Editing Archaeogenetics (section)

=== Fossil DNA preservation ===
[[Fossil]] retrieval starts with selecting an [[Excavation (archaeology)|excavation site]]. Potential excavation sites are usually identified with the [[mineralogy]] of the location and visual detection of bones in the area. However, there are more ways to discover excavation zones using technology such as field portable [[x-ray fluorescence]]<ref>{{Cite journal|last1=Cohen|first1=David R.|last2=Cohen|first2=Emma J.|last3=Graham|first3=Ian T.|last4=Soares|first4=Georgia G.|last5=Hand|first5=Suzanne J.|last6=Archer|first6=Michael|date=October 2017|title=Geochemical exploration for vertebrate fossils using field portable XRF|journal=Journal of Geochemical Exploration|volume=181|pages=1–9|doi=10.1016/j.gexplo.2017.06.012}}</ref> and Dense Stereo Reconstruction.<ref>{{Cite book|last1=Callieri|first1=Marco|last2=Dell'Unto|first2=Nicolo|last3=Dellepiane|first3=Matteo|last4=Scopigno|first4=Roberto|last5=Söderberg|first5=Bengt|last6=Larsson|first6=Lars|date=2011|title=Documentation and Interpretation of an Archeological Excavation: an experience with Dense Stereo Reconstruction tools|url=http://lup.lub.lu.se/record/2062881|journal=[Host publication title missing]|publisher=Eurographics Association|pages=33–40|isbn=978-3905674347}}</ref> Tools used include [[Knife|knives]], [[brush]]es, and pointed [[trowel]]s which assist in the removal of fossils from the earth.<ref name=":9">{{Cite book|title=Digging Up Bones: The Excavation, Treatment, and Study of Human Skeletal Remains|last=Brothwell|first=Don R.|publisher=Cornell University Press|year=1981|isbn=978-0801498756|pages=2–3}}</ref>

To avoid [[Contamination|contaminating]] the [[ancient DNA]], [[Sample (material)|specimens]] are handled with gloves and stored in -20&nbsp;°C immediately after being unearthed. Ensuring that the fossil sample is analyzed in a lab that has not been used for other [[DNA]] analysis could prevent contamination as well.<ref name=":9" /><ref name=":10">{{Cite journal|last1=Scholz|first1=Michael|last2=Bachmann|first2=Lutz|last3=Nicholson|first3=Graeme J.|last4=Bachmann|first4=Jutta|last5=Giddings|first5=Ian|last6=Rüschoff-Thale|first6=Barbara|last7=Czarnetzki|first7=Alfred|last8=Pusch|first8=Carsten M.|date=2000-06-01|title=Genomic Differentiation of Neanderthals and Anatomically Modern Man Allows a Fossil–DNA-Based Classification of Morphologically Indistinguishable Hominid Bones|journal=The American Journal of Human Genetics|volume=66|issue=6|pages=1927–32|doi=10.1086/302949|pmid=10788336|pmc=1378053}}</ref> Bones are [[milling (grinding)|milled]] to a powder and treated with a solution before the polymerase chain reaction (PCR) process.<ref name=":10" /> Samples for [[Polymerase chain reaction|DNA amplification]] may not necessarily be fossil bones. Preserved skin, salt-preserved or air-dried, can also be used in certain situations.<ref>{{Cite journal|last1=Yang|first1=H.|last2=Golenberg|first2=E.M.|last3=Shoshani|first3=J.|date=June 1997|title=Proboscidean DNA from museum and fossil specimens: an assessment of ancient DNA extraction and amplification techniques|journal=Biochemical Genetics|volume=35|issue=5–6|pages=165–79|issn=0006-2928|pmid=9332711|doi=10.1023/A:1021902125382|hdl=2027.42/44162|s2cid=2144662|url=https://deepblue.lib.umich.edu/bitstream/2027.42/44162/1/10528_2004_Article_413527.pdf|hdl-access=free}}</ref>

DNA preservation is difficult because the bone [[fossilisation]] degrades and DNA is chemically modified, usually by [[bacteria]] and [[Fungus|fungi]] in the soil. The best time to extract DNA from a fossil is when it is freshly out of the ground as it contains six times the DNA when compared to stored bones. The temperature of extraction site also affects the amount of obtainable DNA, evident by a decrease in success rate for DNA amplification if the fossil is found in warmer regions. A drastic change of a fossil's environment also affects DNA preservation. Since excavation causes an abrupt change in the fossil's environment, it may lead to [[Physiological chemistry|physiochemical]] change in the DNA molecule. Moreover, DNA preservation is also affected by other factors such as the treatment of the unearthed fossil like (e.g. washing, brushing and sun drying), [[pH]], [[irradiation]], the chemical composition of bone and soil, and [[hydrology]]. There are three perseveration diagenetic phases. The first phase is bacterial [[putrefaction]], which is estimated to cause a 15-fold degradation of DNA. Phase 2 is when bone chemically degrades, mostly by [[depurination]]. The third diagenetic phase occurs after the fossil is excavated and stored, in which bone DNA degradation occurs most rapidly.<ref name=":10"/>