
MI Arnone and EH Davidson. 1997. The hardwiring of development: organization and function of genomic regulatory systems.
EH Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic Press, 2006.
S Barolo and JW Posakony. 2002. "Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling". Genes and Development. 16:1167-1181
EN Trifonov and ZM Frenkel. 2009. "Evolution of protein modularity. Current Opinion in Structural Biology". 19:335-340.
CR Baker, LN Booth, TR Sorrells, AD Johnson. 2012. "Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification". Cell. 151:80-95.
Y Pritykin and M Singh. 2012. "Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks". PLoS Computational Biology. 9(10): e1003243
GP Wagner. 1989. "Origin of Morphological Characters and the Biological Basis of Homology". Evolution. 43(6):1157-1171
SB Carroll, J Grenier, and S Weatherbee. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Wiley-Blackwell, 2002.
== Further reading ==
W Bateson. Materials for the Study of Variation. London:Macmillan, 1984.
R Raff. The Shape of Life. University of Chicago Press, 1996.
EH Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic Press, 2006.
M Ptashne and A Gann. Genes and Signals. Cold Spring Harbor Press, 2002.

42
data/en.wikipedia.org/wiki/Molluscivore-0.md Normal file
View File

@ -0,0 +1,42 @@
---
title: "Molluscivore"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Molluscivore"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:58.235461+00:00"
instance: "kb-cron"
---
A molluscivore is a carnivorous animal that specialises in feeding on molluscs such as gastropods, bivalves, brachiopods and cephalopods. Known molluscivores include numerous predatory (and often cannibalistic) molluscs, (e.g. octopuses, murexes, decollate snails and oyster drills), arthropods such as crabs and firefly larvae, and vertebrates such as fish, birds and mammals. Molluscivory is performed in a variety of ways with some animals highly adapted to this method of feeding. A similar behaviour, durophagy, describes the feeding of animals that consume hard-shelled or exoskeleton bearing organisms, such as corals, shelled molluscs, or crabs.
== Description ==
Molluscivory can be performed in several ways:
In some cases, the mollusc prey are simply swallowed entire, including the shell, whereupon the prey is killed through suffocation and/or exposure to digestive enzymes. Only cannibalistic sea slugs, snail-eating cone shells of the taxon Coninae, and some sea anemones use this method.
One method, used especially by vertebrate molluscivores, is to break the shell, either by exerting force on the shell until it breaks, often by biting the shell, like with oyster crackers, mosasaurs, and placodonts, or hammering at the shell, e.g. oystercatchers and crabs, or by simply dashing the mollusc on a rock (e.g. song thrushes, gulls, and sea otters). It is hypothesized that human archaic ancestors such as early-Pleistocene Homo erectus on Java were predominantly molluscivorous: stone tool use, pachyosteosclerotic skeleton (slow+shallow diving), much larger brains (seafoods + DHA), fossilisations amid edible mussels (Pseudodon, Elongaria), island colonisations (e.g. Flores), early-Pleistocene intercontinental dispersal along coasts and rivers, enamel damage caused by "oral processing of marine mollusks" (Towle cs 2022 AJPA), ear exostoses (chronic cold-water irrigation), shell engravings (google "Joordens Munro"), etc., google "gondwanatalks verhaegen".
Another method is to remove the shell from the prey. Molluscs are attached to their shell by strong muscular ligaments, making the shell's removal difficult. Molluscivorous birds, such as oystercatchers and the Everglades snail kite, insert their elongate beak into the shell to sever these attachment ligaments, facilitating removal of the prey. The carnivorous terrestrial pulmonate snail known as the "decollate snail" ("decollate" being a synonym for "decapitate") uses a similar method: it reaches into the opening of the prey's shell and bites through the muscles in the prey's neck, whereupon it immediately begins devouring the fleshy parts of its victim. The walrus sucks meat out of bivalve molluscs by sealing its powerful lips to the organism and withdrawing its piston-like tongue rapidly into its mouth, creating a vacuum.
Another method, used by octopuses, nautilii and most molluscivoruous sea snails, is to use their radula to drill a hole through the shell, then inject venom and digestive enzymes through the hole, after which the digested prey can be sucked out through the hole.
The larvae of glowworms and fireflies are simply small enough to enter the shells of terrestrial snails and begin eating immediately.
== In marine mammals ==
Whales: Sperm whales, pilot whales, Cuvier's beaked whale, Risso's dolphin and species in the genera Mesoplodon, and Hyperoodon and the superfamily Physeteroidea are classified as molluscivores, eating mainly squid.
Pinnipeds: Elephant seals, Ross seals and South American fur seals are classed as molluscivores. The walrus eats benthic bivalve molluscs, especially clams, for which it forages by grazing along the sea bottom, searching and identifying prey with its sensitive vibrissae. The walrus sucks the meat out by sealing its powerful lips to the organism and withdrawing its piston-like tongue rapidly into its mouth, creating a vacuum. The walrus palate is uniquely vaulted, enabling effective suction.
== In fish ==
Several species of pufferfish and loaches are molluscivores. As many molluscs are protected by a shell, the feeding techniques applied amongst molluscivore fish are highly specialized and usually divided into two groups: "crushers" and "slurpers." Pufferfish tend to be crushers and will use their beak-like teeth to break the shell in order to gain access to the meat inside. Loaches are specialized slurpers, and will make use of their characteristically shaped snout in order to grab hold of, then suck out the animal living inside the shell.
The black carp (Mylopharyngodon piceus) commonly feeds by crushing large molluscs with pharyngeal teeth, extracting soft tissue, and spitting out shell fragments. Four-year-old juveniles are capable of consuming approximately 1–2 kg of molluscs per day. This bottom-dwelling molluscivore was purposely imported into the United States in the early 1970s for use as a food fish and also as a biological control agent for snails—an intermediate host for a trematode parasite in fish reared on fish farms. Two snail-eating cichlids, Trematocranus placodon and Maravichromis anaphyrmis, have been tried as biological control agents of schistosomes in fish ponds in Africa. Redear sunfish (Lepomis micropholus) and bluegill (Lepomis macrochirus) have been used to control quagga mussels (Dreissena bugensis) in the lower Colorado River in the US.
The common name of some fish reflects their molluscivorous feeding, for example, the "snail-crusher hap" (Trematocranus placodon), ""red rock sheller" (Haplochromis sp.), "Rusinga oral sheller" (Haplochromis sp.) and "rainbow sheller" (Haplochromis sp.). The redear sunfish is also known as the "shellcracker".
== In reptiles ==
Gray's monitor (or "butaan") is well known for its diet, which consists primarily of ripe fruit; however, several prey items are also consumed, including snails.
Monitors are generally carnivorous animals, which makes the Gray's monitor somewhat of an exception amongst the varanid family.
The prehistoric placodont reptiles is an extinct taxon of marine animals that superficially resembled lizards and turtles, most of whose dentition of peg-like incisors and enormous, molar-like teeth allowed them to prey on molluscs and brachiopods by plucking their prey off of the substrate, and crushing the shells.
== In birds ==
Among birds, the eponymous shorebirds known as oystercatchers are renowned for feeding upon bivalves. At least one bird of prey is also primarily a molluscivore—the snail kite, Rostrhamus sociabilis. The limpkin is a small rail-like bird that feeds almost entirely on apple snails. Other birds that will eat molluscs occasionally include mergansers, ducks, coots, dippers and spoonbills.
== In invertebrates ==

16
data/en.wikipedia.org/wiki/Molluscivore-1.md Normal file
View File

@ -0,0 +1,16 @@
---
title: "Molluscivore"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Molluscivore"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:58.235461+00:00"
instance: "kb-cron"
---
Cone snails: Some cone snails hunt and eat other kinds of snails, such as cowries, olive shells, turbo snails, and conch snails, while others will eat other cone snails. Conus marmoreus and Conus omaria are able to kill and swallow prey that are larger than themselves; some Conus species can swallow prey that weigh up to half of their own weight. Snails' bodies are attached to their shell by a columellar muscle that holds onto the columella, the axis of the snail. This muscle also allows the snail to retract back into its shell. If this muscle is broken, the snail will lose its shell and die. It is hard to detach this muscle in a live snail, or even in a dead snail. It is thought that the conotoxins in the venom of cone snails are able to completely relax this muscle so that the body can be pulled out from its shell. The cone snail uses its foot to hold the shell of its prey. Using a strong, steady pulling motion, the body of the snail can be forced out and then swallowed whole. Complete digestion of a snail can take many hours, even days.
Starfish: Primitive starfish, such as Astropecten and Luidia, swallow their prey whole and start to digest it in their cardiac stomachs. Shell valves and other inedible materials are ejected through their mouths. The semi-digested fluid is passed into their pyloric stomachs and caeca where digestion continues and absorption occurs. The margined sea star (Astropecten articulatus) is a well known molluscivore. It catches prey with its arms which it then takes to the mouth. The prey is then trapped by the long, moving prickles around the mouth cavity and swallowed food.
In more advanced species of starfish, the cardiac stomach can be everted from the organism's body to engulf and digest food. When the prey is a clam, the starfish pulls with its tube feet to separate the two valves slightly, and inserts a small section of its stomach, which releases enzymes to digest the prey. The stomach and the partially digested prey are later retracted into the disc. Here the food is passed on to the pyloric stomach, which always remains inside the disc. Because of this ability to digest food outside the body, starfish can hunt prey much larger than their mouths.
Crabs: The freshwater crabs Syntripsa matannensis and Syntripsa flavichela are classed as molluscivores. Using their massive and powerful claws, adult Florida stone crabs (Menippe mercenaria) feed on acorn barnacles, hard-shelled clams, scallops, and conch.
== References ==

20
data/en.wikipedia.org/wiki/Monoclonality-0.md Normal file
View File

@ -0,0 +1,20 @@
---
title: "Monoclonality"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Monoclonality"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:15:59.386578+00:00"
instance: "kb-cron"
---
In biology, monoclonality refers to the state of a line of cells that have been derived from a single clonal origin. Thus, "monoclonal cells" can be said to form a single clone. The term monoclonal comes from Ancient Greek monos 'alone, single' and klonos 'clone'.
The process of replication can occur in vivo, or may be stimulated in vitro for laboratory manipulations. The use of the term typically implies that there is some method to distinguish between the cells of the original population from which the single ancestral cell is derived, such as a random genetic alteration, which is inherited by the progeny.
Common usages of this term include:
Monoclonal antibody: a single hybridoma cell, which by chance includes the appropriate V(D)J recombination to produce the desired antibody, is cloned to produce a large population of identical cells. In informal laboratory jargon, the monoclonal antibodies isolated from cell culture supernatants of these hybridoma clones (hybridoma lines) are simply called monoclonals.
Monoclonal neoplasm (tumor): A single aberrant cell which has undergone carcinogenesis reproduces itself into a cancerous mass.
Monoclonal plasma cell (also called plasma cell dyscrasia): A single aberrant plasma cell which has undergone carcinogenesis reproduces itself, which in some cases is cancerous.
== References ==

30
data/en.wikipedia.org/wiki/Monogastric-0.md Normal file
View File

@ -0,0 +1,30 @@
---
title: "Monogastric"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Monogastric"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:00.599009+00:00"
instance: "kb-cron"
---
A monogastric organism defines one of the many types of digestive tracts found among different species of animals. The defining feature of a monogastric is that it has a simple single-chambered stomach (one stomach). A monogastric can be classified as an herbivore, an omnivore (facultative carnivore), or a carnivore (obligate carnivore). Herbivores have a plant-based diet, omnivores have a plant and meat-based diet, and carnivores only eat meat. Examples of monogastric herbivores include horses, rabbits, and guinea pigs. Examples of monogastric omnivores include humans, pigs, and hamsters. Furthermore, there are monogastric carnivores such as cats and seals.
A monogastric digestive tract is slightly different from other types of digestive tracts such as a ruminant and avian. Ruminant organisms have a four-chambered complex stomach and avian organisms have a two-chambered stomach. An example of a ruminant and avian are cattle and chickens.
== Digestive System ==
The digestive system of a monogastric is a one way tract that can be divided into two section: the foregut and the hindgut. The foregut consists of the mouth, esophagus, stomach, and small intestine. The hindgut consists of the large intestine, cecum, colon, and rectum. Each organ has its own role in the break down and digestion of food consumed by the animal.
=== Foregut ===
The digestive system and foregut start in the mouth. The mouth is in charge of the simplest form of break down of food throughout the digestion process. The mouth masticates, commonly known as chewing, food taken in by the organism. Saliva produced by the salivary glands within the mouth helps further break down the food with enzymes and aids the organism in swallowing. Amylase is an example of an enzyme found within many monogastric omnivore's saliva to help break down starches. Once food is swallowed, food travels down the esophagus. The esophagus does not participate in any food break down. Its main function is to perform contractions called peristalsis to push food towards the stomach. Located at the end of the esophagus is the lower esophageal sphincter, which keeps stomach acid from flowing into the esophagus. Animals such as horses and rabbits cannot vomit due to this strong muscle.
The stomach follows the esophagus and contains several muscles, acid, and enzymes. Its main function is to further break down food into a substance that is digestible for the small intestine. The lower muscles in the stomach mix the food with stomach acid. Stomach acid is made up of mainly hydrochloric acid (HCl), which has a pH of around 1.0 to 2.5. The acidity of stomach acid denatures consumed proteins, which helps digestive enzymes break down peptide bonds within the molecules. An example of this enzyme is pepsin.
The last organ in the foregut is the small intestine. The small intestine, like the esophagus, uses peristalsis to push food through the tract. It contains three parts: the duodenum, jejunum, ileum. The duodenum takes the partially digested food from the stomach and further breaks it down into digestible nutrients such as carbohydrates, lipids, and vitamins. The jejunum and ileum are responsible for absorbing most of the nutrients that pass through the digestive system. These sections contain a large number of villi that increase the surface area of the intestinal lining and help absorb the broken down nutrients.
=== Hindgut ===
The hindgut begins right after the small intestine and begins with the cecum, which is the first part of the large intestine. The cecum within monogastric animals can vary drastically. Carnivores contain a small cecum, while herbivores contain a large one due to their need of fermentation. The function of the cecum in monogastric carnivores and some omnivores is water and salt absorption. The cecum plays a much bigger role in monogastric herbivores that need a way to ferment cellulose for energy. Horses for example ferment their carbohydrates in the cecum and large intestine with the help of microbes, which makes them hindgut fermenters. This is opposed to foregut fermenters, or ruminants.
The large intestine is responsible for absorbing water into the bloodstream and turning leftover waste into stool. Waste includes large nutrient particles, dead cells, and other fluid. Bacteria in the large intestine break down some of the remaining nutrients in the food, while some vitamin and minerals continue to be absorbed. Peristalsis is used to push the stool into the rectum. The colon is similar to the large intestine. Its main function is forming stool and absorbing water. The rectum holds stool until its ready to be released through the anus. This is the last organ in the monogastric digestive system.
== References ==

23
data/en.wikipedia.org/wiki/Mycobiota-0.md Normal file
View File

@ -0,0 +1,23 @@
---
title: "Mycobiota"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Mycobiota"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:02.079658+00:00"
instance: "kb-cron"
---
Mycobiota (plural noun, no singular) are a group of all the fungi present in a particular geographic region (e.g. "the mycobiota of Ireland") or habitat type (e.g. "the mycobiota of cocoa"). An analogous term for Mycobiota is funga.
== Human mycobiota ==
Mycobiota exist on the surface and in the gastrointestinal system of humans. There are as many as sixty-six genera and 184 species in the gastrointestinal tract of healthy people. Most of these are in the Candida genera.
Though found to be present on the skin and in the gi tract in healthy individuals, the normal resident mycobiota can become pathogenic in those who are immunocompromised. Such multispecies infections lead to higher mortalities. In addition hospital-acquired infections by C. albicans have become a cause of major health concerns. A high mortality rate of 40-60% is associated with systemic infection. The best-studied of these are Candida species due to their ability to become pathogenic in immunocompromised and even in healthy hosts. Yeasts are also present on the skin, such as Malassezia species, where they consume oils secreted from the sebaceous glands. Pityrosporum (Malassezia) ovale, which is lipid-dependent and found only on humans. P. ovale was later divided into two species, P. ovale and P. orbiculare, but current sources consider these terms to refer to a single species of fungus, with M. furfur the preferred name.
== Other uses ==
There is a peer reviewed mycological journal titled Mycobiota.
== References ==

29
data/en.wikipedia.org/wiki/Natural_competence-0.md Normal file
View File

@ -0,0 +1,29 @@
---
title: "Natural competence"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Natural_competence"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:03.334926+00:00"
instance: "kb-cron"
---
In microbiology, genetics, cell biology, and molecular biology, competence is the ability of a cell to alter its genetics by taking up extracellular DNA from its environment through a process called transformation. Competence can be differentiated between natural competence and induced or artificial competence. Natural competence is a genetically specified ability of bacteria that occurs under natural conditions as well as in the laboratory. Artificial competence arises when cells in laboratory cultures are treated to make them transiently permeable to DNA. Competence allows for rapid adaptation and DNA repair of the cell.
== History ==
Natural competence was discovered by Frederick Griffith in 1928, when he showed that a preparation of killed cells of a pathogenic bacterium contained something that could transform related non-pathogenic cells into the pathogenic type. In 1944 Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that this 'transforming factor' was pure DNA. This was the first compelling evidence that DNA carries the genetic information of the cell.
Since then, natural competence has been studied in a number of different bacteria, particularly Bacillus subtilis, Streptococcus pneumoniae, Neisseria gonorrhoeae, Haemophilus influenzae and members of the Acinetobacter genus. Areas of active research include the mechanisms of DNA transport, the regulation of competence in different bacteria, and the evolutionary function of competence.
== Mechanisms of DNA uptake ==
In the laboratory, DNA is provided by the researcher, often as a genetically engineered fragment or plasmid. During uptake, DNA is transported across the cell membrane(s), and the cell wall if one is present. Once the DNA is inside the cell it may be degraded to nucleotides, which are reused for DNA replication and other metabolic functions. Alternatively it may be recombined into the cell's genome by its DNA repair enzymes. If this recombination changes the cell's genotype the cell is said to have been transformed. Artificial competence and transformation are used as research tools in many organisms.
In almost all naturally competent bacteria components of extracellular filaments called type IV pili bind extracellular double stranded DNA. The DNA is then translocated across the membrane (or membranes for gram negative bacteria) through multi-component protein complexes driven by the degradation of one strand of the DNA. Single stranded DNA in the cell is bound by a well-conserved protein, DprA, which loads the DNA onto RecA, which mediates homologous recombination through the classic DNA repair pathway.
== Regulation of competence ==
In laboratory cultures, natural competence is usually tightly regulated and often triggered by nutritional shortages or adverse conditions. However, the specific inducing signals and regulatory machinery are much more variable than the uptake machinery, regulation systems can vary in different species. Transcription factors have been discovered which regulate competence; an example is sxy (also known as tfoX) which has been found to be regulated in turn by a 5' non-coding RNA element. In bacteria capable of forming spores, conditions inducing sporulation often overlap with those inducing competence. Thus cultures or colonies containing sporulating cells often also contain competent cells.
Most naturally competent bacteria are thought to take up all DNA molecules with roughly equal efficiencies. However, bacteria in some families, such as Neisseriaceae and Pasteurellaceae, preferentially take up DNA fragments containing uptake signal sequences, which are short sequences that are frequent in their own genomes. In Neisseriaceae these sequences are referred as DNA uptake sequence (DUS), while in Pasteurellaceae they're termed uptake signal sequence (USS). Neisserial genomes contain thousands of copies of the preferred sequence GCCGTCTGAA, and Pasteurellacean genomes contain either AAGTGCGGT or ACAAGCGGT.
== Evolutionary functions and consequences of competence ==
Most proposals made for the primary evolutionary function of natural competence as a part of natural bacterial transformation fall into three categories: (1) the selective advantage of genetic diversity; (2) DNA uptake as a source of nucleotides (DNA as “food”); and (3) the selective advantage of a new strand of DNA to promote homologous recombinational repair of damaged DNA (DNA repair). It is possible that multiple proposals are true for different organisms. A secondary suggestion has also been made, noting the occasional advantage of horizontal gene transfer.
=== Hypothesis of genetic diversity ===
According to one hypothesis, bacterial transformation may play the same role in increasing genetic diversity that sex plays in higher organisms. However, the theoretical difficulties associated with the evolution of sex suggest that sex for genetic diversity is problematic. In the case of bacterial transformation, competence requires the high cost of a global protein synthesis switch, with, for example, more than 16 genes that are switched on only during competence of Streptococcus pneumoniae. However, since bacteria tend to grow in clones, the DNA available for transformation would generally have the same genotype as that of the recipient cells. Thus, there is always a high cost in protein expression without, in general, an increase in diversity. Other differences between competence and sex have been considered in models of the evolution of genes causing competence. These models found that competence's postulated recombinational benefits were even more elusive than those of sex.

24
data/en.wikipedia.org/wiki/Natural_competence-1.md Normal file
View File

@ -0,0 +1,24 @@
---
title: "Natural competence"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Natural_competence"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:03.334926+00:00"
instance: "kb-cron"
---
=== Hypothesis of DNA as food ===
The second hypothesis, DNA as food, relies on the fact that cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesize, these may make a significant contribution to the cell's energy budget. Some naturally competent bacteria also secrete nucleases into their surroundings, and all bacteria can take up the free nucleotides these nucleases generate from environmental DNA. The energetics of DNA uptake are not understood in any system, so it is difficult to compare the efficiency of nuclease secretion to that of DNA uptake and internal degradation. In principle the cost of nuclease production and the uncertainty of nucleotide recovery must be balanced against the energy needed to synthesize the uptake machinery and to pull DNA in. Other important factors are the likelihoods that nucleases and competent cells will encounter DNA molecules, the relative inefficiencies of nucleotide uptake from the environment and from the periplasm (where one strand is degraded by competent cells), and the advantage of producing ready-to-use nucleotide monophosphates from the other strand in the cytoplasm. Another complicating factor is the self-bias of the DNA uptake systems of species in the family Pasteurellaceae and the genus Neisseria, which could reflect either selection for recombination or for mechanistically efficient uptake.
=== Hypothesis of repair of DNA damage ===
In bacteria, the problem of DNA damage is most pronounced during periods of stress, particularly oxidative stress, that occur during crowding or starvation conditions. Some bacteria induce competence under such stress conditions, supporting the hypothesis that transformation helps DNA repair. In experimental tests, bacterial cells exposed to agents damaging their DNA, and then undergoing transformation, survived better than cells exposed to DNA damage that did not undergo transformation. In addition, competence to undergo transformation is often inducible by known DNA damaging agents. Thus, a strong short-term selective advantage for natural competence and transformation would be its ability to promote homologous recombinational DNA repair under conditions of stress.
=== Horizontal gene transfer ===
A long-term advantage may occasionally be conferred by occasional instances of horizontal gene transfer also called lateral gene transfer, (which might result from non-homologous recombination after competence is induced), that could provide for antibiotic resistance or other advantages.
Regardless of the nature of selection for competence, the composite nature of bacterial genomes provides abundant evidence that the horizontal gene transfer caused by competence contributes to the genetic diversity that makes evolution possible.
== See also ==
Transformation (genetics)
== References ==

24
data/en.wikipedia.org/wiki/Natural_landscape-0.md Normal file
View File

@ -0,0 +1,24 @@
---
title: "Natural landscape"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Natural_landscape"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:04.505812+00:00"
instance: "kb-cron"
---
A natural landscape is the original landscape that exists before it is acted upon by human culture. The natural landscape and the cultural landscape are separate parts of the landscape. However, in the 21st century, landscapes that are totally untouched by human activity no longer exist, so that reference is sometimes now made to degrees of naturalness within a landscape.
In Silent Spring (1962) Rachel Carson describes a roadside verge as it used to look: "Along the roads, laurel, viburnum and alder, great ferns and wildflowers delighted the traveler’s eye through much of the year" and then how it looks now following the use of herbicides: "The roadsides, once so attractive, were now lined with browned and withered vegetation as though swept by fire". Even though the landscape before it is sprayed is biologically degraded, and may well contains alien species, the concept of what might constitute a natural landscape can still be deduced from the context.
The phrase "natural landscape" was first used in connection with landscape painting, and landscape gardening, to contrast a formal style with a more natural one, closer to nature. Alexander von Humboldt (1769 – 1859) was to further conceptualize this into the idea of a natural landscape separate from the cultural landscape. Then in 1908 geographer Otto Schlüter developed the terms original landscape (Urlandschaft) and its opposite cultural landscape (Kulturlandschaft) in an attempt to give the science of geography a subject matter that was different from the other sciences. An early use of the actual phrase "natural landscape" by a geographer can be found in Carl O. Sauer's paper "The Morphology of Landscape" (1925).
== Origins of the term ==
The concept of a natural landscape was first developed in connection with landscape painting, though the actual term itself was first used in relation to landscape gardening. In both cases it was used to contrast a formal style with a more natural one, that is closer to nature. Chunglin Kwa suggests, "that a seventeenth-century or early-eighteenth-century pen could experience natural scenery 'just like on a painting,’ and so, with or without the use of the word itself, designate it as a landscape." With regard to landscape gardening John Aikin, commented in 1794: "Whatever, therefore, there be of novelty in the singular scenery of an artificial garden, it is soon exhausted, whereas the infinite diversity of a natural landscape presents an inexhaustible flore of new forms". Writing in 1844 the prominent American landscape gardener Andrew Jackson Downing comments: "straight canals, round or oblong pieces of water, and all the regular forms of the geometric mode ... would evidently be in violent opposition to the whole character and expression of natural landscape".
In his extensive travels in South America, Alexander von Humboldt became the first to conceptualize a natural landscape separate from the cultural landscape, though he does not actually use these terms. Andrew Jackson Downing was aware of, and sympathetic to, Humboldt's ideas, which therefore influenceded American landscape gardening
Subsequently, the geographer Otto Schlüter, in 1908, argued that by defining geography as a Landschaftskunde (landscape science) would give geography a logical subject matter shared by no other discipline. He defined two forms of landscape: the Urlandschaft (original landscape) or landscape that existed before major human induced changes and the Kulturlandschaft (cultural landscape) a landscape created by human culture. Schlüter argued that the major task of geography was to trace the changes in these two landscapes.
The term natural landscape is sometimes used as a synonym for wilderness, but for geographers natural landscape is a scientific term which refers to the biological, geological, climatological and other aspects of a landscape, not the cultural values that are implied by the word wilderness.
=== The natural and conservation ===
Matters are complicated by the fact that the worlds nature and natural have more than one meaning. On the one hand there is the main dictionary meaning for nature: "The phenomena of the physical world collectively, including plants, animals, the landscape, and other features and products of the earth, as opposed to humans or human creations." On the other hand, there is the growing awareness, especially since Charles Darwin, of humanities biological affinity with nature.
The dualism of the first definition has its roots is an "ancient concept", because early people viewed "nature, or the nonhuman world […] as a divine brother, godlike in its separation from humans." In the West, Christianity's myth of the fall, that is the expulsion of humankind from the Garden of Eden, where all creation lived in harmony, into an imperfect world, has been the major influence. Cartesian dualism, from the seventeenth century on, further reinforced this dualistic thinking about nature.
With this dualism goes value judgement as to the superiority of the natural over the artificial. Modern science, however, is moving towards a holistic view of naturetion.

