View source for Biology:Genetic history of Africa

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[[File:ADMIXTURE analysis of Horn of Africa populations in a broad context.png|thumb|Population structure of African populations in a broad context. ADMIXTURE analysis of 2,194 individuals from 81 populations for 16,420 SNPs reveals both well-established and novel ancestry components in African populations.]]

The '''genetic history of Africa''' is composed of the overall genetic history of African populations in [[Earth:Africa|Africa]], including the regional genetic histories of [[Biology:Genetic history of North Africa|North Africa]], [[Biology:Genetic history of West Africa|West Africa]], East Africa, [[Biology:Genetic history of Central Africa|Central Africa]], and [[Biology:Genetic history of Southern Africa|Southern Africa]], as well as the [[Biology:Recent African origin of modern humans|recent origin of modern humans in Africa]]. The Sahara served as a trans-regional passageway and place of dwelling for people in Africa during various humid phases<ref name="Osborne">{{cite journal |last1=Osborne |first1=Anne H. |display-authors=0 |title=A humid corridor across the Sahara for the migration of early modern humans out of Africa 120,000 years ago |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=43 |pages=16444–16447 |date=October 2008 |pmid=18936490 |pmc=2575439 |doi=10.1073/pnas.0804472105 |s2cid=10418009 |doi-access=free |bibcode=2008PNAS..10516444O}}</ref><ref name="Drake">{{cite book |last1=Drake |first1=Nick |last2=Breeze |first2=Paul |title=Africa from MIS 6-2 |chapter=Climate Change and Modern Human Occupation of the Sahara from MIS 6-2 |chapter-url=https://link.springer.com/chapter/10.1007/978-94-017-7520-5_6 |series=Vertebrate Paleobiology and Paleoanthropology |year=2016 |pages=103–122 |publisher=Africa from MIS 6-2 |doi=10.1007/978-94-017-7520-5_6 |isbn=978-94-017-7519-9 |s2cid=131383927}}</ref><ref name="El-Shenawy">{{cite journal |last1=El-Shenawy |first1=Mohammed I. |display-authors=0 |title=Speleothem evidence for the greening of the Sahara and its implications for the early human dispersal out of sub-Saharan Africa |url=https://www.sciencedirect.com/science/article/abs/pii/S0277379117307436 |journal=Quaternary Science Reviews |year=2018 |volume=188 |pages=67–76 |doi=10.1016/j.quascirev.2018.03.016 |bibcode=2018QSRv..188...67E |s2cid=134694090}}</ref> and periods throughout the history of Africa.<ref name="Scheele">{{cite book |last1=Scheele |first1=Judith |title=Crossroads Regions: The Sahara |url=https://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199935369.001.0001/oxfordhb-9780199935369-e-18 |date=Aug 2016 |publisher=Oxford Handbooks Online |doi=10.1093/oxfordhb/9780199935369.013.18|isbn=978-0-19-993536-9 }}</ref><ref name="Wippel">{{cite journal |last1=Wippel |first1=Steffen |title=The Sahara as a Bridge, Not a Barrier: An Essay and Book Review on Recent Transregional Perspectives |journal=Neue Politische Literatur |year=2020 |volume=65 |issue=3 |pages=449–472 |doi=10.1007/s42520-020-00318-y |s2cid=224855920 |doi-access=free}}</ref>

==Overview==
[[File:PCA of sub-Saharan Africa populations.png|thumb|(A) the origin of the 46 African ethnic groups used in the analysis; ethnic groups from similar regions are given the same colour, but different shapes. (B) PCA shows that the first major axis of variation in Africa (PC1, y-axis) splits southern groups from the rest of Africa, each symbol represents an individual; PC2 (x-axis) reflects ethno-linguistic differences, with Niger-Congo and Nilo-Saharan speakers split from Afroasiatic speakers. (C) The third principal component (PC3, x-axis) represents geographical separation of Niger-Congo speakers, forming a cline from west to east Africans.]]

The peoples of [[Earth:Africa|Africa]] are characterized by regional genetic substructure and heterogeneity, depending on the respective ethno-linguistic identity, and, in part, explainable by the "multiregional evolution" of modern human lineages in various multiple regions of the African continent, as well as later admixture events, including back-migrations from Eurasia, of both highly differentiated West- and East-Eurasian components.<ref name="The deep population history in Afri">{{cite journal |vauthors=Hollfelder N, Breton G, Sjödin P, Jakobsson M |title=The deep population history in Africa |journal=Human Molecular Genetics |volume=30 |issue=R1 |pages=R2–R10 |date=April 2021 |pmid=33438014 |pmc=8117439 |doi=10.1093/hmg/ddab005}}</ref>

Africans' genetic ancestry is largely partitioned by [[Earth:Geography|geography]] and [[Social:Language family|language family]], with populations belonging to the same ethno-linguistic groupings showing high genetic homogeneity and coherence. Gene flow, consistent with both short- and long-range migration events followed by extensive admixture and bottleneck events, have influenced the regional genetic makeup and demographic structure of Africans. The historical [[History:Bantu expansion|Bantu expansion]] had lasting impacts on the modern demographic make up of Africa, resulting in a greater genetic and linguistic homogenization.<ref name="Fan 82">{{cite journal |vauthors=Fan S, Kelly DE, Beltrame MH, Hansen ME, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson N, Reich D, Tishkoff SA |display-authors=6 |title=African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations |journal=Genome Biology |volume=20 |issue=1 |pages=82 |date=April 2019 |pmid=31023338 |pmc=6485071 |doi=10.1186/s13059-019-1679-2 |doi-access=free }}</ref> Genetic, archeologic, and linguistic studies added extra insight into this movement: "Our results reveal a genetic continuum of Niger–Congo speaker populations across the continent and extend our current understanding of the routes, timing and extent of the Bantu migration."<ref>{{Cite web |title=A great African gene migration |url=https://cosmosmagazine.com/science/a-great-migration-of-genes-in-africa/ |access-date=2022-01-11 |website=cosmosmagazine.com |date=29 October 2020 |language=en-AU}}</ref>

Overall, different African populations display genetic diversity and substructure, but can be clustered in distinct but partially overlapping groupings:<ref name=":5">{{Cite web |author1=Ananyo Choudhury |author2=Shaun Aron |author3=Dhriti Sengupta |author4=Scott Hazelhurst |author5=Michèle Ramsay |date=1 August 2018 |title=African genetic diversity provides novel insights into evolutionary history and local adaptations |url=https://academic.oup.com/hmg/article/27/R2/R209/4993963 |access-date=2022-10-21 |website=academic.oup.com}}</ref>

* Khoisan hunter-gatherer lineages from [[Place:Southern Africa|Southern Africa]] represent the deepest lineages, forming a divergent and distinct cluster, shifted away from contemporary "Sub-Saharan Africans", and are further diverged from them than the various Eurasian lineages are. The diverging date of these "Southern hunter-gatherers" from all other human populations is estimated to over 100,000 years ago respectively, with the Khoisan later diverging into two subgroups, northern and southern Khoisan,~30,000 years ago.{{Efn|Although the estimated date of this event varies across studies, there is general consensus that the split occurred over 100 thousand years ago (kya) (8,23).}}
* Rain forest foragers such as the Baka and the Mbuti diverged from other Sub-Saharan African groups over 60,000 years ago. Eastern groups such as the Mbuti split from Western groups such as the Baka ~20,000 years ago.
* The various [[Social:Afroasiatic languages|Afroasiatic]] speakers are suggested to have diverged from other African groups ~50,000 years ago.<ref name="ReferenceA">{{Cite journal |last1=Baker |first1=Jennifer L. |last2=Rotimi |first2=Charles N. |last3=Shriner |first3=Daniel |date=2017-05-08 |title=Human ancestry correlates with language and reveals that race is not an objective genomic classifier |journal=Scientific Reports |language=en |volume=7 |issue=1 |pages=1572 |doi=10.1038/s41598-017-01837-7 |pmid=28484253 |pmc=5431528 |bibcode=2017NatSR...7.1572B |issn=2045-2322}}</ref>
* Niger-Congo and [[Social:Nilo-Saharan languages|Nilo-Saharan]] speakers split around 28,000 years ago.<ref name=":5" />
* [[Social:Austronesian languages|Austronesian-speaking]] Malagasy people in {{wipe|Madagascar}} have received significant East/Southeast Asian admixture, less among some groups of coastal Southern, Eastern and the Horn of Africa. The estimated date of geneflow is 2,200 years ago.<ref>{{Cite journal |last1=Kusuma |first1=Pradiptajati |last2=Brucato |first2=Nicolas |last3=Cox |first3=Murray P. |last4=Pierron |first4=Denis |last5=Razafindrazaka |first5=Harilanto |last6=Adelaar |first6=Alexander |last7=Sudoyo |first7=Herawati |last8=Letellier |first8=Thierry |last9=Ricaut |first9=François-Xavier |date=2016-05-18 |title=Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy |journal=Scientific Reports |volume=6 |pages=26066 |doi=10.1038/srep26066 |issn=2045-2322 |pmc=4870696 |pmid=27188237|bibcode=2016NatSR...626066K }}</ref><ref>{{cite journal |vauthors=Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA |display-authors=6 |title=A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes |journal=American Journal of Human Genetics |volume=70 |issue=5 |pages=1197–1214 |date=May 2002 |pmid=11910562 |pmc=447595 |doi=10.1086/340257}}</ref><ref>{{cite journal |vauthors=Pakstis AJ, Speed WC, Soundararajan U, Rajeevan H, Kidd JR, Li H, Kidd KK |title=Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels |journal=Scientific Reports |volume=9 |issue=1 |pages=18874 |date=December 2019 |pmid=31827153 |pmc=6906462 |doi=10.1038/s41598-019-55175-x |bibcode=2019NatSR...918874P}}</ref><ref name="Fan 82" /><ref name="Identifying and Interpreting Appare">{{cite journal |vauthors=Chen L, Wolf AB, Fu W, Li L, Akey JM |title=Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals |journal=Cell |volume=180 |issue=4 |pages=677–687.e16 |date=February 2020 |pmid=32004458 |doi=10.1016/j.cell.2020.01.012 |s2cid=210955842|doi-access=free }}</ref><ref name=":2">{{Cite journal |last1=van de Loosdrecht |first1=Marieke |last2=Bouzouggar |first2=Abdeljalil |last3=Humphrey |first3=Louise |last4=Posth |first4=Cosimo |last5=Barton |first5=Nick |last6=Aximu-Petri |first6=Ayinuer |last7=Nickel |first7=Birgit |last8=Nagel |first8=Sarah |last9=Talbi |first9=El Hassan |last10=El Hajraoui |first10=Mohammed Abdeljalil |last11=Amzazi |first11=Saaïd |last12=Hublin |first12=Jean-Jacques |last13=Pääbo |first13=Svante |last14=Schiffels |first14=Stephan |last15=Meyer |first15=Matthias |date=2018-05-04 |title=Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations |journal=Science |language=en |volume=360 |issue=6388 |pages=548–552 |doi=10.1126/science.aar8380 |pmid=29545507 |bibcode=2018Sci...360..548V |s2cid=206666517 |issn=0036-8075|doi-access=free }}</ref>

[[File:Overall genetic position of worldwide populations.jpg|thumb|Geographic location of the samples analyzed in this study (A). PCA of the Khoe-San individuals, Eurasians, West and East Africans before (unmasked, B) and after (masked, C) applying the local ancestry pipeline (146,696 independent SNPs).]]

