---
title: "Archaeogenetics"
chunk: 3/5
source: "https://en.wikipedia.org/wiki/Archaeogenetics"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T13:58:24.541020+00:00"
instance: "kb-cron"
---

Bone specimen is cleaned and the outer layer is scraped off
Sample is collected from preferably compact section
Sample is ground to fine powder and added to an extraction solution to release DNA
Silica solution is added and centrifuged to facilitate DNA binding
Binding solution is removed and a buffer is added to the solution to release the DNA from the silica
One of the main advantages of silica-based DNA extraction is that it is relatively quick and efficient, requiring only a basic laboratory setup and chemicals. It is also independent of sample size, as the process can be scaled to accommodate larger or smaller quantities. Another benefit is that the process can be executed at room temperature. However, this method does contain some drawbacks. Mainly, silica-based DNA extraction can only be applied to bone and teeth samples; they cannot be used on soft tissue. While they work well with a variety of different fossils, they may be less effective in fossils that are not fresh (e.g. treated fossils for museums). Also, contamination poses a risk for all DNA replication in general, and this method may result in misleading results if applied to contaminated material.
Polymerase chain reaction is a process that can amplify segments of DNA and is often used on extracted ancient DNA. It has three main steps: denaturation, annealing, and extension. Denaturation splits the DNA into two single strands at high temperatures. Annealing involves attaching primer strands of DNA to the single strands that allow Taq polymerase to attach to the DNA. Extension occurs when Taq polymerase is added to the sample and matches base pairs to turn the two single strands into two complete double strands. This process is repeated many times, and is usually repeated a higher number of times when used with ancient DNA. Some issues with PCR is that it requires overlapping primer pairs for ancient DNA due to the short sequences. There can also be "jumping PCR" which causes recombination during the PCR process which can make analyzing the DNA more difficult in inhomogeneous samples.

=== Methods of DNA analysis ===
DNA extracted from fossil remains is primarily sequenced using Massive parallel sequencing, which allows simultaneous amplification and sequencing of all DNA segments in a sample, even when it is highly fragmented and of low concentration. It involves attaching a generic sequence to every single strand that generic primers can bond to, and thus all of the DNA present is amplified. This is generally more costly and time intensive than PCR but due to the difficulties involved in ancient DNA amplification it is cheaper and more efficient. One method of massive parallel sequencing, developed by Margulies et al., employs bead-based emulsion PCR and pyrosequencing, and was found to be powerful in analyses of aDNA because it avoids potential loss of sample, substrate competition for templates, and error propagation in replication.
The most common way to analyze an aDNA sequence is to compare it with a known sequence from other sources, and this could be done in different ways for different purposes.
The identity of the fossil remain can be uncovered by comparing its DNA sequence with those of known species using software such as BLASTN. This archaeogenetic approach is especially helpful when the morphology of the fossil is ambiguous. Apart from that, species identification can also be done by finding specific genetic markers in an aDNA sequence. For example, the American indigenous population is characterized by specific mitochondrial RFLPs and deletions defined by Wallace et al.
aDNA comparison study can also reveal the evolutionary relationship between two species. The number of base differences between DNA of an ancient species and that of a closely related extant species can be used to estimate the divergence time of those two species from their last common ancestor. The phylogeny of some extinct species, such as Australian marsupial wolves and American ground sloths, has been constructed by this method. Mitochondrial DNA in animals and chloroplast DNA in plants are usually used for this purpose because they have hundreds of copies per cell and thus are more easily accessible in ancient fossils.
Another method to investigate relationship between two species is through DNA hybridization. Single-stranded DNA segments of both species are allowed to form complementary pair bonding with each other. More closely related species have a more similar genetic makeup, and thus a stronger hybridization signal. Scholz et al. conducted southern blot hybridization on Neanderthal aDNA (extracted from fossil remain W-NW and Krapina). The results showed weak ancient human-Neanderthal hybridization and strong ancient human-modern human hybridization. The human-chimpanzee and Neanderthal-chimpanzee hybridization are of similarly weak strength. This suggests that humans and Neanderthals are not as closely related as two individuals of the same species are, but they are more related to each other than to chimpanzees.
There have also been some attempts to decipher aDNA to provide valuable phenotypic information of ancient species. This is always done by mapping aDNA sequence onto the karyotype of a well-studied closely related species, which share a lot of similar phenotypic traits. For example, Green et al. compared the aDNA sequence from Neanderthal Vi-80 fossil with modern human X and Y chromosome sequence, and they found a similarity in 2.18 and 1.62 bases per 10,000 respectively, suggesting Vi-80 sample was from a male individual. Other similar studies include finding of a mutation associated with dwarfism in Arabidopsis in ancient Nubian cotton, and investigation on the bitter taste perception locus in Neanderthals.

== Applications ==

=== Human archaeology ===