43
data/en.wikipedia.org/wiki/Natural_landscape-1.md Normal file
View File

@ -0,0 +1,43 @@
---
title: "Natural landscape"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Natural_landscape"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:04.505812+00:00"
instance: "kb-cron"
---
==== America ====
What is meant by natural, within the American conservation movement, has been changing over the last century and a half.
In the mid-nineteenth century American began to realize that the land was becoming more and more domesticated and wildlife was disappearing. This led to the creation of American National Parks and other conservation sites. Initially it was believed that all that was needed to do was to separate what was seen as natural landscape and "avoid disturbances such as logging, grazing, fire and insect outbreaks." This, and subsequent environmental policy, until recently, was influenced by ideas of the wilderness. However, this policy was not consistently applied, and in Yellowstone Park, to take one example, the existing ecology was altered, firstly by the exclusion of Native Americans and later with the virtual extermination of the wolf population.
A century later, in the mid-twentieth century, it began to be believed that the earlier policy of "protection from disturbance was inadequate to preserve park values", and that is that direct human intervention was necessary to restore the landscape of National Parks to its ‘'natural'’ condition. In 1963 the Leopold Report argued that "A national park should represent a vignette of primitive America". This policy change eventually led to the restoration of wolves in Yellowstone Park in the 1990s.
However, recent research in various disciplines indicates that a pristine natural or "primitive" landscape is a myth, and it now realised that people have been changing the natural into a cultural landscape for a long while, and that there are few places untouched in some way from human influence. The earlier conservation policies were now seen as cultural interventions. The idea of what is natural and what artificial or cultural, and how to maintain the natural elements in a landscape, has been further complicated by the discovery of global warming and how it is changing natural landscapes.
Also important is a reaction recently amongst scholars against dualistic thinking about nature and culture. Maria Kaika comments: "Nowadays, we are beginning to see nature and culture as intertwined once again – not ontologically separated anymore […].What I used to perceive as a compartmentalized world, consisting of neatly and tightly sealed, autonomous 'space envelopes' (the home, the city, and nature) was, in fact, a messy socio-spatial continuum". And William Cronon argues against the idea of wilderness because it "involves a dualistic vision in which the human is entirely outside the natural" and affirms that "wildness (as opposed to wilderness) can be found anywhere" even "in the cracks of a Manhattan sidewalk." According to Cronon we have to "abandon the dualism that sees the tree in the garden as artificial […] and the tree in the wilderness as natural […] Both in some ultimate sense are wild." Here he bends somewhat the regular dictionary meaning of wild, to emphasise that nothing natural, even in a garden, is fully under human control.
==== Europe ====
The landscape of Europe has considerably altered by people and even in an area, like the Cairngorm Mountains of Scotland, with a low population density, only " the high summits of the Cairngorm Mountains, consist entirely of natural elements. These high summits are of course only part of the Cairngorms, and there are no longer wolves, bears, wild boar or lynx in Scotland's wilderness. The Scots pine in the form of the Caledonian forest also covered much more of the Scottish landscape than today.
The Swiss National Park, however, represent a more natural landscape. It was founded in 1914, and is one of the earliest national parks in Europe.
Visitors are not allowed to leave the motor road, or paths through the park, make fire or camp. The only building within the park is Chamanna Cluozza, mountain hut. It is also forbidden to disturb the animals or the plants, or to take home anything found in the park. Dogs are not allowed. Due to these strict rules, the Swiss National Park is the only park in the Alps who has been categorized by the IUCN as a strict nature reserve, which is the highest protection level.
== History of natural landscape ==
No place on the Earth is unaffected by people and their culture. People are part of biodiversity, but human activity affects biodiversity, and this alters the natural landscape. Mankind have altered landscape to such an extent that few places on earth remain pristine, but once free of human influences, the landscape can return to a natural or near natural state.
Even the remote Yukon and Alaskan wilderness, the bi-national Kluane-Wrangell-St. Elias-Glacier Bay-Tatshenshini-Alsek park system comprising Kluane, Wrangell-St Elias, Glacier Bay and Tatshenshini-Alsek parks, a UNESCO World Heritage Site, is not free from human influence, because the Kluane National Park lies within the traditional territories of the Champagne and Aishihik First Nations and Kluane First Nation who have a long history of living in this region. Through their respective Final Agreements with the Canadian Government, they have made into law their rights to harvest in this region.
=== Procession ===
Through different intervals of time, the process of natural landscapes have been shaped by a series of landforms, mostly due to its factors, including tectonics, erosion, weathering and vegetation.
== Examples of cultural forces ==
Cultural forces intentionally or unintentionally, have an influence upon the landscape. Cultural landscapes are places or artifacts created and maintained by people. Examples of cultural intrusions into a landscape are: fences, roads, parking lots, sand pits, buildings, hiking trails, management of plants, including the introduction of invasive species, extraction or removal of plants, management of animals, mining, hunting, natural landscaping, farming and forestry, pollution. Areas that might be confused with a natural landscape include public parks, farms, orchards, artificial lakes and reservoirs, managed forests, golf courses, nature center trails, gardens.
== See also ==
== Notes ==
== References ==
== External links ==
Developing a forest naturalness indicator for Europe
Scottish heritage: Natural Spaces
Carl O. Sauer. "The Morphology of Landscape", University of California Publications in Geography, vol. 2, No. 2, 12 October 1925, pp. 19–53 (scroll down)

32
data/en.wikipedia.org/wiki/Obligate-0.md Normal file
View File

@ -0,0 +1,32 @@
---
title: "Obligate"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Obligate"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:05.776718+00:00"
instance: "kb-cron"
---
As an adjective, obligate means "by necessity" (antonym facultative) and is used mainly in biology in phrases such as:
Obligate aerobe, an organism that cannot survive without oxygen
Obligate anaerobe, an organism that cannot survive in the presence of oxygen
Obligate air-breather, a term used in fish physiology to describe those that respire entirely from the atmosphere
Obligate biped, an animal that relies solely on walking or running on its two hind limbs for locomotion
Obligate carnivore, an organism dependent for survival on a diet of animal flesh.
Obligate chimerism, a kind of organism with two distinct sets of DNA, always
Obligate hibernation, a state of inactivity in which some organisms survive conditions of insufficiently available resources.
Obligately intracellular parasite, a parasitic microorganism that cannot reproduce without entering a suitable host cell
Obligate necrophage, an animal that uses carrion as its sole or main food source and depends on carrion for survival or reproduction
Obligate parasite, a parasite that cannot reproduce without exploiting a suitable host
Obligate photoperiodic plant, a plant that requires sufficiently long or short nights before it initiates flowering, germination or similarly functions
Obligate scavenger, an animal that uses decaying biomass (e.g. carrion, dead plant material) as its sole or main food source and depends on this for survival or reproduction
Obligate symbionts, organisms that can only live together in a symbiosis
== See also ==
Opportunism (biological)
== References ==

25
data/en.wikipedia.org/wiki/Oophagy-0.md Normal file
View File

@ -0,0 +1,25 @@
---
title: "Oophagy"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Oophagy"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:07.109473+00:00"
instance: "kb-cron"
---
Oophagy ( oh-OFF-ə-jee) or ovophagy, literally "egg eating", is the practice of
embryos feeding on eggs produced by the ovary while still inside the mother's uterus. The word oophagy is formed from the classical Greek ᾠόν (ōion, "egg") and classical Greek φᾱγεῖν (phāgein, "to eat"). In contrast, adelphophagy is the cannibalism of a multi-celled embryo.
Oophagy is thought to occur in all sharks in the order Lamniformes and has been recorded in the bigeye thresher (Alopias superciliosus), the pelagic thresher (A. pelagicus), the shortfin mako (Isurus oxyrinchus) and the porbeagle (Lamna nasus) among others. It also occurs in the tawny nurse shark (Nebrius ferrugineus), and in the family Pseudotriakidae.
This practice may lead to larger embryos or prepare the embryo for a predatory lifestyle.
There are variations in the extent of oophagy among the different shark species. The grey nurse shark (Carcharias taurus) practices intrauterine cannibalism, the first developed embryo consuming both additional eggs and any other developing embryos. Slender smooth-hounds (Gollum attenuatus), form egg capsules which contain 30-80 ova, within which only one ovum develops; the remaining ova are ingested and their yolks stored in its external yolk sac. The embryo then proceeds to develop normally, without ingesting further eggs.
Oophagy is used as a synonym of the egg predation practised by some snakes and other animals.
Oophagy is used to describe the destruction of non-queen eggs in nests of eusocial insects, especially the social wasps, bees, and ants. This is seen in the wasp species Polistes biglumis and Polistes humilis. Oophagy has been observed in the ant Leptothorax acervorum and the wasp Parachartergus fraternus, where oophagy is practiced to increase energy circulation and provide more dietary protein.
The social wasp Polistes fuscatus use oophagy as a method to establish a dominance hierarchy; dominant females eat the eggs of subordinate females such that they no longer produce eggs, possibly due to the unnecessary expenditure of energy and resources. This behavior has also been observed in some bee species. Such bee species include Xylocopa sulcatipes and Bombus ruderatus, where queen bees will eat larvae deposited by workers or eject them from the nest in order to maintain dominance over the colony.
== See also ==
Siblicide
== References ==

27
data/en.wikipedia.org/wiki/Oxford_Dictionary_of_Biology-0.md Normal file
View File

@ -0,0 +1,27 @@
---
title: "Oxford Dictionary of Biology"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Oxford_Dictionary_of_Biology"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:08.292222+00:00"
instance: "kb-cron"
---
Oxford Dictionary of Biology (often abbreviated to ODB) is a multiple editions dictionary published by the English Oxford University Press. With more than 5,500 entries, it contains comprehensive information in English on topics relating to biology, biophysics, and biochemistry. The first edition was published in 1985 as A Concise Dictionary of Biology. The seventh edition, A Dictionary of Biology, was published in 2015 and it was edited by Robert Hine and Elizabeth Martin.
Robert Hine studied at King's College London and University of Aberdeen and since 1984 he has contributed to numerous journals and books.
== Digital and on-line availability ==
The sixth and seventh editions of the ODB are available online for members of subscribed institutions and for subscribed individuals via Oxford Reference.
== Editions ==
The first edition of Oxford Dictionary of Biology was first published in 1985 and the seventh edition in 2015.
== References ==
== External links ==
Oxford Reference Online

39
data/en.wikipedia.org/wiki/Paratype-0.md Normal file
View File

@ -0,0 +1,39 @@
---
title: "Paratype"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Paratype"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:09.515534+00:00"
instance: "kb-cron"
---
In zoology and botany, a paratype is a specimen of an organism that helps define what the scientific name of a species and other taxon actually represents, but it is not the holotype (and in botany is also neither an isotype nor a syntype). Often there is more than one paratype. Paratypes are usually held in museum research collections.
The exact meaning of the term paratype when it is used in zoology is not the same as the meaning when it is used in botany. In both cases however, this term is used in conjunction with holotype.
== Zoology ==
In zoological nomenclature, a paratype is officially defined as "Each specimen of a type series other than the holotype."
In turn, this definition relies on the definition of a "type series". A type series is the material (specimens of organisms) that was cited in the original publication of the new species or subspecies, and was not excluded from being type material by the author (this exclusion can be implicit, e.g., if an author mentions "paratypes" and then subsequently mentions "other material examined", the latter are not included in the type series), nor referred to as a variant, or only dubiously included in the taxon (e.g., a statement such as "I have before me a specimen which agrees in most respects with the remainder of the type series, though it may yet prove to be distinct" would exclude this specimen from the type series).
Thus, in a type series of five specimens, if one is the holotype, the other four will be paratypes.
A paratype may originate from a different locality than the holotype. A paratype cannot become a lectotype, though it is eligible (and often desirable) for designation as a neotype.
The International Code of Zoological Nomenclature (ICZN) has not always required a type specimen, but any species or subspecies newly described after the end of 1999 must have a designated holotype or syntypes.
A related term is allotype, a term that indicates a specimen that exemplifies the opposite sex of the holotype, and is almost without exception designated in the original description, and, accordingly, part of the type series, and thus a paratype; in such cases, it is functionally no different from any other paratype. It has no nomenclatural standing whatsoever, and although the practice of designating an allotype is recognized by the ICZN, it is not a "name-bearing type" and there are no formal rules controlling how one is designated. Apart from species exhibiting strong sexual dimorphism, relatively few authors take the trouble to designate such a specimen. It is not uncommon for an allotype to be a member of an entirely different species from the holotype, because of an incorrect association by the original author.
== Botany ==
In botanical nomenclature, a paratype is a specimen cited in the original description that may not have been said to be a type. It is not the holotype nor an isotype (duplicate of the holotype).
If no types were specified, then all specimens cited are syntypes.
If more than one specimen was cited as the type, then they are all syntypes, but specimens cited but not listed as types are paratypes. (Articles 9.5 and 9.6).
Like other types, a paratype may be specified for taxa at the rank of family or below (Article 7).
A paratype may be designated as a lectotype if no holotype, isotype, syntype, or isosyntype (duplicate of a syntype) is extant (Article 9.12).
== See also ==
Biological type
Scientific name
Binomial nomenclature
== References ==

48
data/en.wikipedia.org/wiki/Patch_dynamics-0.md Normal file
View File

@ -0,0 +1,48 @@
---
title: "Patch dynamics"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Patch_dynamics"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:10.796882+00:00"
instance: "kb-cron"
---
Patch dynamics is an ecological perspective that the structure, function, and dynamics of ecological systems can be understood through studying their interactive patches. Patch dynamics, as a term, may also refer to the spatiotemporal changes within and among patches that make up a landscape. Patch dynamics is ubiquitous in terrestrial and aquatic systems across organizational levels and spatial scales. From a patch dynamics perspective, populations, communities, ecosystems, and landscapes may all be studied effectively as mosaics of patches that differ in size, shape, composition, history, and boundary characteristics.
The idea of patch dynamics dates back to the 1940s when plant ecologists studied the structure and dynamics of vegetation in terms of the interactive patches that it comprises. A mathematical theory of patch dynamics was developed by Simon Levin and Robert Paine in the 1970s, originally to describe the pattern and dynamics of an intertidal community as a patch mosaic created and maintained by tidal disturbances. Patch dynamics became a dominant theme in ecology between the late 1970s and the 1990s.
Patch dynamics is a conceptual approach to ecosystem and habitat analysis that emphasizes dynamics of heterogeneity within a system (i.e. that each area of an ecosystem is made up of a mosaic of small 'sub-ecosystems').
Diverse patches of habitat created by natural disturbance regimes are seen as critical to the maintenance of this diversity (ecology). A habitat patch is any discrete area with a definite shape, spatial and configuration used by a species for breeding or obtaining other resources. Mosaics are the patterns within landscapes that are composed of smaller elements, such as individual forest stands, shrubland patches, highways, farms, or towns.
== Patches and mosaics ==
Historically, due to the short time scale of human observation, mosaic landscapes were perceived to be static patterns of human population mosaics. This focus centered on the idea that the status of a particular population, community, or ecosystem could be understood by studying a particular patch within a mosaic. However, this perception ignored the conditions that interact with, and connect patches. In 1979, Bormann and Likens coined the phrase shifting mosaic to describe the theory that landscapes change and fluctuate, and are in fact dynamic. This is related to the battle of cells that occurs in a Petri dish.
Patch dynamics refers to the concept that landscapes are dynamic. There are three states that a patch can exist in: potential, active, and degraded. Patches in the potential state are transformed into active patches through colonization of the patch by dispersing species arriving from other active or degrading patches. Patches are transformed from the active state to the degraded state when the patch is abandoned, and patches change from degraded to active through a process of recovery.
Logging, fire, farming, and reforestation can all contribute to the process of colonization, and can effectively change the shape of the patch. Patch dynamics also refers to changes in the structure, function, and composition of individual patches that can, for example, affect the rate of nutrient cycling.
Patches are also linked. Although patches may be separated in space, migration can occur from one patch to another. This migration maintains the population of some patches, and can be the mechanism by which some plant species spread. This implies that ecological systems within landscapes are open, rather than closed and isolated.
== Conservation efforts ==
Recognizing the patch dynamics within a system is needed for conservation efforts to succeed. Successful conservation includes understanding how a patch changes and predicting how they will be affected by external forces. These externalities include natural effects, such as land use, disturbance, restoration, and succession, and the effects of human activities. In a sense, conservation is the active maintenance of patch dynamics. The analysis of patch dynamics could be used to predict changes in biodiversity of an ecosystem. When patches of species can be tracked, it has been shown that fluctuations on the biggest patch (the most dominant species) can be used as an early warning of a biodiversity collapse. That means that if external conditions, like climate change and habitat fragmentation, change the internal dynamics of patches, a sharp reduction in biodiversity can be detected before it is produced.
== See also ==
Conservation biology – Study of threats to biological diversity
Edge effect – Ecological conceptPages displaying short descriptions of redirect targets
Forest dynamics – Biotic and abiotic ecosystem influences
Habitat conservation – Management practice for protecting types of environments
Habitat corridor – Connecting wild territories for animalsPages displaying short descriptions of redirect targets
Habitat fragmentation – Discontinuities in an organism's environment causing population fragmentation
Island biogeography – Study of the ecology of isolated habitatsPages displaying short descriptions of redirect targets
Landscape ecology – Relationships between ecological processes in the environment and particular ecosystems
Spatial ecology – Study of the distribution or space occupied by species
== References ==
== Further reading ==
Forman, Richard T. T. (2014). "Land Mosaics: The Ecology of Landscapes and Regions". Foundations:The Ecological Design and Planning Reader. pp. 217–234. doi:10.5822/978-1-61091-491-8_21.
Levin, Simon A.; Paine, R. T. (July 1974). "Disturbance, Patch Formation, and Community Structure". Proceedings of the National Academy of Sciences. 71 (7): 2744–2747. doi:10.1073/pnas.71.7.2744. PMC 388546. PMID 4527752.
Simon A. Levin; Thomas M. Powell; John W. Steele, eds. (1993). Patch Dynamics (1st 1993 ed.). Berlin, Heidelberg: Springer Berlin Heidelberg. doi:10.1007/978-3-642-50155-5. ISBN 978-3-540-56525-3.
Wu, Jianguo; Loucks, Orie L. (December 1995). "From Balance of Nature to Hierarchical Patch Dynamics: A Paradigm Shift in Ecology". The Quarterly Review of Biology. 70 (4): 439–466. doi:10.1086/419172.
Wu, Jianguo (2013-05-28). "Ecological Succession, Species Interactions & Landscape Ecology". Encyclopedia Britannica. Retrieved 2026-01-22.

33
data/en.wikipedia.org/wiki/Perceptual_trap-0.md Normal file
View File

@ -0,0 +1,33 @@
---
title: "Perceptual trap"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Perceptual_trap"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:12.018213+00:00"
instance: "kb-cron"
---
A perceptual trap is an ecological scenario in which environmental change, typically anthropogenic, leads an organism to avoid an otherwise high-quality habitat. The concept is related to that of an ecological trap, in which environmental change causes preference towards a low-quality habitat.
== History ==
In a 2004 article discussing source–sink dynamics, James Battin did not distinguish between high-quality habitats that are preferred or avoided, labelling both "sources". The latter scenario, in which a high-quality habitat is avoided, was first recognised as an important phenomenon in 2007 by Gilroy and Sutherland, who described them as "undervalued resources". The term "perceptual trap" was first proposed by Michael Patten and Jeffrey Kelly in a 2010 article. Hans Van Dyck argues that the term is misleading because perception is also a major component in other cases of trapping.
== Description ==
Animals use discrete environmental cues to select habitat. A perceptual trap occurs if change in an environmental cue leads an organism to avoid a high-quality habitat. It differs, therefore, from simple habitat avoidance, which may be a correct decision given the habitat's quality. The concept of a perceptual trap is related to that of an ecological trap, in which environmental change causes preference towards a low-quality habitat. There is expected to be strong natural selection against ecological traps, but not necessarily against perceptual traps, as Allee effects may restrict a population’s ability to establish itself.
== Examples ==
To support the concept of a perceptual trap, Patten and Kelly cited a study of the lesser prairie-chicken (Tympanuchus pallidicinctus). The species' natural environment, shinnery oak grassland, is often treated with the herbicide tebuthiuron to increase grass cover for cattle grazing. Herbicide treatment resulted in less shrub cover, a habitat cue that caused female lesser prairie-chickens to avoid the habitat in favour of untreated areas. However, females who nested in herbicide-treated areas achieved comparable nesting successes and clutch sizes to those in untreated areas. Patten and Kelly suggest that the adverse effects of tebuthiuron treatment on nesting success are countered by various effects, such as greater nest concealment through increased grass cover. Therefore, female birds are erroneously avoiding a high-quality habitat. Patten and Kelly also cited as a possible perceptual trap the cases of the spotted towhee (Pipilo maculatus) and rufous-crowned sparrow (Aimophila ruficeps), which tend to avoid habitat fragments, even though birds nesting in habitat fragments achieve increased nesting success due to a reduction in snake predation.
== See also ==
Ecological trap
Source–sink dynamics
Type I and type II errors
== References ==

21
data/en.wikipedia.org/wiki/Perennation-0.md Normal file
View File

@ -0,0 +1,21 @@
---
title: "Perennation"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Perennation"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:13.223016+00:00"
instance: "kb-cron"
---
In botany, perennation is the ability of organisms, particularly plants, to survive from one germinating season to another, especially under unfavourable conditions such as drought or winter cold. It typically involves development of a perennating organ, which stores enough nutrients to sustain the organism during the unfavourable season, and develops into one or more new plants the following year. Perennation is done by stem in plants to tide over unfavourable condition. Common forms of perennating organs are storage organs (e.g. bulbs, tubers, rhizomes and corm), buds and oxalis . Perennation is closely related with vegetative reproduction, as the organisms commonly use the same organs for both survival and reproduction.
== See also ==
Overwintering
Plant pathology
Sclerotium
Turion (botany)
== References ==

17
data/en.wikipedia.org/wiki/Permanent_vegetative_cover-0.md Normal file
View File

@ -0,0 +1,17 @@
---
title: "Permanent vegetative cover"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Permanent_vegetative_cover"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:14.512123+00:00"
instance: "kb-cron"
---
Permanent vegetative cover refers to trees, perennial bunchgrasses and grasslands, legumes, and shrubs with an
expected life span of at least 5 years.
In the United States, permanent cover is required on cropland entered into the Conservation Reserve Program.
== References ==
This article incorporates public domain material from Jasper Womach. Report for Congress: Agriculture: A Glossary of Terms, Programs, and Laws, 2005 Edition (PDF). Congressional Research Service.

20
data/en.wikipedia.org/wiki/Permissiveness_(endocrinology)-0.md Normal file
View File

@ -0,0 +1,20 @@
---
title: "Permissiveness (endocrinology)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Permissiveness_(endocrinology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:15.770918+00:00"
instance: "kb-cron"
---
In endocrinology, permissiveness is a biochemical phenomenon in which the presence of one hormone is required in order for another hormone to exert its full effects on a target cell. Hormones can interact in permissive, synergistic, or antagonistic ways. The chemical classes of hormones include amines, polypeptides, glycoproteins and steroids. Permissive hormones act as precursors to active hormones and may be classified as either prohormones or prehormones. It stimulate the formation of receptors of that hormone.
== Examples ==
Thyroid hormone increases the number of beta-adrenergic receptors available for epinephrine at the latter's target cell, thereby increasing epinephrine's effect on that cell. Specially in cardiac cell. Without the thyroid hormone, epinephrine would have only a weak effect.
Cortisol is required for the response of vascular and bronchial smooth muscle to catecholamines. Cortisol is also required for the lipolytic effect of catecholamines, ACTH, and growth hormone on fat cells. Cortisol is also required for the calorigenic effects of glucagon and catecholamines.
The effects of a hormone in the body depend on its concentration. Permissive actions of glucocorticoids like cortisol generally occur at low concentrations. Abnormally high amounts of a hormone can result in atypical effects. Glucocorticoids function by attaching to cytoplasmic receptors to either enhance or suppress changes in the transcription of DNA and thus the synthesis of proteins. Glucocorticoids also inhibit the secretion of cytokines via post-translational modification effects.
== References ==

28
data/en.wikipedia.org/wiki/Photoautotroph-0.md Normal file
View File

@ -0,0 +1,28 @@
---
title: "Photoautotroph"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Photoautotroph"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:16.929231+00:00"
instance: "kb-cron"
---
Photoautotrophs are organisms that can utilize light energy from sunlight, and elements (such as carbon) from inorganic compounds, to produce organic materials needed to sustain their own metabolism (i.e. autotrophy). Such biological activities are known as photosynthesis, and examples of such organisms include plants, algae and cyanobacteria.
Eukaryotic photoautotrophs absorb photonic energy through the photopigment chlorophyll (a porphyrin derivative) in their endosymbiont chloroplasts, while prokaryotic photoautotrophs use chlorophylls and bacteriochlorophylls present in free-floating cytoplasmic thylakoids. Plants, algae, and cyanobacteria perform oxygenic photosynthesis that produces oxygen as a byproduct, while some bacteria perform anoxygenic photosynthesis.
== Origin and the Great Oxidation Event ==
Chemical and geological evidence indicate that photosynthetic cyanobacteria existed about 2.6 billion years ago and anoxygenic photosynthesis had been taking place since a billion years before that. Oxygenic photosynthesis was the primary source of free oxygen and led to the Great Oxidation Event roughly 2.4 to 2.1 billion years ago during the Neoarchean-Paleoproterozoic boundary. Although the end of the Great Oxidation Event was marked by a significant decrease in gross primary productivity that eclipsed extinction events, the development of aerobic respiration enabled more energetic metabolism of organic molecules, leading to symbiogenesis and the evolution of eukaryotes, and allowing the diversification of complex life on Earth.
== Prokaryotic photoautotrophs ==
Prokaryotic photoautotrophs include Cyanobacteria, Pseudomonadota, Chloroflexota, Acidobacteriota, Chlorobiota, Bacillota, Gemmatimonadota, and Eremiobacterota.
Cyanobacteria is the only prokaryotic group that performs oxygenic photosynthesis. Anoxygenic photosynthetic bacteria use PSI- and PSII-like photosystems, which are pigment protein complexes for capturing light. Both of these photosystems use bacteriochlorophyll. There are multiple hypotheses for how oxygenic photosynthesis evolved. The loss hypothesis states that PSI and PSII were present in anoxygenic ancestor cyanobacteria from which the different branches of anoxygenic bacteria evolved. The fusion hypothesis states that the photosystems merged later through horizontal gene transfer. The most recent hypothesis suggests that PSI and PSII diverged from an unknown common ancestor with a protein complex that was coded by one gene. These photosystems then specialized into the ones that are found today.
== Eukaryotic photoautotrophs ==
Eukaryotic photoautotrophs include red algae, haptophytes, stramenopiles, cryptophytes, chlorophytes, and land plants. These organisms perform photosynthesis through organelles called chloroplasts and are believed to have originated about 2 billion years ago. Comparing the genes of chloroplast and cyanobacteria strongly suggests that chloroplasts evolved as a result of endosymbiosis with cyanobacteria that gradually lost the genes required to be free-living. However, it is difficult to determine whether all chloroplasts originated from a single, primary endosymbiotic event, or multiple independent events. Some brachiopods (Gigantoproductus) and bivalves (Tridacna) also evolved photoautotrophy.
== References ==

46
data/en.wikipedia.org/wiki/Photoheterotroph-0.md Normal file
View File

@ -0,0 +1,46 @@
---
title: "Photoheterotroph"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Photoheterotroph"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:18.165326+00:00"
instance: "kb-cron"
---
Photoheterotrophs (Gk: photo = light, hetero = (an)other, troph = nourishment) are heterotrophic phototrophs—that is, they are organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source. Consequently, they use organic compounds from the environment to satisfy their carbon requirements; these compounds include carbohydrates, fatty acids, and alcohols. Examples of photoheterotrophic organisms include purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria. These microorganisms are ubiquitous in aquatic habitats, occupy unique niche-spaces, and contribute to global biogeochemical cycling. Recent research has also indicated that the oriental hornet and some aphids may be able to use light to supplement their energy supply. Some recent research has even found hints of photoheterotrophy in a few eukaryotes, though it's still being studied.
== Research ==
Studies have shown that mammalian mitochondria can also capture light and synthesize ATP when mixed with pheophorbide, a light-capturing metabolite of chlorophyll. Research demonstrated that the same metabolite when fed to the worm Caenorhabditis elegans leads to increase in ATP synthesis upon light exposure, along with an increase in life span.
Furthermore, inoculation experiments suggest that mixotrophic Ochromonas danica (i.e., Golden algae)—and comparable eukaryotes—favor photoheterotrophy in oligotrophic (i.e., nutrient-limited) aquatic habitats. This preference may increase energy-use efficiency and growth by reducing investment in inorganic carbon fixation (e.g., production of autotrophic machineries such as RuBisCo and PSII).
== Energy and carbon sources ==
Photoheterotrophs get energy from light and carbon from organic substances like carbohydrates, fatty acids, or alcohols.
They're different from photoautotrophs, which use carbon dioxide for carbon, and from chemoheterotrophs, which get both energy and carbon from organic compounds. Photoheterotrophy tends to be useful in places where light is available but carbon dioxide is in short supply—like some parts of the ocean or shallow water environments.
== Metabolism ==
Photoheterotrophs generate ATP using light, in one of two ways: they use a bacteriochlorophyll-based reaction center, or they use a bacteriorhodopsin. The chlorophyll-based mechanism is similar to that used in photosynthesis, where light excites the molecules in a reaction center and causes a flow of electrons through an electron transport chain (ETC). This flow of electrons through the proteins causes hydrogen ions (protons) to be pumped across a membrane. The energy stored in this proton gradient is used to drive ATP synthesis. Unlike in photoautotrophs, the electrons flow only in a cyclic pathway: electrons released from the reaction center flow through the ETC and return to the reaction center. They are not utilized to reduce any organic compounds. Purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria are examples of bacteria that carry out this scheme of photoheterotrophy.
Other organisms, including halobacteria, flavobacteria, and vibrios, have purple-rhodopsin-based proton pumps that supplement their energy supply. The archaeal version is called bacteriorhodopsin, while the eubacterial version is called proteorhodopsin. The pump consists of a single protein bound to a Vitamin A derivative: retinal. The pump may have accessory pigments (e.g., carotenoids) associated with the protein. When light is absorbed by the retinal molecule, the molecule isomerises. This drives the protein to change shape and pump a proton across the membrane. The proton gradient can then be used to generate ATP, transport solutes across the membrane, or drive a flagellar motor. One particular flavobacterium cannot reduce carbon dioxide using light, but uses the energy from its rhodopsin system to fix carbon dioxide through anaplerotic fixation. The flavobacterium is still a heterotroph as it needs reduced carbon compounds to live and cannot subsist on only light and CO2. It cannot carry out reactions in the form of
n CO2 + 2n H2D + photons → (CH2O)n + 2n D + n H2O,
where H2D may be water, H2S or another compound/compounds providing the reducing electrons and protons; the 2D + H2O pair represents an oxidized form.
However, it can fix carbon in reactions like:
CO2 + pyruvate + ATP (from photons) → malate + ADP +Pi
where malate or other useful molecules are otherwise obtained by breaking down other compounds by
carbohydrate + O2 → malate + CO2 + energy.
This method of carbon fixation is useful when reduced carbon compounds are scarce and cannot be wasted as CO2 during interconversions, but energy is plentiful in the form of sunlight.
== Examples of photoheterotrophs ==
Organisms that are known to be photoheterotrophic include:
Members of the Heliobacteria
Purple non-sulfur bacteria like Rhodospirillum rubrum
Green non-sulfur bacteria such as Chloroflexus aurantiacus
Salt-loving archaea like Halobacterium salinarum
Some marine bacteria, especially aerobic anoxygenic phototrophs and those with proteorhodopsin
Some other organisms—though not true photoheterotrophs—have interesting features that might be similar. For example, the Oriental hornet can absorb light with pigments in its body and may use that light for energy. Certain aphids have also been shown to make light-sensitive carotenoids that could help them get energy from sunlight. A few recent studies even suggest that yeast cells can be modified to respond to light by inserting genes that allow them to use rhodopsin.
== Ecology ==

27
data/en.wikipedia.org/wiki/Photoheterotroph-1.md Normal file
View File

@ -0,0 +1,27 @@
---
title: "Photoheterotroph"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Photoheterotroph"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:18.165326+00:00"
instance: "kb-cron"
---
=== Distribution and niche partitioning ===
Photoheterotrophs are found in many different water-based environments like oceans, lakes, and even rice paddies. They tend to live near the surface of the water, where there's enough light but not much carbon dioxide.
Photoheterotrophs—either 1) cyanobacteria (i.e. facultative heterotrophs in nutrient-limited environments like Synechococcus and Prochlorococcus), 2) aerobic anoxygenic photoheterotrophic bacteria (AAP; employing bacteriochlorophyll-based reaction centers), 3) proteorhodopsin (PR)-containing bacteria and archaea, and 4) heliobacteria (i.e., the only phototroph with bacteriochlorophyll g pigments, or Gram-positive membrane) are found in various aquatic habitats including oceans, stratified lakes, rice fields, and environmental extremes.
In oceans' photic zones, up to 10% of bacterial cells are capable of AAP, whereas greater than 50% of net marine microorganisms house PR—reaching up to 90% in coastal biomes. As demonstrated in inoculation experiments, photoheterotrophy may provide these planktonic microbes competitive advantages 1) relative to chemoheterotrophs in oligotrophic (i.e., nutrient-poor) environments via increased nutrient use-efficiency (i.e., organic carbon fuels biosynthesis, excessively, versus energy production) and 2) by eliminating investment in physiologically costly autotrophic enzymes/complexes (RuBisCo and PSII). Furthermore, in Arctic oceans, AAP and PR photoheterotrophs are prominent in ice-covered regions during wintertime per light scarcity. Lastly, seasonal turnover has been observed in marine AAPs as ecotypes (i.e., genetically similar taxa with differing functional trait and/or environmental preferences) segregate into temporal niches.
In stratified (i.e., euxinic) lakes, photoheterotrophs—alongside other anoxygenic phototrophs (e.g., purple/green sulfur bacteria fixing carbon dioxide via electron donors such as ferrous iron, sulfide, and hydrogen gas)—often occupy the chemocline in the water column and/or sediments. In this zone, dissolved oxygen is reduced, light is limited to long wavelengths (e.g., red and infrared) left-over by oxygenic phototrophs (e.g., cyanobacteria), and anaerobic metabolisms (i.e., those occurring in the absence of oxygen) begin introducing sulfide and bioavailable nutrients (e.g., organic carbon, phosphate, and ammonia) through upward diffusion.
Heliobacteria are obligate anaerobes primarily located in rice fields, where low sulfide concentrations prevent competitive exclusion of purple/green sulfur bacteria. These waterlogged environments may facilitate symbiotic relationships between heliobacteria and rice plants as fixed nitrogen—from the former—is exchanged for carbon-rich root exudates.
Observation studies have characterized photoheterotrophs (e.g., Green non-sulfur bacteria such as Chloroflexi and AAPs) within photosynthetic mats at environmental extremes (e.g., hot springs and hypersaline lagoons). Notably, temperature and pH drive anoxygenic phototroph community composition in Yellowstone National Park's geothermal features. In addition, various, light-dependent niches in the Great Salt Lake's hypersaline mats support phototrophic diversity as microbes optimize energy production and combat osmotic stress.
=== Biogeochemical cycling ===
Photoheterotrophs influence global carbon cycling by assimilating dissolved organic carbon (DOC). Therefore, when harvesting light-energy, carbon is maintained in the microbial loop without corresponding respiration (i.e., carbon dioxide release to the atmosphere as DOC is oxidized to fuel energy production). This disconnect, the discovery of facultative photoheterotrophs (e.g., AAPs with flexible energy sources), and previous measurements taken in the dark (i.e., to avoid skewed oxygen consumption values due to photooxidation, UV light, and oxygenic photosynthesis) lead to overestimated aquatic CO2 emissions. For example, a 15.2% decrease in community respiration was observed in Cep Lake, Czechia—alongside preferential glucose and pyruvate uptake—is attributed to facultative photoheterotrophs preferring light-energy during the daytime, given fitness benefits mentioned previously.
== Flowchart ==
== See also ==
Primary nutritional groups
== References ==