===Indigenous Africans===


[[File:Procrustes-transformed PCA plot of genetic variation of worldwide populations.png|thumb|PCA plot of genetic variation of worldwide populations. ('''A''') Geographic coordinates of 53 populations. ('''B''') Procrustes-transformed PCA plot of genetic variation.<ref>{{cite journal |vauthors=Wang C, Zöllner S, Rosenberg NA |title=A quantitative comparison of the similarity between genes and geography in worldwide human populations |journal=PLOS Genetics |volume=8 |issue=8 |pages=e1002886 |date=August 2012 |pmid=22927824 |pmc=3426559 |doi=10.1371/journal.pgen.1002886 |doi-access=free }}</ref>]]

The [[Social:Niger–Congo languages|Niger–Congo languages]] probably originated in or near the area where these languages were spoken prior to [[History:Bantu expansion|Bantu expansion]] (i.e. [[Place:West Africa|West Africa]] or [[Place:Central Africa|Central Africa]]). Its expansion may have been associated with the expansion of agriculture, in the [[History:Neolithic|African Neolithic]] period, following the [[Earth:African humid period#End|desiccation of the Sahara]] in c. 3500 BCE. Proto-Niger-Congo may have originated about 10,000 years before present in the "Green Sahara" of Africa (roughly the [[Place:Sahel|Sahel]] and southern Sahara), and that its dispersal can be correlated with the spread of the [[Bow and arrow|bow and arrow]] by migrating [[Biology:Hunter-gatherer|hunter-gatherer]]s, which later developed agriculture.<ref>{{Cite journal |vauthors=Manning K, Timpson A |date=2014-10-01 |title=The demographic response to Holocene climate change in the Sahara |journal=Quaternary Science Reviews |language=en |volume=101 |pages=28–35 |doi=10.1016/j.quascirev.2014.07.003 |bibcode=2014QSRv..101...28M |s2cid=54923700 |issn=0277-3791|doi-access=free }}</ref><ref name="BlenchAfricanPast">{{Cite book |vauthors=Blench R |title=Archaeology, language, and the African past |publisher=AltaMira Press |year=2006 |isbn=9780759104655}}</ref><ref>{{cite conference |vauthors=Blench R |url=https://llacan.cnrs.fr/nigercongo2/discussions/Can_we_visit_the_graves_of_the_first_Niger.pdf |title=Can we visit the graves of the first Niger-Congo speakers? |conference=2nd International Congress: Towards Proto-Niger-Congo: Comparison and Reconstruction |location=Paris |date=September 2016}}</ref>

Although the validity of the [[Social:Nilo-Saharan languages|Nilo-Saharan family]] remains controversial, the region between Chad, Sudan, and the Central African Republic is seen as a likely candidate for its homeland prior to its dispersal around 10,000–8,000 BCE.<ref>{{Cite book |vauthors=Vossen R, Dimmendaal GJ |url=https://books.google.com/books?id=wcjXDwAAQBAJ&pg=PA380 |title=The Oxford Handbook of African Languages |date=2020-03-13 |publisher=Oxford University Press |isbn=978-0-19-960989-5 |language=en}}</ref>

The Southern African hunter-gatherers (Khoisan) are suggested to represent the autochthonous hunter-gatherer population of southern Africa, prior to the expansion of Bantu-speakers from Western/Central Africa and East African pastoralists. Khoisan show evidence for Bantu-related admixture, ranging from nearly ~0% to up to ~87.1%.<ref>{{cite journal |vauthors=Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM |title=Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations |journal=Molecular Biology and Evolution |volume=36 |issue=9 |pages=1849–1861 |date=September 2019 |pmid=31288264 |pmc=6735883 |doi=10.1093/molbev/msz089}}</ref>

===Out-of-Africa event===
{{Main|Biology:Recent African origin of modern humans}}
[[File:Human migration routes following Out-of-Africa.png|thumb|Human migration routes following Out-of-Africa.]]
[[File:Migraciones humanas en haplogrupos de ADN-Y.PNG|thumb|Most modern Africans display a high level of genetic homogeneity, but  contributions from Eurasian populations are substantial, mostly concentrated in the Northeastern part of Africa and Madagascar.]]

The "[[Biology:Recent African origin of modern humans|recent African origin of modern humans]]" model proposes a "single origin" of ''Homo sapiens'' in Africa the taxonomic sense. Recent genetic and archeologic data suggests that Homo sapiens-subgroups originated in multiple regions of Africa, not confined to a single region of origin. The ''H. sapiens'' ancestral to proper Eurasians most likely left Northeastern Africa between 50,000 and 100,000 years ago.<ref name=":2" /> The "recent African origin" model proposes that all modern non-African populations descend from one or several waves of ''H. sapiens'' that left Africa 70,000-60,000 years ago.<ref>{{cite journal |vauthors=López S, van Dorp L, Hellenthal G |title=Human Dispersal Out of Africa: A Lasting Debate |journal=Evolutionary Bioinformatics Online |volume=11 |issue=Suppl 2 |pages=57–68 |date=2016-04-21 |pmid=27127403 |pmc=4844272 |doi=10.4137/EBO.S33489}}</ref><ref>{{cite journal |vauthors=Scerri EM, Thomas MG, Manica A, Gunz P, Stock JT, Stringer C, Grove M, Groucutt HS, Timmermann A, Rightmire GP, d'Errico F, Tryon CA, Drake NA, Brooks AS, Dennell RW, Durbin R, Henn BM, Lee-Thorp J, deMenocal P, Petraglia MD, Thompson JC, Scally A, Chikhi L |display-authors=6 |title=Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? |language=English |journal=Trends in Ecology & Evolution |volume=33 |issue=8 |pages=582–594 |date=August 2018 |pmid=30007846 |pmc=6092560 |doi=10.1016/j.tree.2018.05.005}}</ref><ref>{{Cite web |title=One Species, Many Origins |url=https://www.shh.mpg.de/1474609/pan-african-origins |access-date=2022-01-11 |website=www.shh.mpg.de |language=en}}</ref><ref>{{Cite web |last=Vallini |first=Leonardo |display-authors=et al. |date=7 April 2022 |title=Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa |url=https://academic.oup.com/gbe/article/14/4/evac045/6563828 |access-date=2023-02-21 |website=academic.oup.com}}</ref>
[[File:Simplifed_Y_tree_is_shown_as_reference_for_colours.png|thumb|300x300px|According to serial founder model, the earliest-branching non-African lineages are expected to have expanded in the Middle East, after the Out-of-Africa event (a), but have their deepest divergence in modern-day East or Southeast Asia (b), suggesting either rapid diversification and substructure within the early Eurasians, or replacement and loss of deep lineages in Western Eurasia. Simplified Y tree is shown as reference for colours.<ref>{{Cite journal |vauthors=Hallast P, Agdzhoyan A, Balanovsky O, Xue Y, Tyler-Smith C |date=February 2021 |title=A Southeast Asian origin for present-day non-African human Y chromosomes |journal=Human Genetics |volume=140 |issue=2 |pages=299–307 |doi=10.1007/s00439-020-02204-9 |pmc=7864842 |pmid=32666166}}</ref>]]
According to Durvasula et al. (2020), there are indications that 2% to 19% (≃6.6 to 7.0%) of the DNA of West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, Durvasula et al. (2020) also suggests that at least part of this archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans).<ref>{{cite journal |vauthors=Durvasula A, Sankararaman S |date=February 2020 |title=Recovering signals of ghost archaic introgression in African populations |journal=Science Advances |volume=6 |issue=7 |pages=eaax5097 |bibcode=2020SciA....6.5097D |doi=10.1126/sciadv.aax5097 |pmc=7015685 |pmid=32095519 |doi-access=free}} "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations...One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population...Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..."</ref><ref>''[https://www.science.org/doi/10.1126/sciadv.aax5097] {{Webarchive|url=https://web.archive.org/web/20201207165127/https://advances.sciencemag.org/content/advances/suppl/2020/02/10/6.7.eaax5097.DC1/aax5097_SM.pdf|date=7 December 2020}} Supplementary Materials for ''Recovering signals of ghost archaic introgression in African populations", section "S8.2" "We simulated data using the same priors in Section S5.2, but computed the spectrum for both YRI [West African Yoruba] and CEU [a population of European origin] . We found that the best fitting parameters were an archaic split time of 27,000 generations ago (95% HPD: 26,000-28,000), admixture fraction of 0.09 (95% HPD: 0.04-0.17), admixture time of 3,000 generations ago (95% HPD: 2,800-3,400), and an effective population size of 19,700 individuals (95% HPD: 19,300-20,200). We find that the lower bound of the admixture time is further back than the simulated split between CEU and YRI (2155 generations ago), providing some evidence in favor of a pre-Out-of-Africa event. This model suggests that many populations outside of Africa should also contain haplotypes from this introgression event, though detection is difficult because many methods use unadmixed outgroups to detect introgressed haplotypes [Browning et al., 2018, Skov et al., 2018, Durvasula and Sankararaman, 2019] (5, 53, 22). It is also possible that some of these haplotypes were lost during the Out-of-Africa bottleneck."</ref><ref>{{cite journal |vauthors=Durvasula A, Sankararaman S |date=February 2020 |title=Recovering signals of ghost archaic introgression in African populations |journal=Science Advances |volume=6 |issue=7 |pages=eaax5097 |bibcode=2020SciA....6.5097D |doi=10.1126/sciadv.aax5097 |pmc=7015685 |pmid=32095519}}</ref> Chen et al. (2020) found that Africans have higher [[Biology:Neanderthal|Neanderthal]] ancestry than previously thought. 2,504 African samples from all over Africa were analyzed and tested on Neanderthal ancestry. All African samples showed evidence for minor Neanderthal ancestry, but always at lower levels than observed in Eurasians.<ref name="Identifying and Interpreting Appare2">{{cite journal |vauthors=Chen L, Wolf AB, Fu W, Li L, Akey JM |date=February 2020 |title=Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals |journal=Cell |volume=180 |issue=4 |pages=677–687.e16 |doi=10.1016/j.cell.2020.01.012 |pmid=32004458 |s2cid=210955842|doi-access=free }}</ref>

===Geneflow between Eurasian and African populations===
[[File:Pre-Neolithic and Neolithic migration events in Africa (excluding Basal-West-Eurasian geneflow during the Paleolithic).jpg|thumb|Pre-Neolithic and Neolithic migration events in Africa.<ref name="sciencedirect.com">{{Cite journal |last1=Vicente |first1=Mário |last2=Schlebusch |first2=Carina M |date=2020-06-01 |title=African population history: an ancient DNA perspective |journal=Current Opinion in Genetics & Development |series=Genetics of Human Origin |language=en |volume=62 |pages=8–15 |doi=10.1016/j.gde.2020.05.008 |pmid=32563853 |s2cid=219974966 |issn=0959-437X|doi-access=free }}</ref>]]

Significant Eurasian admixture is found in Northern Africa, and among specific ethnic groups of the [[Place:Horn of Africa|Horn of Africa]], as well as among the Malagasy people of {{wipe|Madagascar}}. Various genome studies found evidence for multiple [[History:Prehistory|prehistoric]] back-migrations from various [[Earth:Eurasia|Eurasia]]n populations and subsequent admixture with native groups.<ref>{{cite journal |vauthors=Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC |display-authors=6 |title=Admixture into and within sub-Saharan Africa |journal=eLife |volume=5 |date=June 2016 |pmid=27324836 |pmc=4915815 |doi=10.7554/eLife.15266 |doi-access=free }}</ref> West-Eurasian geneflow arrived to Northern Africa during the Paleolithic (30,000 to 15,000 years ago), followed by other pre-Neolithic and Neolithic migration events. Genetic data on the Taforalt samples "demonstrated that Northern Africa received significant amounts of gene-flow from Eurasia predating the Holocene and development of farming practices". Medieval geneflow events, such as the Arab expansion also left traces in various African populations.<ref name=":2"/><ref name="sciencedirect.com"/><ref>{{Cite journal |last1=Serra-Vidal |first1=Gerard |last2=Lucas-Sanchez |first2=Marcel |last3=Fadhlaoui-Zid |first3=Karima |last4=Bekada |first4=Asmahan |last5=Zalloua |first5=Pierre |last6=Comas |first6=David |date=2019-11-18 |title=Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa |journal=Current Biology |language=en |volume=29 |issue=22 |pages=3953–3959.e4 |doi=10.1016/j.cub.2019.09.050 |pmid=31679935 |s2cid=204972040 |issn=0960-9822|doi-access=free }}</ref> Pickrell et al. (2014) indicated that Western Eurasian ancestry eventually arrived through [[Place:Northeast Africa|Northeast Africa]] (particularly the Horn of Africa) to [[Place:Southern Africa|Southern Africa]].<ref name=":3">{{cite journal |display-authors=6 |vauthors=Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D |date=February 2014 |title=Ancient west Eurasian ancestry in southern and eastern Africa |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=111 |issue=7 |pages=2632–2637 |arxiv=1307.8014 |bibcode=2014PNAS..111.2632P |doi=10.1073/pnas.1313787111 |pmc=3932865 |pmid=24550290 |doi-access=free}}</ref>

Ramsay et al. (2018) also found evidence for significant Western Eurasian admixture in various parts of Africa, from both ancient and more recent migrations, being highest among populations from [[Place:North Africa|Northern Africa]], and some groups of the [[Place:Horn of Africa|Horn of Africa]]:<ref name="Ramsay">{{cite journal |vauthors=Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M |title=African genetic diversity provides novel insights into evolutionary history and local adaptations |journal=Human Molecular Genetics |volume=27 |issue=R2 |pages=R209–R218 |date=August 2018 |pmid=29741686 |pmc=6061870 |doi=10.1093/hmg/ddy161}}</ref>

<blockquote>In addition to the intrinsic diversity within the continent due to population structure and isolation, migration of Eurasian populations into Africa has emerged as a critical contributor to the genetic diversity. These migrations involved the influx of different Eurasian populations at different times and to different parts of Africa. Comprehensive characterization of the details of these migrations through genetic studies on existing populations could help to explain the strong genetic differences between some geographically neighbouring populations.

This distinctive Eurasian admixture appears to have occurred over at least three time periods with ancient admixture in central west Africa (e.g., Yoruba from Nigeria) occurring between ~7.5 and 10.5 kya, older admixture in east Africa (e.g., Ethiopia) occurring between ~2.4 and 3.2 kya and more recent admixture between ~0.15 and 1.5 kya in some east African (e.g., Kenyan) populations.

