Editing Archaeogenetics (section)

== Applications ==

=== Human archaeology ===

==== Africa ====
Modern humans are thought to have evolved in Africa at least 200 kya (thousand years ago),<ref name=":0">{{Cite journal|last1=Campbell|first1=Michael C.|last2=Tishkoff|first2=Sarah A.|date=2010-02-23|title=The Evolution of Human Genetic and Phenotypic Variation in Africa|url= |journal=Current Biology|language=en|volume=20|issue=4|pages=R166–73|doi=10.1016/j.cub.2009.11.050|issn=0960-9822|pmid=20178763|pmc=2945812}}</ref> with some evidence suggesting a date of over 300 kya.<ref>{{Cite journal|last1=Schlebusch|first1=Carina M.|last2=Malmström|first2=Helena|last3=Günther|first3=Torsten|last4=Sjödin|first4=Per|last5=Coutinho|first5=Alexandra|last6=Edlund|first6=Hanna|last7=Munters|first7=Arielle R.|last8=Vicente|first8=Mário|last9=Steyn|first9=Maryna|date=2017-11-03|title=Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago|journal=Science|language=en|volume=358|issue=6363|pages=652–55|doi=10.1126/science.aao6266|pmid=28971970|issn=0036-8075|doi-access=free|bibcode=2017Sci...358..652S}}</ref> Examination of mitochondrial DNA (mtDNA), Y-chromosome DNA, and X-chromosome DNA indicate that the earliest population to leave Africa consisted of approximately 1500 males and females.<ref name=":0" /> It has been suggested by various studies that populations were geographically “structured” to some degree prior to the expansion out of Africa; this is suggested by the antiquity of shared mtDNA lineages.<ref name=":0" /> One study of 121 populations from various places throughout the continent found 14 genetic and linguistic “clusters,” suggesting an ancient geographic structure to African populations.<ref name=":0" /> In general, genotypic and phenotypic analysis have shown “large and subdivided throughout much of their evolutionary history.”<ref name=":0" />

Genetic analysis has supported archaeological hypotheses of a large-scale migrations of Bantu speakers into Southern Africa approximately 5 kya.<ref name=":0" /> Microsatellite DNA, single nucleotide polymorphisms (SNPs), and insertion/deletion polymorphisms (INDELS) have shown that Nilo-Saharan speaking populations originate from Sudan.<ref name=":0" /> Furthermore, there is genetic evidence that Chad-speaking descendants of Nilo-Saharan speakers migrated from Sudan to Lake Chad about 8 kya.<ref name=":0" /> Genetic evidence has also indicated that non-African populations made significant contributions to the African gene pool.<ref name=":0" /> For example, the Saharan African Beja people have high levels of Middle-Eastern as well as East African Cushitic DNA.<ref name=":0" />

==== Europe ====
[[File:Genealogy of bashkirian kipchak clan.jpg|thumb|Genealogy of Bashkirian Kipchak Clan]]
Analysis of mtDNA shows that modern humans occupied Eurasia in a single migratory event between 60 and 70 kya.<ref name=":1">{{Cite journal|last1=Soares|first1=Pedro|last2=Achilli|first2=Alessandro|last3=Semino|first3=Ornella|last4=Davies|first4=William|last5=Macaulay|first5=Vincent|last6=Bandelt|first6=Hans-Jürgen|last7=Torroni|first7=Antonio|last8=Richards|first8=Martin B.|date=2010-02-23|title=The Archaeogenetics of Europe|journal=Current Biology|language=en|volume=20|issue=4|pages=R174–83|doi=10.1016/j.cub.2009.11.054|pmid=20178764|s2cid=7679921|issn=0960-9822|doi-access=free}}</ref> Genetic evidence shows that occupation of the Near East and Europe happened no earlier than 50 kya.<ref name=":1" /> Studying haplogroup U has shown separate dispersals from the Near East both into Europe and into North Africa.<ref name=":1" />