22
data/en.wikipedia.org/wiki/Photokinesis-0.md Normal file
View File

@ -0,0 +1,22 @@
---
title: "Photokinesis"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Photokinesis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:19.384164+00:00"
instance: "kb-cron"
---
Photokinesis is a change in the velocity of movement of an organism as a result of changes in light intensity. The alteration in speed is independent of the direction from which the light is shining. Photokinesis is described as positive if the velocity of travel is greater with an increase in light intensity and negative if the velocity is slower. If a group of organisms with a positive photokinetic response is swimming in a partially shaded environment, there will be fewer organisms per unit of volume in the sunlit portion than in the shaded parts. This may be beneficial for the organisms if it is unfavourable to their predators, or it may be propitious to them in their quest for prey.
In photosynthetic prokaryotes, the mechanism for photokinesis appears to be an energetic process. In cyanobacteria, for example, an increase in illumination results in an increase of photophosphorylation which enables an increase in metabolic activity. However the behaviour is also found among eukaryotic microorganisms, including those like Astasia longa which are not photosynthetic, and in these, the mechanism is not fully understood. In Euglena gracilis, the rate of swimming has been shown to speed up with increased light intensity until the light reaches a certain saturation level, beyond which the swimming rate declines.
The sea slug Discodoris boholiensis also displays positive photokinesis; it is nocturnal and moves slowly at night, but much faster when caught in the open during daylight hours. Moving faster in the exposed environment should reduce predation and enable it to conceal itself as soon as possible, but its brain is quite incapable of working this out. Photokinesis is common in tunicate larvae, which accumulate in areas with low light intensity just before settlement, and the behaviour is also present in juvenile fish such as sockeye salmon smolts.
== See also ==
Kinesis (biology)
Phototaxis
Phototropism
== References ==

44
data/en.wikipedia.org/wiki/Photoperiodism-0.md Normal file
View File

@ -0,0 +1,44 @@
---
title: "Photoperiodism"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Photoperiodism"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:20.769311+00:00"
instance: "kb-cron"
---
Photoperiod is the change of day length over the seasons. Earth's rotation around its axis produces 24-hour changes in light (daytime) and dark (night) cycles on Earth. The length of the light and dark in each phase varies across the seasons due to the axial tilt of Earth. The photoperiod defines the length of the light. For example, in summer the length of light could be 16 hours while the dark is 8 hours, whereas in winter the length of day could be 8 hours, while the dark is 16 hours. Importantly, the axial tilt of the Earth causes the opposing seasons in the Northern and Southern Hemispheres.
Photoperiodism is the physiological reaction of organisms to the length of light or a dark period. It occurs in plants and animals. Plant photoperiodism can also be defined as the developmental responses of plants to the relative lengths of light and dark periods. They are classified under three groups according to the photoperiods: short-day plants, long-day plants, and day-neutral plants.
In animals, photoperiodism (sometimes called seasonality) is the suite of physiological changes that occur in response to changes in day length. This allows animals to respond to a temporally changing environment associated with changing seasons as the earth orbits the sun.
== Plants ==
In 1920, W. W. Garner and H. A. Allard published their discoveries on photoperiodism and felt it was the length of daylight that was critical, but it was later discovered that the length of the night was the controlling factor. Photoperiodic flowering plants are classified as long-day plants or short-day plants even though night is the critical factor because of the initial misunderstanding about daylight being the controlling factor. Along with long-day plants and short-day plants, there are plants that fall into a "dual-day length category". These plants are either long-short-day plants (LSDP) or short-long-day plants (SLDP). LSDPs flower after a series of long days followed by short days whereas SLDPs flower after a series of short days followed by long days. Each plant has a different length critical photoperiod, or critical night length.
Many flowering plants (angiosperms) use a circadian rhythm together with photoreceptor protein, such as phytochrome or cryptochrome, to sense seasonal changes in night length, or photoperiod, which they take as signals to flower. In a further subdivision, obligate photoperiodic plants absolutely require a long or short enough night before flowering, whereas facultative photoperiodic plants are more likely to flower under one condition.
Phytochrome comes in two forms: Pr and Pfr. Red light (which is present during the day) converts phytochrome to its active form (Pfr) which then stimulates various processes such as germination, flowering or branching. In comparison, plants receive more far-red in the shade, and this converts phytochrome from Pfr to its inactive form, Pr, inhibiting germination. This system of Pfr to Pr conversion allows the plant to sense when it is night and when it is day. Pfr can also be converted back to Pr by a process known as dark reversion, where long periods of darkness trigger the conversion of Pfr. This is important in regards to plant flowering. Experiments by Halliday et al. showed that manipulations of the red-to far-red ratio in Arabidopsis can alter flowering. They discovered that plants tend to flower later when exposed to more red light, proving that red light is inhibitory to flowering. Other experiments have proven this by exposing plants to extra red-light in the middle of the night. A short-day plant will not flower if light is turned on for a few minutes in the middle of the night and a long-day plant can flower if exposed to more red-light in the middle of the night.
Cryptochromes are another type of photoreceptor that is important in photoperiodism. Cryptochromes absorb blue light and UV-A. Cryptochromes entrain the circadian clock to light. It has been found that both cryptochrome and phytochrome abundance relies on light and the amount of cryptochrome can change depending on day-length. This shows how important both of the photoreceptors are in regards to determining day-length.
Modern biologists believe that it is the coincidence of the active forms of phytochrome or cryptochrome, created by light during the daytime, with the rhythms of the circadian clock that allows plants to measure the length of the night. Other than flowering, photoperiodism in plants includes the growth of stems or roots during certain seasons and the loss of leaves. Artificial lighting can be used to induce extra-long days.
=== Long-day plants ===
Long-day plants flower when the night length falls below their critical photoperiod. These plants typically flower during late spring or early summer as days are getting longer. In the northern hemisphere, the longest day of the year (summer solstice) is on or about 21 June. After that date, days grow shorter (i.e. nights grow longer) until 21 December (the winter solstice). This situation is reversed in the southern hemisphere (i.e., longest day is 21 December and shortest day is 21 June).
Some long-day obligate plants are:
Carnation (Dianthus)
Henbane (Hyoscyamus)
Oat (Avena)
Some long-day facultative plants are:
Pea (Pisum sativum)
Barley (Hordeum vulgare)
Lettuce (Lactuca sativa)
Wheat (Triticum aestivum)
=== Short-day plants ===
Short-day (also called long-night) plants flower when the night lengths exceed their critical photoperiod. They cannot flower under short nights or if a pulse of artificial light is shone on the plant for several minutes during the night; they require a continuous period of darkness before floral development can begin. Natural nighttime light, such as moonlight or lightning, is not of sufficient brightness or duration to interrupt flowering.
Short-day plants flower as days grow shorter (and nights grow longer) after 21 September in the northern hemisphere, which is during summer or fall. The length of the dark period required to induce flowering differs among species and varieties of a species.
Photoperiodism affects flowering by inducing the shoot to produce floral buds instead of leaves and lateral buds.
Some short-day facultative plants are:

50
data/en.wikipedia.org/wiki/Photoperiodism-1.md Normal file
View File

@ -0,0 +1,50 @@
---
title: "Photoperiodism"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Photoperiodism"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:20.769311+00:00"
instance: "kb-cron"
---
Kenaf (Hibiscus cannabinus)
Marijuana (Cannabis)
Cotton (Gossypium)
Rice (Oryza)
Sorghum (Sorghum bicolor)
Green gram (Mung bean, Vigna radiata)
Soybeans (Glycine max)
=== Day-neutral plants ===
Day-neutral plants, such as cucumbers, roses, tomatoes, and Ruderalis (autoflowering cannabis) do not initiate flowering based on photoperiodism. Instead, they may initiate flowering after attaining a certain overall developmental stage or age, or in response to alternative environmental stimuli, such as vernalisation (a period of low temperature).
== Animals ==
Day length, and thus knowledge of the season of the year, is vital to many animals. A number of biological and behavioural changes are dependent on this knowledge. Together with temperature changes, photoperiod provokes changes in the color of fur and feathers, migration, entry into hibernation, sexual behaviour, and even the resizing of organs.
In insects, sensitivity to photoperiod has been proven to be initiated by photoreceptors located in the brain. Photoperiod can affect insects at different life stages, serving as an environmental cue for physiological processes such as diapause induction and termination, and seasonal morphs. In the water strider Aquarius paludum, for instance, photoperiod conditions during nymphal development have been shown to trigger seasonal changes in wing frequency and also induce diapause, although the threshold critical day lengths for the determination of both traits diverged by about an hour. In Gerris buenoi, another water strider species, photoperiod has also been shown to be the cause of wing polyphenism, although the specific day lengths changed between species, suggesting that phenotypic plasticity in response to photoperiod has evolved even between relatively closely related species.
The singing frequency of birds such as the canary depends on the photoperiod. In the spring, when the photoperiod increases (more daylight), the male canary's testes grow. As the testes grow, more androgens are secreted and song frequency increases. During autumn, when the photoperiod decreases (less daylight), the male canary's testes regress and androgen levels drop dramatically, resulting in decreased singing frequency. Not only is singing frequency dependent on the photoperiod but the song repertoire is also. The long photoperiod of spring results in a greater song repertoire. Autumn's shorter photoperiod results in a reduction in song repertoire. These behavioral photoperiod changes in male canaries are caused by changes in the song center of the brain. As the photoperiod increases, the high vocal center (HVC) and the robust nucleus of the archistriatum (RA) increase in size. When the photoperiod decreases, these areas of the brain regress.
== Mammals ==
In mammals, day length is registered in the suprachiasmatic nucleus (SCN), which is informed by retinal light-sensitive ganglion cells, which are not involved in vision. The information travels through the retinohypothalamic tract (RHT). In most species the hormone melatonin is produced by the pineal gland only during the hours of darkness, influenced by the light input through the RHT and by innate circadian rhythms. This hormonal signal, combined with outputs from the SCN inform the rest of the body about the time of day, and the length of time that melatonin is secreted is how the time of year is perceived.
Many mammals, particularly those inhabiting temperate and polar regions, exhibit a remarkable degree of seasonality in response to changes in daylight hours(photoperiod). This seasonality manifests in a broad spectrum of behaviors and physiology, including hibernation, seasonal migrations, and coat color changes. A prime example of the adaptation to photoperiods is the seasonal coat color (SCC) species. These animals undergo molting, transforming from dark summer fur to white coat in winter, that provides crucial camouflage in snowy environments.
=== Humans ===
The view has been expressed that humans' seasonality is largely believed to be evolutionary baggage.. Human birth rate varies throughout the year, and the peak month of births appears to vary by latitude. Seasonality in human birth rate appears to have largely decreased since the industrial revolution.
== Other organisms ==
Photoperiodism has also been demonstrated in other organisms besides plants and animals. The fungus Neurospora crassa as well as the dinoflagellate Lingulodinium polyedra and the unicellular green alga Chlamydomonas reinhardtii have been shown to display photoperiodic responses.
== See also ==
Chronobiology
Circadian clock
Circadian rhythm
Florigen
Photobiology
Seasonal Breeder
Scotobiology
Epigenetics of plant growth and development § Photoperiodism
== References ==
== Further reading ==

21
data/en.wikipedia.org/wiki/Phototaxis-0.md Normal file
View File

@ -0,0 +1,21 @@
---
title: "Phototaxis"
chunk: 1/5
source: "https://en.wikipedia.org/wiki/Phototaxis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:22.043277+00:00"
instance: "kb-cron"
---
Phototaxis is a kind of taxis, or locomotory movement, that occurs when a whole organism moves towards or away from a stimulus of light. This is advantageous for phototrophic organisms as they can orient themselves most efficiently to receive light for photosynthesis. Phototaxis is called positive if the movement is in the direction of increasing light intensity and negative if the direction is opposite.
Phototaxis has been described in microorganisms and algea, insects and other invertebrates, and vertebrates. Typically nocturnal insects can show positive phototaxis, while nocturnal mammals often show negative phototaxis.
== Phototaxis in bacteria and archea ==
Phototaxis can be advantageous for phototrophic bacteria as they can orient themselves most efficiently to receive light for photosynthesis. Phototaxis is called positive if the movement is in the direction of increasing light intensity and negative if the direction is opposite.
Two types of positive phototaxis are observed in prokaryotes (bacteria and archea). The first is called "scotophobotaxis" (from the word "scotophobia"), which is observed only under a microscope. This occurs when a bacterium swims by chance out of the area illuminated by the microscope. Entering darkness signals the cell to reverse flagella rotation direction and reenter the light. The second type of phototaxis is true phototaxis, which is a directed movement up a gradient to an increasing amount of light. This is analogous to positive chemotaxis except that the attractant is light rather than a chemical.
Phototactic responses are observed in a number of bacteria and archae, such as Serratia marcescens. Photoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are bacteriorhodopsin and bacteriophytochromes in some bacteria. See also: phytochrome and phototropism.
Most prokaryotes (bacteria and archaea) are unable to sense the direction of light, because at such a small scale it is very difficult to make a detector that can distinguish a single light direction. Still, prokaryotes can measure light intensity and move in a light-intensity gradient. Some gliding filamentous prokaryotes can even sense light direction and make directed turns, but their phototactic movement is very slow. Some bacteria and archaea are phototactic.
In most cases the mechanism of phototaxis is a biased random walk, analogous to bacterial chemotaxis. Halophilic archaea, such as Halobacterium salinarum, use sensory rhodopsins (SRs) for phototaxis. Rhodopsins are 7 transmembrane proteins that bind retinal as a chromophore. Light triggers the isomerization of retinal, which leads to phototransductory signalling via a two-component phosphotransfer relay system. Halobacterium salinarum has two SRs, SRI and SRII, which signal via the transducer proteins Htr1 and Htr2 (halobacterial transducers for SRs I and II), respectively. The downstream signalling in phototactic archaebacteria involves CheA, a histidine kinase, which phosphorylates the response regulator, CheY. Phosphorylated CheY induces swimming reversals. The two SRs in Halobacterium have different functions. SRI acts as an attractant receptor for orange light and, through a two-photon reaction, a repellent receptor for near-UV light, while SRII is a repellent receptor for blue light. Depending on which receptor is expressed, if a cell swims up or down a steep light gradient, the probability of flagellar switch will be low. If light intensity is constant or changes in the wrong direction, a switch in the direction of flagellar rotation will reorient the cell in a new, random direction. As the length of the tracks is longer when the cell follows a light gradient, cells will eventually get closer to or further away from the light source. This strategy does not allow orientation along the light vector and only works if a steep light gradient is present (i.e. not in open water).
Some cyanobacteria (e.g. Anabaena, Synechocystis) can slowly orient along a light vector. This orientation occurs in filaments or colonies, but only on surfaces and not in suspension. The filamentous cyanobacterium Synechocystis is capable of both positive and negative two-dimensional phototactic orientation. The positive response is probably mediated by a bacteriophytochrome photoreceptor, TaxD1. This protein has two chromophore-binding GAF domains, which bind biliverdin chromophore, and a C-terminal domain typical for bacterial taxis receptors (MCP signal domain). TaxD1 also has two N-terminal transmembrane segments that anchor the protein to the membrane. The photoreceptor and signalling domains are cytoplasmic and signal via a CheA/CheY-type signal transduction system to regulate motility by type IV pili. TaxD1 is localized at the poles of the rod-shaped cells of Synechococcus elongatus, similarly to MCP containing chemosensory receptors in bacteria and archaea. How the steering of the filaments is achieved is not known. The slow steering of these cyanobacterial filaments is the only light-direction sensing behaviour prokaryotes could evolve owing to the difficulty in detecting light direction at this small scale.

18
data/en.wikipedia.org/wiki/Phototaxis-1.md Normal file
View File

@ -0,0 +1,18 @@
---
title: "Phototaxis"
chunk: 2/5
source: "https://en.wikipedia.org/wiki/Phototaxis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:22.043277+00:00"
instance: "kb-cron"
---
The ability to link light perception to control of motility is found in a very wide variety of prokaryotes, indicating that this ability must confer a range of physiological advantages. Most directly, the light environment is crucial to phototrophs as their energy source. Phototrophic prokaryotes are extraordinarily diverse, with a likely role for horizontal gene transfer in spreading phototrophy across multiple phyla. Thus, different groups of phototrophic prokaryotes may have little in common apart from their exploitation of light as an energy source, but it should be advantageous for any phototroph to be able to relocate in search of better light environments for photosynthesis. To do this efficiently requires the ability to control motility in response to integrated information on the intensity of light, the spectral quality of light and the physiological status of the cell. A second major reason for light-controlled motility is to avoid light at damaging intensities or wavelengths: this factor is not confined to photosynthetic bacteria since light (especially in the UV region) can be dangerous to all prokaryotes, primarily because of DNA and protein damage  and inhibition of the translation machinery by light-generated reactive oxygen species.
Finally, light signals potentially contain rich and complex information about the environment, and the possibility should not be excluded that bacteria make sophisticated use of this information to optimize their location and behavior. For example, plant or animal pathogens could use light information to control their location and interaction with their hosts, and in fact light signals are known to regulate development and virulence in several non-phototrophic prokaryotes. Phototrophs could also benefit from sophisticated information processing, since their optimal environment is defined by a complex combination of factors including light intensity, light quality, day and night cycles, the availability of raw materials and alternative energy sources, other beneficial or harmful physical and chemical factors and sometimes the presence of symbiotic partners. Light quality strongly influences specialized developmental pathways in certain filamentous cyanobacteria, including the development of motile hormogonia and nitrogen-fixing heterocysts. Since hormogonia are important for establishing symbiotic partnerships between cyanobacteria and plants, and heterocysts are essential for nitrogen fixation in those partnerships, it is tempting to speculate that the cyanobacteria may be using light signals as one way to detect the proximity of a plant symbiotic partner. Within a complex and heterogeneous environment such as a phototrophic biofilm, many factors crucial for growth could vary dramatically even within the limited region that a single motile cell could explore. We should therefore expect that prokaryotes living in such environments might control their motility in response to a complex signal transduction network linking a range of environmental cues.
The photophobic response is a change in the direction of motility in response to a relatively sudden increase in illumination: classically, the response is to a temporal change in light intensity, which the bacterium may experience as it moves into a brightly illuminated region. The directional switch may consist of a random selection of a new direction ('tumbling') or it may be a simple reversal in the direction of motility. Either has the effect of repelling cells from a patch of unfavorable light. Photophobic responses have been observed in prokaryotes as diverse as Escherichia coli, purple photosynthetic bacteria and haloarchaea.
The scotophobic (fear of darkness) response is the converse of the photophobic response described above: a change in direction (tumbling or reversal) is induced when the cell experiences a relatively sudden drop in light intensity. Photophobic and scotophobic responses both cause cells to accumulate in regions of specific (presumably favorable) light intensity and spectral quality. Scotophobic responses have been well documented in purple photosynthetic bacteria, starting with the classic observations of Engelmann in 1883, and in cyanobacteria. Scotophobic/photophobic responses in flagellated bacteria closely resemble the classic 'biased random walk' mode of bacterial chemotaxis, which links perception of temporal changes in the concentration of a chemical attractant or repellent to the frequency of tumbling. The only significant distinction is that the scotophobic/photophobic responses involve perception of temporal changes in light intensity rather than the concentration of a chemical.
Photokinesis is a light-induced change in the speed (but not direction) of movement. Photokinesis may be negative (light-induced reduction of motility) or positive (light-induced stimulation of motility). Photokinesis can cause cells to accumulate in regions of favorable illumination: they linger in such regions or accelerate out of regions of unfavorable illumination. Photokinesis has been documented in cyanobacteria and purple photosynthetic bacteria.
True phototaxis consists of directional movement which may be either towards a light source (positive phototaxis) or away from a light source (negative phototaxis). In contrast to the photophobic/scotophobic responses, true phototaxis is not a response to a temporal change in light intensity. Generally, it seems to involve direct sensing of the direction of illumination rather than a spatial gradient of light intensity. True phototaxis in prokaryotes is sometimes combined with social motility, which involves the concerted movement of an entire colony of cells towards or away from the light source. This phenomenon could also be described as community phototaxis. True phototaxis is widespread in eukaryotic green algae, but among the prokaryotes it has been documented only in cyanobacteria, and in social motility of colonies of the purple photosynthetic bacterium Rhodocista centenaria.
== Phototaxis in protists ==

24
data/en.wikipedia.org/wiki/Phototaxis-2.md Normal file
View File

@ -0,0 +1,24 @@
---
title: "Phototaxis"
chunk: 3/5
source: "https://en.wikipedia.org/wiki/Phototaxis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:22.043277+00:00"
instance: "kb-cron"
---
Some protists (unicellular eukaryotes) can also move toward or away from light, by coupling their locomotion strategy with a light-sensing organ. Eukaryotes evolved for the first time in the history of life the ability to follow light direction in three dimensions in open water. The strategy of eukaryotic sensory integration, sensory processing and the speed and mechanics of tactic responses is fundamentally different from that found in prokaryotes.
Both single-celled and multi-cellular eukaryotic phototactic organisms have a fixed shape, are polarized, swim in a spiral and use cilia for swimming and phototactic steering. Signalling can happen via direct light-triggered ion currents, adenylyl cyclases or trimeric G-proteins. The photoreceptors used can also be very different (see below). However, signalling in all cases eventually modifies the beating activity of cilia. The mechanics of phototactic orientation is analogous in all eukaryotes. A photosensor with a restricted view angle rotates to scan the space and signals periodically to the cilia to alter their beating, which will change the direction of the helical swimming trajectory. Three-dimensional phototaxis can be found in five out of the six eukaryotic major groups (opisthokonts, Amoebozoa, plants, chromalveolates, excavates, rhizaria).
Pelagic phototaxis is present in green algae – it is not present in glaucophyte algae or red algae. Green algae have a "stigma" located in the outermost portion of the chloroplast, directly underneath the two chloroplast membranes. The stigma is made of tens to several hundreds of lipid globules, which often form hexagonal arrays and can be arranged in one or more rows. The lipid globules contain a complex mixture of carotenoid pigments, which provide the screening function and the orange-red colour, as well as proteins that stabilize the globules. The stigma is located laterally, in a fixed plane relative to the cilia, but not directly adjacent to the basal bodies. The fixed position is ensured by the attachment of the chloroplast to one of the ciliary roots. The pigmented stigma is not to be confused with the photoreceptor. The stigma only provides directional shading for the adjacent membrane-inserted photoreceptors (the term "eyespot" is therefore misleading). Stigmata can also reflect and focus light like a concave mirror, thereby enhancing sensitivity.
In the best-studied green alga, Chlamydomonas reinhardtii, phototaxis is mediated by a rhodopsin pigment, as first demonstrated by the restoration of normal photobehaviour in a blind mutant by analogues of the retinal chromophore. Two archaebacterial-type rhodopsins, channelrhodopsin-1 and -2, were identified as phototaxis receptors in Chlamydomonas. Both proteins have an N-terminal 7-transmembrane portion, similar to archaebacterial rhodopsins, followed by an approximately 400 residue C-terminal membrane-associated portion. CSRA and CSRB act as light-gated cation channels and trigger depolarizing photocurrents. CSRA was shown to localize to the stigma region using immunofluorescence analysis (Suzuki et al. 2003). Individual RNAi depletion of both CSRA and CSRB modified the light-induced currents and revealed that CSRA mediates a fast, high-saturating current while CSRB a slow, low-saturating one. Both currents are able to trigger photophobic responses and can have a role in phototaxis, although the exact contribution of the two receptors is not yet clear.
As in all bikonts (plants, chromalveolates, excavates, rhizaria), green algae have two cilia, which are not identical. The anterior cilium is always younger than the posterior one. In every cell cycle, one daughter cell receives the anterior cilium and transforms it into a posterior one. The other daughter inherits the posterior, mature cilium. Both daughters then grow a new anterior cilium.
As all other ciliary swimmers, green algae always swim in a spiral. The handedness of the spiral is robust and is guaranteed by the chirality of the cilia. The two cilia of green algae have different beat patterns and functions. In Chlamydomonas, the phototransduction cascade alters the stroke pattern and beating speed of the two cilia differentially in a complex pattern. This results in the reorientation of the helical swimming trajectory as long as the helical swimming axis is not aligned with the light vector.
== Phototaxis in invertebrates ==
=== Jellyfish ===
Positive and negative phototaxis can be found in several species of jellyfish such as those from the genus Polyorchis. Jellyfish use ocelli to detect the presence and absence of light, which is then translated into anti-predatory behaviour in the case of a shadow being cast over the ocelli, or feeding behaviour in the case of the presence of light. Many tropical jellyfish have a symbiotic relationship with photosynthetic zooxanthellae that they harbor within their cells. The zooxanthellae nourish the jellyfish, while the jellyfish protects them, and moves them toward light sources such as the sun to maximize their light-exposure for efficient photosynthesis. In a shadow, the jellyfish can either remain still, or quickly move away in bursts to avoid predation and also re-adjust toward a new light source.
This motor response to light and absence of light is facilitated by a chemical response from the ocelli, which results in a motor response causing the organism to swim toward a light source.
=== Marine ragworm ===

24
data/en.wikipedia.org/wiki/Phototaxis-3.md Normal file
View File

@ -0,0 +1,24 @@
---
title: "Phototaxis"
chunk: 4/5
source: "https://en.wikipedia.org/wiki/Phototaxis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:22.043277+00:00"
instance: "kb-cron"
---
Phototaxis has been well studied in the marine ragworm Platynereis dumerilii. Both Platynereis dumerilii trochophore and its metatrochophore larvae are positively phototactic. Phototaxis is mediated by simple eyespots that consists of a pigment cell and a photoreceptor cell. The photoreceptor cell synapses directly onto ciliated cells, which are used for swimming. The eyespots do not give spatial resolution, therefore the larvae are rotating to scan their environment for the direction where the light is coming from.
Platynereis dumerilii larvae (nectochaete) can switch between positive and negative phototaxis. Phototaxis there is mediated by two pairs of more complex pigment cup eyes. These eyes contain more photoreceptor cells that are shaded by pigment cells forming a cup. The photoreceptor cells do not synapse directly onto ciliated cells or muscle cells but onto inter-neurons of a processing center. This way the information of all four eye cups can be compared and a low-resolution image of four pixels can be created telling the larvae where the light is coming from. This way the larva does not need to scan its environment by rotating. This is an adaption for living on the bottom of the sea the lifestyle of the larva while scanning rotation is more suited for living in the open water column, the lifestyle of the trochophore larva. Phototaxis in the Platynereis dumerilii larva has a broad spectral range which is at least covered by three opsins that are expressed by the cup eyes: Two rhabdomeric opsins and a Go-opsin.
However, not every behavior that looks like phototaxis is phototaxis: Platynereis dumerilii nechtochate and metatrochophore larvae swim up first when they are stimulated with UV-light from above. But after a while, they change the direction and avoid the UV-light by swimming down. This looks like a change from positive to negative phototaxis (see video left), but the larvae also swim down if UV-light comes non-directionally from the side. And so they do not swim to or away from the light, but swim down, this means to the center of gravity. Thus this is a UV-induced positive gravitaxis. Positive phototaxis (swimming to the light from the surface) and positive gravitaxis (swimming to the center of gravity) are induced by different ranges of wavelengths and cancel out each other at a certain ratio of wavelengths. Since the wavelengths compositions change in water with depth: Short (UV, violet) and long (red) wavelengths are lost first, phototaxis and gravitaxis form a ratio-chromatic depth gauge, which allows the larvae to determine their depth by the color of the surrounding water. This has the advantage over a brightness based depth gauge that the color stays almost constant independent of the time of the day or whether it is cloudy.
In the diagram on the right, the larvae start swimming upwards when UV-light switched on (marked by the violet square). But later, they are swimming downward. The larval tracks are color coded: Red for upward and blue for downward swimming larvae. The video runs at double speed.
=== Insects ===
Positive phototaxis can be found in many flying insects such as moths, grasshoppers, and flies. Drosophila melanogaster has been studied extensively for its innate positive phototactic response to light sources, using controlled experiments to help understand the connection between airborne locomotion toward a light source. This innate response is common among insects that fly primarily during the night utilizing transverse orientation vis-à-vis the light of the moon for orientation. Artificial lighting in cities and populated areas results in a more pronounced positive response compared to that with the distant light of the moon, resulting in the organism repeatedly responding to this new supernormal stimulus and innately flying toward it.
Evidence for the innate response of positive phototaxis in Drosophila melanogaster was carried out by altering the wings of several individual specimens, both physically (via removal) and genetically (via mutation). In both cases there was a noticeable lack of positive phototaxis, demonstrating that flying toward light sources is an innate response to the organisms' photoreceptors receiving a positive response.
Negative phototaxis can be observed in larval drosophila melanogaster within the first three developmental instar stages, despite adult insects displaying positive phototaxis. This behaviour is common among other species of insects which possess a flightless larval and adult stage in their life cycles, only switching to positive phototaxis when searching for pupation sites. Tenebrio molitor by comparison is one species which carries its negative phototaxis into adulthood.
== Relation to magnetic fields ==
Under experimental conditions, organisms that use positive phototaxis have also shown a correlation with light and magnetic fields. Under homogeneous light conditions with a shifting magnetic field, Drosophila melanogaster larvae reorient themselves toward predicted directions of greater or lesser light intensities as expected by a rotating magnetic field. In complete darkness, the larvae orient randomly without any notable preference. This suggests the larvae can observe a visible pattern in combination with light.