Subsequent studies based on LD decay and haplotype sharing in an extensive set of African and Eurasian populations confirmed the presence of Eurasian signatures in west, east and southern Africans. In the west, in addition to Niger-Congo speakers from The Gambia and Mali, the Mossi from Burkina Faso showed the oldest Eurasian admixture event ~7 kya. In the east, these analyses inferred Eurasian admixture within the last 4000 years in Kenya.<ref name="Ramsay" /></blockquote>

There is no definitive agreement on when or where the original homeland of the [[Social:Afroasiatic languages|Afroasiatic language family]] existed. Some have suggested that they were spread by people with largely West-Eurasian ancestry during the [[History:Neolithic Revolution|Neolithic Revolution]], towards Northern Africa and the Horn of Africa, outgoing from the [[Place:Middle East|Middle East]], specifically from the [[Place:Levant|Levant]]. This hypothesis does not account for the domestication of plants [[Biology:Endemism|endemic]] to the Horn of Africa such as [[Biology:Teff|teff]], [[Biology:Ensete ventricosum|ensete]], and [[Biology:Guizotia abyssinica|Niger seed]], nor does it account for the lack of evidence of intrusive agricultural populations or the cultivation of [[Biology:Wheat|wheat]], [[Biology:Barley|barley]], or [[Biology:Sorghum|sorghum]] in that region prior to 3000 B.C.<ref>{{Cite book |last1=Clark |first1=JD |title=From Hunters to Farmers: The Causes and Consequences of Food Production in Africa |last2=Brandt |first2=SA |publisher=University of California Press |year=1984 |isbn=978-0520045743 |pages=180 |language=English}}</ref><ref>{{cite journal |vauthors=Diamond J, Bellwood P |date=April 2003 |title=Farmers and their languages: the first expansions |journal=Science |volume=300 |issue=5619 |pages=597–603 |bibcode=2003Sci...300..597D |doi=10.1126/science.1078208 |pmid=12714734 |s2cid=13350469}}</ref> Others argue that the first speakers of Proto-Afroasiatic were based in Northeast Africa because that region includes the majority of the diversity of the Afroasiatic language family and has very diverse groups in close geographic proximity, which is sometimes considered a telltale sign for a linguistic geographic origin.<ref>{{Cite book |last=Campbell |first=Lyle |title=Historical Linguistics, Fourth Edition |publisher=The MIT Press |year=2021 |isbn=978-0262542180 |pages=399–400 |language=English}}</ref> A subset of the Proto-Afroasiatic population would have migrated to the [[Place:Levant|Levant]] during the late [[Earth:Paleolithic|Paleolithic]], merging with local West-Eurasians and resulting in a population which would later give rise to Natufian culture, associated with the early development of [[Earth:Agriculture|agriculture]] and early Afroasiatic languages, or specifically pre-[[Social:Proto-Semitic language|proto-Semitic]].<ref>{{Cite book |last1=Jarvie |title=Transition to Modernity: Essays on Power, Wealth and Belief |last2=Hall |publisher=Cambridge University Press |year=2005 |isbn=9780521022279 |pages=27 |language=English}}</ref><ref>{{Cite book |last=Shirai |first=Noriyuki |url=http://worldcat.org/oclc/852516752 |title=The archaeology of the first farmer-herders in Egypt: new insights into the Fayum Epipalaeolithic and Neolithic |date=2010 |publisher=Leiden University Press |isbn=978-90-485-1269-0 |oclc=852516752}}</ref>{{Page needed|date=March 2022}}<ref name="Early back-to-Africa migration into">{{cite journal |vauthors=Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL |date=June 2014 |title=Early back-to-Africa migration into the Horn of Africa |journal=PLOS Genetics |volume=10 |issue=6 |pages=e1004393 |doi=10.1371/journal.pgen.1004393 |pmc=4055572 |pmid=24921250 |doi-access=free }}</ref><ref>{{Cite book |last=Blench |first=Roger |title=Archaeology, Language, and the African Past |publisher=AltaMira Press |year=2006 |isbn=978-0759104662 |pages=150–163 |language=English}}</ref><ref name=":4">{{Cite journal |last=Ehret |first=Christopher |date=1979 |title=On the Antiquity of Agriculture in Ethiopia |url=https://www.jstor.org/stable/181512 |journal=The Journal of African History |volume=20 |issue=2 |pages=161–177 |doi=10.1017/S002185370001700X |jstor=181512 |s2cid=162986221 |via=JSTOR}}</ref><ref>{{Cite book |last=Nöth |first=Winfried |title=Origins of Semiosis: Sign Evolution in Nature and Culture |publisher=De Gruyter Mouton |year=2011 |isbn=9781134816231 |pages=293 |language=English}}</ref> In addition, [[Biology:Human Y-chromosome DNA haplogroup|Y-haplogroup]] sub-lineage [[Biology:Haplogroup E-M215 (Y-DNA)|E-M215]] (also known as "E1b1b) and its derivative E-M35 are quite common among Afroasiatic speakers, and southwestern Ethiopia is a plausible source of these haplogroups.<ref name=":1">{{Cite journal |last=Shriner |first=Daniel |date=2018 |title=Re-analysis of Whole Genome Sequence Data From 279 Ancient Eurasians Reveals Substantial Ancestral Heterogeneity |journal=Frontiers in Genetics |volume=9 |page=268 |doi=10.3389/fgene.2018.00268 |issn=1664-8021 |pmc=6062619 |pmid=30079081 |quote=and a sub-Saharan African component in Natufians that localizes to present-day southern Ethiopia. |doi-access=free}}</ref> The linguistic group and carriers of this lineage would have arisen and dispersed together from Northeast Africa in the Mesolithic, plausibly having already developed [[Social:Subsistence pattern|subsistence pattern]]s of pastoralism and intensive plant usage and collection.<ref>{{Cite journal |last1=Underhill |first1=P. A. |last2=Passarino |first2=G. |last3=Lin |first3=A. A. |last4=Shen |first4=P. |last5=Mirazón Lahr |first5=M. |last6=Foley |first6=R. A. |last7=Oefner |first7=P. J. |last8=Cavalli-Sforza |first8=L. L. |date=January 2001 |title=The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations |journal=Annals of Human Genetics |volume=65 |issue=Pt 1 |pages=43–62 |doi=10.1046/j.1469-1809.2001.6510043.x |issn=0003-4800 |pmid=11415522 |s2cid=9441236 |doi-access=free}}</ref><ref>{{Cite journal |last=Ibrahim |first=Muntaser E. |date=2021-04-26 |title=Genetic diversity of the Sudanese: insights on origin and implications for health |journal=Human Molecular Genetics |volume=30 |issue=R1 |pages=R37–R41 |doi=10.1093/hmg/ddab028 |issn=1460-2083 |pmc=8223596 |pmid=33864377}}</ref><ref>{{Cite journal |last1=Ehret |first1=Christopher |last2=Keita |first2=S. O. Y. |last3=Newman |first3=Paul |date=2004-12-03 |title=The origins of Afroasiatic |journal=Science |volume=306 |issue=5702 |pages=1680; author reply 1680 |doi=10.1126/science.306.5702.1680c |issn=1095-9203 |pmid=15576591 |s2cid=8057990}}</ref><ref>{{Cite journal |last=Ehret |first=Christopher |date=1979 |title=On the Antiquity of Agriculture in Ethiopia |journal=The Journal of African History |volume=20 |issue=2 |pages=161–177 |doi=10.1017/S002185370001700X |issn=0021-8537 |jstor=181512 |s2cid=162986221}}</ref> According to historian and linguist Christopher Ehret, the form of intensive plant collection practiced by the Proto-Afroasiatic population in Northeast Africa may have been a precursor to the agricultural practices that would later independently develop in the [[Place:Fertile Crescent|Fertile Crescent]] and the Horn of Africa.<ref name=":4" /><ref>{{Citation |last1=Bultosa |first1=G. |title=TEFF |date=2004-01-01 |url=https://www.sciencedirect.com/science/article/pii/B0127654909001725 |encyclopedia=Encyclopedia of Grain Science |pages=281–290 |editor-last=Wrigley |editor-first=Colin |access-date=2022-03-29 |place=Oxford |publisher=Elsevier |language=en |doi=10.1016/b0-12-765490-9/00172-5 |isbn=978-0-12-765490-4 |last2=Taylor |first2=J. R. N.}}</ref><ref>{{Cite journal |last1=Schlebusch |first1=Carina M. |last2=Jakobsson |first2=Mattias |date=2018-08-31 |title=Tales of Human Migration, Admixture, and Selection in Africa |journal=Annual Review of Genomics and Human Genetics |volume=19 |pages=405–428 |doi=10.1146/annurev-genom-083117-021759 |issn=1545-293X |pmid=29727585 |s2cid=19155657|doi-access=free }}</ref> 

[[File:E of Y-DNA migrations.png|thumb|Proposed migration routes of paternal lineage E.]]

====Horn of Africa====

While many studies conducted on Horn of Africa populations estimate a West-Eurasian admixture event around 3,000 years ago,<ref name=":0" /><ref name="Ramsay" /><ref name=":3" /><ref>{{Cite journal |last1=Molinaro |first1=Ludovica |last2=Montinaro |first2=Francesco |last3=Yelmen |first3=Burak |last4=Marnetto |first4=Davide |last5=Behar |first5=Doron M. |last6=Kivisild |first6=Toomas |last7=Pagani |first7=Luca |date=2019-12-11 |title=West Asian sources of the Eurasian component in Ethiopians: a reassessment |journal=Scientific Reports |language=en |volume=9 |issue=1 |pages=18811 |doi=10.1038/s41598-019-55344-y |pmid=31827175 |pmc=6906521 |bibcode=2019NatSR...918811M |issn=2045-2322}}</ref> Hodgson et al. (2014) found a distinct West-Eurasian ancestral component among studied Afroasiatic-speaking groups in the Horn of Africa (and to a lesser extent in North Africa and [[Place:Western Asia|West Asia]]), most prevalent among the Somali. This ancestral component dubbed "Ethio-Somali" is most closely related to the "Maghrebi" (peaking in Tunisians) component and is believed to have diverged from other non-African ancestries around 23,000 years ago, and migrated back to Africa prior to developing agriculture (12–23 ka) from the Near East. This population would have crossed via the Sinai Peninsula and then split into two, with one branch continuing west across North Africa and the other heading south into the Horn of Africa. The authors propose that "Ethio-Somali" may have been a substantial ancestral component of the Proto-Afroasiatic-speaking population. Later migration from Arabia into the HOA beginning around 3 ka would explain the origin of the Ethiosemitic languages at this time.<ref name="Early back-to-Africa migration into" /> An [[Biology:Mitochondrial DNA|mtDNA]] analysis by Gandini et al. (2016) has produced additional evidence in support of a pre-agricultural back-migration from West-Eurasia into the [[Place:Horn of Africa|Horn of Africa]] with an estimated date of arrival into the Horn of Africa in the early [[Earth:Holocene|Holocene]], possibly as a result of [[Chemistry:Obsidian|obsidian]] exchange networks across the Red Sea.<ref>{{Cite journal |last1=Gandini |first1=Francesca |last2=Achilli |first2=Alessandro |last3=Pala |first3=Maria |last4=Bodner |first4=Martin |last5=Brandini |first5=Stefania |last6=Huber |first6=Gabriela |last7=Egyed |first7=Balazs |last8=Ferretti |first8=Luca |last9=Gómez-Carballa |first9=Alberto |last10=Salas |first10=Antonio |last11=Scozzari |first11=Rosaria |date=2016-05-05 |title=Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes |journal=Scientific Reports |language=en |volume=6 |issue=1 |pages=25472 |doi=10.1038/srep25472 |pmid=27146119 |pmc=4857117 |bibcode=2016NatSR...625472G |issn=2045-2322}}</ref> Hodgson et al. also confirmed the existence of an ancestral component indigenous to the Horn of Africa - "Ethiopic" or "Omotic" (Pagani et al.) - which is most prevalent among speakers of the [[Social:Omotic languages|Omotic]] branch of Afroasiatic in southwestern Ethiopia.<ref name="Early back-to-Africa migration into" /><ref name=":0" /> This lineage is associated with that of a 4,500 year-old fossil (Mota) found in a cave in southwestern Ethiopia, which has high genetic affinity to modern Ethiopian groups, especially the [[Biology:Endogamy|endogamous]] blacksmith [[Social:Caste|caste]] of the Omotic Aari people. Like Mota, Aari blacksmiths do not show evidence for admixture with West-Eurasians, demonstrating a degree of population continuity in this region for at least 4,500 years. In a comparative analysis of Mota's genome referencing modern populations, Gallego et al. (2016) concluded that the divergence of Omotic from other Afroasiatic languages may have resulted from the relative isolation of its speakers from external groups.<ref>{{Cite journal |date=2016-02-19 |title=Erratum for the Report "Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa" (previously titled "Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent") by M. Gallego Llorente, E. R. Jones, A. Eriksson, V. Siska, K. W. Arthur, J. W. Arthur, M. C. Curtis, J. T. Stock, M. Coltorti, P. Pieruccini, S. Stretton, F. Brock, T. Higham, Y. Park, M. Hofreiter, D. G. Bradley, J. Bhak, R. Pinhasi, A. Manica |journal=Science |volume=351 |issue=6275 |pages=aaf3945 |doi=10.1126/science.aaf3945 |issn=1095-9203 |pmid=26912899|doi-access=free }}</ref> In an analysis of 68 Ethiopian ethnic groups, Lopez et al. (2021) revealed that several groups belonging to the three AA classifications of Cushitic, Omotic and Semitic show high genetic similarity to each other on average. Furthermore, the Nilo-Saharan speakers in the southwest shared more recent ancestry with Bantu and Nilotics, in contrast Afro-Asiatic speakers in the northeast shared more recent ancestry with Egyptians and other West Eurasians. The data also supported widespread recent intermixing among various ethnic groups.<ref>{{Cite journal |last1=López |first1=Saioa |last2=Tarekegn |first2=Ayele |last3=Band |first3=Gavin |last4=van Dorp |first4=Lucy |last5=Bird |first5=Nancy |last6=Morris |first6=Sam |last7=Oljira |first7=Tamiru |last8=Mekonnen |first8=Ephrem |last9=Bekele |first9=Endashaw |last10=Blench |first10=Roger |last11=Thomas |first11=Mark G. |date=2021-06-11 |title=Evidence of the interplay of genetics and culture in Ethiopia |journal=Nature Communications |language=en |volume=12 |issue=1 |pages=3581 |doi=10.1038/s41467-021-23712-w |pmid=34117245 |pmc=8196081 |bibcode=2021NatCo..12.3581L |issn=2041-1723}}</ref> 

====Madagascar====
[[File:Austronesia with hypothetical greatest expansion extent (Blench, 2009) 01.png|thumb|Austronesian expansion, outgoing from Taiwan and the northern {{wipe|Philippines}}.]]