Much of the work done in archaeogenetics focuses on the [[Neolithic transition]] in Europe.<ref name=":2">{{Cite book|title=The Cambridge World History, Volume II|last=Baker|first=Graeme|publisher=Cambridge University Press|year=2015|isbn=978-0521192187|location=Cambridge|oclc=889666433}}</ref> Cavalli-Svorza's analysis of genetic-geographic patterns led him to conclude that there was a massive influx of Near Eastern populations into Europe at the start of the Neolithic.<ref name=":2" /> This view led him “to strongly emphasize the expanding early farmers at the expense of the indigenous Mesolithic foraging populations.”<ref name=":2" /> mtDNA analysis in the 1990s, however, contradicted this view. M.B. Richards estimated that 10–22% of extant European mtDNA's had come from Near Eastern populations during the Neolithic.<ref name=":2" /> Most mtDNA's were “already established” among existing Mesolithic and Paleolithic groups.<ref name=":2" /> Most “control-region lineages” of modern European mtDNA are traced to a founder event of reoccupying northern Europe towards the end of the [[Last Glacial Maximum]] (LGM).<ref name=":1" /> One study of extant European mtDNA's suggest this reoccupation occurred after the end of the LGM, although another suggests it occurred before.<ref name=":1" /><ref name=":2" /> Analysis of haplogroups V, H, and U5 support a “pioneer colonization” model of European occupation, with incorporation of foraging populations into arriving Neolithic populations.<ref name=":2" /> Furthermore, analysis of ancient DNA, not just extant DNA, is shedding light on some issues. For instance, comparison of Neolithic and mesolithic DNA has indicated that the development of dairying preceded widespread [[lactose tolerance]].<ref name=":2" />

==== South Asia ====
South Asia has served as the major early corridor for geographical dispersal of modern humans from out-of-Africa.<ref name=":3" /> Based on studies of mtDNA line M, some have suggested that the first occupants of India were Austro-Asiatic speakers who entered about 45–60 kya.<ref name=":3">{{Cite journal|last=Majumder|first=Partha P.|date=2010-02-23|title=The Human Genetic History of South Asia|journal=Current Biology|language=en|volume=20|issue=4|pages=R184–87|doi=10.1016/j.cub.2009.11.053|issn=0960-9822|pmid=20178765|s2cid=1490419|doi-access=free}}</ref> The Indian gene pool has contributions from earliest settlers, as well as West Asian and Central Asian populations from migrations no earlier than 8 kya.<ref name=":3" /> The lack of variation in mtDNA lineages compared to the Y-chromosome lineages indicate that primarily males partook in these migrations.<ref name=":3" /> The discovery of two subbranches U2i and U2e of the U mtDNA lineage, which arose in Central Asia has “modulated” views of a large migration from Central Asia into India, as the two branches diverged 50 kya.<ref name=":3" /> Furthermore, U2e is found in large percentages in Europe but not India, and vice versa for U2i, implying U2i is native to India.<ref name=":3" />

==== East Asia ====
Analysis of mtDNA and NRY (non-recombining region of Y chromosome) sequences have indicated that the first major dispersal out of Africa went through Arabia and the Indian coast 50–100 kya, and a second major dispersal occurred 15–50 kya north of the Himalayas.<ref name=":4">{{Cite journal|last1=Stoneking|first1=Mark|last2=Delfin|first2=Frederick|date=2010-02-23|title=The Human Genetic History of East Asia: Weaving a Complex Tapestry|journal=Current Biology|language=en|volume=20|issue=4|pages=R188–R193|doi=10.1016/j.cub.2009.11.052|pmid=20178766|s2cid=18777315|issn=0960-9822|doi-access=free}}</ref>