24
data/en.wikipedia.org/wiki/Phototaxis-4.md Normal file
View File

@ -0,0 +1,24 @@
---
title: "Phototaxis"
chunk: 5/5
source: "https://en.wikipedia.org/wiki/Phototaxis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:22.043277+00:00"
instance: "kb-cron"
---
== Light based vertical movement ==
A depth can also be selected based on light levels: The brightness decreases with depth, but depends on the weather (e.g. whether it is sunny or cloudy) and the time of the day. Also the color depends on the water depth and dissolved and suspended matter. The only consistent factor is that at a given place, deeper water is darker.
In water, light attenuates differently for each wavelength. The UV, violet (> 420 nm), and red (< 500 nm) wavelengths disappear before blue light (470 nm), which penetrates clear water the deepest. The wavelength composition is constant for each depth and is almost independent of time of the day and the weather. To gauge depth, an animal would need two photopigments sensitive to different wavelengths to compare different ranges of the spectrum. Such pigments may be expressed in different structures.
Such different structures are found in the polychaete Torrea candida. Its eyes have a main and two accessory retinae. The accessory retinae sense UV-light (λmax = 400 nm) and the main retina senses blue-green light (λmax = 560 nm). If the light sensed from all retinae is compared, the depth can be estimated, and so for Torrea candida such a ratio-chromatic depth gauge has been proposed.
A ratio chromatic depth gauge has been found in larvae of the polychaete Platynereis dumerilii. The larvae have two structures: The rhabdomeric photoreceptor cells of the eyes and in the deep brain the ciliary photoreceptor cells. The ciliary photoreceptor cells express a ciliary opsin, which is a photopigment maximally sensitive to UV-light (λmax = 383 nm). Thus, the ciliary photoreceptor cells react on UV-light and make the larvae swimming down gravitactically. The gravitaxis here is countered by phototaxis, which makes the larvae swimming up to the light coming from the surface. Phototaxis is mediated by the rhabdomeric eyes. The eyes express at least three opsins (at least in the older larvae), and one of them is maximally sensitive to cyan light (λmax = 483 nm) so that the eyes cover a broad wavelength range with phototaxis. When phototaxis and gravitaxis have leveled out, the larvae have found their preferred depth.
== See also ==
Photokinesis
Phototropism (more relevant to plants and fungi)
== References ==
== Further reading ==

47
data/en.wikipedia.org/wiki/Phototroph-0.md Normal file
View File

@ -0,0 +1,47 @@
---
title: "Phototroph"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Phototroph"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:23.246471+00:00"
instance: "kb-cron"
---
Phototrophs (from Ancient Greek φῶς, φωτός (phôs, phōtós) 'light' and τροφή (trophḗ) 'nourishment') are organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs photosynthesize: they anabolically convert carbon dioxide into biomolecules to be utilized structurally (e.g. cellulose and membrane lipids), functionally (e.g. vitamins, nucleotides, and amino acids), or as a source for later catabolic processes (e.g. starches, sugars and fats). All phototrophs either use electron transport chains or direct proton pumping to establish an electrochemical gradient, which is utilized by ATP synthase to provide adenosine triphosphate (ATP) for the cell. Phototrophs can be either autotrophs or heterotrophs. If their electron and hydrogen donors are inorganic compounds (e.g., Na2S2O3, as in some purple sulfur bacteria, or H2S, as in some green sulfur bacteria) they can be also called lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms are Rhodobacter capsulatus, Chromatium, and Chlorobium.
== History ==
Originally used with a different meaning, the term took its current definition after Lwoff and collaborators (1946).
== Photoautotroph ==
Most well-known phototrophs are photoautotrophs, which means they synthesize their own food from inorganic substances (i.e. carbon dioxide) in a process called carbon fixation, using light as an energy source. Green plants and most photosynthetic bacteria are photoautotrophs. Photoautotrophic organisms are sometimes referred to as holophytic.
Oxygenic photosynthetic organisms use photosystem II to capture light-energy and oxidize water (H2O), splitting it into molecular oxygen (O2) and 4 protons (H+) in the process called photolysis.
=== Ecology ===
In an ecological context, photoautotrophs are often the food source for neighboring heterotrophic life. In terrestrial environments, plants are the predominant variety, while aquatic environments include a range of phototrophic organisms such as algae (e.g., kelp), other protists (such as euglena), phytoplankton, and bacteria (such as cyanobacteria).
Cyanobacteria, which are prokaryotic organisms which carry out oxygenic photosynthesis, occupy many environmental conditions, including fresh water, seas, soil, and lichen. Cyanobacteria carry out plant-like photosynthesis because the organelle in plants that carries out photosynthesis is derived from an endosymbiotic cyanobacterium. This bacterium can use water as a source of electrons in order to perform CO2 reduction reactions.
A photolithoautotroph is an autotrophic organism that uses light energy, and an inorganic electron donor (e.g., H2O, H2, H2S), and CO2 as its carbon source.
== Photoheterotroph ==
In contrast to photoautotrophs, photoheterotrophs are organisms that depend solely on light for their energy, and consumption of organic compounds for biomolecules. Photoheterotrophs produce ATP through photophosphorylation but use environmentally obtained organic compounds to build structures and other biomolecules.
== Classification by light-capturing molecule ==
Most phototrophs use chlorophyll or the related bacteriochlorophyll to capture light and are known as chlorophototrophs. Others, however, use retinal and are retinalophototrophs.
== Flowchart ==
== See also ==
Primary nutritional groups
Prototroph
== References ==

18
data/en.wikipedia.org/wiki/Phototropism-0.md Normal file
View File

@ -0,0 +1,18 @@
---
title: "Phototropism"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Phototropism"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:24.492344+00:00"
instance: "kb-cron"
---
In biology, phototropism, formerly called heliotropism, is the growth of an organism in response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi. The cells on the plant that are farthest from the light contain a hormone called auxin that reacts when phototropism occurs. This causes the plant to have elongated cells on the furthest side from the light. Phototropism is one of the many plant tropisms, or movements, which respond to external stimuli. Growth towards a light source is called positive phototropism, while growth away from light is called negative phototropism. Negative phototropism is not to be confused with skototropism, which is defined as the growth towards darkness, whereas negative phototropism can refer to either the growth away from a light source or towards the darkness. Most plant shoots exhibit positive phototropism, and rearrange their chloroplasts in the leaves to maximize photosynthetic energy and promote growth. Some vine shoot tips exhibit negative phototropism, which allows them to grow towards dark, solid objects and climb them. The combination of phototropism and gravitropism allow plants to grow in the correct direction.
== Mechanism ==
There are several signaling molecules that help the plant determine where the light source is coming from, and these activate several genes, which change the hormone gradients allowing the plant to grow towards the light. The very tip of the plant is known as the coleoptile, which is necessary in light sensing. The middle portion of the coleoptile is the area where the shoot curvature occurs. The Cholodny–Went hypothesis, developed in the early 20th century, predicts that in the presence of asymmetric light, auxin will move towards the shaded side and promote elongation of the cells on that side to cause the plant to curve towards the light source. Auxins activate proton pumps, decreasing the pH in the cells on the dark side of the plant. This acidification of the cell wall region activates enzymes known as expansins which disrupt hydrogen bonds in the cell wall structure, making the cell walls less rigid. In addition, increased proton pump activity leads to more solutes entering the plant cells on the dark side of the plant, which increases the osmotic gradient between the symplast and apoplast of these plant cells. Water then enters the cells along its osmotic gradient, leading to an increase in turgor pressure. The decrease in cell wall strength and increased turgor pressure above a yield threshold causes cells to swell, exerting the mechanical pressure that drives phototropic movement.
Proteins encoded by a second group of genes, PIN genes, have been found to play a major role in phototropism. They are auxin transporters, and it is thought that they are responsible for the polarization of auxin location. Specifically PIN3 has been identified as the primary auxin carrier. It is possible that phototropins receive light and inhibit the activity of PINOID kinase (PID), which then promotes the activity of PIN3. This activation of PIN3 leads to asymmetric distribution of auxin, which then leads to asymmetric elongation of cells in the stem. pin3 mutants had shorter hypocotyls and roots than the wild-type, and the same phenotype was seen in plants grown with auxin efflux inhibitors. Using anti-PIN3 immunogold labeling, movement of the PIN3 protein was observed. PIN3 is normally localized to the surface of hypocotyl and stem, but is also internalized in the presence of Brefeldin A (BFA), an exocytosis inhibitor. This mechanism allows PIN3 to be repositioned in response to an environmental stimulus. PIN3 and PIN7 proteins were thought to play a role in pulse-induced phototropism. The curvature responses in the "pin3" mutant were reduced significantly, but only slightly reduced in "pin7" mutants. There is some redundancy among "PIN1", "PIN3", and "PIN7", but it is thought that PIN3 plays a greater role in pulse-induced phototropism.
There are phototropins that are highly expressed in the upper region of coleoptiles. There are two main phototropism they are phot1 and phot2. phot2 single mutants have phototropic responses like that of the wild-type, but phot1 phot2 double mutants do not show any phototropic responses. The amounts of PHOT1 and PHOT2 present are different depending on the age of the plant and the intensity of the light. There is a high amount of PHOT2 present in mature Arabidopsis leaves and this was also seen in rice orthologs. The expression of PHOT1 and PHOT2 changes depending on the presence of blue or red light. There was a downregulation of PHOT1 mRNA in the presence of light, but upregulation of PHOT2 transcript. The levels of mRNA and protein present in the plant were dependent upon the age of the plant. This suggests that the phototropin expression levels change with the maturation of the leaves.
Mature leaves contain chloroplasts that are essential in photosynthesis. Chloroplast rearrangement occurs in different light environments to maximize photosynthesis. There are several genes involved in plant phototropism including the NPH1 and NPL1 gene. They are both involved in chloroplast rearrangement. The nph1 and npl1 double mutants were found to have reduced phototropic responses. In fact, the two genes are both redundant in determining the curvature of the stem.
Recent studies reveal that multiple AGC kinases, except for PHOT1 and PHOT2, are involved in plant phototropism. Firstly, PINOID, exhibiting a light-inducible expression pattern, determines the subcellular relocation of PIN3 during phototropic responses via a direct phosphorylation. Secondly, D6PK and its D6PKL homologs modulates the auxin transport activity of PIN3, likely through phosphorylation as well. Third, upstream of D6PK/D6PKLs, PDK1.1 and PDK1.2 acts an essential activator for these AGC kinases. Interestingly, different AGC kinases might participate in different steps during the progression of a phototropic response. D6PK/D6PKLs exhibit an ability to phosphorylate more phosphosites than PINOID.

45
data/en.wikipedia.org/wiki/Phototropism-1.md Normal file
View File

@ -0,0 +1,45 @@
---
title: "Phototropism"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Phototropism"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:24.492344+00:00"
instance: "kb-cron"
---
=== Five models of auxin distribution in phototropism ===
In 2012, Sakai and Haga outlined how different auxin concentrations could be arising on shaded and lighted side of the stem, giving birth to phototropic response. Five models in respect to stem phototropism have been proposed, using Arabidopsis thaliana as the study plant.
First model
In the first model incoming light deactivates auxin on the light side of the plant allowing the shaded part to continue growing and eventually bend the plant over towards the light.
Second model
In the second model light inhibits auxin biosynthesis on the light side of the plant, thus decreasing the concentration of auxin relative to the unaffected side.
Third model
In the third model there is a horizontal flow of auxin from both the light and dark side of the plant. Incoming light causes more auxin to flow from the exposed side to the shaded side, increasing the concentration of auxin on the shaded side and thus more growth occurring.
Fourth model
In the fourth model it shows the plant receiving light to inhibit auxin basipetal down to the exposed side, causing the auxin to only flow down the shaded side.
Fifth model
Model five encompasses elements of both model 3 and 4. The main auxin flow in this model comes from the top of the plant vertically down towards the base of the plant with some of the auxin travelling horizontally from the main auxin flow to both sides of the plant. Receiving light inhibits the horizontal auxin flow from the main vertical auxin flow to the irradiated exposed side. And according to the study by Sakai and Haga, the observed asymmetric auxin distribution and subsequent phototropic response in hypocotyls seems most consistent with this fifth scenario.
== Effects of wavelength ==
Phototropism in plants such as Arabidopsis thaliana is directed by blue light receptors called phototropins. Other photosensitive receptors in plants include phytochromes that sense red light and cryptochromes that sense blue light. Different organs of the plant may exhibit different phototropic reactions to different wavelengths of light. Stem tips exhibit positive phototropic reactions to blue light, while root tips exhibit negative phototropic reactions to blue light. Both root tips and most stem tips exhibit positive phototropism to red light. Cryptochromes are photoreceptors that absorb blue/ UV-A light, and they help control the circadian rhythm in plants and timing of flowering. Phytochromes are photoreceptors that sense red/far-red light, but they also absorb blue light; they can control flowering in adult plants and the germination of seeds, among other things. The combination of responses from phytochromes and cryptochromes allow the plant to respond to various kinds of light. Together phytochromes and cryptochromes inhibit gravitropism in hypocotyls and contribute to phototropism.
== Gallery ==
== See also ==
Etiolation
Scotobiology
Cholodny–Went model
== References ==
== Bibliography ==
== External links ==
Media related to Phototropism at Wikimedia Commons
Time lapse films, Plants-In-Motion

35
data/en.wikipedia.org/wiki/Plant_litter-0.md Normal file
View File

@ -0,0 +1,35 @@
---
title: "Plant litter"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Plant_litter"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:25.712317+00:00"
instance: "kb-cron"
---
Plant litter (also leaf litter, tree litter, soil litter, litterfall, or duff) is dead plant material (such as leaves, bark, needles, twigs, and cladodes) that has fallen to the ground. This detritus or dead organic material and its constituent nutrients are added to the top layer of soil, commonly known as the litter layer or O-horizon ("O" for "organic"). Litter is an important factor in ecosystem dynamics, as it is indicative of ecological productivity and may be useful in predicting regional nutrient cycling and soil fertility.
== Characteristics and variability ==
Litterfall is characterized as fresh, undecomposed, and easily recognizable (by species and type) plant debris. This can be anything from leaves, cones, needles, twigs, bark, seeds/nuts, logs, or reproductive organs (e.g. the stamen of flowering plants). Items larger than 2 cm diameter are referred to as coarse litter, while anything smaller is referred to as fine litter or litter. The type of litterfall is most directly affected by ecosystem type.
For example, leaf tissues account for about 70 percent of litterfall in forests, but woody litter tends to increase with forest age. In grasslands, there is very little aboveground perennial tissue so the annual litterfall is very low and quite nearly equal to the net primary production.
In soil science, soil litter is classified in three layers, which form on the surface of the O Horizon. These are the L, F, and H layers:
The litter layer is quite variable in its thickness, decomposition rate and nutrient content and is affected in part by seasonality, plant species, climate, soil fertility, elevation, and latitude, as well as water retention of the soil. The most extreme variability of litterfall is seen as a function of seasonality; each individual species of plant has seasonal losses of certain parts of its body, which can be determined by the collection and classification of plant litterfall throughout the year, and in turn affects the thickness of the litter layer. In tropical environments, the largest amount of debris falls in the latter part of dry seasons and early during wet season. As a result of this variability due to seasons, the decomposition rate for any given area will also be variable.
Latitude also has a strong effect on litterfall rates and thickness. Specifically, litterfall declines with increasing latitude. In tropical rainforests, there is a thin litter layer due to the rapid decomposition, while in boreal forests, the rate of decomposition is slower and leads to the accumulation of a thick litter layer, also known as a mor. Net primary production works inversely to this trend, suggesting that the accumulation of organic matter is mainly a result of decomposition rate.
Surface detritus facilitates the capture and infiltration of rainwater into lower soil layers. The surface detritus also protects soil from excess drying and warming. Soil litter protects soil aggregates from raindrop impact, preventing the release of clay and silt particles from plugging soil pores. Releasing clay and silt particles reduces the capacity for soil to absorb water and increases cross surface flow, accelerating soil erosion. In addition soil litter reduces wind erosion by preventing soil from losing moisture and providing cover preventing soil transportation.
Organic matter accumulation also helps protect soils from wildfire damage. Soil litter can be completely removed depending on intensity and severity of wildfires and season. Regions with high frequency wildfires have reduced vegetation density and reduced soil litter accumulation. Climate also influences the depth of plant litter. Typically humid tropical and sub-tropical climates have reduced organic matter layers and horizons due to year-round decomposition and high vegetation density and growth. In temperate and cold climates, litter tends to accumulate and decompose slower due to a shorter growing season as decomposers work faster in environments with a stable temperature.
== Net primary productivity ==
Net primary production and litterfall are intimately connected. In every terrestrial ecosystem, the largest fraction of all net primary production is lost to herbivores and litter fall. Due to their interconnectedness, global patterns of litterfall are similar to global patterns of net primary productivity. Plant litter, which can be made up of fallen leaves, twigs, seeds, flowers, and other woody debris, makes up a large portion of above ground net primary production of all terrestrial ecosystems. Fungus plays a large role in cycling the nutrients from the plant litter back into the ecosystem.
== Habitat and food ==
Litter provides habitat for a variety of organisms.
=== Plants ===
Certain plants are specially adapted for germinating and thriving in the litter layers. For example, bluebell (Hyacinthoides non-scripta) shoots puncture the layer to emerge in spring. Some plants with rhizomes, such as common wood sorrel (Oxalis acetosella) do well in this habitat.
=== Detritivores and other decomposers ===

28
data/en.wikipedia.org/wiki/Plant_litter-1.md Normal file
View File

@ -0,0 +1,28 @@
---
title: "Plant litter"
chunk: 2/3
source: "https://en.wikipedia.org/wiki/Plant_litter"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:25.712317+00:00"
instance: "kb-cron"
---
Many organisms that live on the forest floor are decomposers, such as fungi. Organisms whose diet consists of plant detritus, such as earthworms, are termed detritivores. The community of decomposers in the litter layer also includes bacteria, amoeba, nematodes, rotifer, tardigrades, springtails, cryptostigmata, potworms, insect larvae, mollusks, oribatid mites, woodlice, and millipedes. Even some species of microcrustaceans, especially copepods (for instance Bryocyclops spp., Graeteriella spp.,Olmeccyclops hondo, Moraria spp.,Bryocamptus spp., Atheyella spp.) live in moist leaf litter habitats and play an important role as predators and decomposers.
The consumption of the litterfall by decomposers results in the breakdown of simple carbon compounds into carbon dioxide (CO2) and water (H2O), and releases inorganic ions (like nitrogen and phosphorus) into the soil where the surrounding plants can then reabsorb the nutrients that were shed as litterfall. In this way, litterfall becomes an important part of the nutrient cycle that sustains forest environments.
As litter decomposes, nutrients are released into the environment. The portion of the litter that is not readily decomposable is known as humus. Litter aids in soil moisture retention by cooling the ground surface and holding moisture in decaying organic matter. The flora and fauna working to decompose soil litter also aid in soil respiration. A litter layer of decomposing biomass provides a continuous energy source for macro- and micro-organisms.
=== Larger animals ===
Numerous reptiles, amphibians, birds, and even some mammals rely on litter for shelter and forage. Amphibians such as salamanders and caecilians inhabit the damp microclimate underneath fallen leaves for part or all of their life cycle. This makes them difficult to observe. A BBC film crew captured footage of a female caecilian with young for the first time in a documentary that aired in 2008.
Some species of birds, such as the ovenbird of eastern North America for example, require leaf litter for both foraging and material for nests. Sometimes litterfall even provides energy to much larger mammals, such as in boreal forests where lichen litterfall is one of the main constituents of wintering deer and elk diets. In the inland rainforests of British Columbia, heavy litterfall of "hair" lichens such as Bryoria and Alectoria plays a similar role for deep-snow mountain caribou. Each winter, large amounts of fragmented lichen thalli are shed from the forest canopy and accumulate on the snow surface, where they remain accessible as forage for several months. Researchers have described this continual replenishment of edible fragments as the "manna effect", a process that helps sustain caribou during periods when other food sources are buried under deep snow.
== Nutrient cycle ==
During leaf senescence, a portion of the plant's nutrients are reabsorbed from the leaves. The nutrient concentrations in litterfall differ from the nutrient concentrations in the mature foliage by the reabsorption of constituents during leaf senescence. Plants that grow in areas with low nutrient availability tend to produce litter with low nutrient concentrations, as a larger proportion of the available nutrients is reabsorbed. After senescence, the nutrient-enriched leaves become litterfall and settle on the soil below.
Litterfall is the dominant pathway for nutrient return to the soil, especially for nitrogen (N) and phosphorus (P). The accumulation of these nutrients in the top layer of soil is known as soil immobilization. Once the litterfall has settled, decomposition of the litter layer, accomplished through the leaching of nutrients by rainfall and throughfall and by the efforts of detritivores, releases the breakdown products into the soil below and therefore contributes to the cation exchange capacity of the soil. This holds especially true for highly weathered tropical soils. Decomposition rate is tied to the type of litterfall present.
Leaching is the process by which cations such as iron (Fe) and aluminum (Al), as well as organic matter are removed from the litterfall and transported downward into the soil below. This process is known as podzolization and is particularly intense in boreal and cool temperate forests that are mainly constituted by coniferous pines whose litterfall is rich in phenolic compounds and fulvic acid.
By the process of biological decomposition by microfauna, bacteria, and fungi, CO2 and H2O, nutrient elements, and a decomposition-resistant organic substance called humus are released. Humus composes the bulk of organic matter in the lower soil profile.
The decline of nutrient ratios is also a function of decomposition of litterfall (i.e. as litterfall decomposes, more nutrients enter the soil below and the litter will have a lower nutrient ratio). Litterfall containing high nutrient concentrations will decompose more rapidly and asymptote as those nutrients decrease. Knowing this, ecologists have been able to use nutrient concentrations as measured by remote sensing as an index of a potential rate of decomposition for any given area. Globally, data from various forest ecosystems shows an inverse relationship in the decline in nutrient ratios to the apparent nutrition availability of the forest.
Once nutrients have re-entered the soil, the plants can then reabsorb them through their roots. Therefore, nutrient reabsorption during senescence presents an opportunity for a plant's future net primary production use. A relationship between nutrient stores can also be defined as:
annual storage of nutrients in plant tissues + replacement of losses from litterfall and leaching = the amount of uptake in an ecosystem

98
data/en.wikipedia.org/wiki/Plant_litter-2.md Normal file
View File

@ -0,0 +1,98 @@
---
title: "Plant litter"
chunk: 3/3
source: "https://en.wikipedia.org/wiki/Plant_litter"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:25.712317+00:00"
instance: "kb-cron"
---
== Non-terrestrial litterfall ==
Non-terrestrial litterfall follows a very different path. Litter is produced both inland by terrestrial plants and moved to the coast by fluvial processes, and by mangrove ecosystems. From the coast Robertson & Daniel 1989 found it is then removed by the tide, crabs and microbes. They also noticed that which of those three is most significant depends on the tidal regime. Nordhaus et al. 2011 find crabs forage for leaves at low tide and if their detritivory is the predominant disposal route, they can take 80% of leaf material. Bakkar et al 2017 studied the chemical contribution of the resulting crab defecation. They find crabs pass a noticeable amount of undegraded lignins to both the sediments and water composition. They also find that the exact carbonaceous contribution of each plant species can be traced from the plant, through the crab, to its sediment or water disposition in this way. Crabs are usually the only significant macrofauna in this process, however Raw et al 2017 find Terebralia palustris competes with crabs unusually vigorously in southeast Asia.
== Collection and analysis ==
The main objectives of litterfall sampling and analysis are to quantify litterfall production and chemical composition over time in order to assess the variation in litterfall quantities, and hence its role in nutrient cycling across an environmental gradient of climate (moisture and temperature) and soil conditions.
Ecologists employ a simple approach to the collection of litterfall, most of which centers around one piece of equipment, known as a litterbag. A litterbag is simply any type of container that can be set out in any given area for a specified amount of time to collect the plant litter that falls from the canopy above.
Litterbags are generally set in random locations within a given area and marked with GPS or local coordinates, and then monitored on a specific time interval. Once the samples have been collected, they are usually classified on type, size and species (if possible) and recorded on a spreadsheet. When measuring bulk litterfall for an area, ecologists will weigh the dry contents of the litterbag. By this method litterfall flux can be defined as:
litterfall (kg m−2 yr−1) = total litter mass (kg) / litterbag area (m2)
The litterbag may also be used to study decomposition of the litter layer. By confining fresh litter in the mesh bags and placing them on the ground, an ecologist can monitor and collect the decay measurements of that litter. An exponential decay pattern has been produced by this type of experiment:
X
X
o
=
e
−
k
{\displaystyle {\frac {X}{X_{o}}}=e^{-k}}
, where
X
o
{\displaystyle X_{o}}
is the initial leaf litter and
k
{\displaystyle k}
is a constant fraction of detrital mass.
The mass-balance approach is also utilized in these experiments and suggests that the decomposition for a given amount of time should equal the input of litterfall for that same amount of time.
litterfall = k(detrital mass)
For study various groups from edaphic fauna you need a different mesh sizes in the litterbags
== Issues ==
=== Change due to invasive earthworms ===
In some regions of glaciated North America, earthworms have been introduced where they are not native. Non-native earthworms have led to environmental changes by accelerating the rate of decomposition of litter. These changes are being studied, but may have negative impacts on some inhabitants such as salamanders.
=== Forest litter raking ===
Leaf litter accumulation depends on factors like wind, decomposition rate and species composition of the forest. The quantity, depth and humidity of leaf litter varies in different habitats. The leaf litter found in primary forests is more abundant, deeper and holds more humidity than in secondary forests. This condition also allows for a more stable leaf litter quantity throughout the year. This thin, delicate layer of organic material can be easily affected by humans. For instance, forest litter raking as a replacement for straw in husbandry is an old non-timber practice in forest management that has been widespread in Europe since the seventeenth century. In 1853, an estimated 50 Tg of dry litter per year was raked in European forests, when the practice reached its peak. This human disturbance, if not combined with other degradation factors, could promote podzolisation; if managed properly (for example, by burying litter removed after its use in animal husbandry), even the repeated removal of forest biomass may not have negative effects on pedogenesis.
== See also ==
Coarse woody debris
Detritus
Forest floor
Leaf litter sieve
Leaf mold (a type of compost)
Soil horizon
== References ==
== External links ==
forestresearch.gov.uk

49
data/en.wikipedia.org/wiki/Postglacial_vegetation-0.md Normal file
View File

@ -0,0 +1,49 @@
---
title: "Postglacial vegetation"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Postglacial_vegetation"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:27.073439+00:00"
instance: "kb-cron"
---
Postglacial vegetation refers to plants that colonize the newly exposed substrate after a glacial retreat. The term "postglacial" typically refers to processes and events that occur after the departure of glacial ice or glacial climates.
== Climate Influence ==
Climate change is the main force behind changes in species distribution and abundance. Repeated changes in climate throughout the Quaternary Period are thought to have had a significant impact on the current vegetation species diversity present today. Functional and phylogenetic diversity are considered to be closely related to changing climatic conditions and this indicates that trait differences are extremely important in long term responses to climate change. During the transition from the last glaciation of the Pleistocene to the Holocene period, climate warming resulted in the expansion of taller plants and larger seed bearing plants which resulted in lower proportions of vegetation regeneration. Hence, low temperatures can be strong environmental filters that prevent tall and large-seeded plants from establishing in postglacial environments.
Throughout Europe vegetation dynamics within the first half of the Holocene appear to have been influenced mainly by climate and the reorganization of atmospheric circulation associated with the disappearance of the North American ice sheet. This is evident in the rapid increase of forestation and changing biomes during the postglacial period between 11500ka and 8000ka before the present.
Vegetation development periods of post-glacial land forms on Ellesmere Island, Northern Canada, is assumed to have been at least ca. 20,000 years in duration. This slow progression is mostly due to climatic restrictions such as an estimated annual rainfall amount of only 64mm and a mean annual temperature of -19.7 degrees Celsius. The length in time of vegetation development observed on Ellesmere Island is evidence that post glacial vegetation development is much more restricted in the Arctic and colder climates as compared to milder climatic regions such as the boreal, temperate and tropical zones.
== Vegetation Responses ==
As land became exposed following the glaciation of the last ice age, a variety of geographic settings ranging from the tropics to the Arctic and Antarctic became available for the establishment of vegetation. Species that now exist on formerly glaciated terrain must have undergone a change in distribution of hundreds to thousands of kilometers, or have evolved from other taxa that have once done so in the past. In a newly developing environment, plant growth is often strongly influenced by the introduction of new organisms into that environment, where competitive or mutualistic relationships may develop. Often, competitive balances are eventually reached and species abundances remain somewhat constant over a period of generations.
Studies done on the Norwegian Island of Svalbard, have been very useful in understanding the behavior of postglacial vegetation. Studies show that many vascular plants that are considered pioneers of vegetation development, eventually become less frequent. For example, the abundance of species such as Braya purpurascens has fallen nearly 30% due to the introduction of new species in the area.
== Postglacial Vegetation in North America ==
Arctic vegetation has distinct postglacial development characteristics compared to the more temperate zones of lower latitudes. A study of postglacial moraines conducted in the Canadian Arctic on Ellesmere Island have found that dwarf shrubs of Dryas integrifolia and Cassiope tetragona are often good indicators of vegetation development and progression. Dwarf shrubs have been found to increase with the age of the moraine, with Dryas integrifolia becoming the most predominant. As well the cover of vegetation, including lichens and bryophytes showed consistent increase with the moraine age, suggesting directional vegetation development. It is also suggested that part of the high proportions of polypoids occurring in arctic floras is the result of speciation as continental ice-sheets withdrew.
Pollen diagrams from northern Quebec, Canada, show advances throughout the Holocene of post-glacial vegetation development. The initial phase of open vegetation began about 6000 years before the present. Following deglaciation, shrub and herbaceous tundra plants dominated for a brief period of time. Plants such as the Larix laricina, Populus and Juniperus, were also important in the initial vegetation development. Some species that followed later include: Alnus crispa, and Betula. Though later vegetation development was mainly dominated by Picea, shortly following deglaciation, they reached their present day limit. Today black spruce is mainly dominant throughout much of northern Quebec.
The continental U.S. is considered to have strongly contributed to the re-establishment of postglacial vegetation in Canada following the last ice age. Roughly 300 taxa of vascular plants and mosses that were found to have existed below the extent of the last glacial period within the United States were also found to have migrated to Canada. These patterns are recorded within either pollen or macro fossils.
== Anthropogenic Impact ==
Studies done by Reitalu, (2015) have found that human impact throughout much of Europe has negatively influenced plant diversity by suppressing the establishment of tall-growing, large seeded taxa. Although human influence has facilitated many ruderal species, this is believed to have led to an overall decrease in phylogenetic diversity.
== Research Methods ==
Many pollen diagrams around the world indicate that major climate changes caused the last continental ice sheets to retreat, leading to dramatic effects on the distribution and abundance of plants. By converting pollen data into plant functional type (PFT) assemblages and interpolating the data, researchers have been able to reconstruct postglacial vegetation patterns around the world. Core sampling and analysis of lake sediments that contain pollen and other plant remains are often used to obtain good records of past pollination cycles. Such paleorecords preserved in lake sediments can be used to reconstruct the history of post glacial vegetation. Lake sediments have an advantage over other core sampling sites, such as fen and bog peats, as they provide no overwhelming local pollen components. As well, lake sediments contain stratigraphic changes in soil character, which are useful for understanding changes in vegetation development over a period of time. Macrofossils that are obtained from sedimentary deposits are also useful for constructing the history of changing postglacial vegetation.
== Notes ==
== References ==
Bennett, Keith (1988). "Post-glacial vegetation history: ecological considerations". Handbook of Vegetation Science. Vol. 7. pp. 699–724. Retrieved January 3, 2013.
Ritchie, J. C. (2004). Post-glacial Vegetation of Canada. Cambridge University Press. ISBN 0521544092. Retrieved 2021-08-12.
== Further reading ==
Heinselman, Miron (1999). Boundary Waters: Wilderness Ecosystem. U of Minnesota Press. pp. 34–36. ISBN 081662805X. Retrieved 2021-08-12.
Winkler, Marjorie Green (1982). Late-glacial and postglacial vegetation history of Cape Cod and the paleolimnology of Duck Pond, South Wellfleet, Massachusetts. University of Wisconsin-Madison. Retrieved 2021-08-12.