Specific East Asian-related ancestry is found among the Malagasy speakers of {{wipe|Madagascar}} at a medium frequency. The presence of this East Asian-related ancestry is mostly linked to the Austronesian peoples expansion from [[Place:Southeast Asia|Southeast Asia]].<ref>{{Cite journal |vauthors=Dewar RE, Wright HT |date=1993-12-01|title=The culture history of Madagascar |journal=Journal of World Prehistory |language=en |volume=7 |issue=4 |pages=417–466 |doi=10.1007/BF00997802 |hdl=2027.42/45256 |s2cid=21753825 |hdl-access=free}}</ref><ref>{{cite journal | vauthors = Burney DA, Burney LP, Godfrey LR, Jungers WL, Goodman SM, Wright HT, Jull AJ | title = A chronology for late prehistoric Madagascar | journal = Journal of Human Evolution | volume = 47 | issue = 1–2 | pages = 25–63 | date = 2004-07-01 | pmid = 15288523 | doi = 10.1016/j.jhevol.2004.05.005 }}</ref><ref>{{cite journal | vauthors = Pierron D, Razafindrazaka H, Pagani L, Ricaut FX, Antao T, Capredon M, Sambo C, Radimilahy C, Rakotoarisoa JA, Blench RM, Letellier T, Kivisild T | display-authors = 6 | title = Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 3 | pages = 936–941 | date = January 2014 | pmid = 24395773 | pmc = 3903192 | doi = 10.1073/pnas.1321860111 | doi-access = free | bibcode = 2014PNAS..111..936P }}</ref><ref name="Kusuma_2016">{{cite journal | vauthors = Kusuma P, Brucato N, Cox MP, Pierron D, Razafindrazaka H, Adelaar A, Sudoyo H, Letellier T, Ricaut FX | display-authors = 6 | title = Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy | journal = Scientific Reports | volume = 6 | issue = 1 | pages = 26066 | date = May 2016 | pmid = 27188237 | pmc = 4870696 | doi = 10.1038/srep26066 | bibcode = 2016NatSR...626066K }}</ref> The peoples of Borneo were identified to resemble the East Asian voyagers, who arrived on Madagascar. East Asian ancestry among Malagasy people was estimated at a mean average of 33%, but as high as ~75% among some Highlander groups and upper caste groups.<ref name="Heiske"/><ref>{{Cite web |last=Nicolas |first=Brucato |display-authors=0 |date=4 February 2019 |title=Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia |url=https://academic.oup.com/gbe/article/11/3/748/5306180 |website=Genome Biology and Evolution, Volume 11, Issue 3}}</ref><ref name="Kusuma_2016" />

====Northern Africa====

Dobon et al. (2015) identified an autosomal ancestral component that is commonly found among modern Afroasiatic-speaking populations (as well as Nubians) in Northeast Africa. This Coptic component peaks among [[Religion:Copts|Copts]] in Sudan, which is differentiated by its lack of Arab influence, but shares common ancestry with the North African/Middle Eastern populations. It appears alongside a component that defines [[Social:Nilo-Saharan languages|Nilo-Saharan]] speakers of southwestern Sudan and South Sudan.<ref>{{cite journal |display-authors=6 |vauthors=Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A, Wijmenga C, Tahir H, Comas D, Netea MG, Bertranpetit J |date=May 2015 |title=The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape |journal=Scientific Reports |volume=5 |pages=9996 |bibcode=2015NatSR...5E9996D |doi=10.1038/srep09996 |pmc=4446898 |pmid=26017457}}</ref> Arauna et al. (2017), analyzing existing genetic data obtained from [[Place:North Africa|Northern African]] populations, such as Berbers, described them as a mosaic of North African (Taforalt), Middle Eastern, European (Early European Farmers), and [[Place:Sub-Saharan Africa|Sub-Saharan Africa]]n-related ancestries.<ref>{{Citation |title=Genetic Heterogeneity between Berbers and Arabs |date=2017 |work=eLS |pages=1–7 |publisher=John Wiley & Sons, Ltd |language=en |doi=10.1002/9780470015902.a0027485 |isbn=978-0-470-01590-2 |vauthors=Arauna LR, Comas D}}</ref>

Chen et al. (2020) analyzed 2,504 African samples from all over Africa, and found archaic Neanderthal ancestry, among all tested African samples at low frequency. They also identified a European-related (West-Eurasian) ancestry segment, which seems to largely correspond with the detected Neanderthal ancestry components. European-related admixture among Africans was estimated to be between ~0% to up to ~30%, with a peak among Northern Africans.<ref name="Identifying and Interpreting Appare" /> According to Chen et al. (2020), "These data are consistent with the hypothesis that back-migration contributed to the signal of Neanderthal ancestry in Africans. Furthermore, the data indicates that this back-migration came after the split of Europeans and East Asians, from a population related to the European lineage."<ref name="Identifying and Interpreting Appare" />

There is a minor geneflow from North Africa in parts of [[Place:Southern Europe|Southern Europe]], this is supported by the presence of an African-specific mitochondrial haplogroup among one of four 4,000 year old samples.<ref>{{Cite journal |last1=González-Fortes |first1=G. |last2=Tassi |first2=F. |last3=Trucchi |first3=E. |last4=Henneberger |first4=K. |last5=Paijmans |first5=J. L. A. |last6=Díez-del-Molino |first6=D. |last7=Schroeder |first7=H. |last8=Susca |first8=R. R. |last9=Barroso-Ruíz |first9=C. |last10=Bermudez |first10=F. J. |last11=Barroso-Medina |first11=C. |last12=Bettencourt |first12=A. M. S. |last13=Sampaio |first13=H. A. |last14=Grandal-d'Anglade |first14=A. |last15=Salas |first15=A. |date=2019-01-30 |title=A western route of prehistoric human migration from Africa into the Iberian Peninsula |journal=Proceedings of the Royal Society B: Biological Sciences |volume=286 |issue=1895 |pages=20182288 |doi=10.1098/rspb.2018.2288 |issn=0962-8452 |pmc=6364581 |pmid=30963949}}</ref> Multiple studies found also evidence for geneflow of African ancestry towards Eurasia, specifically Europe and the Middle East. The analysis of 40 different West-Eurasian populations found African admixture at a frequency of 0% to up to ~15%.<ref>{{Cite journal |last1=Moorjani |first1=Priya |last2=Patterson |first2=Nick |last3=Hirschhorn |first3=Joel N. |last4=Keinan |first4=Alon |last5=Hao |first5=Li |last6=Atzmon |first6=Gil |last7=Burns |first7=Edward |last8=Ostrer |first8=Harry |last9=Price |first9=Alkes L. |last10=Reich |first10=David |date=April 2011 |title=The history of African gene flow into Southern Europeans, Levantines, and Jews |journal=PLOS Genetics |volume=7 |issue=4 |pages=e1001373 |doi=10.1371/journal.pgen.1001373 |issn=1553-7404 |pmc=3080861 |pmid=21533020 |doi-access=free}}</ref><ref>{{Cite journal |last1=Botigué |first1=Laura R. |last2=Henn |first2=Brenna M. |last3=Gravel |first3=Simon |last4=Maples |first4=Brian K. |last5=Gignoux |first5=Christopher R. |last6=Corona |first6=Erik |last7=Atzmon |first7=Gil |last8=Burns |first8=Edward |last9=Ostrer |first9=Harry |last10=Flores |first10=Carlos |last11=Bertranpetit |first11=Jaume |date=2013-07-16 |title=Gene flow from North Africa contributes to differential human genetic diversity in southern Europe |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=110 |issue=29 |pages=11791–11796 |bibcode=2013PNAS..11011791B |doi=10.1073/pnas.1306223110 |issn=0027-8424 |pmc=3718088 |pmid=23733930 |doi-access=free}}</ref><ref>{{Cite journal |last1=Auton |first1=Adam |last2=Bryc |first2=Katarzyna |last3=Boyko |first3=Adam R. |last4=Lohmueller |first4=Kirk E. |last5=Novembre |first5=John |last6=Reynolds |first6=Andy |last7=Indap |first7=Amit |last8=Wright |first8=Mark H. |last9=Degenhardt |first9=Jeremiah D. |last10=Gutenkunst |first10=Ryan N. |last11=King |first11=Karen S. |date=May 2009 |title=Global distribution of genomic diversity underscores rich complex history of continental human populations |journal=Genome Research |volume=19 |issue=5 |pages=795–803 |doi=10.1101/gr.088898.108 |issn=1088-9051 |pmc=2675968 |pmid=19218534}}</ref><ref>{{Cite journal |last1=Reich |first1=David |last2=Price |first2=Alkes L. |last3=Patterson |first3=Nick |date=May 2008 |title=Principal component analysis of genetic data |url=https://www.nature.com/articles/ng0508-491 |journal=Nature Genetics |language=en |volume=40 |issue=5 |pages=491–492 |doi=10.1038/ng0508-491 |issn=1546-1718 |pmid=18443580 |s2cid=34837532}}</ref>

====Western Africa====

Hollfelder et al. (2021) concluded that West African Yoruba people, which were previously used as "unadmixed reference population" for indigenous Africans, harbor minor levels of Neanderthal ancestry, which can be largely associated with back-migration of an "Ancestral European-like" source population.<ref name="The deep population history in Afri" /> 

A genome-wide study of a Fulani community from Burkina Faso inferred two major admixture events in this group, dating to ~1800 ya, and 300 ya. The first admixture event took place between the West African ancestors of the Fula and ancestral North African nomadic groups. The second admixture event, relatively recent, inferred a source from Southwestern Europe, or suggests either an additional gene flow between the Fulani and Northern African groups, who carry admixture proportions from Europeans.<ref>{{Cite journal |last1=Černý |first1=Viktor |last2=Fortes-Lima |first2=Cesar |last3=Tříska |first3=Petr |date=2021-04-26 |title=Demographic history and admixture dynamics in African Sahelian populations |journal=Human Molecular Genetics |volume=30 |issue=R1 |pages=R29–R36 |doi=10.1093/hmg/ddaa239 |issn=1460-2083 |pmid=33105478 |doi-access=free}}</ref> Sahelian populations like the Toubou also showed admixture coming from Eurasians.<ref name="Chad Genetic Diversity Reveals an A">{{cite journal |last1=Haber |first1=Marc |last2=Mezzavilla |first2=Massimo |last3=Bergström |first3=Anders |last4=Prado-Martinez |first4=Javier |last5=Hallast |first5=Pille |last6=Saif-Ali |first6=Riyadh |last7=Al-Habori |first7=Molham |last8=Dedoussis |first8=George |last9=Zeggini |first9=Eleftheria |last10=Blue-Smith |first10=Jason |last11=Wells |first11=R. Spencer |last12=Xue |first12=Yali |last13=Zalloua |first13=Pierre A. |last14=Tyler-Smith |first14=Chris |date=December 2016 |title=Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations |url=https://www.cell.com/ajhg/pdf/S0002-9297(16)30448-7.pdf |journal=The American Journal of Human Genetics |volume=99 |issue=6 |pages=1316–1324 |doi=10.1016/j.ajhg.2016.10.012 |pmc=5142112 |pmid=27889059 |s2cid=38169172}}</ref>

====Southern Africa====

Low levels of West Eurasian ancestry (European or Middle Eastern) are found in Khoe–Kwadi Khoesan-speakers. It could have been acquired indirectly by admixture with migrating pastoralists from East Africa. This hypothesis of gene flow from eastern to southern Africa is further supported by other genetic and archaeological data documenting the spread of pastoralism from East to South Africa.<ref>{{Cite journal |last1=Campbell |first1=Michael C |last2=Hirbo |first2=Jibril B |last3=Townsend |first3=Jeffrey P |last4=Tishkoff |first4=Sarah A |date=2014-12-01 |title=The peopling of the African continent and the diaspora into the new world |journal=Current Opinion in Genetics & Development |volume=29 |pages=120–132 |doi=10.1016/j.gde.2014.09.003 |issn=0959-437X |pmc=4308437 |pmid=25461616}}</ref>

