Editing Archaeogenetics (section)

===Methods of DNA analysis===
DNA extracted from fossil remains is primarily sequenced using [[Massive parallel sequencing]],<ref name=":33">{{Cite journal|last1=Pääbo|first1=Svante|last2=Poinar|first2=Hendrik|last3=Serre|first3=David|last4=Jaenicke-Despres|first4=Viviane|last5=Hebler|first5=Juliane|last6=Rohland|first6=Nadin|last7=Kuch|first7=Melanie|last8=Krause|first8=Johannes|last9=Vigilant|first9=Linda|date=2004|title=Genetic analyses from ancient DNA|journal=Annual Review of Genetics|volume=38|issue=1 |pages=645–79|doi=10.1146/annurev.genet.37.110801.143214|issn=0066-4197|pmid=15568989|doi-access=free}}</ref> which allows simultaneous amplification and sequencing of all DNA segments in a sample, even when it is highly fragmented and of low concentration.<ref name=":03"/> 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.<ref name=":03" /> One method of [[massive parallel sequencing]], developed by Margulies et al., employs bead-based emulsion [[Polymerase chain reaction|PCR]] and [[pyrosequencing]],<ref>{{Cite journal|last1=Margulies|first1=Marcel|last2=Egholm|first2=Michael|last3=Altman|first3=William E.|last4=Attiya|first4=Said|last5=Bader|first5=Joel S.|last6=Bemben|first6=Lisa A.|last7=Berka|first7=Jan|last8=Braverman|first8=Michael S.|last9=Chen|first9=Yi-Ju|date=2005-09-15|title=Genome sequencing in microfabricated high-density picolitre reactors|journal=Nature|volume=437|issue=7057|pages=376–380|doi=10.1038/nature03959|issn=1476-4687|pmc=1464427|pmid=16056220|bibcode=2005Natur.437..376M}}</ref> 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.<ref name=":13">{{Cite journal|last1=Green|first1=Richard E.|last2=Krause|first2=Johannes|last3=Ptak|first3=Susan E.|last4=Briggs|first4=Adrian W.|last5=Ronan|first5=Michael T.|last6=Simons|first6=Jan F.|last7=Du|first7=Lei|last8=Egholm|first8=Michael|last9=Rothberg|first9=Jonathan M.|date=2006-11-16|title=Analysis of one million base pairs of Neanderthal DNA|journal=Nature|language=en|volume=444|issue=7117|pages=330–36|doi=10.1038/nature05336|pmid=17108958|issn=0028-0836|bibcode=2006Natur.444..330G|s2cid=4320907|doi-access=free}}</ref>

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.<ref name=":13"/> This archaeogenetic approach is especially helpful when the [[Morphology (biology)|morphology]] of the fossil is ambiguous.<ref name=":23">{{Cite journal|last1=Palmer|first1=Sarah A.|last2=Smith|first2=Oliver|last3=Allaby|first3=Robin G.|date=2012-01-20|title=The blossoming of plant archaeogenetics|journal=Annals of Anatomy - Anatomischer Anzeiger|series=Special Issue: Ancient DNA|volume=194|issue=1|pages=146–56|doi=10.1016/j.aanat.2011.03.012|pmid=21531123}}</ref> Apart from that, species identification can also be done by finding specific [[genetic marker]]s in an aDNA sequence. For example, the [[American indigenous people|American indigenous population]] is characterized by specific mitochondrial [[Restriction fragment length polymorphism|RFLPs]] and [[Deletion (genetics)|deletions]] defined by Wallace et al.<ref>{{Cite journal|last1=Kolman|first1=Connie J.|last2=Tuross|first2=Noreen|date=2000-01-01|title=Ancient DNA analysis of human populations|url=https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-8644(200001)111:1%3C5::AID-AJPA2%3E3.0.CO;2-3
|journal=American Journal of Physical Anthropology|language=en|volume=111|issue=1|pages=5–23|doi=10.1002/(sici)1096-8644(200001)111:1<5::aid-ajpa2>3.0.co;2-3|pmid=10618586 |url-access=subscription}}</ref>

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 [[Genetic divergence|divergence]] time of those two species from their last [[common ancestor]].<ref name=":33"/> The [[Phylogenetic tree|phylogeny]] of some extinct species, such as Australian marsupial wolves and American ground [[sloth]]s, has been constructed by this method.<ref name=":33" /> [[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.<ref name=":33" />

Another method to investigate relationship between two species is through [[Nucleic acid hybridization|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 [[Nucleic acid hybridization|hybridization]] signal. Scholz et al. conducted [[Southern blot|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.<ref name=":10"/>

There have also been some attempts to decipher aDNA to provide valuable [[Phenotype|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.<ref name=":13"/> 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.<ref name=":13" /> Other similar studies include finding of a [[mutation]] associated with dwarfism in ''Arabidopsis'' in ancient Nubian [[cotton]],<ref name=":23"/> and investigation on the bitter taste perception locus in Neanderthals.<ref>{{Cite journal|last1=Lalueza-Fox|first1=Carles|last2=Gigli|first2=Elena|last3=Rasilla|first3=Marco de la|last4=Fortea|first4=Javier|last5=Rosas|first5=Antonio|date=2009-08-12|title=Bitter taste perception in Neanderthals through the analysis of the TAS2R38 gene|journal=Biology Letters|volume=5|issue=6|language=en|pages=809–11|doi=10.1098/rsbl.2009.0532|issn=1744-9561|pmid=19675003|pmc=2828008}}</ref>