17
data/en.wikipedia.org/wiki/Predation_rates-0.md Normal file
View File

@ -0,0 +1,17 @@
---
title: "Predation rates"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Predation_rates"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:28.250216+00:00"
instance: "kb-cron"
---
The term predation rate refers to the frequency with which an organism captures and consumes its prey in an ecosystem. Coupled with the kill rate, the predation rate drives the population dynamics of predation. This statistic is related to Predator–prey dynamics and may be influenced by several factors.
In order for predation to occur, a predator and its prey must encounter one another. A low concentration of prey decreases the likelihood of such encounters. The prey encounter rate is determined by the abundance of organisms and a predator’s ability to locate its prey. Covering more territory increases the likelihood that a predator will meet its prey. In areas of low prey density, predators are adapted to be more motile, engage in filter feeding, or use attractants such as chemical lures.
If predation increased simply with prey concentration, the relationship would be linear until a limit is reached. This scenario is represented by Holling's type I functional response, which is rarely observed in nature. Several factors affect this relationship, including handling time (the time required for a predator to consume its prey), selective feeding behaviors, and learning. In contrast, Holling's type II and type III functional responses account for the time predators spend handling prey and the reduced efficiency in locating prey at low densities.
Predation rate is also influenced by spatial and temporal mismatch. An extreme example occurred in the Arctic in May of 2021 and 2022, when large blooms of Phytoplankton were observed alongside low concentrations of grazers. As the phytoplankton bloomed and died, the energy was not transferred into the Food web. Although primary production was high, the food web experienced an energy deficit. Spatial mismatch is particularly concerning under Climate change, as changing environmental parameters—such as rising Sea surface temperature and alterations in terrestrial habitats (e.g., loss of Tundra and melting Sea ice)—can create conditions that are no longer conducive to the populations they once supported
== References ==

28
data/en.wikipedia.org/wiki/Prehensility-0.md Normal file
View File

@ -0,0 +1,28 @@
---
title: "Prehensility"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Prehensility"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:29.527669+00:00"
instance: "kb-cron"
---
Prehensility is the quality of an appendage or organ that has adapted for grasping or holding. The word is derived from the Latin term prehendere, meaning "to grasp". The ability to grasp is likely derived from a number of different origins. The most common are tree-climbing and the need to manipulate food.
== Examples ==
Appendages that can become prehensile include:
== Uses ==
Prehensility affords animals a great natural advantage in manipulating their environment for feeding, climbing, digging, and defense. It enables many animals, such as primates, to use tools to complete tasks that would otherwise be impossible without highly specialized anatomy. For example, chimpanzees have the ability to use sticks to obtain termites and grubs in a manner similar to human fishing. However, not all prehensile organs are applied to tool use; the giraffe tongue, for instance, is instead used in feeding and self-cleaning.
== See also ==
Robot end effector
== References ==

35
data/en.wikipedia.org/wiki/Proteostasis-0.md Normal file
View File

@ -0,0 +1,35 @@
---
title: "Proteostasis"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Proteostasis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:30.910694+00:00"
instance: "kb-cron"
---
Proteostasis is the dynamic regulation of a balanced, functional proteome. The proteostasis network includes competing and integrated biological pathways within cells that control the biogenesis, folding, trafficking, and degradation of proteins present within and outside the cell. Loss of proteostasis is central to understanding the cause of diseases associated with excessive protein misfolding and degradation leading to loss-of-function phenotypes, as well as aggregation-associated degenerative disorders. Therapeutic restoration of proteostasis may treat or resolve these pathologies.
Cellular proteostasis is key to ensuring successful development, healthy aging, resistance to environmental stresses, and to minimize homeostatic perturbations from pathogens such as viruses. Cellular mechanisms for maintaining proteostasis include regulated protein translation, chaperone assisted protein folding, and protein degradation pathways. Adjusting each of these mechanisms based on the need for specific proteins is essential to maintain all cellular functions relying on a correctly folded proteome.
== Mechanisms of proteostasis ==
=== The roles of the ribosome in proteostasis ===
One of the first points of regulation for proteostasis is during translation. This regulation is accomplished via the structure of the ribosome, a complex central to translation. Its characteristics shape the way the protein folds, and influence the protein's future interactions. The synthesis of a new peptide chain using the ribosome is very slow; the ribosome can even be stalled when it encounters a rare codon, a codon found at low concentrations in the cell. The slow synthesis rate and any such pauses provide an individual protein domain with the necessary time to become folded before the production of subsequent domains. This facilitates the correct folding of multi-domain proteins.
The newly synthesized peptide chain exits the ribosome into the cellular environment through the narrow ribosome exit channel (width: 10Å to 20Å, length 80Å). Characteristics of the exit channel control the formation of secondary and limited tertiary structures in the nascent chain. For example, an alpha helix is a structural property that is commonly induced in this exit channel. At the same time, the exit channel prevents premature folding by impeding large scale interactions within the peptide chain that would require more space.
=== Molecular chaperones and post-translational maintenance in proteostasis ===
In order to maintain protein homeostasis post-translationally, the cell makes use of molecular chaperones sometimes including chaperonins, which aid in the assembly or disassembly of proteins. They recognize exposed segments of hydrophobic amino acids in the nascent peptide chain and then work to promote the proper formation of noncovalent interactions that lead to the desired folded state.
Chaperones begin to assist in protein folding as soon as a nascent chain longer than 60 amino acids emerges from the ribosome exit channel.
One of the most studied ribosome binding chaperones is trigger factor (TF). TF works to stabilize the peptide, promotes its folding, prevents aggregation, and promotes refolding of denatured model substrates. Ribosome profiling experiments have shown that TF predominantly targets ribosomes translating outer membrane proteins in vivo, and moreover are underrepresented on ribosomes translating inner membrane proteins. TF not only directly works to properly fold the protein but also recruits other chaperones to the ribosome, such as Hsp70. Hsp70 surrounds an unfolded peptide chain, thereby preventing aggregation and promoting folding.
Chaperonins are a special class of chaperones that promote native state folding by cyclically encapsulating the peptide chain. Chaperonins are divided into two groups. Group 1 chaperonins are commonly found in bacteria, chloroplasts, and mitochondria. Group 2 chaperonins are found in the cytosol of eukaryotic cells as well as in archaea. Group 2 chaperonins also contain an additional helical component which acts as a lid for the cylindrical protein chamber, unlike Group 1 which instead relies on an extra cochaperone to act as a lid. All chaperonins exhibit two states (open and closed), between which they can cycle. This cycling process is important during the folding of an individual polypeptide chain as it helps to avoid undesired interactions as well as to prevent the peptide from entering into kinetically trapped states.
=== Regulating proteostasis by protein degradation ===
The third component of the proteostasis network is the protein degradation machinery. Protein degradation occurs in proteostasis when the cellular signals indicate the need to decrease overall cellular protein levels. The effects of protein degradation can be local, with the cell only experiencing effects from the loss of the degraded protein itself or widespread, with the entire protein landscape changing due to loss of other proteins' interactions with the degraded protein.
Multiple substrates are targets for proteostatic degradation. These degradable substrates include nonfunctional protein fragments produced from ribosomal stalling during translation, misfolded or unfolded proteins, aggregated proteins, and proteins that are no longer needed to carry out cellular function.
Several different pathways exist for carrying out these degradation processes. When proteins are determined to be unfolded or misfolded, they are typically degraded via the unfolded protein response (UPR) or endoplasmic-reticulum-associated protein degradation (ERAD). Substrates that are unfolded, misfolded, or no longer required for cellular function can also be ubiquitin tagged for degradation by ATP dependent proteases, such as the proteasome in eukaryotes or ClpXP in prokaryotes. Autophagy, or self engulfment, lysosomal targeting, and phagocytosis (engulfment of waste products by other cells) can also be used as proteostatic degradation mechanisms.
== Signaling events in proteostasis ==
Protein misfolding is detected by mechanisms that are specific for the cellular compartment in which they occur. Distinct surveillance mechanisms that respond to unfolded protein have been characterized in the cytoplasm, endoplasmatic reticulum (ER) and mitochondria. This response acts locally in a cell autonomous fashion but can also extend to intercellular signaling to protect the organism from anticipated proteotoxic stress.
=== Cell-autonomous stress responses ===
Cellular stress response pathways detect and alleviate proteotoxic stress which is triggered by imbalances in proteostasis. The cell-autonomous regulation occurs through direct detection of misfolded proteins or inhibition of pathway activation by sequestering activating components in response to heat shock. Cellular responses to this stress signaling include transcriptional activation of chaperone expression, increased efficiency in protein trafficking and protein degradation and translational reduction.

42
data/en.wikipedia.org/wiki/Proteostasis-1.md Normal file
View File

@ -0,0 +1,42 @@
---
title: "Proteostasis"
chunk: 2/3
source: "https://en.wikipedia.org/wiki/Proteostasis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:30.910694+00:00"
instance: "kb-cron"
---
=== Cytosolic heat shock response ===
The cytosolic heat shock response (HSR) is mainly mediated by the transcription factor family HSF (heat shock family). HSF is constitutively bound by Hsp90. Upon a proteotoxic stimulus Hsp90 is recruited away from HSF, which can then bind to heat response elements in the DNA and upregulate gene expression of proteins involved in the maintenance of proteostasis.
=== ER unfolded protein response ===
The unfolded protein response (UPR) in the ER is activated by imbalances of unfolded proteins inside the ER and the proteins mediating protein homeostasis. Different "detectors" - such as IRE1, ATF6 and PERK - can recognize misfolded proteins in the ER and mediate transcriptional responses which help alleviate the effects of ER stress.
=== Mitochondrial unfolded protein response ===
The mitochondrial unfolded protein response detects imbalances in protein stoichiometry of mitochondrial proteins and misfolded proteins. The expression of mitochondrial chaperones is upregulated by the activation of the transcription factors ATF1 and/or DVE-1 with UBL5.
=== Systemic stress signaling ===
Stress responses can also be triggered in a non-cell autonomous fashion by intercellular communication. The stress that is sensed in one tissue could thereby be communicated to other tissues to protect the proteome of the organism or to regulate proteostasis systemically. Cell non-autonomous activation can occur for all three stress responses.
Work on the model organism C. elegans has shown that neurons play a role in this intercellular communication of cytosolic HSR. Stress induced in the neurons of the worm can in the long run protect other tissues such as muscle and intestinal cells from chronic proteotoxicity. Similarly ER and mitochondrial UPR in neurons are relayed to intestinal cells . These systemic responses have been implicated in mediating systemic proteostasis; they also influence organismal aging.
== Diseases of proteostasis ==
=== Proteostasis and diseases of protein folding ===
Dysfunction in proteostasis can arise from errors in or misregulation of protein folding. The classic examples are missense mutations and deletions that change the thermodynamic and kinetic parameters for the protein folding process. These mutations are often inherited and range in phenotypic severity from having no noticeable effect to embryonic lethality. Disease develops when these mutations render a protein significantly more susceptible to misfolding, aggregation, and degradation.
If these effects only alter the mutated protein, the negative consequences will only be local loss of function. However, if these mutations occur in a chaperone or a protein that interacts with many other proteins, dramatic global alterations in the proteostasis boundary will occur. Examples of diseases resulting from proteostatic changes from errors in protein folding include cystic fibrosis, Huntington's disease, Alzheimer's disease, lysosomal storage disorders, and others.
=== The role of model systems in the elucidation of protein-misfolding diseases ===
Small animal model systems have been and continue to be instrumental in the identification of functional mechanisms that safeguard proteostasis. Model systems of diverse misfolding-prone disease proteins have so far revealed numerous chaperone and co-chaperone modifiers of proteotoxicity.
=== Proteostasis and cancer ===
The unregulated cell division that marks cancer development requires increased protein synthesis for cancer cell function and survival. This increased protein synthesis is typically seen in proteins that modulate cell metabolism and growth processes. Cancer cells are sometimes susceptible to drugs that inhibit chaperones and disrupt proteostasis, such as Hsp90 inhibitors or proteasome inhibitors.
Furthermore, cancer cells tend to produce misfolded proteins, which are removed mainly by proteolysis. Inhibitors of proteolysis allow accumulation of both misfolded protein aggregates, as well as apoptosis signaling proteins in cancer cells. This can change the sensitivity of cancer cells to antineoplastic drugs; cancer cells either die at a lower drug concentration, or survive, depending on the type of proteins that accumulate, and the function these proteins have. Proteasome inhibitor bortezomib was the first drug of this type to receive approval for treatment of multiple myeloma.
=== Proteostasis and obesity ===
A hallmark of cellular proteostatic networks is their ability to adapt to stress via protein regulation. Metabolic disease, such as that associated with obesity, alters the ability of cellular proteostasis networks to adapt to stress, often with detrimental health effects. For example, when insulin production exceeds the cell's insulin secretion capacity, proteostatic collapse occurs and chaperone production is severely impaired. This disruption leads to the disease symptoms exhibited in individuals with diabetes.
=== Proteostasis and aging ===
Over time, the proteostasis network becomes burdened with proteins modified by reactive oxygen species and metabolites that induce oxidative damage. These byproducts can react with cellular proteins to cause misfolding and aggregation (especially in nondividing cells like neurons). This risk is particularly high for intrinsically disordered proteins. The insulin-like growth factor 1 receptor (IGF-1R) pathway has been shown in C. elegans to protect against these harmful aggregates, and some experimental work has suggested that upregulation of IGF-1R may stabilize proteostatic network and prevent detrimental effects of aging.
Expression of the chaperome, the ensemble of chaperones and co-chaperones that interact in a complex network of molecular folding machines to regulate proteome function, is dramatically repressed in human aging brains and in the brains of patients with neurodegenerative diseases. Functional assays in C. elegans and human cells have identified a conserved chaperome sub-network of 16 chaperone genes, corresponding to 28 human orthologs as a proteostasis safeguard in aging and age-onset neurodegenerative disease.

20
data/en.wikipedia.org/wiki/Proteostasis-2.md Normal file
View File

@ -0,0 +1,20 @@
---
title: "Proteostasis"
chunk: 3/3
source: "https://en.wikipedia.org/wiki/Proteostasis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:30.910694+00:00"
instance: "kb-cron"
---
=== Pharmacologic intervention in proteostasis ===
There are two main approaches that have been used for therapeutic development targeting the proteostatic network: pharmacologic chaperones and proteostasis regulators. The principle behind designing pharmacologic chaperones for intervention in diseases of proteostasis is to design small molecules that stabilize proteins exhibiting borderline stability.
Previously, this approach has been used to target and stabilize G-protein coupled receptors, neurotransmitter receptors, glycosidases, lysosomal storage proteins, and the mutant CFTR protein that causes cystic fibrosis and transthyretin, which can misfiled and aggregate leading to amyloidoses. Vertex Pharmaceuticals and Pfizer sell regulatory agency approved pharmacologic chaperones for ameliorating cystic fibrosis and the transthyretin amyloidoses, respectively. Amicus sells a regulatory agency approved pharmacologic chaperone for Fabry disease–a lysosomal storage disease.
The principle behind proteostasis regulators is different. These molecules alter the biology of protein folding and/or degradation by altering the stoichiometry of the proteostasis network components in a given sub cellular compartment. For example, some proteostasis regulators initiate stress responsive signaling, such as the unfolded protein response, which transcriptionally reprograms the endoplasmic reticulum proteostasis network.
It has been suggested that this approach could even be applied prophylactically, such as upregulating certain protective pathways before experiencing an anticipated severe cellular stress. One theoretical mechanism for this approach includes upregulating the heat shock response to rescue proteins from degradation during cellular stress.
== See also ==
Molecular chaperone therapy
== References ==

18
data/en.wikipedia.org/wiki/Psammon-0.md Normal file
View File

@ -0,0 +1,18 @@
---
title: "Psammon"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Psammon"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:32.210054+00:00"
instance: "kb-cron"
---
Psammon (from Greek "psammos", "sand") is an ecological community of organisms inhabiting coastal sand. It consists of biota buried in moist sediments. Psammon is also sometimes considered a part of benthos due to its near-bottom distribution. Psammon term is commonly used to refer to freshwater reservoirs such as lakes.
== See also ==
Epipsammon
== References ==

60
data/en.wikipedia.org/wiki/Psammophyte-0.md Normal file
View File

@ -0,0 +1,60 @@
---
title: "Psammophyte"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Psammophyte"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:33.528329+00:00"
instance: "kb-cron"
---
A psammophyte is a plant that grows in sandy and often unstable soils. Psammophytes are commonly found growing on beaches, deserts, and sand dunes. Because they thrive in these challenging or inhospitable habitats, psammophytes are considered extremophiles, and are further classified as a type of psammophile.
== Etymology ==
The word "psammophyte" consists of two Greek roots, psamm-, meaning "sand", and -phyte, meaning "plant". The term "psammophyte" first entered English in the early twentieth century via German botanical terminology.
== Description ==
Psammophytes are found in many different plant families, so may not share specific morphological or phytochemical traits. They also come in a variety of plant life-forms, including annual ephemerals, perennials, subshrubs, hemicryptophytes, and many others. What the many diverse psammophytes have in common is a resilience to harsh or rapidly fluctuating environmental factors, such as shifting soils, strong winds, intense sunlight exposure, or saltwater exposure, depending on the habitat. Psammophytes often have specialized traits, such as unusually tenacious or resilient roots that enable them to anchor and thrive despite various environmental stressors. Those growing in arid regions have evolved highly efficient physiological mechanisms that enable them to survive despite limited water availability, similar to those in other xerophytes.
== Distribution and habitat ==
Psammophytes grow in regions all over the world and can be found on sandy, unstable soils of beaches, deserts, and sand dunes. In China's autonomous Inner Mongolia region, psammophytic woodlands are found in steppe habitats.
== Ecology ==
Psammophytes often play an important ecological role by contributing some degree of soil stabilization in their sandy habitats. They can also play an important role in soil nutrient dynamics. Depending on the factors at play at a given site, psammophyte communities exhibit varying degrees of species diversity. For example, in the dunes of the Sahara Desert, psammophyte communities exhibit limited diversity and are predominantly made up of plants from the grass and mustard families.
Like many other types of plants, psammophytes can have symbiotic relationships with microorganisms called endophytes that live inside of their tissues, which can impart enhanced growth or other benefits.
== Conservation ==
A major threat to psammophytes in many regions is dune destabilization, which is exacerbated by human development projects and factors associated with climate change, such as drought and temperature increases. Encroachment of non-psammophytic plants and invasive species poses another threat to psammophyte species in some areas. Ecological restoration efforts in psammophyte habitats often aim to utilize the natural soil stabilizing and nutrient enhancement abilities of psammophytes as part of restoration strategies. Another important strategy is restoring and protecting the requisite soil microbiome some psammophytes require to thrive.
China's Minqin Garden of Desert Plants is one organization that is actively working on efforts to conserve both wild and horticultural psammophyte species.
== Examples ==
Some examples of psammophyte species include:
Agriophyllum squarrosum (sand rice)
Haloxylon ammodendron (saxaul)
Linaria arenaria (sand toadflax)
Omphalodes kuzinskyanae (Kuzinsky navelwort)
Stipagrostis pungens (madjiugu)
Corynephorus canescens (grey hair-grass or gray clubawn grass)
Plantago arenaria (branched plantain, sand plantain, or black psyllium)
== See also ==
Extremophile
Goravan Sands Sanctuary
Psammophile
Xerophyte
== References ==
== External links ==
Minqin Garden of Desert Plants

25
data/en.wikipedia.org/wiki/Pyrrolizidine_alkaloid_sequestration-0.md Normal file
View File

@ -0,0 +1,25 @@
---
title: "Pyrrolizidine alkaloid sequestration"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Pyrrolizidine_alkaloid_sequestration"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:34.807727+00:00"
instance: "kb-cron"
---
Pyrrolizidine alkaloid sequestration by insects is a strategy to facilitate defense and mating. Various species of insects have been known to use molecular compounds from plants for their own defense and even as their pheromones or precursors to their pheromones. A few Lepidoptera have been found to sequester chemicals from plants which they retain throughout their life and some members of Erebidae are examples of this phenomenon. Starting in the mid-twentieth century researchers investigated various members of Arctiidae, and how these insects sequester pyrrolizidine alkaloids (PAs) during their life stages, and use these chemicals as adults for pheromones or pheromone precursors. PAs are also used by members of the Arctiidae for defense against predators throughout the life of the insect.
== Overview ==
Pyrrolizidine alkaloids are a group of chemicals produced by plants as secondary metabolites, all of which contain a pyrrolizidine nucleus. This nucleus is made up of two pyrrole rings bonded by one carbon and one nitrogen. There are two forms in which PAs can exist and will readily interchange between: a pro-toxic free base form, also called a tertiary amine, or in a non-toxic form of N-oxide.
Researchers have collected data that strongly suggests that PAs can be registered by taste receptors of predators, acting as a deterrent from being ingested. Taste receptors are also used by the various moth species that sequester PAs, which often stimulates them to feed. As of 2005, all of the PA sequestering insects that have been studied have all evolved a system to keep concentrations of the PA pro-toxic form low within the insect's tissues.
Researchers have found a number of Arctiidae that use PAs for protection and for male pheromones or precursors of the male pheromones, and some studies have found evidence suggesting PAs have behavioral and developmental effects. Estigmene acrea, Cosmosoma myrodora, Utetheisa ornatrix, Creatonotos gangis and Creatonotos transiens are all members of the family Arctiidae and found to use PAs for their defense and/or male pheromones. Parsimony suggests that the sequestering of PAs in the larval stage evolved in the subfamily Arctiinae common ancestor. The loss of ability to sequester and use PAs has occurred in a number of species, along with the switch from larval uptake to adult uptake of PAs occurring multiple times within the Arctiinae taxon.
Members of Arctiidae typically sequester PAs from their diets, but sometimes must specifically ingest fluids excreted by plants that are not a part of their diets. Sequestered PAs are kept in various tissues and varying concentration which is dependent upon the species. PAs are found in the cuticle of all studied Arctiidae mentioned here, but some also package these chemicals into their spermatophores as seen in Creatonotos gangis and Creatonotos transiens. The display of PAs on the exoskeleton is believed to cue predators to the unpalatability of the prey.
Eisner and Eisner looked at the palatability of PA positive and negative U. ornatrix to wolf spiders, Lycosa ceratiola, in both the larval form and adult form. They found that the pyrrolizidine-positive organisms were typically released unharmed by spiders except in two field circumstances where the larvae were probably envenomated prior to the spider's release and died two days after the attack. All of the PA-negative organisms were eaten by spiders. These findings were in line with prior studies done by Eisner and Meinwald which looked at orb weavers and U. ornatrix, along with spiders being fed beetle larva covered in PAs, which they rejected. All of these findings support PAs being used for defense against predation.
Studies have further elucidated the defenses and uses of PAs in Arctiidae. One study researched C. myrodora and how PAs protect this species from spider predation among other things. It found that PAs ingested from fluids excreted by plants aided in defense from predation. All organisms permitted access to PA-containing diets that were fed to spiders were cut loose from the webs. Females that had PA-deprived diets, but were allowed to mate with PA-positive males, were also released from the spider's webs. Further observations showed that male C. myrodora have a pair of pouches where they produce PA-laden filaments, which are typically released over the female prior to copulation as a nuptial gift. Experiments show that the filaments give the females more PAs, explaining why spiders released mated PA-negative females from their webs. Most of the PAs from the males were subsequently transferred to the eggs when deposited. Three clusters of eggs that were laid after copulation with a PA-positive male all tested positive for alkaloids and the one cluster that resulted from a PA-negative male copulation tested negative. By the eggs getting a dose of PAs, the authors suggest that the eggs are being protected from predators such as Coccinellidae beetles.
Jordan and others’ study found a very interesting effect of the larval ingestion of PAs. Male Estigmene acrea moths that consumed PAs in their diet as larvae produced hydroxydanaidal, a volatile PA compound, and displayed their coremata: a bifid, inflatable male-specific organ, used in dispersing pheromones in the adult stage. Larvae that were fed diets without PAs rarely displayed their coremata and did not produce hydroxydanaidal. E. acrea have been observed in the wild displaying their coremata, an activity which attracts both males and females and is known as lekking. Lekking was described by Willis and Birch in 1982, but larvae raised in the laboratory prior to this study rarely engaged in lekking or corematal displays. Scientists were unsure of why this phenomenon didn't occur in the lab, but laboratory raised larvae were usually reared on commercially available food which lacks PAs. The authors suggest that the PAs are used by the males to attract other moths by releasing the volatile PA hydroxydanaidal into the air. It is suggested in this study that this strategy of mate attraction came about by tapping into the PA affinity already programmed into the moths for feeding, which is further supported by the observation that E. acrea females release their pheromones a little bit later in the evening than the males.
Similar uses of coremata to attract other moths have been observed in C. gangis and C. transiens along with altered development of coremata when larvae are reared without PAs. Boppre and Schneider observed adult males of these two species that were not permitted to eat PAs. Their coremata only developed into two, stalk-like projections with very few hairs arising from these stalks. Males that were given plants that produced PAs to feed upon, developed long coremata with four tubes, each longer than the males body, and each tube was highly pubescent. The authors suggest from this observation that there is a basic corematal phenotype, the two stalked coremata, and that PAs are required to form full coremata which is much larger and more elaborate than the basic corematal expression. These observations were further investigated by feeding larvae different amounts of PAs which had a direct correlation to the development of the coremata, which reached a maximum plateau around 2 mg of PAs ingested while in larval form. Similar to Jordan and others’ findings, the males raised on a diet devoid of PAs did not produce hydroxydanaidal.
== References ==

21
data/en.wikipedia.org/wiki/Range_state-0.md Normal file
View File

@ -0,0 +1,21 @@
---
title: "Range state"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Range_state"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:36.174449+00:00"
instance: "kb-cron"
---
Range state is a term generally used in zoogeography and conservation biology to refer to any nation that exercises jurisdiction over any part of a range which a particular species, taxon or biotope inhabits, or crosses or overflies at any time on its normal migration route. The term is often expanded to also include, particularly in international waters, any nation with vessels flying their flag that engage in exploitation (e.g. hunting, fishing, capturing) of that species. Countries in which a species occurs only as a vagrant or ‘accidental’ visitor outside of its normal range or migration route are not usually considered range states.
Because governmental conservation policy is often formulated on a national scale, and because in most countries, both governmental and private conservation organisations are also organised at the national level, the range state concept is often used by international conservation organizations in formulating their conservation and campaigning policy.
An example of one such organization is the Convention on the Conservation of Migratory Species of Wild Animals (CMS, or the “Bonn Convention”). It is a multilateral treaty focusing on the conservation of critically endangered and threatened migratory species, their habitats and their migration routes. Because such habitats and/or migration routes may span national boundaries, conservation efforts are less likely to succeed without the cooperation, participation, and coordination of each of the range states.
== External links ==
Bonn Convention (CMS) — Text of Convention Agreement
Bonn Convention (CMS): List of Range States for Critically Endangered Migratory Species
== References ==

696
data/en.wikipedia.org/wiki/Redundancy_principle_(biology)-0.md Normal file
View File

@ -0,0 +1,696 @@
---
title: "Redundancy principle (biology)"
chunk: 1/5
source: "https://en.wikipedia.org/wiki/Redundancy_principle_(biology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:37.452192+00:00"
instance: "kb-cron"
---
The redundancy principle in biology expresses the need of many copies of the same entity (cells, molecules, ions) to fulfill a biological function. Examples are numerous: disproportionate numbers of spermatozoa during fertilization compared to one egg, large number of neurotransmitters released during neuronal communication compared to the number of receptors, large numbers of released calcium ions during transient in cells, and many more in molecular and cellular transduction or gene activation and cell signaling. This redundancy is particularly relevant when the sites of activation are physically separated from the initial position of the molecular messengers. The redundancy is often generated for the purpose of resolving the time constraint of fast-activating pathways. It can be expressed in terms of the theory of extreme statistics to determine its laws and quantify how the shortest paths are selected. The main goal is to estimate these large numbers from physical principles and mathematical derivations.
When a large distance separates the source and the target (a small activation site), the redundancy principle explains that this geometrical gap can be compensated by large number. Had nature used less copies than normal, activation would have taken a much longer time, as finding a small target by chance is a rare event and falls into narrow escape problems.
== Molecular rate ==
The time for the fastest particles to reach a target in the context of redundancy depends on the numbers and the local geometry of the target. In most of the time, it is the rate of activation. This rate should be used instead of the classical Smoluchowski's rate describing the mean arrival time, but not the fastest. The statistics of the minimal time to activation set kinetic laws in biology, which can be quite different from the ones associated to average times.
== Physical models ==
=== Stochastic process ===
The motion of a particle located at position
X
t
{\displaystyle X_{t}}
can be described by the Smoluchowski's limit of the Langevin equation:
d
X
t
=
2
D
d
B
t
+
1
γ
F
(
x
)
d
t
,
{\displaystyle dX_{t}={\sqrt {2D}}\,dB_{t}+{\frac {1}{\gamma }}F(x)dt,}
where
D
{\displaystyle D}
is the diffusion coefficient of the particle,
γ
{\displaystyle \gamma }
is the friction coefficient per unit of mass,
F
(
x
)
{\displaystyle F(x)}
the force per unit of mass, and
B
t
{\displaystyle B_{t}}
is a Brownian motion. This model is classically used in molecular dynamics simulations.
=== Jump processes ===
x
n
+
1
=
{
x
n
−
a
,
with probability
l
(
x
n
)
x
n
+
b
,
with probability
r
(
x
n
)
{\displaystyle {\begin{aligned}x_{n+1}={\begin{cases}x_{n}-a,&{\text{with probability }}l(x_{n})\\x_{n}+b,&{\text{ with probability }}r(x_{n})\end{cases}}\end{aligned}}}
, which is for example a model of telomere length dynamics. Here
r
(
x
)
=
1
1
+
β
x
,
{\displaystyle r(x)={\frac {1}{1+\beta x}},}
, with
r
(
x
)
+
l
(
x
)
=
1
{\displaystyle r(x)+l(x)=1}
.
=== Directed motion process ===
X
˙
=
v
0
u
,
{\displaystyle {\dot {X}}=v_{0}{\bf {u,}}}
where
u
{\displaystyle {\bf {u}}}
is a unit vector chosen from a uniform distribution. Upon hitting an obstacle at a boundary point
X
0
∈
∂
Ω
{\displaystyle X_{0}\in \partial \Omega }
, the velocity changes to
X
˙
=
v
0
v
,
{\displaystyle {\dot {X}}=v_{0}{\bf {v,}}}
where
v
{\displaystyle {\bf {v}}}
is chosen on the unit sphere in the supporting half space at
X
0
{\displaystyle X_{0}}
from a uniform distribution, independently of
u
{\displaystyle {\bf {u}}}
. This rectilinear with constant velocity is a simplified model of spermatozoon motion in a bounded domain
Ω
{\displaystyle \Omega }
. Other models can be diffusion on graph, active graph motion.
== Mathematical formulation: Computing the rate of arrival time for the fastest ==
The mathematical analysis of large numbers of molecules, which are obviously redundant in the traditional activation theory, is used to compute the in vivo time scale of stochastic chemical reactions. The computation relies on asymptotics or probabilistic approaches to estimate the mean time of the fastest to reach a small target in various geometries.
With N non-interacting i.i.d. Brownian trajectories (ions) in a bounded domain Ω that bind at a site, the shortest arrival time is by definition
τ
1
=
min
(
t
1
,
…
,
t
N
)
,
{\displaystyle \tau ^{1}=\min(t_{1},\ldots ,t_{N}),}
where
t
i
{\displaystyle t_{i}}
are the independent arrival times of the N ions in the medium. The survival distribution of arrival time of the fastest
P
r
(
τ
1
>
t
)
{\displaystyle Pr(\tau ^{1}>t)}
is expressed in terms of a single particle,
P
r
(
τ
1
>
t
)
=
P
r
N
(
t
1
>
t
)
{\displaystyle Pr(\tau ^{1}>t)=Pr^{N}(t_{1}>t)}
. Here
P
r
{
t
1
>
t
}
{\displaystyle Pr\{t_{1}>t\}}
is the survival probability of a single particle prior to binding at the target.This probability is computed from the solution of the diffusion equation in a domain
Ω
{\displaystyle \Omega }
:
∂
p
(
x
,
t
)
∂
t
=
D
Δ
p
(
x
,
t
)
for
x
∈
Ω
,
t
>
0
{\displaystyle {\frac {\partial p(x,t)}{\partial t}}=D\Delta p(x,t){\hbox{ for }}x\in \Omega ,t>0}
p
(
x
,
0
)
=
p
0
(
x
)
for
x
∈
Ω
∂
p
∂
n
(
x
,
t
)
=
0
for
x
∈
∂
Ω
r
p
(
x
,
t
)
=
0
for
x
∈
∂
Ω
a
,
{\displaystyle {\begin{aligned}p(x,0)=&p_{0}(x){\hbox{ for }}x\in \Omega \\{\frac {\partial p}{\partial n}}(x,t)&=0{\hbox{ for }}x\in \partial \Omega _{r}\\p(x,t)&=0{\hbox{ for }}x\in \partial \Omega _{a},\end{aligned}}}

1326
data/en.wikipedia.org/wiki/Redundancy_principle_(biology)-1.md Normal file
View File

File diff suppressed because it is too large Load Diff

1075
data/en.wikipedia.org/wiki/Redundancy_principle_(biology)-2.md Normal file
View File