==Regional genomic overview==

===North Africa===
{{Main|Biology:Genetic history of North Africa}}

====Archaic Human DNA====

While [[History:Denisovan|Denisovan]] and [[Biology:Neanderthal|Neanderthal]] ancestry in non-Africans outside of Africa are more certain, archaic human ancestry in Africans is less certain and is too early to be established with certainty.<ref name="Bergström">{{cite journal | vauthors = Bergström A, Stringer C, Hajdinjak M, Scerri EM, Skoglund P | title = Origins of modern human ancestry | journal = Nature | volume = 590 | issue = 7845 | pages = 229–237 | date = February 2021 | pmid = 33568824 | doi = 10.1038/s41586-021-03244-5 | s2cid = 231883210 | bibcode = 2021Natur.590..229B }}</ref>

====Ancient DNA====
Daniel Shriner (2018), using modern populations as a reference, showed that the Natufians carried 61.2% Arabian, 21.2% Northern African, 10.9% Western Asian, and a small portion of Eastern African ancestry at 6.8%, which is associated with the modern Omotic-speaking groups found in southern Ethiopia.<ref name=":1" />

=====Egypt=====

Khnum-aa, Khnum-Nakht, Nakht-Ankh and JK2911 carried maternal [[Biology:Haplogroup M (mtDNA)#Haplogroup M1|haplogroup M1a1]].<ref name="Gad" /><ref name=":0">{{Cite journal |last1=Schuenemann |first1=Verena J. |last2=Peltzer |first2=Alexander |last3=Welte |first3=Beatrix |last4=van Pelt |first4=W. Paul |last5=Molak |first5=Martyna |last6=Wang |first6=Chuan-Chao |last7=Furtwängler |first7=Anja |last8=Urban |first8=Christian |last9=Reiter |first9=Ella |last10=Nieselt |first10=Kay |last11=Teßmann |first11=Barbara |date=2017-05-30 |title=Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods |journal=Nature Communications |volume=8 |issue=1 |page=15694 |doi=10.1038/ncomms15694 |pmid=28556824 |issn=2041-1723 |doi-access=free |bibcode=2017NatCo...815694S |pmc=5459999}}</ref>

Djehutynakht (10A) carried maternal haplogroup [[Biology:Haplogroup U (mtDNA)#Haplogroup U5|U5b2b5]].<ref name="Loreille 135">{{Cite journal |last1=Loreille |first1=Odile |last2=Ratnayake |first2=Shashikala |last3=Bazinet |first3=Adam L. |last4=Stockwell |first4=Timothy B. |last5=Sommer |first5=Daniel D. |last6=Rohland |first6=Nadin |last7=Mallick |first7=Swapan |last8=Johnson |first8=Philip L. F. |last9=Skoglund |first9=Pontus |last10=Onorato |first10=Anthony J. |last11=Bergman |first11=Nicholas H. |date=March 2018 |title=Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens |journal=Genes |volume=9 |issue=3 |pages=135 |doi=10.3390/genes9030135 |pmid=29494531 |pmc=5867856 |doi-access=free}}</ref> JK2888 carried maternal haplogroup [[Biology:Haplogroup U (mtDNA)|U6a2]].<ref name=":0" />

Thuya, Tiye, Tutankhamen's mother, and Tutankhamen carried the maternal [[Biology:Haplogroup K (mtDNA)|haplogroup K]].<ref name="Gad" />

JK2134 carried maternal haplogroup [[Biology:Haplogroup J (mtDNA)|J1d]]<ref name=":0" /> and JK2887 carried maternal haplogroup [[Biology:Haplogroup J (mtDNA)|J2a1a1]].<ref name=":0" />

Amenhotep III, [[Biography:Akhenaten|Akhenaten]], and Tutankhamen carried the paternal [[Biology:Haplogroup R1b|haplogroup R1b]].<ref name="Gad">{{cite journal |vauthors=Gad YZ, Hassan NA, Mousa DM, Fouad FA, El-Sayed SG, Abdelazeem MA, Mahdy SM, Othman HY, Ibrahim DW, Khairat R, Ismail S |display-authors=6 |title=Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship |journal=Human Molecular Genetics |volume=30 |issue=R1 |pages=R24–R28 |date=April 2021 |pmid=33059357 |doi=10.1093/hmg/ddaa223 |doi-access=free}}</ref>

Ramesses III and "Unknown Man E", possibly Pentawere, carried paternal haplogroup E1b1a.<ref name="Gad" /><ref name="Hawass">{{cite journal |vauthors=Hawass Z, Ismail S, Selim A, Saleem SN, Fathalla D, Wasef S, Gad AZ, Saad R, Fares S, Amer H, Gostner P, Gad YZ, Pusch CM, Zink AR |display-authors=6 |title=Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study |journal=BMJ |volume=345 |pages=e8268 |date=December 2012 |pmid=23247979 |doi=10.1136/bmj.e8268 |hdl-access=free |s2cid=206896841 |hdl=10072/62081}}</ref><ref name="Gourdine">{{cite journal | vauthors = Gourdine JP, Keita S, Gourdine JL, Anselin A |title=Ancient Egyptian Genomes from northern Egypt: Further discussion |url=https://www.researchgate.net/publication/327065612 |journal=Nature Communications}}</ref>

JK2134 and JK2911 carried paternal haplogroup [[Biology:Haplogroup J (Y-DNA)|J]].<ref name=":0" />

Takabuti carried maternal haplogroup [[Biology:Haplogroup H (mtDNA)|H4a1]]<ref>{{Cite web |url=https://www.manchester.ac.uk/discover/news/shocking-truth-behind-takabutis-death-revealed/ |title=Shocking truth behind Takabuti's death revealed |language=en |access-date=2020-01-29}}</ref> and YM:KMM A 63 carried maternal haplogroup [[Biology:Haplogroup HV (mtDNA)|HV]].<ref name=":10">{{Cite journal |last1=Oras |first1=Ester |last2=Anderson |first2=Jaanika |last3=Tõrv |first3=Mari |last4=Vahur |first4=Signe |last5=Rammo |first5=Riina |last6=Remmer |first6=Sünne |last7=Mölder |first7=Maarja |last8=Malve |first8=Martin |last9=Saag |first9=Lehti |last10=Saage |first10=Ragnar |last11=Teearu-Ojakäär |first11=Anu |date=2020-01-16 |title=Multidisciplinary investigation of two Egyptian child mummies curated at the University of Tartu Art Museum, Estonia (Late/Graeco-Roman Periods) |journal=PLOS ONE |language=en |volume=15 |issue=1 |pages=e0227446 |doi=10.1371/journal.pone.0227446 |pmid=31945091 |pmc=6964855 |bibcode=2020PLoSO..1527446O |issn=1932-6203 |doi-access=free}}</ref>

OM:KMM A 64 carried maternal haplogroup [[Biology:Haplogroup T (mtDNA)|T2c1a]].<ref name=":10" />

JK2888 carried paternal haplogroup [[Biology:Haplogroup E-M215 (Y-DNA)|E1b1b1a1b2]].<ref name=":0" />

=====Libya=====

At [[History:Takarkori|Takarkori]] rockshelter, in [[Place:Libya|Libya]], two naturally mummified women, dated to the Middle Pastoral Period (7000 BP), carried [[Biology:Basal (phylogenetics)|basal]] maternal [[Biology:Haplogroup N (mtDNA)|haplogroup N]].<ref name="Vai">{{cite journal | vauthors = Vai S, Sarno S, Lari M, Luiselli D, Manzi G, Gallinaro M, Mataich S, Hübner A, Modi A, Pilli E, Tafuri MA, Caramelli D, di Lernia S | display-authors = 6 | title = Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara | journal = Scientific Reports | volume = 9 | issue = 1 | pages = 3530 | date = March 2019 | pmid = 30837540 | pmc = 6401177 | doi = 10.1038/s41598-019-39802-1 | bibcode = 2019NatSR...9.3530V }}</ref>

=====Morocco=====

Van de Loorsdrecht et al. (2018)  found that of seven samples of Taforalts of Morocco, radiocarbon dated to between 15,100 cal BP and 13,900 cal BP, six were found to carry maternal haplogroup [[Biology:Haplogroup U (mtDNA)|U6a]], and one was found to carry maternal haplogroup [[Biology:Haplogroup M (mtDNA)|M1b]]. Six of six males were found to carry paternal haplogroup [[Biology:Haplogroup E-M215 (Y-DNA)|E1b1b]]. They were found to harbor 63.5% Natufian-related ancestry and 36.5% Sub-Saharan African-related ancestry. The Sub-Saharan component is most strongly drawn out by modern West African groups such as the Yoruba and the Mende. The samples also contain an additional affinity to South, Central, and East African outgroups that cannot be explained by any known ancient or modern populations.<ref name="Van De Loosdrecht">{{cite journal | vauthors = van de Loosdrecht M, Bouzouggar A, Humphrey L, Posth C, Barton N, Aximu-Petri A, Nickel B, Nagel S, Talbi EH, El Hajraoui MA, Amzazi S, Hublin JJ, Pääbo S, Schiffels S, Meyer M, Haak W, Jeong C, Krause J | display-authors = 6 | title = Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations | journal = Science | volume = 360 | issue = 6388 | pages = 548–552 | date = May 2018 | pmid = 29545507 | doi = 10.1126/science.aar8380 | s2cid = 206666517 | doi-access = free | bibcode = 2018Sci...360..548V }}</ref> When projected onto a principal component analysis graph of African and west Eurasian populations, the Taforalt individuals form a distinct cluster in an intermediate position between modern North Africans (e.g., Berbers, Mozabites, Saharawis) and East Africans (e.g., Afars, Oromos, Somalis).<ref name="Van De Loosdrecht"/> Jeong (2020), comparing the Taforalt people of the Iberomaurusian culture to modern populations, found that the Taforalt's Sub-Saharan African genetic component may be best represented by modern West Africans (e.g., Yoruba).<ref name="Jeong" />

====Y-Chromosomal DNA====

====Mitochondrial DNA====

Amid the [[Earth:Holocene|Holocene]], including the Holocene Climate Optimum in 8000 BP, Africans bearing haplogroup L2 spread within West Africa and Africans bearing haplogroup L3 spread within East Africa.<ref name="Sá" /> As the largest migration since the Out of Africa migration, migration from Sub-Saharan Africa toward the North Africa occurred, by West Africans, Central Africans, and East Africans, resulting in migrations into [[Earth:Europe|Europe]] and [[Earth:Asia|Asia]]; consequently, Sub-Saharan African mitochondrial DNA was introduced into Europe and Asia.<ref name="Sá" /> During the early period of the [[Earth:Holocene|Holocene]], 50% of [[Biology:Macro-haplogroup L (mtDNA)|Sub-Saharan African mitochondrial DNA]] was introduced into [[Place:North Africa|North Africa]] by [[Place:West Africa#Demographics and languages|West Africans]] and the other 50% was introduced by [[Place:East Africa#Demographics|East Africans]].<ref name="Sá" /> During the modern period, a greater number of West Africans introduced Sub-Saharan African mitochondrial DNA into North Africa than East Africans.<ref name="Sá" />

Mitochondrial haplogroups L3, M, and N are found among Sudanese peoples (e.g., Beja, Nilotics, Nuba, Nubians), who have no known interaction (e.g., history of migration/admixture) with Europeans or Asians; rather than having developed in a post-Out-of-Africa migration context, mitochondrial macrohaplogroup L3/M/N and its subsequent development into distinct mitochondrial haplogroups (e.g., [[Biology:Haplogroup L3|Haplogroup L3]], [[Biology:Haplogroup M (mtDNA)|Haplogroup M]], [[Biology:Haplogroup N (mtDNA)|Haplogroup N]]) may have occurred in [[Place:East Africa|East Africa]] at a time that considerably predates the Out-of-Africa migration event of 50,000 BP.<ref name="Osman">{{cite journal |vauthors=Osman MM, Hassan HY, Elnour MA, Makkan H, Gebremeskel EI, Gais T, Koko ME, Soodyall H, Ibrahim ME |display-authors=6 |title=Mitochondrial HVRI and whole mitogenome sequence variations portray similar scenarios on the genetic structure and ancestry of northeast Africans |url=http://81.95.108.158/return-files/Mitochondrial%20HVRI.pdf |journal=Meta Gene |access-date=2021-05-12 |archive-date=2021-06-25 |archive-url=https://web.archive.org/web/20210625003807/http://81.95.108.158/return-files/Mitochondrial%20HVRI.pdf |url-status=dead }}</ref>

====Autosomal DNA====

====Medical DNA====

The genomes of Africans commonly found to undergo [[Biology:Adaptation|adaptation]] are [[Biology:Regulation of gene expression|regulatory DNA]], and many cases of adaptation found among Africans relate to [[Biology:Nutritional epigenetics|diet]], [[Biology:Physiology|physiology]], and [[Biology:Evolutionary pressure|evolutionary pressure]]s from pathogens.<ref name="Pfennig" />