Much work has been done to discover the extent of north-to-south and south-to-north migrations within Eastern Asia.<ref name=":4" /> Comparing the genetic diversity of northeastern groups with southeastern groups has allowed archaeologists to conclude many of the northeast Asian groups came from the southeast.<ref name=":4" /> The Pan-Asian SNP (single nucleotide polymorphism) study found “a strong and highly significant correlation between haplotype diversity and latitude,” which, when coupled with demographic analysis, supports the case for a primarily south-to-north occupation of East Asia.<ref name=":4" /> Archaeogenetics has also been used to study hunter-gatherer populations in the region, such as the [[Ainu people|Ainu]] from Japan and [[Negrito]] groups in the Philippines.<ref name=":4" /> For example, the Pan-Asian SNP study found that Negrito populations in Malaysia and the Negrito populations in the Philippines were more closely related to non-Negrito local populations than to each other, suggesting Negrito and non-Negrito populations are linked by one entry event into East Asia; although other Negrito groups do share affinities, including with [[Aboriginal Australians|Indigenous Australians]].<ref name=":4" /> A possible explanation of this is a recent admixture of some Negrito groups with their local populations.

==== Americas ====
{{further|Genetic history of Indigenous peoples of the Americas}}
Archaeogenetics has been used to better understand the populating of the Americas from Asia.<ref name=":5">{{Cite journal|last1=O'Rourke|first1=Dennis H.|last2=Raff|first2=Jennifer A.|author-link2=Jennifer Raff|date=2010-02-23|title=The Human Genetic History of the Americas: The Final Frontier|journal=Current Biology|language=en|volume=20|issue=4|pages=R202–07|doi=10.1016/j.cub.2009.11.051|pmid=20178768|s2cid=14479088|issn=0960-9822|doi-access=free}}</ref> Native American mtDNA haplogroups have been estimated to be between 15 and 20 kya, although there is some variation in these estimates.<ref name=":5" /> Genetic data has been used to propose various theories regarding how the Americas were colonized.<ref name=":5" /> Although the most widely held theory suggests “three waves” of migration after the LGM through the Bering Strait, genetic data have given rise to alternative hypotheses.<ref name=":5" /> For example, one hypothesis proposes a migration from Siberia to South America 20–15 kya and a second migration that occurred after glacial recession.<ref name=":5" /> Y-chromosome data has led some to hold that there was a single migration starting from the Altai Mountains of Siberia between 17.2 and 10.1 kya, after the LGM.<ref name=":5" /> Analysis of both mtDNA and Y-chromosome DNA reveals evidence of “small, founding populations.”<ref name=":5" /> Studying haplogroups has led some scientists to conclude that a southern migration into the Americas from one small population was impossible, although separate analysis has found that such a model is feasible if such a migration happened along the coasts.<ref name=":5" />

==== Australia and New Guinea ====
Finally, archaeogenetics has been used to study the occupation of Australia and New Guinea.<ref name=":6">{{Cite journal|last=Kayser|first=Manfred|date=2010-02-23|title=The Human Genetic History of Oceania: Near and Remote Views of Dispersal|journal=Current Biology|language=en|volume=20|issue=4|pages=R194–R201|doi=10.1016/j.cub.2009.12.004|issn=0960-9822|pmid=20178767|s2cid=7282462|doi-access=free}}</ref> The Indigenous people of Australia and New Guinea are phenotypically very similar, but mtDNA has shown that this is due to convergence from living in similar conditions.<ref name=":6" /> Non-coding regions of mt-DNA have shown “no similarities” between the aboriginal populations of Australia and New Guinea.<ref name=":6" /> Furthermore, no major NRY lineages are shared between the two populations. The high frequency of a single NRY lineage unique to Australia coupled with “low diversity of lineage-associated Y-chromosomal short tandem repeat (Y-STR) haplotypes” provide evidence for a “recent founder or bottleneck” event in Australia.<ref name=":6" /> But there is relatively large variation in mtDNA, which would imply that the bottleneck effect impacted males primarily.<ref name=":6" /> Together, NRY and mtDNA studies show that the splitting event between the two groups was over 50&nbsp;kya, casting doubt on recent common ancestry between the two.<ref name=":6" />

=== Plants and animals ===
Archaeogenetics has been used to understand the development of [[domestication]] of plants and animals.