File diff suppressed because it is too large Load Diff

1280
data/en.wikipedia.org/wiki/Redundancy_principle_(biology)-3.md Normal file
View File

File diff suppressed because it is too large Load Diff

340
data/en.wikipedia.org/wiki/Redundancy_principle_(biology)-4.md Normal file
View File

@ -0,0 +1,340 @@
---
title: "Redundancy principle (biology)"
chunk: 5/5
source: "https://en.wikipedia.org/wiki/Redundancy_principle_(biology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:37.452192+00:00"
instance: "kb-cron"
---
where the integral is taken over all paths starting at y(0) and exiting at time
m
Δ
t
{\displaystyle m\Delta t}
. This formula suggests that when n is large, only the paths that minimize the integrant will contribute. For large n, this formula suggests that paths that will contribute the most are the ones that will minimize the exponent, which allows selecting the paths for which the energy functional is minimal, that is
E
=
min
X
∈
P
t
∫
0
T
x
˙
2
d
s
,
{\displaystyle E=\min _{X\in {\mathcal {P}}_{t}}\int \limits _{0}^{T}{\dot {x}}^{2}ds,}
where the integration is taken over the ensemble of regular paths
P
t
{\displaystyle {\mathcal {P}}_{t}}
inside
Ω
{\displaystyle \Omega }
starting at y and exiting in
∂
Ω
a
{\displaystyle \partial \Omega _{a}}
, defined as
P
T
=
{
P
(
0
)
=
y
,
P
(
T
)
∈
∂
Ω
a
and
P
(
s
)
∈
Ω
and
0
≤
s
≤
T
}
.
{\displaystyle {\mathcal {P}}_{T}=\{P(0)=y,P(T)\in \partial \Omega _{a}{\hbox{ and }}P(s)\in \Omega {\hbox{ and }}0\leq s\leq T\}.}
This formal argument shows that the random paths associated to the fastest exit time are concentrated near the shortest paths. Indeed, the Euler-Lagrange equations for the extremal problem are the classical geodesics between y and a point in the narrow window
∂
Ω
a
{\displaystyle \partial \Omega _{a}}
.
=== Fastest escape from a cusp in two dimensions ===
The formula for the fastest escape can generalize to the case where the absorbing window is located in funnel cusp and the initial particles are distributed outside the cusp. The cusp has a size
ϵ
{\displaystyle \epsilon }
in the opening and a curvature R. The diffusion coefficient is D. The shortest arrival time, valid for large n is given by
τ
(
n
)
≈
π
2
R
3
4
ϵ
D
(
1
−
cos
⁡
(
c
ϵ
~
)
ϵ
~
)
2
log
⁡
(
2
n
π
)
.
{\displaystyle \tau ^{(n)}\approx {\frac {\pi ^{2}R^{3}}{4\epsilon D({\frac {1-\cos(c{\sqrt {\tilde {\epsilon }}})}{\tilde {\epsilon }}})^{2}\log({\frac {2n}{\sqrt {\pi }}})}}.}
Here
ϵ
~
=
ϵ
R
{\displaystyle {\tilde {\epsilon }}={\frac {\epsilon }{R}}}
and c is a constant that depends on the diameter of the domain. The time taken by the first arrivers is proportional to the reciprocal of the size of the narrow target
ϵ
{\displaystyle \epsilon }
. This formula is derived for fixed geometry and large n and not in the opposite limit of large n and small epsilon.
== Concluding remarks ==
How nature sets the disproportionate numbers of particles remain unclear, but can be found using the theory of diffusion. One example is the number of neurotransmitters around 2000 to 3000 released during synaptic transmission, that are set to compensate the low copy number of receptors, so the probability of activation is restored to one.
In natural processes these large numbers should not be considered wasteful, but are necessary for generating the fastest possible response and make possible rare events that otherwise would never happen. This property is universal, ranging from the molecular scale to the population level.
Nature's strategy for optimizing the response time is not necessarily defined by the physics of the motion of an individual particle, but rather by the extreme statistics, that select the shortest paths. In addition, the search for a small activation site selects the particle to arrive first: although these trajectories are rare, they are the ones that set the time scale. We may need to reconsider our estimation toward numbers when punctioning nature in agreement with the redundant principle that quantifies the request to achieve the biological function.
== References ==

49
data/en.wikipedia.org/wiki/Relict-0.md Normal file
View File

@ -0,0 +1,49 @@
---
title: "Relict"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Relict"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:38.757493+00:00"
instance: "kb-cron"
---
A relict is a surviving remnant of a natural phenomenon.
== Biology ==
A relict is an organism that at an earlier time was abundant in a large area but now occurs at only one or a few small areas.
== Geology and geomorphology ==
In geology, a relict is a structure or mineral from a parent rock that did not undergo metamorphosis when the surrounding rock did, or a rock that survived a destructive geologic process.
In geomorphology, a relict landform is a landform formed by either erosive or constructive surficial processes that are no longer active as they were in the past.
A glacial relict is a cold-adapted organism that is a remnant of a larger distribution that existed in the ice ages.
== Human populations ==
As revealed by DNA testing, a relict population is an ancient people in an area, who have been largely supplanted by a later group of migrants and their descendants.
In various places around the world, minority ethnic groups represent lineages of ancient human migrations in places now occupied by more populous ethnic groups, whose ancestors arrived later. For example, the first human groups to inhabit the Caribbean islands were hunter-gatherer tribes from South and Central America. Genetic testing of natives of Cuba show that, in late pre-Columbian times, the island was home to agriculturalists of Taino ethnicity. In addition, a relict population of the original hunter-gatherers remained in western Cuba as the Ciboney people.
== Other uses ==
In ecology, an ecosystem which originally ranged over a large expanse, but is now narrowly confined, may be termed a relict.
In agronomy, a relict crop is a crop which was previously grown extensively, but is now only used in one limited region, or a small number of isolated regions.
In real estate law, reliction is the gradual recession of water from its usual high-water mark so that the newly uncovered land becomes the property of the adjoining riparian property owner.
"Relict" was an ancient term still used in colonial (British) America, and in England and Ireland of that era, now archaic, for a widow; it has come to be a generic or collective term for widows and widowers.
In historical linguistics, a relict is a word that is a survivor of a form or forms that are otherwise archaic.
== See also ==
The dictionary definition of relict at Wiktionary
Endemism
Hysteresis
Living fossil
Refugium (population biology)
Relic
Palaeochannel
== References ==

23
data/en.wikipedia.org/wiki/Reproductive_interference-0.md Normal file
View File

@ -0,0 +1,23 @@
---
title: "Reproductive interference"
chunk: 1/4
source: "https://en.wikipedia.org/wiki/Reproductive_interference"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:39.962893+00:00"
instance: "kb-cron"
---
Reproductive interference is the interaction between individuals of different species during mate acquisition that leads to a reduction of fitness in one or more of the individuals involved. The interactions occur when individuals make mistakes or are unable to recognise their own species, labelled as ‘incomplete species recognition'. Reproductive interference has been found within a variety of taxa, including insects, mammals, birds, amphibians, marine organisms, and plants.
There are seven causes of reproductive interference, namely signal jamming, heterospecific rivalry, misdirected courtship, heterospecific mating attempts, erroneous female choice, heterospecific mating, and hybridisation. All types have fitness costs on the participating individuals, generally from a reduction in reproductive success, a waste of gametes, and the expenditure of energy and nutrients. These costs are variable and dependent on numerous factors, such as the cause of reproductive interference, the sex of the parent, and the species involved.
Reproductive interference occurs between species that occupy the same habitat and can play a role in influencing the coexistence of these species. It differs from competition as reproductive interference does not occur due to a shared resource. Reproductive interference can have ecological consequences, such as through the segregation of species both spatially and temporally. It can also have evolutionary consequences, for example; it can impose a selective pressure on the affected species to evolve traits that better distinguish themselves from other species.
== Causes of reproductive interference ==
Reproductive interference can occur at different stages of mating, from locating a potential mate, to the fertilisation of an individual of a different species. There are seven causes of reproductive interference that each have their own consequences on the fitness of one or both of the involved individuals.
=== Signal jamming ===
Signal jamming refers to the interference of one signal by another. Jamming can occur by signals emitted from environmental sources (e.g. noise pollution), or from other species. In the context of reproductive interference, signal jamming only refers to the disruption of the transmission or retrieval of signals by another species. The process of mate attraction and acquisition involves signals to aid in locating and recognising potential mates. Signals can also give the receiver an indication of the quality of a potential mate. Signal jamming can occur in different types of communication. Auditory signal jamming, otherwise labelled as auditory masking, is when a noisy environment created by heterospecific signals causes difficulties in identifying conspecifics. Likewise in chemical signals, pheromones that are meant to attract conspecifics and drive off others may overlap with heterospecific pheromones, leading to confusion. Difficulties in recognising and locating conspecifics can result in a reduction of encounters with potential mates and a decrease in mating frequencies.
==== Examples ====
Vibrational signalling in the American grapevine leafhopper - Individuals of the American grapevine leafhopper communicate with each other through vibrational signals that they transmit through the host plant. American grapevine leafhoppers are receptive of signals within their receptor’s sensitivity range of 50 to 1000 Hz. The vibrations can be used to identify and locate potential female mates. To successfully communicate, a duet is performed between the male and female American grapevine leafhopper. The female replies within a specific timeframe after the male signal, and the male may use the timing of her reply to identify her. However, vibrational signals are prone to disruption and masking by heterospecific signals, conspecific signals, and background noise that are within their species-specific sensitivity range. The interference of the duet between a male and female American grapevine leafhopper can reduce the male’s success in identifying and locating the female, which can reduce the frequency of mating.

26
data/en.wikipedia.org/wiki/Reproductive_interference-1.md Normal file
View File

@ -0,0 +1,26 @@
---
title: "Reproductive interference"
chunk: 2/4
source: "https://en.wikipedia.org/wiki/Reproductive_interference"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:39.962893+00:00"
instance: "kb-cron"
---
Auditory signalling in the gray treefrog (Hyla versicolor) and the Cope's gray treefrogs (Hyla chrysoscelis) – The success of reproduction is dependent on a female’s ability to correctly identify and respond to the advertisement call of a potential mate. At a breeding site with high densities of males, the male’s chorus may overlap with heterospecific calls, making it difficult for the female to successfully locate a mate. When the advertisement calls of the male gray treefrog and male Cope’s gray treefrog overlap, female gray treefrogs make mistakes and choose the heterospecific call. The amount of errors the female makes is dependent on the amount of overlap between signals. Female Cope’s gray treefrogs can better differentiate the signals and are only significantly affected when heterospecifics completely overlap conspecific male signals. However, female Cope’s gray treefrogs prefer conspecific male signals that have less overlap (i.e. less interference). Furthermore, females have longer response times to overlapped calls, where it takes longer for them to choose a mate. Signal jamming can affect both males and females as difficulties in identifying and locating a mate reduces their mating frequencies. Females may have more costs if they mate with a male of a lower quality, and may be susceptible to a higher risk of predation by predators within the breeding site if they take longer to choose and locate a male. Heterospecific mating between the gray treefrog and Cope’s gray treefrogs also can form an infertile hybrid which is highly costly to both parents due to the wastage of gametes.
Chemical signalling in ticks – Female ticks produce a pheromone that is a species-specific signal to attract conspecific males that are attached to the host. Female ticks also produce a pheromone that is not species-specific which can attract males that are in a close proximity to her. Pheromones emitted from closely related species can mix and lead to interference. Three species of ticks: Aponomma hydrosauri, Amblyomma albolimbatum, and Amblyomma limbatum, are closely related and can interfere with one another when attached to the same host. When two of the species of tick are attached on the same host, males have difficulties locating a female of the same species, potentially due to the mixing of pheromones. The pheromone that is not species-specific also has the capability of attracting males of all three species when they are in close proximity to the female. The presence of a heterospecific female can also reduce the time a male spends with conspecific females, leading to a reduction of reproductive success. Furthermore, when Amblyomma albolimbatum males attach to Aponomma hydrosauri females to mate, despite being unsuccessful, they remain attached which physically inhibits following males from mating.
=== Heterospecific rivalry ===
Heterospecific rivalry occurs between males, when a male of a different species is mistaken as a rival for mates (i.e. mistaken for a conspecific male). In particular, heterospecific rivalry is hard to differentiate from other interspecific interactions, such as the competition over food and other resources. Costs to the mistaken males can include the wastage of time and energy, and a higher risk of injury and predation if they leave their mating territory to pursue the heterospecific male. Males that chase off a heterospecific male may also leave females exposed to following intruders, whether it be a conspecific or heterospecific male.
==== Examples ====
Eastern amberwing dragonfly (Perithemis tenera) – Male Eastern amberwing dragonflies are territorial as they defend mating territories from rival conspecific males. The male will perch around their territory and pursue conspecifics that fly near the perch. When the male is approached by a species of horsefly and butterfly, they are similarly pursued. The horsefly and butterfly do not compete over a common resource with the Eastern amberwing dragonfly, have not been seen interfering with the mating within the territory, and are neither a predator nor prey of the Eastern amberwing dragonfly. Instead, they are pursued potentially due to being mistaken for a rival conspecific as they share similar characteristics in size, colour, and flight height. The similar characteristics may be cues used by the male Eastern amberwing dragonfly to identify conspecifics. The heterospecific pursuit is costly for the male as they waste energy and time, have a higher risk of injury, and may lose opportunities to defend their territory against subsequent intruders.
=== Misdirected courtship ===
Misdirected courtship occurs when males display courtship towards individuals of a different species of either sex. The misdirection is caused by a mistake during species recognition, or by an attraction towards heterospecifics that possess desirable traits. Such desirable traits are those traits that normally are an indicator of conspecific mate quality, such as body size. Costs associated with misdirecting courtship for males include the wasted energy investment in the attempt to court heterospecifics, and a decrease in mating frequency within species.
==== Examples ====
Waxbill – Waxbills are monogamous, where an individual only has one partner. Parents also display biparental care, where both the mother and father contribute to the care of the offspring. The combination of monogamy and biparental investment suggest that both male and female waxbills should be ‘choosy’ and have strong preferences to reduce the chances of mating with a heterospecific female. Males of the three species of waxbill: blue breast (Uraeginthus angolensis), red cheek (Uraeginthus bengalus), and blue cap (Uraeginthus cyanocephalus), have differing strengths of preferences for conspecific females when also presented with a heterospecific female. The differing preferences is affected by the body size of the females, potentially due to body size being an indicator of fecundity, which is the ability to produce offspring. Blue breast males prefer conspecifics over red cheek females that are smaller; however, have a weaker preference for conspecifics over blue breast females that are only slightly smaller. Red cheek males have no preference for conspecifics in the presence of a larger blue breast female or blue cap female. Blue cap males prefer conspecifics over red cheek females; however, have no preference for conspecifics in the presence of a larger blue breast male.

31
data/en.wikipedia.org/wiki/Reproductive_interference-2.md Normal file
View File

@ -0,0 +1,31 @@
---
title: "Reproductive interference"
chunk: 3/4
source: "https://en.wikipedia.org/wiki/Reproductive_interference"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:39.962893+00:00"
instance: "kb-cron"
---
Atlantic salmon (Salmo salar) – Atlantic salmon that were once native to Lake Ontario were reintroduced to the lake to study their spawning interactions with other species of fish, including the chinook salmon, coho salmon, and brown trout. Chinook salmon interacted with Atlantic salmon the most, where male chinooks attempted to court female Atlantic salmon. Male chinooks also chased away, and in some interactions, behaved aggressively towards other Atlantic salmon that approached female Atlantic salmon. A male brown trout was also observed to court a female Atlantic salmon. Misdirected courtship towards the Atlantic salmon can cause problems in waters that the Atlantic salmon currently occupy, and towards conservation efforts to reintroduce the Atlantic salmon to Lake Ontario. Implications of misdirected courtship on the Atlantic salmon can cause the delay or prevention of spawning, and the hybridisation of the Atlantic salmon with other species.
=== Heterospecific mating attempts ===
Heterospecific mating attempts occur when males attempt to mate with females of a different species, regardless of whether courtship occurs. During each mating attempt, sperm transfer may or may not occur. Both sexes have costs when a heterospecific attempts to mate. Costs associated with heterospecific mating attempts include wasted energy, time, and potentially gametes if sperm transfer occurs. There is also a risk of injury and increased risk of predation for both sexes.
==== Examples ====
Cepero's grasshopper (Tetrix ceperoi) and the slender groundhopper (Tetrix subulata) – Naturally the distribution of the Cepero’s grasshopper and slender groundhopper overlap; however, they rarely co-exist. The reproductive success of the Cepero’s grasshopper decreases when housed within the same enclosure as high numbers of the slender groundhopper. The reduction of reproductive success stems from an increase in mating attempts by the Cepero's grasshopper towards the slender groundhopper, which may be due to their larger body size. However, these mating attempts are generally unsuccessful as the mate recognition of female slender groundhoppers are reliable, which may be due to the different courtship displays of the two species. The reduced reproductive success can cause the displacement in one of the species, potentially a factor as to why the species rarely co-exist despite sharing similar habitat preferences.
Italian agile frog (Rana latastei) - The distribution of Italian agile frog and the agile frog (Rana dalmatina) overlap naturally in ponds and drainage ditches. In the areas of overlap, the abundance of agile frogs is higher than Italian agile frogs. When there is a higher abundance of agile frogs, the mating between Italian agile frogs is interfered with. Male agile frogs attempt to displace male Italian agile frogs during amplexus, which is a type of mating position where the male grasps onto the female. The Italian agile frog and agile frog have been seen in amplexus when co-existing. The mating attempts by the agile frog reduces the reproductive success of the Italian agile frog. The Italian agile frog also produces a lower number of viable eggs in the presence of the agile frog, potentially due to sperm competition between the male Italian agile frog and agile frog.
Species and sex-recognition errors among true toads are very well studied. Toads are known to have amplexus with species from other genera in the same family, and species belonging to other families. Hybridization cases have also been reported among toads.
=== Erroneous female choice ===
Erroneous female choice refers to mistakes made by females when differentiating males of the same species from males of a different species. Female choice may occur at different stages of mating, including male courtship, copulation, or after copulation. Female choice can depend on the availability of appropriate males. When there are less available conspecific males, females may make more mistakes as they become less ‘choosy’.
==== Examples ====
Striped ground cricket (Allonemobius fasciatus) and Southern ground cricket (Allonemobius socius) - The striped ground cricket and the Southern ground cricket are closely related species that have an overlapping distribution. Both crickets use calling songs in order to identify and locate potential mates. The songs of the two species have a different frequency and period. Females of both species show little preference between the songs from conspecific and heterospecific males. The minor preference disappears if the intensity of the calls are altered. The lack of ability to differentiate between the two songs can result in erroneous female choice. Erroneous female choice has costs, including energy wastage, and increases in predation risk when searching for a conspecific. Additionally, it is highly costly when the mistake leads to heterospecific mating, which involves the wastage of gametes. However, the cost of erroneous female choice may be small for the striped ground and Southern ground cricket due to their high abundance. The lack of ability to differentiate between the calling songs is proposed to be due to the weak selective pressure on the females.
=== Heterospecific mating ===
Heterospecific mating is when two individuals from different species mate. After the male transfers his sperm into the heterospecific female, different processes can occur that may change the outcome of the copulation. Heterospecific mating may result in the production of a hybrid in some pairings. Costs associated to heterospecific mating include the wastage of time, energy, and gametes.

25
data/en.wikipedia.org/wiki/Reproductive_interference-3.md Normal file
View File

@ -0,0 +1,25 @@
---
title: "Reproductive interference"
chunk: 4/4
source: "https://en.wikipedia.org/wiki/Reproductive_interference"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:39.962893+00:00"
instance: "kb-cron"
---
==== Examples ====
Spider mites – two closely related Panonychus mites: the Panonychus citri and Panonychus mori, are generally geographically segregated and on occasion co-exist. However, the co-existence is not stable as the Panonychus mori is eventually excluded. The exclusion is a result of reproductive interference and also due to the higher reproductive rate of the Panonychus citri. Heterospecific mating occurs between the two species which can produce infertile eggs or infertile hybrid females. Furthermore, females are not able to produce female offspring after mating with a heterospecific. In addition to the wastage of energy, time, and gametes, the inability to produce female offspring after heterospecific mating skews the sex ratio of the co-existing populations. The high costs associated with heterospecific mating along with the higher reproductive rate of the Panonychus citri lead to the displacement of the Panonychus mori.
Black-legged meadow katydid (Orchelimum nigripes) and the handsome meadow katydid (Orchelimum pulchellum) – The two closely related species of katydid have the same habitat preferences and co-exist along the Potomac River. Females of both species that mate heterospecifically have a large reduction in fecundity compared to conspecific pairings. Heterospecific mating either produces no eggs or male hybrids that may be sterile. Both individuals suffer a large fitness cost from the wastage of energy, time, and gametes, as they unsuccessfully pass on their genes. However, females may be able to offset this cost through multiple mating, as they receive nutritional benefits from consuming a nuptial food gift from the male, otherwise known as the spermatophylax.
=== Hybridisation ===
Hybridisation, in the context of reproductive interference, is defined as the mating between individuals of different species that can lead to a hybrid, an inviable egg, or an inviable offspring. The frequency of hybridisation increases if it is hard to recognise potential mates, especially when heterospecifics share similarities, such as body size, colouration, and acoustic signals. Costs associated with hybridisation are dependent on the level of parental investment and on the product of the pairing (hybrid). Hybrids have the potential to become invasive if they develop traits that make them more successful than their parent species in surviving within new and changing habitats, otherwise known as hybrid vigor or heterosis. Compared to each individual parent species, they hold a different combination of characteristics that can be more adaptable and 'fit' within particular environments. If an inviable product is produced, both parents suffer from the cost of unsuccessfully passing on their genes.
==== Examples ====
California Tiger Salamanders (Ambystoma californiense) x Barred Tiger Salamanders (Ambystoma mavortium) - California tiger salamanders are native to California, and were geographically isolated from Barred tiger salamanders. Barred tiger salamanders were then introduced by humans to California, and the mating between these two species led to the formation of a population of hybrids. The hybrids have since established in their parent habitat and spread into human modified environments. Within hybrids, the survivability of individuals with a mixed-ancestry is higher than individuals with a highly native or highly introduced genetic background. Stable populations can form as populations with a large native ancestry become mixed with more introduced genes, and vice versa. Hybrids pose both ecological and conservation consequences as they threaten the population viability of the native California tiger salamanders, which is currently listed as an endangered species. The hybrids may also affect the viability of other native organisms within the invaded regions, as they consume large quantities of aquatic invertebrate and tadpole.
Red deer (Cervus elaphus) x sika deer (Cervus nippon) - The sika deer were originally introduced by humans to Britain and has since established and spread through deliberate reintroductions and escape. The red deer are native to Britain and hybridise with the sika deer in areas which they co-exist. Heterospecific mating between the red deer and sika deer can produce viable hybrids. Sika deer and the hybrids may outcompete and displace native deer from dense woodland. As the complete eradication of sika and the hybrids is impractical, management efforts are directed at minimising spread by not planting vegetation that would facilitate their spread into regions where the red deer still persist.
== References ==

32
data/en.wikipedia.org/wiki/Retinalophototroph-0.md Normal file
View File

@ -0,0 +1,32 @@
---
title: "Retinalophototroph"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Retinalophototroph"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:41.252337+00:00"
instance: "kb-cron"
---
A retinalophototroph is one of two different types of phototrophs, and are named for retinal-binding proteins (microbial rhodopsins) they utilize for cell signaling and converting light into energy. Like all phototrophs, retinalophototrophs absorb photons to initiate their cellular processes. In contrast with chlorophototrophs, retinalophototrophs do not use chlorophyll or an electron transport chain to power their chemical reactions. This means retinalophototrophs are incapable of traditional carbon fixation, a fundamental photosynthetic process that transforms inorganic carbon (carbon contained in molecular compounds like carbon dioxide) into organic compounds. For this reason, experts consider them to be less efficient than their chlorophyll-using counterparts, chlorophototrophs.
== Energy conversion ==
Retinalophototrophs achieve adequate energy conversion via a proton-motive force. In retinalophototrophs, proton-motive force is generated from rhodopsin-like proteins, primarily bacteriorhodopsin and proteorhodopsin, acting as proton pumps along a cellular membrane.
To capture photons needed for activating a protein pump, retinalophototrophs employ organic pigments known as carotenoids, namely beta-carotenoids. Beta-carotenoids present in retinalophototrophs are unusual candidates for energy conversion, but they possess high Vitamin-A activity necessary for retinaldehyde, or retinal, formation. Retinal, a chromophore molecule configured from Vitamin A, is formed when bonds between carotenoids are disrupted in a process called cleavage. Due to its acute light sensitivity, retinal is ideal for activation of proton-motive force and imparts a unique purple coloration to retinalophototrophs. Once retinal absorbs enough light, it isomerizes, thereby forcing a conformational (i.e., structural) change among the covalent bonds of the rhodopsin-like proteins. Upon activation, these proteins mimic a gateway, allowing passage of ions to create an electrochemical gradient between the interior and exterior of the cellular membrane. Ions diffusing outwards across the gradient through proton pumps are then bound to ATP synthase proteins on the cell's surface. As they diffuse back into the cell, their protons catalyze the creation of ATP (from ADP and a phosphorus ion), providing energy for retinalophototrophic self-sustenance and proliferation.
== Interaction with carbon ==
Many, if not all, retinalophototrophs are photoheterotrophs: although sufficient ATP is produced by light, they cannot subsist on light and inorganic substances alone because they cannot produce needed organic materials from only CO2. This category includes retinalophototrophs that perform anaplerotic fixation, such as a flavobacterium that can use pyruvate and CO2 to make malate. This ability does, however, help "stretch" limited supplies of carbon.
== Taxonomy ==
Retinalophototrophs are found across all domains of life but predominantly in the Bacteria and Archaea taxonomic groups. Scientists believe retinalophototroph's general ecological abundance correlates to horizontal gene transfer since only two genes are required for retinalophototrophy to occur: essentially, one gene for retinal-binding protein synthesis (bop) and one for retinal chromophore synthesis (blh).
== Interactions with environment ==
Despite their apparent simplicity, retinalophototrophs boast versatile ion usage that translates to their existence in relatively extreme environments. For instance, retinalophototrophs can thrive at depths over 200 meters where, despite a lack of inorganic carbon, sufficient light as well as sodium, hydrogen, or chloride concentrations harbor conditions capable of supporting their vital metabolic processes. Studies have also shown sodium and hydrogen ions correlate directly with retinalophototroph's nutrient uptake and ATP synthesis, while chloride drives processes responsible for osmotic equilibrium. Even though retinalophototrophs are widespread, research has shown they can be niche too. Depending on their proximity to the oceans surface, retinalophototrophs have evolved to be better at absorbing light within specific wavelengths. Most importantly, retinalophototrophs prevalence as a primary producer contributes substantially to the bottom-up mechanics of marine environments and, consequently, success of fauna and flora worldwide.
Although retinalophototrophs are less efficient at converting light than chlorophototrophs, the simplicity makes it the preferred system in a large number of environments. For example, because retinalophototrophs requires no iron in the reaction center, they are well-adapted to the iron-poor ocean environment. At high light level, they are more efficient in terms of protein investment to energy output due to the small size.
== References ==

16
data/en.wikipedia.org/wiki/Rimose-0.md Normal file
View File

@ -0,0 +1,16 @@
---
title: "Rimose"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Rimose"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:42.501491+00:00"
instance: "kb-cron"
---
Rimose is an adjective used to describe a surface that is cracked or fissured.
The term is often used in describing crustose lichens. A rimose surface of a lichen is sometimes contrasted to the surface being areolate. Areolate is an extreme form of being rimose, where the cracks or fissures are so deep that they create island-like pieces called areoles, which look the "islands" of mud on the surface of a dry lake bed. Rimose and areolate are contrasted with being verrucose, or "warty". Verrucose surfaces have warty bumps which are distinct, but not separated by cracks.
In mycology the term describes mushrooms whose caps crack in a radial pattern, as commonly found in the genera Inocybe and Inosperma.
== References ==

39
data/en.wikipedia.org/wiki/Runt-0.md Normal file
View File

@ -0,0 +1,39 @@
---
title: "Runt"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Runt"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:43.749383+00:00"
instance: "kb-cron"
---
A runt is an animal that is unusually small for its species. In veterinary medicine, a runt may also be described using terms such as low-birth weight, intrauterine growth restriction, and small for gestational age. An animal may be defined as small for gestational age (SGA) depending on different criteria, such as size in comparison to littermates', as percent of maternal body weight, as a specific neonate weight threshold for the breed or species, and as different body proportions displayed by runts.
Runts face many challenges in comparison to their normal birth weight peers - they are more likely to contract diseases, and die in the neonatal period, have lower glycogen stores, have developmental delays, insulin resistance, hypothermia, and low blood pressure. Runts are also associated with economic losses in farm animals - SGA adult cows give smaller milk yields and have infertility, intrauterine growth restricted (IUGR) piglets have modifications in their muscle tissue that may affect the taste of their meat, adult IUGR sows have smaller litter sizes and lower birth weight piglets in their litters and adult low birth weight ewes may have poorer quality fleeces.
== Causes ==
SGA has been best studied in pigs, both due to industry pressures of high mortality rates of preweaning piglets and the use of pig as a model organism in science. Runts are caused by interplay between genetics, environment in utero, maternal environment and care. Breeding for larger litter sizes has resulted in there being born more piglets than the teats of the sow, longer birthing times and more hypoxic young. Further causes of fetal malfunctioning can be a circovirus infection, maternal malnutrition or a small or inconveniently placed placenta.
In cattle and sheep, an additional reason may be hot weather during pregnancy. In dairy cows, a contributing factor may be lactating while pregnant, which can overtax the cow's ability to provide sufficient nutrients to the fetus. Nulliparous cows are more at risk of giving birth to SGA calves, and on average give birth to calves of a lower birth weight.
In dogs, a larger litter size may cause more low weight puppies to be born. Typically low weight puppies, like piglets, have smaller placentas in comparison to their normal body weight littermates.
In cats, younger mothers are more likely to give birth to kittens with lower body weight. Likelihood of giving birth to low body weight kittens increases if there is at least one stillbirth in the litter.
== Management ==
For companion animals such as dogs, assisting with whelping, using Apgar scoring and monitoring weight to identify at-risk puppies has been proven to lower mortality rates and equalize early growth among littermates.
However, it is the identification of at-risk puppies that presents a unique challenge in dogs, as dog breeds can vary in weight from less than 1 kg to 120 kg. This discrepancy in size can make it hard to create a uniform guideline for care which breeders and veterinarians can implement in practice. Several identifying tools have been proposed, such as puppy weight - mother weight ratio, which can help identify low birth weight mongrel puppies or breed-specific thresholds, which can be more useful in identifying underweight purebred puppies, as the birth weight of puppies can vary quite a bit among same adult size large and giant breeds.
For livestock like swine, labor-intensive birth assistance has been identified as a major mitigating factor in runt mortality and future outcomes, however such a strategy is cost ineffective in intensive animal farming. Instead, the recommended strategy is managing the sow's nutritional intake and not breeding IUGR piglets.
In cows, it has been found that runt calves are less likely to be effective milk producers and also tend to produce smaller calves in turn. It has been suggested that it would be more effective to redirect SGA calves to veal production, and preferentially breed calves of an average size and good productivity.
== See also ==
Small for gestational age
Low birth weight
Vanishing twin
== References ==
== External links ==
Runt Por Placa

14
data/en.wikipedia.org/wiki/Smash_and_Grab_(biology)-0.md Normal file
View File