=====Lactase Persistence=====

[[History:Neolithic|Neolithic]] agriculturalists, who may have resided in [[Place:Northeast Africa|Northeast Africa]] and the [[Place:Near East|Near East]], may have been the source population for [[Biology:Lactase persistence|lactase persistence]] variants, including –13910*T, and may have been subsequently supplanted by later migrations of peoples.<ref name="Priehodová">{{cite journal |vauthors=Priehodová E, Austerlitz F, Čížková M, Nováčková J, Ricaut FX, Hofmanová Z, Schlebusch CM, Černý V | display-authors = 6 | title = Sahelian pastoralism from the perspective of variants associated with lactase persistence | journal = American Journal of Physical Anthropology | volume = 173 | issue = 3 | pages = 423–436 | date = November 2020 | pmid = 32812238 | doi = 10.1002/ajpa.24116 | s2cid = 221179656 | url = https://hal.archives-ouvertes.fr/hal-02919786/file/ajpa_ms_final.pdf }}</ref> The Sub-Saharan West African Fulani, the North African Tuareg, and European agriculturalists, who are descendants of these Neolithic agriculturalists, share the lactase persistence variant –13910*T.<ref name="Priehodová" /> While shared by Fulani and Tuareg herders, compared to the Tuareg variant, the Fulani variant of –13910*T has undergone a longer period of haplotype differentiation.<ref name="Priehodová" /> The Fulani lactase persistence variant –13910*T may have spread, along with cattle pastoralism, between 9686 BP and 7534 BP, possibly around 8500 BP; corroborating this timeframe for the Fulani, by at least 7500 BP, there is evidence of herders engaging in the act of milking in the Central Sahara.<ref name="Priehodová" />

===West Africa===
{{Main|Biology:Genetic history of West Africa}}
{{Further|Biology:Genetic history of the African diaspora}}

====Archaic Human DNA====

Archaic traits found in human fossils of [[Place:West Africa|West Africa]] (e.g., Iho Eleru fossils, which dates to 13,000 BP) and [[Place:Central Africa|Central Africa]] (e.g., Ishango fossils, which dates between 25,000 BP and 20,000 BP) may have developed as a result of admixture between archaic humans and modern humans or may be evidence of late-persisting early modern humans.<ref name="Bergström"/> While [[History:Denisovan|Denisovan]] and [[Biology:Neanderthal|Neanderthal]] ancestry in non-Africans outside of Africa are more certain, archaic human ancestry in Africans is less certain and is too early to be established with certainty.<ref name="Bergström" />

====Ancient DNA====

As of 2017, human ancient DNA has not been found in the region of [[Place:West Africa|West Africa]].<ref name="Scerri">{{cite book |last1=Scerri |first1=Eleanor |title=Oxford Research Encyclopedia of African History |chapter=The Stone Age Archaeology of West Africa |date=26 October 2017 |publisher=Oxford University Press |isbn=9780190277734 |page=1 |chapter-url=https://ora.ox.ac.uk/objects/uuid:1442d1c1-7f76-454d-97db-8fd52a4c6c1e/files/m02a1cd8d0c2ef8eb3ffee57a58c4b335 |doi=10.1093/acrefore/9780190277734.013.137 |oclc=1013546425 |s2cid=133758803}}</ref> As of 2020, human ancient DNA has not been forthcoming in the region of West Africa.<ref name="Jeong">{{cite book |last1=Jeong |first1=Choongwon |chapter=Current Trends in Ancient DNA Study: Beyond Human Migration in and Around Europe |title=The Handbook of Mummy Studies |chapter-url=https://link.springer.com/referenceworkentry/10.1007%2F978-981-15-1614-6_10-1 |year=2020 |pages=1–16 |publisher=Springer |doi=10.1007/978-981-15-1614-6_10-1 |isbn=978-981-15-1614-6 |oclc=1182512815 |s2cid=226555687}}</ref>

====Y-Chromosomal DNA====

Eight male individuals from Guinea Bissau, two male individuals from Niger, one male individual from Mali, and one male individual from Cabo Verde carried [[Biology:Haplogroup A (Y-DNA)#A1a (A-M31)|haplogroup A1a]].<ref name="Batini">{{cite journal |last1=Batini |first1=Chiara |display-authors=0 |title=Supplementary Data: Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages |journal=Molecular Biology and Evolution |date=September 2011 |volume=28 |issue=9 |pages=2603–2613 |doi=10.1093/molbev/msr089 |pmid=21478374 |url=https://academic.oup.com/mbe/article/28/9/2603/1011779#supplementary-data |issn=0737-4038 |oclc=748733133 |s2cid=11190055|doi-access=free |hdl=10400.13/4486 |hdl-access=free }}</ref>

As a result of haplogroup D0, a basal branch of haplogroup DE, being found in three Nigerian men, it may be the case that [[Biology:Haplogroup DE|haplogroup DE]], as well as its sublineages D0 and E, originated in [[Earth:Africa|Africa]].<ref name="Haber">{{cite journal |last1=Haber |first1=Marc |display-authors=0 |title=A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa |journal=Genetics |volume=212 |issue=4 |pages=1421–1428 |date=August 2019 |pmid=31196864 |pmc=6707464 |doi=10.1534/genetics.119.302368 |issn=0016-6731 |oclc=8291848146 |s2cid=189817793}}</ref>

As of 19,000 years ago, Africans, bearing [[Biology:Haplogroup E-V38|haplogroup E1b1a-V38]], likely traversed across the Sahara, from [[Place:East Africa|east]] to [[Place:West Africa|west]].<ref name="Shriner">{{cite journal |last1=Shriner |first1=Daniel |last2=Rotimi |first2=Charles N. |title=Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase |journal=American Journal of Human Genetics |volume=102 |issue=4 |pages=547–556 |date=April 2018 |pmid=29526279 |pmc=5985360 |issn=0002-9297 |oclc=7353789016 |doi=10.1016/j.ajhg.2018.02.003}}</ref> [[Biology:Haplogroup E-M2|E1b1a1-M2]] likely originated in [[Place:West Africa|West Africa]] or [[Place:Central Africa|Central Africa]].<ref name="Trombetta">{{cite journal |last1=Trombetta |first1=Beniamino |display-authors=0 |title=Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent |journal=Genome Biology and Evolution |volume=7 |issue=7 |pages=1940–1950 |date=June 2015 |pmid=26108492 |pmc=4524485 |issn=0016-6731 |oclc=8291848146 |doi=10.1093/gbe/evv118}}</ref>

====Mitochondrial DNA====
{{Further|Biology:Haplogroup L2 (mtDNA)}}

Around 18,000 BP, Mende people, along with Gambian peoples, grew in population size.<ref name="Miller">{{cite journal |last1=Miller |first1=Eleanor F. |display-authors=0 |title=Global demographic history of human populations inferred from whole mitochondrial genomes |journal=Royal Society Open Science |volume=5 |issue=8 |pages=180543 |date=August 2018 |pmid=30225046 |pmc=6124094 |doi=10.1098/rsos.180543 |bibcode=2018RSOS....580543M |oclc=8582185081 |s2cid=52289534}}</ref>

In 15,000 BP, Niger-Congo speakers may have migrated from the Sahelian region of West Africa, along the Senegal River, and introduced [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a1|L2a1]] into [[Place:North Africa|North Africa]], resulting in modern Mauritanian peoples and Berbers of Tunisia inheriting it.<ref name="Frigi">{{cite journal |last1=Frigi |first1=Sabeh |display-authors=0 |title=Ancient local evolution of African mtDNA haplogroups in Tunisian Berber populations |url=https://www.researchgate.net/publication/47810347 |journal=Human Biology |volume=82 |issue=4 |pages=367–384 |date=August 2010 |pmid=21082907 |doi=10.3378/027.082.0402 |jstor=41466688 |issn=0018-7143 |oclc=4668535228 |s2cid=27594333}}</ref>

Between 11,000 BP and 10,000 BP, Yoruba people and Esan people grew in population size.<ref name="Miller" />

As early as 11,000 years ago, Sub-Saharan West Africans, bearing [[Biology:Macro-haplogroup L (mtDNA)|macrohaplogroup L]] (e.g., [[Biology:Haplogroup L1 (mtDNA)#L1b|L1b1a11]], L1b1a6a, L1b1a8, L1b1a9a1, [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a1|L2a1k]], [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3d1b1a]]), may have migrated through [[Place:North Africa|North Africa]] and into [[Earth:Europe|Europe]], mostly into [[Place:Southern Europe|southern Europe]] (e.g., Iberia).<ref name="Soares">{{cite journal |last1=Podgorná |first1=Eliška |display-authors=0 |title=The genetic impact of the lake chad basin population in North Africa as documented by mitochondrial diversity and internal variation of the L3e5 haplogroup |url=https://onlinelibrary.wiley.com/doi/abs/10.1111/ahg.12040 |journal=Annals of Human Genetics |volume=77 |issue=6 |pages=513–523 |date=November 2013 |pmid=25069842 |doi=10.1111/ahg.12040 |issn=0003-4800 |oclc=6998015647 |s2cid=24672148}}</ref>

====Autosomal DNA====

During the early period of the [[Earth:Holocene|Holocene]], in 9000 BP, Khoisan-related peoples admixed with the ancestors of the Igbo people, possibly in the western Sahara.<ref name="Busby">{{cite journal |last1=Busby |first1=George BJ |display-authors=0 |title=Admixture into and within sub-Saharan Africa |journal=eLife |date=June 21, 2016 |volume=5 |page=e15266 |doi=10.7554/eLife.15266 |pmid=27324836 |pmc=4915815 |s2cid=6885967 |doi-access=free }}</ref><ref name="Gurdasani">{{cite journal |last1=Gurdasani |first1=Deepti |display-authors=0 |title=The African Genome Variation Project shapes medical genetics in Africa |journal=Nature |date=December 3, 2014 |volume=517 |issue=7534 |pages=327–332 |doi=10.1038/nature13997 |pmid=25470054 |issn=0028-0836 |pmc=4297536 |oclc=9018039409 |bibcode=2015Natur.517..327G |s2cid=4463627}}</ref>

Between 2000 BP and 1500 BP, Nilo-Saharan-speakers may have migrated across the [[Place:Sahel|Sahel]], from [[Place:East Africa|East Africa]] into [[Place:West Africa|West Africa]], and admixed with Niger-Congo-speaking Berom people.<ref name="Choudhury II">{{cite journal |last1=Choudhury |first1=Ananyo |display-authors=0 |title=High-depth African genomes inform human migration and health |journal=Nature |volume=586 |issue=7831 |pages=741–748 |date=October 2020 |pmid=33116287 |doi=10.1038/s41586-020-2859-7 |pmc=7759466 |bibcode=2020Natur.586..741C |issn=0028-0836 |oclc=8691160009 |s2cid=226039427}}</ref> In 710 CE, [[Place:West Africa|West Africa]]n-related populations (e.g., Niger-Congo-speaking Berom people, [[Social:Bantu languages|Bantu-speakers]]) and [[Place:East Africa|East Africa]]n-related populations (Nilo-Saharan-speaking Ethiopians, Nilo-Saharan-speaking Chadians) admixed with one another in northern Nigeria and northern Cameroon.<ref name="Bird">{{cite journal |last1=Bird |first1=Nancy |display-authors=0 |title=Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture |journal=Science Advances |date=March 29, 2023 |volume=9 |issue=13 |page=eabq2616 |doi=10.1126/sciadv.abq2616 |pmid=36989356 |pmc=10058250 |bibcode=2023SciA....9.2616B |issn=2375-2548 |oclc=9819554112 |s2cid=257834341}}</ref>

Fan et al. (2019) found that the Fulani people show genetic affinity to isolated [[Social:Afroasiatic languages|Afroasiatic-speaking]] groups in [[Place:East Africa|Eastern Africa]], specifically [[Social:Omotic languages|Omotic-speakers]] such as the Aari people. While the Fulani have nearly exclusive indigenous African ancestry (defined by West and East African ancestry), they also show traces of West-Eurasian-like admixture, supporting an ancestral homeland somewhere in North or Eastern Africa, and westwards expansion during the Neolithic, possibly caused by the arrival and expansion of West-Eurasian-related groups.<ref>{{Cite journal |last1=Fan |first1=Shaohua |last2=Kelly |first2=Derek E. |last3=Beltrame |first3=Marcia H. |last4=Hansen |first4=Matthew E. B. |last5=Mallick |first5=Swapan |last6=Ranciaro |first6=Alessia |last7=Hirbo |first7=Jibril |last8=Thompson |first8=Simon |last9=Beggs |first9=William |last10=Nyambo |first10=Thomas |last11=Omar |first11=Sabah A. |date=2019-04-26 |title=African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations |journal=Genome Biology |volume=20 |issue=1 |pages=82 |doi=10.1186/s13059-019-1679-2 |issn=1474-760X |pmc=6485071 |pmid=31023338 |doi-access=free }}</ref> Fan et al. (2023) found that the Fulani, who have 50% Amhara-related and 50% Tikari-related ancestry as well as occupy regions such as [[Place:West Africa|West Africa]], [[Place:Central Africa|Central Africa]], and the [[Place:Sudan (region)|Sudan]] as [[Social:Nomadic pastoralism|nomadic herders]], may have initially been Afroasiatic speakers that subsequently underwent language replacement and became Niger-Congo speakers.<ref name="Fan">{{cite journal |last1=Fan |first1=Shaohua |display-authors=0 |title=Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation |journal=Cell |date=March 2, 2023 |volume=186 |issue=5 |pages=923–939 |doi=10.1016/j.cell.2023.01.042 |pmid=36868214 |pmc=10568978 |issn=0092-8674 |oclc= 9791150466 |s2cid=257286226 |url=https://www.cell.com/cell/pdf/S0092-8674(23)00101-0.pdf |pmc-embargo-date=March 2, 2024 }}</ref>