==== Domestication of plants ====
The combination of genetics and archeological findings have been used to trace the earliest signs of plant [[Domestication of plants|domestication]] around the world. However, since the nuclear, mitochondrial, and chloroplast [[genome]]s used to trace domestication's moment of origin have evolved at different rates, its use to trace [[genealogy]] have been somewhat problematic.<ref name=":15" /> [[Nuclear DNA]] in specific is used over [[Mitochondrial DNA|mitochondrial]] and [[chloroplast DNA]] because of its faster mutation rate as well as its intraspecific variation due to a higher consistency of [[Polymorphism (biology)|polymorphism]] [[genetic marker]]s.<ref name=":15" /> Findings in crop 'domestication genes' (traits that were specifically selected for or against) include
* tb1 (teosinte branched1) – affecting the [[apical dominance]] in maize<ref name=":15" />
* tga1 (teosinte glume architecture1) – making maize kernels compatible for the convenience of humans <ref name=":15" />
* te1 (Terminal ear1) – affecting the weight of kernels<ref name=":15" />
* fw2.2 – affecting the weight in tomatoes<ref name=":15" />
* BoCal – [[inflorescence]] of broccoli and cauliflower<ref name=":15" />
Through the study of archaeogenetics in plant domestication, signs of the first global economy can also be uncovered. The geographical distribution of new crops highly selected in one region found in another where it would have not originally been introduced serve as evidence of a trading network for the production and consumption of readily available resources.<ref name=":15">{{Cite journal|last=Zeder, Emshwiller, Smith, Bradley|date=March 2006|title=Documenting domestication: the intersection of genetics and archaeology|url=https://anthropology.si.edu/archaeobio/images/zederetal_2006_docdom_tig.pdf|journal=Trends in Genetics|volume=22|issue=3|pages=139–146|via=Science Direct|doi=10.1016/j.tig.2006.01.007|pmid=16458995}}</ref>

==== Domestication of animals ====
Archaeogenetics has been used to study the domestication of animals.<ref name=":8">{{Cite web|url=https://anthropology.si.edu/archaeobio/images/zederetal_2006_docdom_tig.pdf|title=Documenting domestication: the inter- section of genetics and archaeology|last=Zeder |display-authors=etal }}</ref> By analyzing genetic diversity in domesticated animal populations researchers can search for genetic markers in DNA to give valuable insight about possible traits of progenitor species.<ref name=":8" /> These traits are then used to help distinguish archaeological remains between wild and domesticated specimens.<ref name=":8" /> The genetic studies can also lead to the identification of ancestors for domesticated animals.<ref name=":8" /> The information gained from genetics studies on current populations helps guide the Archaeologist's search for documenting these ancestors.<ref name=":8" />

Archaeogenetics has been used to trace the domestication of pigs throughout the old world.<ref name=":11">{{Cite journal|url=http://www.pnas.org/content/104/39/15276.full.pdf|title=Ancient DNA, pig domestication, and the spread of the Neolithic into Europe|last=Larson |display-authors=etal |journal=Proceedings of the National Academy of Sciences}}</ref> These studies also reveal evidence about the details of early farmers.<ref name=":11" /> Methods of Archaeogenetics have also been used to further understand the development of domestication of dogs.<ref name=":14">{{Cite journal|title=Rethinking dog domestication by integrating genetics, archeology, and biogeography|last=Larson |display-authors=etal |pmid=22615366|doi=10.1073/pnas.1203005109|volume=109|pmc=3384140|year=2012|journal=Proc. Natl. Acad. Sci. U.S.A.|issue=23|pages=8878–83|bibcode=2012PNAS..109.8878L|doi-access=free }}</ref> Genetic studies have shown that all dogs are descendants from the gray wolf, however, it is currently unknown when, where, and how many times dogs were domesticated.<ref name=":14" /> Some genetic studies have indicated multiple domestications while others have not.<ref name=":14" /> Archaeological findings help better understand this complicated past by providing solid evidence about the progression of the domestication of dogs.<ref name=":14" /> As early humans domesticated dogs the archaeological remains of buried dogs became increasingly more abundant.<ref name=":14" /> Not only does this provide more opportunities for archaeologists to study the remains, it also provides clues about early human culture.<ref name=":14" />