@ -0,0 +1,14 @@
---
title: "Smash and Grab (biology)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Smash_and_Grab_(biology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:44.953153+00:00"
instance: "kb-cron"
---
Smash and Grab is the name given to a technique developed by Charles S. Hoffman and Fred Winston used in molecular biology to rescue plasmids from yeast transformants into Escherichia coli, also known as E. coli, in order to amplify and purify them. In addition, it can be used to prepare yeast genomic DNA (and DNA from tissue samples) for Southern blot analyses or polymerase chain reaction (PCR).
== References ==

20
data/en.wikipedia.org/wiki/Sociome-0.md Normal file
View File

@ -0,0 +1,20 @@
---
title: "Sociome"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Sociome"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:46.170901+00:00"
instance: "kb-cron"
---
The Sociome is a concept used by scientists in Biology and Sociology referring to the dimensions of existence that are social. The term is also an indication of the convergence of systems biology and the study of society as a complex system that has begun to occur among early 21st Century scientists. Just as the phenome is typically thought of as the set of expressed phenotypes of an organism, the sociome can be thought of as the set of observed characteristics of societies. For example, while all societies consisting of humans might be thought of as having the potential to become egalitarian social democracies, not all observed societies are egalitarian or social democracies. Thus, the sociome can also be thought of indirectly as an ideal type of the unrealized potential of any given organization of social beings.
== Origin of term ==
The first known usage of the term sociome was in 2001 by Daichi Kamiyama. The term has also been utilized by sociologist Adam Thomas Perzynski. The two scientists differ in their usage. Kamiyama's study describes a new scientific "era of the sociome (Sociology[+ome])" characterized by the study of the social activities of molecules. This usage is an anthropomorphism of social behavior, wherein molecules are described as having the ability to socialize. Perzynski's social scientific usage varies from this considerably. While Sociology is the study of society, behavior and social relationships, the sociome is the characterization and quantification of patterns, variables, activities, relationships and attributes across all societies that exist and can be studied. The suffix -ome has been used primarily in biology, as in genome, proteome, microbiome, metabolome and phenome. Basu and colleagues have used the term sociome to refer to a sort of standardized approach to the characterization of geocoded social attributes (e.g. neighborhood level). In 2014, Del Savio and colleagues discussed the blurring of the boundaries between disciplines, and increased enthusiasm for the sociome concept and its importance for research in social science, epigenetics and epidemiology, with cautionary advice about the risks rooted in the marred history of Sociobiology
Still other authors have referred to sociomics as the bidirectional interplay between the field of Science and Technology Studies and all other "-omics" fields.
The -omics Wikipedia entry had previously listed sociome as a proposed new name for sociology, although it is unclear whether this has ever actually been proposed by any credible source. Still others have proposed that sociome is the object of study of Sociometry.
== References ==

37
data/en.wikipedia.org/wiki/Soil_seed_bank-0.md Normal file
View File

@ -0,0 +1,37 @@
---
title: "Soil seed bank"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Soil_seed_bank"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:47.335699+00:00"
instance: "kb-cron"
---
The soil seed bank is the natural storage of seeds, often dormant, within the soil of most ecosystems. The study of soil seed banks started in 1859 when Charles Darwin observed the emergence of seedlings using soil samples from the bottom of a lake. The first scientific paper on the subject was published in 1882 and reported on the occurrence of seeds at different soil depths. Weed seed banks have been studied intensely in agricultural science because of their important economic impacts; other fields interested in soil seed banks include forest regeneration and restoration ecology.
== The ecological importance of seed bank ==
The seed bank is one of the key factors for the persistence and density fluctuations of plant populations, especially for annual plants. Perennial plants have vegetative propagules to facilitate forming new plants, migration into new ground, or reestablishment after being top-killed, which are analogous to seed bank in their persistence ability under disturbance. These propagules are collectively called the 'soil bud bank', and include dormant and adventitious buds on stolons, rhizomes, and bulbs. Moreover, the term soil diaspore bank can be used to include non-flowering plants such as ferns and bryophytes.
Soil seed bank is significant breeding source for vegetation restoration and species-rich vegetation restoration, as they provide memories of past vegetation and represent the structure of future population. Moreover the composition of seed bank is often more stable than the vegetation to environmental changes, although a chronic N deposition can deplete it. In many systems, the density of the soil seed bank is often lower than the vegetation, and there are a large differences in species composition of the seed bank and the composition of the aboveground vegetation. Additionally, it is a key point that the relationship between soil seed bank and original potential to measure the revegetation potential. In endangered habitats, such as mudflats, rare and critically endangered species may be present in high densities, the composition of the seed bank is often more stable than the vegetation to environmental changes.
Soil seed banks are a crucial part of the rapid re-vegetation of sites disturbed by wildfire, catastrophic weather, agricultural operations, and timber harvesting, a natural process known as secondary succession. Soil seed banks are often dominated by pioneer species, those species that are specially adapted to return to an environment first after a disturbance. Forest ecosystems and wetlands contain a number of specialized plant species forming persistent soil seed banks.
The absence of a soil seed bank impedes the establishment of vegetation during primary succession, while presence of a well-stocked soil seed bank permits rapid development of species-rich ecosystems during secondary succession.
== Seed longevity ==
Many taxa have been classified according to the longevity of their seeds in the soil seed bank. Seeds of transient species remain viable in the soil seed bank only to the next opportunity to germinate, while seeds of persistent species can survive longer than the next opportunity—often much longer than one year. Species with seeds that remain viable in the soil longer than five years form the long-term persistent seed bank, while species whose seeds generally germinate or die within one to five years are called short-term persistent. A typical long-term persistent species is Chenopodium album (Lambsquarters); its seeds commonly remain viable in the soil for up to 40 years and in rare situations perhaps as long as 1,600 years. A species forming no soil seed bank at all (except the dry season between ripening and the first autumnal rains) is Agrostemma githago (Corncockle), which was formerly a widespread cereal weed.
Longevity of seeds is very variable and depends on many factors. Seeds buried more deeply tend to be capable of lasting longer. However, few species exceed 100 years. In typical soils the longevity of seeds can range from nearly zero (germinating immediately when reaching the soil or even before) to several hundred years. Some of the oldest still-viable seeds were those of Lotus (Nelumbo nucifera) found buried in the soil of a pond; these seeds were estimated by carbon dating to be around 1,200 years old. One cultivar of date palm, the Judean date palm, successfully sprouted in 2008 after accidental storage for 2,000 years.
== The famous seed longevity experiments ==
One of the longest-running soil seed viability trials was started in Michigan in 1879 by James Beal. The experiment involved the burying of 20 bottles holding 50 seeds from 21 species. Every five years, a bottle from every species was retrieved and germinated on a tray of sterilized soil which was kept in a growth chamber. Later, after responsibility for managing the experiment was delegated to caretakers, the period between retrievals became longer. In 1980, more than 100 years after the trial was started, seeds of only three species were observed to germinate: moth mullein (Verbascum blattaria), common mullein (Verbascum thapsus) and common mallow (Malva neglecta). Several other experiments have been conducted to determine the long-term longevity of seeds in soil seed banks.
== Other studies ==
Species of Striga (witchweed) are known to leave some of the highest seed densities in the soil compared to other plant genera; this is a major factor that aids their invasive potential. Each plant has the capability to produce between 90,000 and 450,000 seeds, although a majority of these seeds are not viable. It has been estimated that only two witchweeds would produce enough seeds required to refill a seed bank after seasonal losses.
Before the advent of herbicides, a good example of a persistent seed bank species was Papaver rhoeas, sometimes so abundant in agricultural fields in Europe that it could be mistaken for a crop.
Studies on the genetic structure of Androsace septentrionalis populations in the seed bank compared to those of established plants showed that diversity within populations is higher below ground than above ground.
== References ==

49
data/en.wikipedia.org/wiki/Storage_organ-0.md Normal file
View File

@ -0,0 +1,49 @@
---
title: "Storage organ"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Storage_organ"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:48.570582+00:00"
instance: "kb-cron"
---
A storage organ is a part of a plant specifically modified for storage of energy
(generally in the form of carbohydrates) or water. Storage organs often grow underground, where they are better protected from attack by herbivores. Plants that have an underground storage organ are called geophytes in the Raunkiær plant life-form classification system. Storage organs often, but not always, act as perennating organs which enable plants to survive adverse conditions (such as cold, excessive heat, lack of light or drought).
== Relationship to perennating organ ==
Storage organs may act as perennating organs ('perennating' as in perennial, meaning "through the year", used in the sense of continuing beyond the year and in due course lasting for multiple years). These are used by plants to survive adverse periods in the plant's life-cycle (e.g. caused by cold, excessive heat, lack of light or drought). During these periods, parts of the plant die and then when conditions become favourable again, re-growth occurs from buds in the perennating organs. For example, geophytes growing in woodland under deciduous trees (e.g. bluebells, trilliums) die back to underground storage organs during summer when tree leaf cover restricts light and water is less available.
However, perennating organs need not be storage organs. After losing their leaves, deciduous trees grow them again from 'resting buds', which are the perennating organs of phanerophytes in the Raunkiær classification, but which do not specifically act as storage organs. Equally, storage organs need not be perennating organs. Many succulents have leaves adapted for water storage, which they retain in adverse conditions.
== Underground storage organ ==
In common parlance, underground storage organs may be generically called roots, tubers, or bulbs, but to the botanist there is more specific technical nomenclature:
True roots:
Storage taproot – e.g. carrot
Tuberous root or root tuber – e.g. Dahlia
Modified stems:
Bulb (a short stem that produces fleshy scale leaves or modified leaf bases) – e.g. Lilium, Narcissus, onion
Caudex – e.g. Adenium (desert-rose)
Corm – e.g. Crocus
Pseudobulb – e.g. Pleione (windowsill orchid)
Rhizome – e.g. Iris pseudacorus (yellow flag iris)
Stem tuber – e.g. Zantedeschia (arum lily), potato
Trophopod (the persistent petiole base of several fern genera) – e.g. Diplazium, Onoclea sensibilis
Others:
Storage hypocotyl (the stem of a seedling) – sometimes called a tuber, as in Cyclamen
Some of the above, particularly pseudobulbs and caudices, may occur wholly or partially above ground. Intermediates and combinations of the above are also found, making classification difficult. As an example of an intermediate, the tuber of Cyclamen arises from the stem of the seedling, which forms the junction of the roots and stem of the mature plant. In some species (e.g. Cyclamen coum) roots come from the bottom of the tuber, suggesting that it is a stem tuber; in others (e.g. Cyclamen hederifolium) roots come largely from the top of the tuber, suggesting that it is a root tuber. As an example of a combination, juno irises have both bulbs and storage roots.
Underground storage organs used for food may be generically called root vegetables, although this phrase should not be taken to imply that the class only includes true roots.
== Other storage organs ==
Succulents are plants which are adapted to withstand periods of drought by their ability to store moisture in specialized storage organs.
Leaf succulents store water in their leaves, which are thus thickened, fleshy and typically covered with a waxy coating or fine hairs to reduce evaporation. They may also contain mucilaginous compounds. Some leaf succulents have leaves which are distributed along the stem in a similar fashion to non-succulent species (e.g. Crassula, Kalanchoe); their stems may also be succulent. In others, the leaves are more compact, forming a rosette (e.g. Echeveria, Aloe). Pebble-plants or living stones (e.g. Lithops, Conophytum) have reduced their leaves to just two, forming a fleshy body, only the top of which may be visible above ground.
Stem succulents are generally either leafless or have leaves which can be quickly shed in the event of drought. Photosynthesis is then taken over by the stems. As with leaf succulents, stems may be covered with a waxy coating or fine hairs to reduce evaporation. The ribbed bodies of cacti may be an adaption to allow shrinkage and expansion with the amount of water stored. Plants of the same general form as cacti are found in other families (e.g. Euphorbia canariensis (family Euphorbiaceae), Stapelia (family Apocynaceae)).
== Notes and references ==

44
data/en.wikipedia.org/wiki/Substrate_(biology)-0.md Normal file
View File

@ -0,0 +1,44 @@
---
title: "Substrate (biology)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Substrate_(biology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:49.725303+00:00"
instance: "kb-cron"
---
In biology, a substrate is the surface on which an organism (such as a plant, fungus, or animal) lives. A substrate can include biotic or abiotic materials and animals. For example, encrusting algae that lives on a rock (its substrate) can be itself a substrate for an animal that lives on top of the algae. Inert substrates are used as growing support materials in the hydroponic cultivation of plants. In biology substrates are often activated by the nanoscopic process of substrate presentation.
== In agriculture and horticulture ==
Cellulose substrate
Expanded clay aggregate (LECA)
Rock wool
Potting soil
Soil
== In animal biotechnology ==
=== Requirements for animal cell and tissue culture ===
Requirements for animal cell and tissue culture are the same as described for plant cell, tissue and organ culture (In Vitro Culture Techniques: The Biotechnological Principles). Desirable requirements are (i) air conditioning of a room, (ii) hot room with temperature recorder, (iii) microscope room for carrying out microscopic work where different types of microscopes should be installed, (iv) dark room, (v) service room, (vi) sterilization room for sterilization of glassware and culture media, and (vii) preparation room for media preparation, etc. In addition the storage areas should be such where following should be kept properly : (i) liquids-ambient (4–20 °C), (ii) glassware-shelving, (iii) plastics-shelving, (iv) small items-drawers, (v) specialized equipments-cupboard, slow turnover, (vi) chemicals-sidled containers.
=== For cell growth ===
There are many types of vertebrate cells that require support for their growth in vitro otherwise they will not grow properly. Such cells are called anchorage-dependent cells. Therefore, many substrates which may be adhesive (e.g. plastic, glass, palladium, metallic surfaces, etc.) or non-adhesive (e.g. agar, agarose, etc.) types may be used as discussed below:
Plastic as a substrate. Disposable plastics are cheaper substrate as they are commonly made up of polystyrene. After use they should be disposed of properly. Before use they are treated with gamma radiation or electric arc simply to develop charges on the surface of substrate. After cell growth its rate of proliferation should be measured. In addition, the other plastic materials used as substrate are teflon or polytetrafluoroethylene (PTFE), thermamox (TPX), polyvinylchloride (PVC), polycarbonate, etc. Monolayer of cell must be grown. Moreover, plastic beads of polystyrene, sephadex and polyacrylamide are also available for cell growth in suspension culture.
Glass as a substrate. Glass is an important substrate used in laboratory in several forms such as test tubes, slides, coverslips, pipettes, flasks, rods, bottles, Petri dishes, several apparatus, etc. These are sterilized by using chemicals, radiations, dry heat (in oven) and moist heat (in autoclave).
Palladium as a substrate. For the first time palladium deposited on agarose was used as a substrate for growth of fibroblast and glia.
== See also ==
== References ==
== External links ==
"Micro-vegetable growing" using abiotic substrates at home

31
data/en.wikipedia.org/wiki/Subvariety_(botany)-0.md Normal file
View File

@ -0,0 +1,31 @@
---
title: "Subvariety (botany)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Subvariety_(botany)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:51.293257+00:00"
instance: "kb-cron"
---
A subvariety (Latin: subvarietas) in botanical nomenclature is a taxonomic rank. They are rarely used to classify organisms.
== Plant taxonomy ==
Subvariety is ranked:
below that of variety (varietas)
above that of form (forma).
Subvariety is an infraspecific taxon.
=== Name ===
Its name consists of three parts:
a genus name (genera)
a specific epithet (species)
an infraspecific epithet (subvariety)
To indicate the subvariety rank, the abbreviation "subvar." is put before the infraspecific epithet.
== References ==

16
data/en.wikipedia.org/wiki/Suctorial-0.md Normal file
View File

@ -0,0 +1,16 @@
---
title: "Suctorial"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Suctorial"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:52.681651+00:00"
instance: "kb-cron"
---
Suctorial pertains to the adaptation for sucking or suction, as possessed by marine parasites such as the Cookiecutter shark, specifically in a specialised lip organ enabling attachment to the host.
Suctorial organs of a different form are possessed by the Solifugae arachnids, enabling the climbing of smooth, vertical surfaces.
Another variation on the suctorial organ can be found as part of the glossa proboscis of Masarinae (pollen wasps), enabling nectar feeding from the deep and narrow corolla of flowers.
== References ==

20
data/en.wikipedia.org/wiki/Syngameon-0.md Normal file
View File

@ -0,0 +1,20 @@
---
title: "Syngameon"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Syngameon"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:54.005494+00:00"
instance: "kb-cron"
---
Syngameon refers to groups of taxa that frequently engage in natural hybridization and lack strong reproductive barriers that prevent interbreeding. Syngameons are more common in plants than animals, with approximately 25% of plant species and 10% of animal species producing natural hybrids. The most well known syngameons include irises of the California Pacific Coast and white oaks of the Eastern United States. Hybridization within a syngameon is typically not equally distributed among species and few species often dominate patterns of hybridization.
The term syngameon comes from the root word syngamy coined by Edward Bagnall Poulton to define groups that freely interbreed. He also coined the word asyngamy referring to groups that do not freely interbreed (with the substantive noun forms Syngamy and Asyngamy). The term syngameon was first used by Johannes Paulus Lotsy, who used it to describe a habitually interbreeding community that was reproductively isolated from other habitually interbreeding communities. Syngameon was used interchangeably with the term species to describe groups of closely related individuals that interbreed to varying degrees. A more specific definition of syngameon has been given to groups of taxa that frequently engage in natural hybridization and lack strong morphological differences that could be used to define them. Taxa in syngameons may have separate species names, but evolutionary biologists often suggest they should be treated as a single species. Variation among species within a syngameon can be due to a number of factors related to their biogeography, ecology, phylogeny, reproductive biology, and genetics.
== Coenospecies ==
The terms coenospecies and syngameons are both used to describe clusters of lineages that are morphologically distinct and lack strong isolation mechanisms. Coenospecies, first coined by Göte Turesson in 1922, refers to the total sum of possible combinations in a genotype compound, which includes hybridization that occurs both naturally and artificially. Coenospecies is often used to describe lineages that can be crossed under cultivation and only a few species pairs are found to form natural hybrids, whereas syngameons refer to species where extensive evidence of natural hybridization occurs. In this sense, definitions of syngameon and coenospecies correspond to the two different definitions of the Biological Species Concept proposed by Ernst Mayr; syngameon is consistent with “actually” interbreeding species, while coenospecies is consistent with “actually or potentially” interbreeding species. The term ecospecies is considered a subdivision of coenospecies that refers to the genotypes within a coenospecies that hybridize and produce viable, fertile offspring.
== References ==

28
data/en.wikipedia.org/wiki/Temperature-sensitive_mutant-0.md Normal file
View File

@ -0,0 +1,28 @@
---
title: "Temperature-sensitive mutant"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Temperature-sensitive_mutant"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:55.194576+00:00"
instance: "kb-cron"
---
Temperature-sensitive mutations are variants of genes that allow the organism to function normally at low temperatures but alter its function at higher temperatures. Cold-sensitive mutants are variants of genes that allow normal function of the organism at higher temperatures but altered function at low temperatures.
== Mechanism ==
Most temperature-sensitive mutations affect proteins, and cause loss of protein function at the non-permissive temperature. The permissive temperature is one at which the protein typically can fold properly or remain properly folded. At higher temperatures, the protein is unstable and ceases to function properly. These mutations are usually recessive in diploid organisms. Temperature -sensitive mutations arrange a reversible mechanism and can reduce particular gene products at varying stages of growth, which is easily done by changing the temperature of growth.
== Permissive temperature ==
The permissive temperature is the temperature at which a temperature-sensitive mutation gene product takes on a normal, functional phenotype. When a temperature-sensitive mutant is grown in a permissive condition, the mutant gene product behaves normally (meaning that the phenotype is not observed), even if there is a mutant allele present. This results in the survival of the cell or organism,as if it were a wild type strain. In contrast, the nonpermissive temperature or restrictive temperature is the temperature at which the mutant phenotype is observed.
Temperature-sensitive mutations are usually missense mutations, which slightly modify the energy landscape of the protein folding. The mutant protein will function at the standard, permissive, low temperature. It will alternatively lack the function at a rather high, non-permissive temperature and display a hypomorphic (partial loss of gene function) at a middle, semi-permissive temperature.
== Developmental Effects ==
Temperature-sensitive mutations can significantly impact an organism's development by altering gene function at specific temperatures. These mutations affect proteins that may function normally at a lower, "permissive" temperature but become dysfunctional or degrade at a higher, "restrictive" temperature. This characteristic allows researchers to study gene function by controlling temperature conditions.
One example is a mutation in the virilizer (vir) gene in Drosophila melanogaster, which prevents the proper development of female traits at elevated temperatures. This demonstrates the crucial role temperature-sensitive mutations play in regulating developmental pathways.
Temperature-sensitive mutations have also been observed in human diseases. For instance, in spinal muscular atrophy (SMA), mutations affecting the Survival of Motor Neuron (SMN) protein can render it unstable at higher temperatures, leading to impaired nerve function.
Researchers have developed methods to introduce temperature-sensitive mutations artificially. One approach utilizes intein-mediated protein splicing, where protein segments remove themselves under specific temperature conditions. A study by Tan et al. (2009) demonstrated how engineered inteins can regulate protein function by allowing the intein to splice at lower temperatures while remaining intact at higher temperatures, thereby disrupting protein activity.
By leveraging temperature-sensitive mutations, scientists can study the functional roles of genes and proteins in both normal development and disease processes.
== Ecological Effects ==
At a base level, all organisms respond to their environment. Specifically, the temperature in an organism's environment can greatly impact many different aspects of its life. Understanding how temperature affects different species is difficult to study due to the fact that each one reacts differently to temperatures. Some may be more susceptible to higher temperatures due to not having the correct machinery to deal with it. Additionally, it is difficult to predict how a species would respond due to the fact that the fitness of the organism is closely intertwined with others inside of a single ecosystem [14].

28
data/en.wikipedia.org/wiki/Temperature-sensitive_mutant-1.md Normal file
View File

@ -0,0 +1,28 @@
---
title: "Temperature-sensitive mutant"
chunk: 2/3
source: "https://en.wikipedia.org/wiki/Temperature-sensitive_mutant"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:55.194576+00:00"
instance: "kb-cron"
---
== Evolutionary Effects ==
Temperature is an environmental factor that influences the evolution of organisms by shaping their genetic variation, physiological traits, adaptations, and survivability. As global temperatures increase due to climate change, species have to adapt to these changes through mutations that affect protein function, such as temperature sensitive mutations. Specifically, higher temperatures can increase mutation rates, alter the stability of proteins, and influence natural selection. These factors can lead to evolutionary changes in populations over time. However, when adapting to these higher temperatures, organisms often experience trade-offs, which are compromises where gaining an advantage in one trait leads to a disadvantage in another.
Higher temperatures can directly influence mutation rates by increasing the rate of spontaneous mutations leading to more errors during DNA replication or increased exposure to mutagens. Studies have shown that these effects are potentially due to enhanced metabolic rates. More specifically, a study involving Daphnia pulex found that spontaneous mutations had varied fitness effects under different thermal conditions, which suggests that temperature plays a role in shaping mutational impacts. In addition, this heightened mutation rate provides a broader range of genetic diversity for natural selection to act upon, allowing populations to adapt more rapidly. However, too many mutations can result in higher rates of genetic disorders or maladaptive traits which reduce the overall fitness.
Since proteins rely on precise folding to function correctly, higher temperatures can destabilize their structure, leading to loss of function. This instability creates challenges for evolution, as living organisms have to find a way to maintain protein function while dealing with temperature changes. As a result, organisms evolving in hotter environments may develop compensatory mutations that enhance protein stability or adopt proteins that assist in proper folding. However, studies have shown that these mutations, which could help restore the function of destabilized proteins, are rare, emphasizing how crucial it is to keep proteins stable. One study by researchers demonstrated how genome-wide CRISPR screens using temperature-sensitive mutations can map critical pathways involved in protein homeostasis and disease regulation. These evolutionary shifts ensure that essential cellular functions remain unharmed despite thermal conditions.
Populations exposed to persistent high temperatures face selective pressures that favor individuals with heat-resistant traits, leading to the spread of beneficial alleles related to thermal tolerance—such as changes in membrane lipids, heat shock proteins, and thermostable enzymes. As global temperatures rise, organisms with temperature-sensitive mutations may experience shifting fitness landscapes, where previously neutral or deleterious mutations become advantageous. This dynamic drives natural selection and rapid adaptation, as seen in experimental evolution studies showing changes in mutation rates and variations in response to elevated temperatures.
Adaptation to higher temperatures is not without costs. Proteins optimized for stability at higher temperatures may show reduced flexibility or functionality at lower temperatures, leading to trade-offs in the performance of organisms across different environments. Another possible trade-off would be the energy required to maintain protein stability can take away resources from other vital processes, such as reproduction and growth. These trade-offs can shape evolutionary trajectories, as organisms must balance between thermal tolerance and overall fitness.
== The Results of Climate Change ==
Climate change is a huge topic in today's science world. Scientists have been asking many questions about how climate change will affect different ecosystems, organisms, and the human race. This question also arises from the standpoint of temperature-sensitive mutations.
As mentioned before, certain species' characteristics or behaviors rely on temperature. With the global climate becoming warmer, the question is what will happen with organisms that are sensitive to temperature change, and it affects their characteristics or ability to obtain nutrients. Though climate change is not necessarily a good thing, some research has shown that some organisms have benefited from the increasing climate temperature. It showed that the rising temperature can increase the fitness of an organism.
Climate change can also begin to effect the outcome of the ratio of male and females in the wild. Some animals mainly reptiles sex is determined by the temperature of the outside world when developing in an egg. Example of this happen in most species of turtles, which the increasing temperature this could lead to more of one sex which would result in less mates being coupled to repopulate. Though this is not a mutation it does show that many processes in certain species are sesntive to temperature.
== Use in research ==
Temperature-sensitive mutantations are useful in biological research. They allow the study of essential processes required for the survival of the cell or organism. Mutations to essential genes are generally lethal, and hence, temperature-sensitive mutations enable researchers to induce the phenotype at restrictive temperatures and study the effects. The temperature-sensitive phenotype could be expressed during a specific developmental stage to study the effects. This is also done to determine what can happen to certain living organisms with the effects of climate change. Temperature sensitive mutations are important for many different kinds of research especially for genetic research which can help determine many aspects of life from a molecular level.
=== Examples ===
In the late 1970s, the Saccharomyces cerevisiae secretory pathway, essential for viability of the cell and for growth of new buds, was dissected using temperature-sensitive mutants, resulting in the identification of twenty-three essential genes.
In the 1970s, several temperature-sensitive mutant genes were identified in Drosophila melanogaster, such as shibirets, which led to the first genetic dissection of synaptic function.< In the 1990s, the heat shock promoter hsp70 was used in temperature-modulated gene expression in the fruit fly.

21
data/en.wikipedia.org/wiki/Temperature-sensitive_mutant-2.md Normal file
View File

@ -0,0 +1,21 @@
---
title: "Temperature-sensitive mutant"
chunk: 3/3
source: "https://en.wikipedia.org/wiki/Temperature-sensitive_mutant"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:55.194576+00:00"
instance: "kb-cron"
---
=== Bacteriophage ===
An infection of an Escherichia coli host cell by a bacteriophage (phage) T4 temperature -ensitive (TS) conditionally lethal mutant at a high restrictive temperature generally leads to no phage growth. However, a co-infection under restrictive conditions with two TS mutants defective in different genes generally leads to robust growth because of intergenic complementation. The discovery of TS mutants of phage T4 and the employment of such mutants in complementation tests contributed to the identification of many of the genes in this organism. Because multiple copies of a polypeptide specified by a gene often form multimers, mixed infections with two different TS mutants defective in the same gene often lead to mixed multimers and partial restoration of function, a phenomenon referred to as intragenic complementation. Intragenic complementation of TS mutants defective in the same gene can provide information on the structural organization of the multimer. The growth of phage TS mutants under partially restrictive conditions has been used to identify the functions of genes. Thus, genes employed in the repair of DNA damages were identified, as well as genes affecting genetic recombination. For example, growing a TS DNA repair mutant at an intermediate temperature will allow some progeny phage to be produced. However, if that TS mutant is irradiated with UV light, its survival will be more strongly reduced compared to the reduction of survival of irradiated wild-type phage T4.
Conditional lethal mutants able to grow at high temperatures but unable to grow at low temperatures were also isolated in phage T4. These cold-sensitive mutants defined a discrete set of genes, some of which had been previously identified by other types of conditional lethal mutants.
== References ==
Febvre C, Goldblatt C, El-Sabaawi R. Thermal performance of ecosystems: Modeling how physiological responses to temperature scale up in communities. Journal of Theoretical Biology. 2024;585:N.PAG. doi:10.1016/j.jtbi.2024.111792
Edelsparre, A. H., Fitzpatrick, M. J., Saastamoinen, M., & Teplitsky, C. (2024). Evolutionary adaptation to climate change. Evolution letters, 8(1), 1–7. https://doi.org/10.1093/evlett/qrad070
Hilfiker, A., Nothiger, R. The temperature-sensitive mutation vir ts(virilizer) identifies a new gene involved in sex determination of Drosophila . Roux's Arch Dev Biol 200, 240–248 (1991). https://doi.org/10.1007/BF00241293
Gonsalvez, J. L., Burghes, A. H., & Kunkel, L. M. (2020). Temperature-sensitive spinal muscular atrophy-causing point mutations destabilize the SMN protein at elevated temperatures. Disease Models & Mechanisms, 13(5), dmm043307. https://doi.org/10.1242/dmm.043307
Tan, G., Chen, M., Foote, C., & Tan, C. (2009). Temperature-sensitive mutations made easy: Generating conditional mutations by using temperature-sensitive inteins. Proceedings of the National Academy of Sciences, 106(24), 9155-9160. https://doi.org/10.1073/pnas.0900235106

35
data/en.wikipedia.org/wiki/Thanatocoenosis-0.md Normal file
View File

@ -0,0 +1,35 @@
---
title: "Thanatocoenosis"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Thanatocoenosis"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:56.407377+00:00"
instance: "kb-cron"
---
Thanatocoenosis (from Greek language thanatos - death and koinos - common) are all the embedded fossils at a single discovery site. This site may be referred to as a "death assemblage". Such groupings are composed of fossils of organisms which may not have been associated during life, often originating from different habitats. Examples include marine fossils having been brought together by a water current or animal bones having been deposited by a predator. A site containing thanatocoenosis elements can also lose clarity in its faunal history by more recent intruding factors such as burrowing microfauna or stratigraphic disturbances born from anthropogenic methods.
This term differs from a related term, biocoenosis, which refers to an assemblage in which all organisms within the community interacted and lived together in the same habitat while alive. A biocoenosis can lead to a thanatocoenosis if disrupted significantly enough to have its dead/fossilized matter scattered. A death community/thanatocoenosis is developed by multiple taphonomic processes (those being ones relating to the different ways in which organismal remains pass through strata and are decomposed and preserved) that are generally categorized into two groups: biostratinomy and diagenesis. As a whole, thanatocoenoses are divided into two categories as well: autochthonous and allochthonous.
Death assemblages and thanatocoenoses can provide insight into the process of early-stage fossilization, as well as information about the species within a given ecosystem. The study of taphonomy can aid in furthering the understanding of the ecological past of species and their fossil records if used in conjunction with research on death assemblages from modern ecosystems.
== History ==
The term "thanatocoenosis" was originally created by Erich Wasmund in 1926, and he was the first to define both the similarities and contrasts between these death communities and biocoenoses. Due to confusion between some distinctions between the two, another researcher, Horst Böger, later classified them further in 1970. Similarly to how the term "biotope" describes biocoenosis, a term analogous to thanatocoenosis, "thanatope", was also created and utilized in related literature. Wasmund proffered that the terms thanatope and biotope were congruent to one another, so long as a death community is autochthonous, but that has since been refuted based on the differences regarding the formation factors involved with the two terms.
== References ==
== Further reading ==
Boucot, A. J., (1953). Life and Death Assemblages Among Fossils. American Journal of Science, 251, 25–40.
Concise Encyclopedia - Biology, Thomas A. Scott, ISBN 3-11-010661-2
Domingo, M., Martin-Perea, D., Badgley, E., Lopez-Guerrero, P., Oliver, A., Negro, J., (2020). Taphonomic Information from the Modern Vertebrate Death Assemblage of Donana National Park, Spain. PLOS ONE, 15(11).
Heinrich, D., (1994). Some Remarks on the Term "Thanatocoenosis" Especially "Anthropogenic Thanatocoenosis", with Particular Reference to Fish Remains. Archaeofauna, 3, 93–97.
== See also ==
Biocoenosis, a life assemblage
Fossils, preserved remains of once-living organisms from past age
Taphonomy, the study of decomposition and fossilization
Biotope, an ecological habitat supporting multiple species