====Medical DNA====

The genomes of Africans commonly found to undergo [[Biology:Adaptation|adaptation]] are [[Biology:Regulation of gene expression|regulatory DNA]], and many cases of adaptation found among Africans relate to [[Biology:Nutritional epigenetics|diet]], [[Biology:Physiology|physiology]], and [[Biology:Evolutionary pressure|evolutionary pressure]]s from pathogens.<ref name="Pfennig" /> Throughout [[Place:Sub-Saharan Africa|Sub-Saharan Africa]], genetic adaptation (e.g., rs334 mutation, Duffy blood group, increased rates of [[Medicine:Glucose-6-phosphate dehydrogenase deficiency|G6PD deficiency]], [[Medicine:Sickle cell disease|sickle cell disease]]) to [[Medicine:Malaria|malaria]] has been found among Sub-Saharan Africans, which may have initially developed in 7300 BP.<ref name="Pfennig" /> [[Place:Sub-Saharan Africa|Sub-Saharan Africa]]ns have more than 90% of the [[Biology:Duffy antigen system|Duffy-null]] genotype.<ref name="Wonkam" />

=====Pediculus=====

During the [[Place:Israel#Bronze and Iron Ages|Copper Age]] and early Islamic era of ancient Israel, [[Place:West Africa|West Africa]]ns may have migrated into ancient Israel and introduced [[Biology:Head louse#Clade E (sister of clade C)|head louse]] from [[Place:West Africa|West Africa]].<ref name="Amanzougaghene">{{cite journal |last1=Amanzougaghene |first1=Nadia |display-authors=0 |title=High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice |journal=PLOS ONE |date=October 14, 2016 |volume=11 |issue=10 |page=e0164659 |doi=10.1371/journal.pone.0164659 |pmid=27741281 |pmc=5065229 |bibcode=2016PLoSO..1164659A |s2cid=14033603 |doi-access=free }}</ref>

=====Sickle Cell=====

Amid the Green Sahara, the mutation for sickle cell originated in the Sahara<ref name="Shriner" /> or in the northwest forest region of western Central Africa (e.g., Cameroon)<ref name="Shriner" /><ref name="Esoh">{{cite journal | vauthors = Esoh K, Wonkam A | title = Evolutionary history of sickle-cell mutation: implications for global genetic medicine | journal = Human Molecular Genetics | volume = 30 | issue = R1 | pages = R119–R128 | date = April 2021 | pmid = 33461216 | pmc = 8117455 | doi = 10.1093/hmg/ddab004 }}</ref> by at least 7,300 years ago,<ref name="Shriner" /><ref name="Esoh" /> though possibly as early as 22,000 years ago.<ref name="Laval">{{cite journal | vauthors = Laval G, Peyrégne S, Zidane N, Harmant C, Renaud F, Patin E, Prugnolle F, Quintana-Murci L | display-authors = 6 | title = Recent Adaptive Acquisition by African Rainforest Hunter-Gatherers of the Late Pleistocene Sickle-Cell Mutation Suggests Past Differences in Malaria Exposure | journal = American Journal of Human Genetics | volume = 104 | issue = 3 | pages = 553–561 | date = March 2019 | pmid = 30827499 | pmc = 6407493 | doi = 10.1016/j.ajhg.2019.02.007 }}</ref><ref name="Esoh" /> The ancestral sickle cell haplotype to modern haplotypes (e.g., Cameroon/Central African Republic and Benin/Senegal haplotypes) may have first arose in the ancestors of modern West Africans, bearing haplogroups [[Biology:Haplogroup E-M2#E1b1a1a1f|E1b1a1-L485]] and [[Biology:Haplogroup E-M2#E1b1a1a1g|E1b1a1-U175]] or their ancestral haplogroup E1b1a1-M4732.<ref name="Shriner" /> West Africans (e.g., Yoruba and Esan of Nigeria), bearing the Benin sickle cell haplotype, may have migrated through the [[Place:Northeast Africa|northeastern region of Africa]] into the western region of Arabia.<ref name="Shriner" /> West Africans (e.g., Mende of Sierra Leone), bearing the Senegal sickle cell haplotype,<ref name="Yaseen">{{cite journal | vauthors = Yaseen NT, Al-Mamoori HS, Hassan MK |title=Sickle β-globin haplotypes among patients with sickle cell anemia in Basra, Iraq: A cross-sectional study | doi = 10.4103/ijh.ijh_20_19 |journal=Iraqi Journal of Hematology | date = January 2020 | volume = 9 | issue = 1 | pages = 23 |s2cid=216082225 | doi-access = free }}</ref><ref name="Shriner" /> may have migrated into Mauritania (77% modern rate of occurrence) and Senegal (100%); they may also have migrated across the Sahara, into [[Place:North Africa|North Africa]], and from North Africa, into [[Place:Southern Europe|Southern Europe]], [[Place:Turkey|Turkey]], and a region near northern Iraq and southern Turkey.<ref name="Yaseen" /> Some may have migrated into and introduced the Senegal and Benin sickle cell haplotypes into [[Place:Basra|Basra]], Iraq, where both occur equally.<ref name="Yaseen" /> West Africans, bearing the Benin sickle cell haplotype, may have migrated into the northern region of Iraq (69.5%), Jordan (80%), [[Place:Lebanon|Lebanon]] (73%), Oman (52.1%), and [[Place:Egypt|Egypt]] (80.8%).<ref name="Yaseen" />

=====Schistosomes=====

According to Steverding (2020), while not definite: Near the [[Place:African Great Lakes|African Great Lakes]], schistosomes (e.g., S. mansoni, S. haematobium) underwent evolution.<ref name="Steverding">{{cite journal |last1=Steverding |first1=Dietmar |title=The spreading of parasites by human migratory activities |journal=Virulence |volume=11 |issue=1 |pages=1177–1191 |date=December 2020 |pmid=32862777 |pmc=7549983 |doi=10.1080/21505594.2020.1809963}}</ref> Subsequently, there was an expansion alongside the Nile.<ref name="Steverding" /> From [[Place:Egypt|Egypt]], the presence of schistosomes may have expanded, via migratory Yoruba people, into Western Africa.<ref name="Steverding" /> Thereafter, schistosomes may have expanded, via migratory Bantu peoples, into the rest of [[Place:Sub-Saharan Africa|Sub-Saharan Africa]] (e.g., [[Place:Southern Africa|Southern Africa]], [[Place:Central Africa|Central Africa]]).<ref name="Steverding" />

=====Thalassemia=====

Through pathways taken by caravans, or via travel amid the [[Place:Almoravid dynasty|Almovarid]] period, a population (e.g., Sub-Saharan [[Place:West Africa#Demographics and languages|West Africans]]) may have introduced the –29 (A → G) [[Medicine:Beta thalassemia|β-thalassemia]] mutation (found in notable amounts among African-Americans) into the North African region of Morocco.<ref name="Agouti">{{cite journal |last1=Agouti |first1=Imane |display-authors=0 |title=Molecular basis of ß-thalassemia in Morocco: possible origins of the molecular heterogeneity |url=https://www.cs.sjsu.edu/~khuri/Rabat_2013/Agouti_2008.pdf |journal=Genetic Testing |volume=12 |issue=4 |pages=563–568 |date=December 2008 |pmid=18976160 |doi=10.1089/gte.2008.0058 |s2cid=46000591}}</ref>

====Domesticated Animal DNA====

While the Niger-Congo migration may have been from West Africa into Kordofan, possibly from Kordofan, Sudan, Niger-Congo speakers accompanied by undomesticated [[Biology:Helmeted guineafowl|helmeted guineafowl]]s, may have traversed into West Africa, domesticated the helmeted guineafowls by 3000 BCE, and via the [[History:Bantu expansion|Bantu expansion]], traversed into other parts of [[Place:Sub-Saharan Africa|Sub-Saharan Africa]] (e.g., [[Place:Central Africa|Central Africa]], [[Place:East Africa|East Africa]], [[Place:Southern Africa|Southern Africa]]).<ref name="Murunga">{{cite journal |last1=Murunga |first1=Philip |display-authors=0 |title=Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism |journal=BioMed Research International |year=2018 |volume=2018 |pages=1–12 |doi=10.1155/2018/7314038 |pmid=30539018 |pmc=6258102 |oclc=8754386965 |s2cid=54463512 |doi-access=free}}</ref>

===Central Africa===
{{Main|Biology:Genetic history of Central Africa}}
{{Further|Biology:Genetic history of the African diaspora}}

====Archaic Human DNA====

Archaic traits found in human fossils of [[Place:West Africa|West Africa]] (e.g., Iho Eleru fossils, which dates to 13,000 BP) and [[Place:Central Africa|Central Africa]] (e.g., Ishango fossils, which dates between 25,000 BP and 20,000 BP) may have developed as a result of admixture between archaic humans and modern humans or may be evidence of late-persisting early modern humans.<ref name="Bergström"/> While [[History:Denisovan|Denisovan]] and [[Biology:Neanderthal|Neanderthal]] ancestry in non-Africans outside of Africa are more certain, archaic human ancestry in Africans is less certain and is too early to be established with certainty.<ref name="Bergström" />

====Ancient DNA====

In 4000 BP, there may have been a population that traversed from [[Earth:Africa|Africa]] (e.g., [[Place:West Africa|West Africa]] or West-[[Place:Central Africa|Central Africa]]), through the Strait of Gibraltar, into the Iberian peninsula, where admixing between Africans and Iberians (e.g., of northern Portugal, of southern {{wipe|Spain}}) occurred.<ref name="RSP">{{cite journal |last1=González-Fortes |first1=G. |display-authors=0 |title=A western route of prehistoric human migration from Africa into the Iberian Peninsula |journal=Proceedings of the Royal Society B: Biological Sciences |volume=286 |issue=1895 |page=20182288 |doi=10.1098/rspb.2018.2288 |pmid=30963949 |pmc=6364581 |s2cid=104296971 |year=2019}}</ref>

=====Cameroon=====

[[History:West African hunter-gatherers|West African hunter-gatherers]], in the region of western Central Africa (e.g., Shum Laka, Cameroon), particularly between 8000 BP and 3000 BP, were found to be related to modern Central African hunter-gatherers (e.g., Baka, Bakola, Biaka, Bedzan).<ref name="Lipson">{{cite journal | vauthors = Lipson M, Ribot I, Mallick S, Rohland N, Olalde I, Adamski N, Broomandkhoshbacht N, Lawson AM, López S, Oppenheimer J, Stewardson K, Asombang RN, Bocherens H, Bradman N, Culleton BJ, Cornelissen E, Crevecoeur I, de Maret P, Fomine FL, Lavachery P, Mindzie CM, Orban R, Sawchuk E, Semal P, Thomas MG, Van Neer W, Veeramah KR, Kennett DJ, Patterson N, Hellenthal G, Lalueza-Fox C, MacEachern S, Prendergast ME, Reich D | display-authors = 6 | title = Ancient West African foragers in the context of African population history | journal = Nature | volume = 577 | issue = 7792 | pages = 665–670 | date = January 2020 | pmid = 31969706 | pmc = 8386425 | doi = 10.1038/s41586-020-1929-1 | s2cid = 210862788 | bibcode = 2020Natur.577..665L }}</ref>

=====Democratic Republic of Congo=====

At Kindoki, in the Democratic Republic of Congo, there were three individuals, dated to the protohistoric period (230 BP, 150 BP, 230 BP); one carried haplogroups [[Biology:Haplogroup E-M2#E1b1a1a1d|E1b1a1a1d1a2 (E-CTS99, E-CTS99)]] and [[Biology:Haplogroup L1 (mtDNA)#L1c|L1c3a1b]], another carried [[Biology:Haplogroup E-M96|haplogroup E (E-M96, E-PF1620)]], and the last carried haplogroups [[Biology:Haplogroup R1b#R1b (R-L278)|R1b1 (R-P25 1, R-M415)]] and [[Biology:Haplogroup L0#Distribution|L0a1b1a1]].<ref name="Wang">{{cite journal | vauthors = Wang K, Goldstein S, Bleasdale M, Clist B, Bostoen K, Bakwa-Lufu P, Buck LT, Crowther A, Dème A, McIntosh RJ, Mercader J, Ogola C, Power RC, Sawchuk E, Robertshaw P, Wilmsen EN, Petraglia M, Ndiema E, Manthi FK, Krause J, Roberts P, Boivin N, Schiffels S | display-authors = 6 | title = Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa | journal = Science Advances | volume = 6 | issue = 24 | pages = eaaz0183 | date = June 2020 | pmid = 32582847 | pmc = 7292641 | doi = 10.1126/sciadv.aaz0183 | bibcode = 2020SciA....6..183W }}</ref><ref name="Wang II">{{cite journal | vauthors = Wang K, Goldstein S, Bleasdale M, Clist B, Bostoen K, Bakwa-Lufu P, Buck LT, Crowther A, Dème A, McIntosh RJ, Mercader J, Ogola C, Power RC, Sawchuk E, Robertshaw P, Wilmsen EN, Petraglia M, Ndiema E, Manthi FK, Krause J, Roberts P, Boivin N, Schiffels S | display-authors = 6 | title = Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa | journal = Science Advances | volume = 6 | issue = 24 | pages = eaaz0183 | date = June 2020 | pmid = 32582847 | doi = 10.1126/sciadv.aaz0183 | pmc = 7292641 | bibcode = 2020SciA....6..183W }}</ref>

