Editing Archaeogenetics (section)

===Methods of DNA extraction===
Once a specimen is collected from an archaeological site, DNA can be extracted through a series of processes.<ref name=":43">{{Cite journal|last1=Hagelberg|first1=Erika|author-link1=Erika Hagelberg|last2=Clegg|first2=J.B.|date=1991-04-22|title=Isolation and Characterization of DNA from Archaeological Bone|journal=Proceedings of the Royal Society of London B: Biological Sciences|language=en|volume=244|issue=1309|pages=45–50|doi=10.1098/rspb.1991.0049|issn=0962-8452|pmid=1677195|bibcode=1991RSPSB.244...45H|s2cid=23859039}}</ref> One of the more common methods utilizes silica and takes advantage of [[polymerase chain reaction]]s in order to collect [[ancient DNA]] from bone samples.<ref name=":53">{{Cite journal|last1=Rohland|first1=Nadin|last2=Hofreiter|first2=Michael|date=July 2007|title=Ancient DNA extraction from bones and teeth|journal=Nature Protocols|language=en|volume=2|issue=7|pages=1756–62|doi=10.1038/nprot.2007.247|pmid=17641642|issn=1754-2189|doi-access=free}}</ref>

There are several challenges that add to the difficulty when attempting to extract ancient DNA from fossils and prepare it for analysis. DNA is continuously being split up. While the organism is alive these splits are repaired; however, once an organism has died, the DNA will begin to deteriorate without repair. This results in samples having strands of DNA measuring around 100 [[base pair]]s in length. Contamination is another significant challenge at multiple steps throughout the process. Often other DNA, such as bacterial DNA, will be present in the original sample. To avoid contamination it is necessary to take many precautions such as separate ventilation systems and workspaces for ancient DNA extraction work.<ref name=":62">{{Cite journal|last1=Handt|first1=O.|last2=Höss|first2=M.|last3=Krings|first3=M.|last4=Pääbo|first4=S.|date=1994-06-01|title=Ancient DNA: Methodological challenges|journal=Experientia|language=en|volume=50|issue=6|pages=524–529|doi=10.1007/BF01921720|pmid=8020612|s2cid=6742827|issn=0014-4754}}</ref> The best samples to use are fresh fossils as uncareful washing can lead to [[Mold (fungus)|mold]] growth.<ref name=":43"/> DNA coming from fossils also occasionally contains a compound that inhibits DNA replication.<ref name=":73">{{Cite journal|last1=Höss|first1=M|last2=Pääbo|first2=S|date=1993-08-11|title=DNA extraction from Pleistocene bones by a silica-based purification method.|pmc=309938|journal=Nucleic Acids Research|volume=21|issue=16|pages=3913–3914|issn=0305-1048|pmid=8396242|doi=10.1093/nar/21.16.3913}}</ref> Coming to a consensus on which methods are best at mitigating challenges is also difficult due to the lack of repeatability caused by the uniqueness of specimens.<ref name=":62" />

[[DNA separation by silica adsorption|Silica-based DNA extraction]] is a method used as a purification step to extract DNA from archaeological bone [[Artifact (archaeology)|artifacts]] and yield DNA that can be amplified using [[Polymerase chain reaction|polymerase chain reaction (PCR)]] techniques.<ref name=":73"/> This process works by using silica as a means to bind DNA and separate it from other components of the fossil process that inhibit [[Polymerase chain reaction|PCR]] amplification. However, silica itself is also a strong PCR [[Reaction inhibitor|inhibitor]], so careful measures must be taken to ensure that silica is removed from the DNA after extraction.<ref>{{Cite journal|last1=Yang|first1=Dongya Y.|last2=Eng|first2=Barry|last3=Waye|first3=John S.|last4=Dudar|first4=J. Christopher|last5=Saunders|first5=Shelley R.|date=1998-04-01|title=Improved DNA extraction from ancient bones using silica-based spin columns|journal=American Journal of Physical Anthropology|language=en|volume=105|issue=4|pages=539–43|doi=10.1002/(sici)1096-8644(199804)105:4<539::aid-ajpa10>3.0.co;2-1|pmid=9584894|issn=1096-8644}}</ref> The general process for extracting DNA using the silica-based method is outlined by the following:<ref name=":53"/>
# 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 [[DNA separation by silica adsorption|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, [[DNA separation by silica adsorption|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 [[museum]]s). Also, contamination poses a risk for all DNA replication in general, and this method may result in misleading results if applied to contaminated material.<ref name=":53"/>

[[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 (biochemistry)|denaturation]], [[Annealing (biology)|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.<ref name=":43"/> This process is repeated many times, and is usually repeated a higher number of times when used with [[ancient DNA]].<ref name=":03">{{Cite journal|last1=Bouwman|first1=Abigail|last2=Rühli|first2=Frank|date=2016-09-01|title=Archaeogenetics in evolutionary medicine|journal=Journal of Molecular Medicine|language=en|volume=94|issue=9|pages=971–77|doi=10.1007/s00109-016-1438-8|pmid=27289479|s2cid=10223726|issn=0946-2716}}</ref> 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.