19
data/en.wikipedia.org/wiki/Tiller_(botany)-0.md Normal file
View File

@ -0,0 +1,19 @@
---
title: "Tiller (botany)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Tiller_(botany)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:57.738914+00:00"
instance: "kb-cron"
---
A tiller is a shoot that arises from the base of a grass plant. The term refers to all shoots that grow after the initial parent shoot grows from a seed. Tillers are segmented, each segment possessing its own two-part leaf. They are involved in vegetative propagation and, in some cases, also seed production.
"Tillering" refers to the production of side shoots and is a property possessed by many species in the grass family. This enables them to produce multiple stems (tillers) starting from the initial single seedling. This ensures the formation of dense tufts and multiple seed heads. Tillering rates are heavily influenced by soil water quantity. When soil moisture is low, grasses tend to develop more sparse and deep root systems (as opposed to dense, lateral systems). Thus, in dry soils, tillering is inhibited: the lateral nature of tillering is not supported by lateral root growth.
== See also ==
Crown (botany)
== References ==

80
data/en.wikipedia.org/wiki/Toxin-0.md Normal file
View File

@ -0,0 +1,80 @@
---
title: "Toxin"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/Toxin"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:59.029271+00:00"
instance: "kb-cron"
---
A toxin is a naturally occurring poison produced by metabolic activities of living cells or organisms. They occur especially as proteins, often conjugated. The term was first used by organic chemist Ludwig Brieger (1849–1919), derived from toxic.
Toxins can be small molecules, peptides, or proteins that are capable of causing disease on contact with or absorption by body tissues interacting with biological macromolecules such as enzymes or cellular receptors. They vary greatly in their toxicity, ranging from usually minor (such as a bee sting) to potentially fatal even at extremely low doses (such as botulinum toxin).
== Terminology ==
Toxins are often distinguished from other chemical agents strictly based on their biological origin.
Less strict understandings embrace naturally occurring inorganic toxins, such as arsenic. Other understandings embrace synthetic analogs of naturally occurring organic poisons as toxins, and may or may not embrace naturally occurring inorganic poisons. It is important to confirm usage if a common understanding is critical.
Toxins are a subset of toxicants. The term toxicant is preferred when the poison is man-made and therefore artificial. The human and scientific genetic assembly of a natural-based toxin should be considered a toxin as it is identical to its natural counterpart. The debate is one of linguistic semantics.
The word toxin does not specify method of delivery (as opposed to venom, a toxin delivered via a bite, sting, etc.). Poison is a related but broader term that encompasses both toxins and toxicants; poisons may enter the body through any means - typically inhalation, ingestion, or skin absorption. Toxin, toxicant, and poison are often used interchangeably despite these subtle differences in definition. The term toxungen has also been proposed to refer to toxins that are delivered onto the body surface of another organism without an accompanying wound.
A rather informal terminology of individual toxins relates them to the anatomical location where their effects are most notable:
Genitotoxin, damages the urinary organs or the reproductive organs
Hemotoxin, causes destruction of red blood cells (hemolysis)
Phototoxin, causes dangerous photosensitivity
Hepatotoxins affect the liver
Neurotoxins affect the nervous system
On a broader scale, toxins may be classified as either exotoxins, excreted by an organism, or endotoxins, which are released mainly when bacteria are lysed.
== Biological ==
The term "biotoxin" is sometimes used to explicitly confirm the biological origin as opposed to environmental or anthropogenic origins. Biotoxins can be classified by their mechanism of delivery as poisons (passively transferred via ingestion, inhalation, or absorption across the skin), toxungens (actively transferred to the target's surface by spitting, spraying, or smearing), or venoms (delivered through a wound generated by a bite, sting, or other such action). They can also be classified by their source, such as fungal biotoxins, microbial toxins, plant biotoxins, or animal biotoxins.
Toxins produced by microorganisms are important virulence determinants responsible for microbial pathogenicity and/or evasion of the host immune response.
Biotoxins vary greatly in purpose and mechanism, and can be highly complex (the venom of the cone snail can contain over 100 unique peptides, which target specific nerve channels or receptors).
Biotoxins in nature have two primary functions:
Predation, such as in the spider, snake, scorpion, jellyfish, and wasp
Defense as in the bee, ant, termite, honey bee, wasp, poison dart frog and plants producing toxins
The toxins used as defense in species among the poison dart frog can also be used for medicinal purposes
Some of the more well known types of biotoxins include:
Cyanotoxins, produced by cyanobacteria
Dinotoxins, produced by dinoflagellates
Necrotoxins cause necrosis (i.e., death) in the cells they encounter. Necrotoxins spread through the bloodstream. In humans, skin and muscle tissues are most sensitive to necrotoxins. Organisms that possess necrotoxins include:
The brown recluse or "fiddle back" spider
Most rattlesnakes and vipers produce phospholipase and various trypsin-like serine proteases
Puff adder
Necrotizing fasciitis (caused by the "flesh eating" bacterium Streptococcus pyogenes) – produces a pore forming toxin
Neurotoxins primarily affect the nervous systems of animals. The group neurotoxins generally consists of ion channel toxins that disrupt ion channel conductance. Organisms that possess neurotoxins include:
The black widow spider.
Most scorpions
The box jellyfish
Elapid snakes
The cone snail
The Blue-ringed octopus
Venomous fish
Frogs
Palythoa coral
Various different types of algae, cyanobacteria and dinoflagellates
Myotoxins are small, basic peptides found in snake and lizard venoms, They cause muscle tissue damage by a non-enzymatic receptor based mechanism. Organisms that possess myotoxins include:
rattlesnakes
Mexican beaded lizard
Cytotoxins are toxic at the level of individual cells, either in a non-specific fashion or only in certain types of living cells:
Ricin, from castor beans
Apitoxin, from honey bees
T-2 mycotoxin, from certain toxic mushrooms
Cardiotoxin III, from Chinese cobra
Hemotoxin, from vipers
=== Weaponry ===
Many living organisms employ toxins offensively or defensively. A relatively small number of toxins are known to have the potential to cause widespread sickness or casualties. They are often inexpensive and easily available, and in some cases it is possible to refine them outside the laboratory. As biotoxins act quickly, and are highly toxic even at low doses, they can be more efficient than chemical agents.
Due to these factors, it is vital to raise awareness of the clinical symptoms of biotoxin poisoning, and to develop effective countermeasures including rapid investigation, response, and treatment.
== Environmental ==
The term "environmental toxin" can sometimes explicitly include synthetic contaminants such as industrial pollutants and other artificially made toxic substances. As this contradicts most formal definitions of the term "toxin", it is important to confirm what the researcher means when encountering the term outside of microbiological contexts.
Environmental toxins from food chains that may be dangerous to human health include:
Paralytic shellfish poisoning (PSP)
Amnesic shellfish poisoning (ASP)
Diarrheal shellfish poisoning (DSP)
Neurotoxic shellfish poisoning (NSP)

27
data/en.wikipedia.org/wiki/Toxin-1.md Normal file
View File

@ -0,0 +1,27 @@
---
title: "Toxin"
chunk: 2/2
source: "https://en.wikipedia.org/wiki/Toxin"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:16:59.029271+00:00"
instance: "kb-cron"
---
== Research ==
In general, when scientists determine the amount of a substance that may be hazardous for humans, animals and/or the environment they determine the amount of the substance likely to trigger effects and if possible establish a safe level. In Europe, the European Food Safety Authority produced risk assessments for more than 4,000 substances in over 1,600 scientific opinions and they provide open access summaries of human health, animal health and ecological hazard assessments in their OpenFoodTox database. The OpenFoodTox database can be used to screen potential new foods for toxicity.
The Toxicology and Environmental Health Information Program (TEHIP) at the United States National Library of Medicine (NLM) maintains a comprehensive toxicology and environmental health web site that includes access to toxins-related resources produced by TEHIP and by other government agencies and organizations. This web site includes links to databases, bibliographies, tutorials, and other scientific and consumer-oriented resources. TEHIP also is responsible for the Toxicology Data Network (TOXNET), an integrated system of toxicology and environmental health databases that are available free of charge on the web.
TOXMAP is a Geographic Information System (GIS) that is part of TOXNET. TOXMAP uses maps of the United States to help users visually explore data from the United States Environmental Protection Agency's (EPA) Toxics Release Inventory and Superfund Basic Research Programs.
== See also ==
== References ==
== External links ==
T3DB: Toxin-target database
ATDB: Animal toxin database
Society of Toxicology
The Journal of Venomous Animals and Toxins including Tropical Diseases
ToxSeek: Meta-search engine in toxicology and environmental health
Website on Models & Ecotoxicology

59
data/en.wikipedia.org/wiki/Tropical_vegetation-0.md Normal file
View File

@ -0,0 +1,59 @@
---
title: "Tropical vegetation"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Tropical_vegetation"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:00.247154+00:00"
instance: "kb-cron"
---
Tropical vegetation, plant life that occurs in climates that are warm year-round, is in general more biologically diverse than in other latitudes. Some tropical areas may receive abundant rain the whole year round, while others have long dry seasons which last several months and may vary in length and intensity with geographic location. These seasonal droughts have a great impact on the vegetation, such as in the Madagascar spiny forests.
Rainforest vegetation can often be categorized into five layers. The top layer is the emergents, the upper tree layer, with the largest and widest trees in all the forest, commonly 50 m (160 ft) and higher. These trees tend to have very large canopies so they can be fully exposed to sunlight. A layer below that is the canopy, or middle tree layer, averaging 30–40 m (98–131 ft) in height. Here there are more compact trees and vegetation. These trees, shaded, tend to be slenderer. The third layer is the lower tree area. These trees tend to be around 5–10 m (16–33 ft) high and tightly compacted. The trees found in the third layer include young trees with the potential to grow into larger canopy trees, and "palmoids" or "corner model trees". The fourth layer is the shrub layer beneath the tree canopy. This layer is mainly populated by sapling trees, shrubs, and seedlings. The fifth and lowest layer is the herb layer which is the forest floor, mainly bare except for various plants, mosses, lycopods and ferns. The forest floor is much more dense than above because of little sunlight and air movement.
Plant species native to the tropics found in tropical ecosystems are known as tropical plants. Some examples of tropical ecosystems are the Guinean Forests of West Africa, the Madagascar dry deciduous forests and the broadleaf forests of the Thai highlands and the El Yunque National Forest in Puerto Rico. Dr. Ghillean Prance has estimated that, as of 1979, there were 155,000 known species of tropical plants, with 90,000 species in the Neotropics, 35,000 in southern Asia and the East Indies and 30,000 in Africa, about half of those in Madagascar. There are also 50,000 Neotropical fungi, and about 20,000 fungal species each from Asia and Africa.
== Description ==
The term "tropical vegetation" is frequently used in the sense of lush and luxuriant, but not all the vegetation of the areas of the Earth in tropical climates can be defined as such. Despite lush vegetation, often the soils of tropical forests are low in nutrients making them quite vulnerable to slash-and-burn deforestation techniques, which are sometimes an element of shifting cultivation agricultural systems.
Tropical vegetation may include the following habitat types:
=== Tropical rainforest ===
Tropical rainforest ecosystems include significant areas of biodiversity, often coupled with high species endemism. Rainforests are home to half of all the living animal and plant species on the planet and roughly two-thirds of all flowering plants can be found in rainforests. The most representative are the Borneo rainforest, one of the oldest rainforests in the world, the Brazilian and Venezuelan Amazon rainforest, and the eastern Costa Rican rainforests.
=== Tropical seasonal forest ===
Seasonal tropical forests generally receive high total rainfall, averaging more than 1000 mm per year, but with a distinct dry season. They include: the Congolian forests, a broad belt of highland tropical moist broadleaf forest which extends across the basin of the Congo River; Central American tropical forests in Panama and Nicaragua; the seasonal forests that predominate across much the Indian subcontinent, Indochina, and Queensland, northern Australia.
=== Tropical dry broadleaf forest ===
Tropical dry broadleaf forests are territories with a forest cover that is not very dense and has often an unkempt, irregular appearance, especially in the dry season. This type of forest often includes bamboo and teak as the dominant large tree species, such as in the Phi Pan Nam Range, part of the Central Indochina dry forests. They are affected by often long seasonal dry periods and, though less biologically diverse than rainforests, tropical dry forests are home to a wide variety of wildlife.
=== Tropical grasslands, savannas, and shrublands ===
Tropical grasslands, savannas, and shrublands are spread over a large area of the tropics with a vegetation made up mainly of low shrubs and grasses, often including sclerophyll species. Some of the most representative are the Western Zambezian grasslands in Zambia and Angola, as well as the Einasleigh upland savanna in Australia and the Everglades in the United States of America. Tree species such as Acacia and baobab may be present in these ecosystems depending on the region.
== See also ==
Biocoenosis
Ecoregion
Jungle
Vegetation type
== Further reading ==
Archibold, O. W. Ecology of World Vegetation. New York: Springer Publishing, 1994.
Barbour, M.G, J.H. Burk, and W.D. Pitts. "Terrestrial Plant Ecology". Menlo Park: Benjamin Cummings, 1987.
Breckle, S-W. Walter's Vegetation of the Earth. New York: Springer Publishing, 2002.
Van der Maarel, E. Vegetation Ecology. Oxford: Blackwell Publishers, 2004.
Geoff Tracey The Vegetation of the Humid Tropical Region of North Queensland. Australia: CSIRO 1982.
Stork, N. E. & Turton, Stephen M. (2008). Living in a dynamic tropical forest landscape. Malden, MA : Blackwell Pub.
Leonard Webb A Physiognomic Classification of Australian Rain Forests Journal of Ecology Vol. 47, No. 3, pp. 551-570 (British Ecological Society), 1959
== References ==
== External links ==
Classifying Vegetation Condition: Vegetation Assets States and Transitions (VAST)

35
data/en.wikipedia.org/wiki/Understory-0.md Normal file
View File

@ -0,0 +1,35 @@
---
title: "Understory"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Understory"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:01.485664+00:00"
instance: "kb-cron"
---
In forestry and ecology, understory (American English), or understorey (Commonwealth English), also known as underbrush or undergrowth, includes plant life growing beneath the forest canopy without penetrating it to any great extent, but above the forest floor. Only a small percentage of light penetrates the canopy, so understory vegetation is generally shade-tolerant. The understory typically consists of trees stunted through lack of light, other small trees with low light requirements, saplings, shrubs, vines, and undergrowth. Small trees such as holly and dogwood are understory specialists.
In temperate deciduous forests, many understory plants start into growth earlier in the year than the canopy trees, to make use of the greater availability of light at that particular time of year. A gap in the canopy caused by the death of a tree stimulates the potential emergent trees into competitive growth as they grow upward to fill the gap. These trees tend to have straight trunks and few lower branches. At the same time, the bushes, undergrowth, and plant life on the forest floor become denser. The understory experiences greater humidity than the canopy, and the shaded ground does not vary in temperature as much as open ground. This causes a proliferation of ferns, mosses, and fungi and encourages nutrient recycling, which provides favorable habitats for many animals and plants.
== Understory structure ==
The understory is the underlying layer of vegetation in a forest or wooded area, especially the trees and shrubs growing between the forest canopy and the forest floor.
Plants in the understory comprise an assortment of seedlings and saplings of canopy trees together with specialist understory shrubs and herbs. Young canopy trees often persist in the understory for decades as suppressed juveniles until an opening in the forest overstory permits their growth into the canopy. In contrast understory shrubs complete their life cycles in the shade of the forest canopy. Some smaller tree species, such as dogwood and holly, rarely grow tall and generally are understory trees.
The canopy of a tropical forest is typically about 10 m (33 ft) thick, and intercepts around 95% of the sunlight. The understory therefore receives less intense light than plants in the canopy and such light as does penetrate is impoverished in wavelengths of light that are most effective for photosynthesis. Understory plants therefore must be shade tolerant—they must be able to photosynthesize adequately using such light as does reach their leaves. They often are able to use wavelengths that canopy plants cannot. In temperate deciduous forests towards the end of the leafless season, understory plants take advantage of the shelter of the still leafless canopy plants to "leaf out" before the canopy trees do. This is important because it provides the understory plants with a window in which to photosynthesize without the canopy shading them. This brief period (usually 1–2 weeks) is often a crucial period in which the plant can maintain a net positive carbon balance over the course of the year.
As a rule forest understories also experience higher humidity than exposed areas. The forest canopy reduces solar radiation, so the ground does not heat up or cool down as rapidly as open ground. Consequently, the understory dries out more slowly than more exposed areas do. The greater humidity encourages epiphytes such as ferns and mosses, and allows fungi and other decomposers to flourish. This drives nutrient cycling, and provides favorable microclimates for many animals and plants, such as the pygmy marmoset.
== See also ==
Fire-stick farming
Layers of rainforests
Overgrazing
== References ==
== External links ==
https://www.eolss.net/sample-chapters/C10/E5-03-01-08.pdf
Media related to underbrush at Wikimedia Commons

39
data/en.wikipedia.org/wiki/Vagrancy_(biology)-0.md Normal file
View File

@ -0,0 +1,39 @@
---
title: "Vagrancy (biology)"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Vagrancy_(biology)"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:02.728436+00:00"
instance: "kb-cron"
---
Vagrancy is a phenomenon in biology whereby an individual animal (usually a bird) appears well outside its normal range; they are known as vagrants. The term accidental is sometimes also used. There are a number of poorly understood factors which might cause an animal to become a vagrant, including internal causes such as navigation errors (endogenous vagrancy) and external causes such as severe weather (exogenous vagrancy). Vagrancy events may lead to colonisation and eventually to speciation.
== Birds ==
In the Northern Hemisphere, adult birds (possibly inexperienced younger adults) of many species are known to continue past their normal breeding range during their spring migration and end up in areas further north (such birds are termed spring overshoots).
In autumn, some young birds, instead of heading to their usual wintering grounds, take "incorrect" courses and migrate through areas which are not on their normal migration path. For example, Siberian passerines which normally winter in Southeast Asia are commonly found in Northwest Europe, e.g. Arctic warblers in Britain. This is reverse migration, where the birds migrate in the opposite direction to that expected (say, flying north-west instead of south-east). The causes of this are unknown, but genetic mutation or other anomaly relating to the bird's magnetic sensibilities is suspected.
Other birds are sent off course by storms and high winds, such as some North American birds blown across the Atlantic Ocean to Europe. Birds can also be blown out to sea, become physically exhausted, land on a ship and end up being carried to the ship's destination.
While many vagrant birds do not survive, if sufficient numbers wander to a new area they can establish new populations. Many isolated oceanic islands are home to species that are descended from landbirds blown out to sea, Hawaiian honeycreepers and Darwin's finches being prominent examples.
== Insects ==
Vagrancy in insects is recorded from many groups—it is particularly well-studied in butterflies and moths, and dragonflies. Vagrancy appears to be highly correlated with migration in certain species of butterfly and dragonfly. In butterfly host-plant sampling, higher frequencies of vagrancy were documented in shrub- and forb-feeding larvae compared to grass-feeding larvae. Vagrant individuals in theTramea genus of dragonflies migrate as well, and may be prone to vagrancy due to elongated hindwings equipped for long, gliding flights. Individuals from a North American dragonfly species, Anax junius, have been reported anomalously in Europe during autumn months when strong westerly winds can redirect migration routes.
== Mammals ==
In mammals, vagrancy has been recorded for bats, pinnipeds (seals), beluga whales, manatees, cougars, and more. Migrating bats may be blown off course during unfavorable winds or extreme weather events. Nomadic Antarctic and sub-Antarctic seal species have been observed in temperate islands in the South Atlantic Ocean. Leopard Seals which breed on Antarctic ice banks have been seen as north as Gough Island (40°20′S 10°00′W) and Tristan da Cunha (37°05′S 12°17′W). Male beluga whales, which breed in the Arctic circle, may turn up as vagrant groups in sub-Arctic waters, with one sole vagrant reported further south off the shore of Baja California, Mexico. Manatee vagrants from small, localized Puerto Rican populations have been observed on several occasions in the U.S. Virgin Islands. Manatees are known to travel long distances to repeat locations, suggesting preference for particular foraging sites. Rarer examples come from individuals traveling from Florida to the northeastern United States. One manatee, named "Chessie," made repeated northward journeys for several summers, possibly indicating destination-directed vagrancy. More examples of transoceanic vagrancy have occurred in small-bodied mammals. At least one instance of mole, shrew, monkey, civet, lemur, and rat vagrants have been demonstrated relocating to new continents via vegetation mats or uprooted tree rafts. Relocation this way, while rare, is possible when individuals lower metabolic activity, allowing them to survive harsh maritime conditions with little food or water.
== Reptiles ==
Vagrancy has been recorded for sea turtles, snakes (e.g. Pelamis platura), crocodilians, and probably also occurs in lizards. It therefore seems to be a fairly widespread phenomenon in reptiles. Saltwater crocodiles are especially prone to vagrancy, with individuals occasionally being recorded in odd places including Fiji, Iwo Jima, and even the Sea of Japan.
== Plants ==
The term vagrant is also used of plants (e.g. Gleason and Cronquist, 1991), to refer to a plant that is growing far away from its species' usual range (especially north of its range) with the connotation of being a temporary population. In the context of lichens, a vagrant form or species occurs unattached to a substrate ("loose"), not necessarily outside its range.
Another definition (de Lange & Molloy, 1995) defined vagrant species in New Zealand flora – although could also be applied for any given region. Their definition was, "taxa whose presence within the New Zealand botanical region is naturally transitory... those which have failed to establish themselves significantly beyond their point of introduction through reproductive failure or for quite specific ecological reasons.". One example was the presence of Atriplex cinerea in New Zealand.
== References ==

46
data/en.wikipedia.org/wiki/Woody_plant-0.md Normal file
View File

@ -0,0 +1,46 @@
---
title: "Woody plant"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Woody_plant"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:03.874797+00:00"
instance: "kb-cron"
---
A woody plant is a plant that produces wood as its structural tissue and thus has a hard stem. In cold climates, woody plants further survive winter or dry season above ground, as opposed to herbaceous plants that die back to the ground until spring.
== Characteristics ==
Woody plants include trees, shrubs, or lianas. These are usually perennials whose stems and larger roots are reinforced with wood produced from secondary xylem. The main stem, larger branches, and roots of these plants are usually covered by a layer of bark. Wood is a structural tissue that allows woody plants to grow from above-ground stems year after year, thus making some woody plants the largest and tallest terrestrial plants.
Woody plants, like herbaceous perennials, typically have a dormant period of the year when growth does not take place. This occurs in temperate and continental areas due to freezing temperatures and lack of daylight during the winter months. Meanwhile, dormancy in subtropical and tropical climates is due to the dry season; when low precipitation limits water available for growth. The dormant period will be accompanied by abscission (if the plant is deciduous). Evergreen plants do not lose all their leaves at once (they instead shed them gradually over the growing season), however growth virtually halts during the dormant season. Many woody plants native to the subtropics and tropics are evergreen due to year-round warm temperatures and rainfall. However, in many regions with a tropical savanna climate or a monsoon subtropical climate, a lengthy dry season precludes evergreen vegetation, instead promoting the predominance of deciduous trees.
During the fall months, each stem in a deciduous plant cuts off the flow of nutrients and water to the leaves. This causes them to change colors as the chlorophyll in the leaves breaks down. Special cells are formed that sever the connection between the leaf and stem, so that it will easily detach. Evergreen plants do not shed their leaves, merely go into a state of low activity during the dormant season (in order to acclimate to cold temperatures or low rainfall). During spring, the roots begin sending nutrients back up to the canopy.
When the growing season resumes, either with warm weather or the wet season, the plant will break bud by sending out new leaf or flower growth. This is accompanied by growth of new stems from buds on the previous season's wood. In colder climates, most stem growth occurs during spring and early summer. When the dormant season begins, the new growth hardens off and becomes woody. Once this happens, the stem will no longer grow in length; however, it will continue to expand in diameter for the rest of the plant's life.
Most woody plants native to colder climates have distinct growth rings produced by each year's production of new vascular tissue. Only the outer handful of rings contain living tissue (the cambium, xylem, phloem, and sapwood). Inner layers contain heartwood, which is dead tissue that serves primarily as structural support.
== Growth ==
Stem growth primarily occurs out of the terminal bud on the tip of the stem. Axillary buds are suppressed by the terminal bud and produce less growth, unless it is removed by human or natural action. Without a terminal bud, the side buds will have nothing to suppress them and begin rapidly sending out growth, if cut during spring. By late summer and early autumn, most active growth for the season has ceased and pruning a stem will result in little or no new growth. Winter buds are formed when the dormant season begins. Depending on the plant, these buds contain either new leaf growth, new flowers, or both.
Terminal buds have a stronger dominance on conifers than broadleaf plants, thus conifers will normally grow a single straight trunk without forking or large side or lateral branches.
As a woody plant grows, it will often lose lower leaves and branches as they become shaded out by the canopy. If a given stem is producing an insufficient amount of energy for the plant, the roots will "abort" it by cutting off the flow of water and nutrients, causing it to gradually die.
Below ground, the root system expands each growing season in much the same manner as the stems. The roots grow in length and send out smaller lateral roots. At the end of the growing season, the newly grown roots become woody and cease future length expansion, but will continue to expand in diameter. However, unlike the above-ground portion of the plant, the root system continues to grow, although at a slower rate, throughout the dormant season. In cold-weather climates, root growth will continue as long as temperatures are above 2 °C (36 °F).
== Tissue composition ==
Wood is primarily composed of xylem cells with cell walls made of cellulose and lignin. Xylem is a vascular tissue which moves water and nutrients from the roots to the leaves. Most woody plants form new layers of woody tissue each year, and so increase their stem diameter from year to year, with new wood deposited on the inner side of a vascular cambium layer located immediately beneath the bark. However, in some monocotyledons such as palms and dracaenas, the wood is formed in bundles scattered through the interior of the trunk. Stem diameter increases continuously throughout the growing season and halts during the dormant period.
== Symbol ==
The symbol for a woody plant, based on Species Plantarum by Linnaeus is .
== See also ==
Arboriculture
Dendrology
Inosculation
Vascular plant
== References ==

98
data/en.wikipedia.org/wiki/Xerophile-0.md Normal file
View File

@ -0,0 +1,98 @@
---
title: "Xerophile"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/Xerophile"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T07:17:05.175036+00:00"
instance: "kb-cron"
---
A xerophile (from Ancient Greek ξηρός (xerós), meaning "dry", and φίλος (phílos), meaning "loving") is an extremophilic organism that can grow and reproduce in conditions with a low availability of water, also known as water activity.
Xerophiles are "xerotolerant", meaning tolerant of dry conditions. They can often survive in environments with water activity below 0.8; above which is typical for most life on Earth. Typically xerotolerance is used with respect to matrix drying, where a substance has a low water concentration. These environments include arid desert soils. The term osmophile, or osmotolerant, is typically applied to microorganisms that can grow in solutions with high solute concentrations (salts, sugars), such as halophiles.
== Physics of water activity ==
Water activity, a thermodynamical value denoted aw, is defined as the partial water vapor pressure p in equilibrium with the substance relative to (divided by) the (partial) vapor pressure of pure water p* at the same temperature:
a
w
≡
p
p
∗
{\displaystyle a_{w}\equiv {\frac {p}{p^{*}}}}
The thermodynamical water activity is thus equal to the relative humidity (RH), and the chemical activity of pure water is equal to one: aw = 1.0.
When the atmosphere above a substance, or a solution, is undersaturated in water vapor (p < p*), its water activity is lower than one.
Water activity in solutions is directly related to osmotic pressure, although the exact relationship is complex and still the subject of study.
=== Adaption to low-water activity areas ===
Eukaryotic and most prokaryotic life will collect or create compatible solutes, also called osmolytes, which establish a counter balance to the osmotic pressures. An example would be some bacteria accumulate KCl to counter-balance NaCl osmotic pressures. Fungi appear to use glycerol as an osmolyte since when cultures are grown in high glycerol concentrations they become better adapted to surviving low water activities.
== Examples of xerophilic species ==
=== Bacteria ===
All taxonomic kingdoms have examples of xerophiles. Microbial xerophiles will usually inhabit environments that are sugar-rich or salt-rich, and xerophilic bacteria will most commonly be found in salt rich areas. Because xerophiles often live in salt-rich environments many halophilic species such as H. halophila, Bacillus halophilus, and H. salina are often also xerophilic.
=== Archaea ===
A xerophilic archaea would be Natronococcus.
=== Eukarya ===
Xerophilic fungi will usually be found in environments that are sugar rich, and some xerophilic fungi have shown extremely low water activity, as low as .61. Xerophilic fungi include Trichosporonoides nigrescens, Zygosaccharomyces, and Aspergillus penicillioides.
Among multi plant life an example of a xerophilic plant group is cacti.
== Impact on humans ==
=== Bioremediation ===
Xerophilic micro organisms can be utilized in efforts of bioremediation. This is especially the case when the environment needing bioremediation has low water activity. Xerotolerant bacteria isolated from areas in Chile have expressed traits allowing it to be used as to begin bioremediation.
=== Agriculture ===
For plants to properly grow in dry areas they will need a usable xerotolerant microbiome. In desert plants xerophiles are set in a plant's microbiome helping with its water management.
=== Food storage ===
Xerophiles are a concern to food storage industry due to their ability to bypass common food preservation methods. Many foods are preserved by creating high osmotic pressures that dry out and kill any microbes that attempt to culture in the food. Foods such as honey or jam have such high levels of sugar and low levels of water normal micro organisms can not grow on them. However, xerophilic organisms can grow in these mediums posing a threat to food safety.
The common food preservation methods of reducing water activity (food drying) may not always be sufficient to prevent the growth of xerophilic organisms, often resulting in food spoilage. Some mold and yeast species are xerophilic. Mold growth on bread is an example of food spoilage by xerophilic organisms.
Complete dehydration based on the freeze-drying technique with effective protection inside a tight packaging system, strictly impervious to water and atmospheric gases (O2 and CO2), may be required for long-term preservation of food and pharmacochemical substances (antibiotics, vaccines…). Freeze drying can limit the microbial activity on the long term, as long as the product remains perfectly dry in a hermetically sealed and intact package, but it is not a sterilisation technique per se, because after rehydration, even if many dehydrated cells suffer irreversible and lethal damages, some resistant spores and bacterial endospores can still be revived again, and multiplied, by means of microbiological cultures if the product was not initially sterilized by applying a proven technique.
=== Museum conservation ===
Humidity and temperature control to prevent bacterial and fungal growth is a key part of museum conservation. There is increasing evidence that xerophilic moulds are more common in museums than is generally admitted, with destructive effects on their collections, and this may have been exacerbated by the inadvertent creation of a xerophile-friendly environment.
== See also ==
Extremophile – Organisms capable of living in extreme environments
Ombrophobe – Plant adverse to rainfall
Osmophile – Organism tolerant osmotic effects from a low water activity
Xerocole – Any animal adapted to live in the desert
Xerophyte – Plants able to survive in an environment with little liquid water
== References ==

Some files were not shown because too many files have changed in this diff Show More