====Y-Chromosomal DNA====

[[Biology:Haplogroup R1b#R1b1b (R-V88)|Haplogroup R-V88]] may have originated in western Central Africa (e.g., Equatorial Guinea), and, in the middle of the [[Earth:Holocene|Holocene]], arrived in [[Place:North Africa|North Africa]] through population migration.<ref name="González-Santos">{{cite journal | vauthors = González M, Gomes V, López-Parra AM, Amorim A, Carracedo A, Sánchez-Diz P, Arroyo-Pardo E, Gusmão L | display-authors = 6 | title = The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88 | journal = European Journal of Human Genetics | volume = 21 | issue = 3 | pages = 324–331 | date = March 2013 | pmid = 22892526 | doi = 10.1038/ejhg.2012.167 | pmc = 3573200 }}</ref>

====Mitochondrial DNA====
{{Further|Biology:Haplogroup L1 (mtDNA)|Biology:Haplogroup L2 (mtDNA)}}

In 150,000 BP, Africans (e.g., [[Place:Central Africa|Central Africa]]ns, [[Place:East Africa|East Africa]]ns) bearing [[Biology:Haplogroup L1 (mtDNA)|haplogroup L1]] diverged.<ref name="Sá" /> Between 75,000 BP and 60,000 BP, Africans bearing [[Biology:Haplogroup L3 (mtDNA)|haplogroup L3]] emerged in [[Place:East Africa|East Africa]] and eventually migrated into and became present in modern [[Place:West Africa|West Africa]]ns, Central Africans, and non-Africans.<ref name="Sá" /> Amid the Holocene, including the Holocene Climate Optimum in 8000 BP, Africans bearing haplogroup L2 spread within West Africa and Africans bearing haplogroup L3 spread within East Africa.<ref name="Sá" /> As the largest migration since the Out of Africa migration, migration from Sub-Saharan Africa toward the North Africa occurred, by West Africans, Central Africans, and East Africans, resulting in migrations into [[Earth:Europe|Europe]] and [[Earth:Asia|Asia]]; consequently, Sub-Saharan African mitochondrial DNA was introduced into Europe and Asia.<ref name="Sá" />

Mitochondrial [[Biology:Haplogroup L1 (mtDNA)|haplogroup L1c]] is strongly associated with pygmies, especially with Bambenga groups.<ref name="Quintana08">{{cite journal | vauthors = Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, Patin E, Sica L, Mouguiama-Daouda P, Comas D, Tzur S, Balanovsky O, Kidd KK, Kidd JR, van der Veen L, Hombert JM, Gessain A, Verdu P, Froment A, Bahuchet S, Heyer E, Dausset J, Salas A, Behar DM | display-authors = 6 | title = Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 5 | pages = 1596–1601 | date = February 2008 | pmid = 18216239 | pmc = 2234190 | doi = 10.1073/pnas.0711467105 | doi-access = free | bibcode = 2008PNAS..105.1596Q }}</ref> L1c prevalence was variously reported as: 100% in Ba-Kola, 97% in Aka (Ba-Benzélé), and 77% in Biaka,<ref name="Tishkoff">Sarah A. Tishkoff et al. 2007, [https://web.archive.org/web/20080517050807/http://mbe.oxfordjournals.org/cgi/content/full/24/10/2180 History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation.] Molecular Biology and Evolution 2007 24(10):2180-2195</ref> 100% of the Bedzan (Tikar), 97% and 100% in the Baka people of Gabon and Cameroon, respectively,<ref>Lluis Quintana-Murci et al. MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism. CNRS-Institut Pasteur, Paris</ref> 97% in Bakoya (97%), and 82% in Ba-Bongo.<ref name="Quintana08" /> Mitochondrial haplogroups [[Biology:Haplogroup L2 (mtDNA)|L2a]] and [[Biology:Haplogroup L0|L0a]] are prevalent among the Bambuti.<ref name="Quintana08"/><ref>{{cite journal | vauthors = Silva M, Alshamali F, Silva P, Carrilho C, Mandlate F, Jesus Trovoada M, Černý V, Pereira L, Soares P | display-authors = 6 | title = 60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2 | journal = Scientific Reports | volume = 5 | pages = 12526 | date = July 2015 | pmid = 26211407 | pmc = 4515592 | doi = 10.1038/srep12526 | bibcode = 2015NatSR...512526S }}</ref>

====Autosomal DNA====

Genetically, African pygmies have some key difference between them and Bantu peoples.<ref>{{cite journal | vauthors = Jarvis JP, Scheinfeldt LB, Soi S, Lambert C, Omberg L, Ferwerda B, Froment A, Bodo JM, Beggs W, Hoffman G, Mezey J, Tishkoff SA | display-authors = 6 | title = Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies | journal = PLOS Genetics | volume = 8 | issue = 4 | pages = e1002641 | year = 2012 | pmid = 22570615 | pmc = 3343053 | doi = 10.1371/journal.pgen.1002641 | doi-access = free }}</ref><ref>{{cite journal | vauthors = López Herráez D, Bauchet M, Tang K, Theunert C, Pugach I, Li J, Nandineni MR, Gross A, Scholz M, Stoneking M | display-authors = 6 | title = Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs | journal = PLOS ONE | volume = 4 | issue = 11 | pages = e7888 | date = November 2009 | pmid = 19924308 | pmc = 2775638 | doi = 10.1371/journal.pone.0007888 | doi-access = free | bibcode = 2009PLoSO...4.7888L }}</ref>

====Medical DNA====

Evidence suggests that, when compared to other Sub-Saharan African populations, African pygmy populations display unusually low levels of expression of the genes encoding for human growth hormone and its receptor associated with low serum levels of insulin-like growth factor-1 and short stature.<ref name='Bozzola, 2009'>{{cite journal | vauthors = Bozzola M, Travaglino P, Marziliano N, Meazza C, Pagani S, Grasso M, Tauber M, Diegoli M, Pilotto A, Disabella E, Tarantino P, Brega A, Arbustini E | display-authors = 6 | title = The shortness of Pygmies is associated with severe under-expression of the growth hormone receptor | journal = Molecular Genetics and Metabolism | volume = 98 | issue = 3 | pages = 310–313 | date = November 2009 | pmid = 19541519 | doi = 10.1016/j.ymgme.2009.05.009 }}</ref>

The genomes of Africans commonly found to undergo [[Biology:Adaptation|adaptation]] are [[Biology:Regulation of gene expression|regulatory DNA]], and many cases of adaptation found among Africans relate to [[Biology:Nutritional epigenetics|diet]], [[Biology:Physiology|physiology]], and [[Biology:Evolutionary pressure|evolutionary pressure]]s from pathogens.<ref name="Pfennig" /> Throughout [[Place:Sub-Saharan Africa|Sub-Saharan Africa]], genetic adaptation (e.g., rs334 mutation, Duffy blood group, increased rates of [[Medicine:Glucose-6-phosphate dehydrogenase deficiency|G6PD deficiency]], [[Medicine:Sickle cell disease|sickle cell disease]]) to [[Medicine:Malaria|malaria]] has been found among Sub-Saharan Africans, which may have initially developed in 7300 BP.<ref name="Pfennig" /> [[Place:Sub-Saharan Africa|Sub-Saharan Africa]]ns have more than 90% of the [[Biology:Duffy antigen system|Duffy-null]] genotype.<ref name="Wonkam" /> In the rainforests of [[Place:Central Africa|Central Africa]], genetic adaptation for non-height-related factors (e.g., [[Biology:Immune system|immune traits]], reproduction, [[Biology:Thyroid|thyroid]] function) and short stature (e.g., EHB1 and PRDM5 – [[Biology:Bone#Development|bone synthesis]]; OBSCN and COX10 – [[Biology:Muscular system|muscular development]]; [[Biology:HESX1|HESX1]] and ASB14 – [[Medicine:Pituitary gland|pituitary gland]]’s growth hormone production/secretion) has been found among rainforest hunter-gatherers.<ref name="Pfennig" /> 

===Eastern Africa===
{{Main|Biology:Genetic history of Eastern Africa}}
{{Further|Biology:Genetic history of the African diaspora}}

From the region of Kenya and Tanzania to {{wipe|South Africa}}, eastern [[Social:Bantu languages|Bantu-speaking]] Africans constitute a north to south genetic [[Biology:Cline|cline]]; additionally, from eastern Africa to toward [[Place:Southern Africa|southern Africa]], evidence of genetic homogeneity is indicative of a [[Biology:Founder effect#Serial founder effect|serial founder effect]] and [[Biology:Genetic admixture|admixture]] events having occurred between Bantu-speaking Africans and [[History:Bantu expansion#Pre-expansion-era demography|other African populations]] by the time the Bantu migration had spanned into South Africa.<ref name="Pfennig" />

====Archaic Human DNA====

While [[History:Denisovan|Denisovan]] and [[Biology:Neanderthal|Neanderthal]] ancestry in non-Africans outside of Africa are more certain, archaic human ancestry in Africans is less certain and is too early to be established with certainty.<ref name="Bergström"/>

====Ancient DNA====

=====Ethiopia=====

At Mota, in Ethiopia, an individual, estimated to date to the 5th millennium BP, carried haplogroups [[Biology:Haplogroup E-P2|E1b1]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3x2a]].<ref name="Llorente">{{cite journal | vauthors = Llorente MG, Jones ER, Eriksson A, Siska V, Arthur KW, Arthur JW, Curtis MC, Stock JT, Coltorti M, Pieruccini P, Stretton S, Brock F, Higham T, Park Y, Hofreiter M, Bradley DG, Bhak J, Pinhasi R, Manica A | display-authors = 6 | title = Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent | journal = Science | volume = 350 | issue = 6262 | pages = 820–822 | date = November 2015 | pmid = 26449472 | doi = 10.1126/science.aad2879 | bibcode = 2015Sci...350..820L | hdl = 2318/1661894 | s2cid = 25743789 | hdl-access = free }}</ref><ref name="Llorente II">{{cite journal | vauthors = Llorente MG, Jones ER, Eriksson A, Siska V, Arthur KW, Arthur JW, Curtis MC, Stock JT, Coltorti M, Pieruccini P, Stretton S, Brock F, Higham T, Park Y, Hofreiter M, Bradley DG, Bhak J, Pinhasi R, Manica A | display-authors = 6 |title=Supplementary Materials for Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa |url=https://www.science.org/doi/10.1126/science.aad2879 |journal=Science | date = 13 November 2015 | volume = 350 | issue = 6262 | pages = 820–822 | doi = 10.1126/science.aad2879 | pmid = 26449472 | bibcode = 2015Sci...350..820L | hdl = 2318/1661894 | s2cid = 25743789 | hdl-access = free }}</ref> The individual of Mota is genetically related to groups residing near the region of Mota, and in particular, are considerably genetically related to the Aari people, especially the blacksmith caste of that group.<ref name="Hellenthal">{{cite journal | vauthors = Hellenthal G, Bird N, Morris S | title = Structure and ancestry patterns of Ethiopians in genome-wide autosomal DNA | journal = Human Molecular Genetics | volume = 30 | issue = R1 | pages = R42–R48 | date = April 2021 | pmid = 33547782 | pmc = 8242491 | doi = 10.1093/hmg/ddab019 }}</ref><ref>{{Cite journal |last1=Pagani |first1=Luca |last2=Kivisild |first2=Toomas |last3=Tarekegn |first3=Ayele |last4=Ekong |first4=Rosemary |last5=Plaster |first5=Chris |last6=Gallego Romero |first6=Irene |last7=Ayub |first7=Qasim |last8=Mehdi |first8=S. Qasim |last9=Thomas |first9=Mark G. |last10=Luiselli |first10=Donata |last11=Bekele |first11=Endashaw |date=2012-07-13 |title=Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool |journal=American Journal of Human Genetics |volume=91 |issue=1 |pages=83–96 |doi=10.1016/j.ajhg.2012.05.015 |issn=1537-6605 |pmc=3397267 |pmid=22726845}}</ref>

=====Kenya=====

At Jawuoyo Rockshelter, in Kisumu County, Kenya, a forager of the Later Stone Age carried haplogroups [[Biology:Haplogroup E-V68#E-V22|E1b1b1a1b2/E-V22]] and [[Biology:Haplogroup L4 (mtDNA)|L4b2a2c]].<ref name="Prendergast">{{cite journal | vauthors = Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Culleton BJ, Eccles L, Harper TK, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zalzala F, Ambrose SH, Ayodo G, Gates HL, Gidna AO, Katongo M, Kwekason A, Mabulla AZ, Mudenda GS, Ndiema EK, Nelson C, Robertshaw P, Kennett DJ, Manthi FK, Reich D | display-authors = 6 | title = Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa | journal = Science | volume = 365 | issue = 6448 | date = July 2019 | pmid = 31147405 | doi = 10.1126/science.aaw6275 | pmc = 6827346 | bibcode = 2019Sci...365.6275P }}</ref><ref name="Prendergast II">{{cite journal | vauthors = Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Culleton BJ, Eccles L, Harper TK, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zalzala F, Ambrose SH, Ayodo G, Gates HL, Gidna AO, Katongo M, Kwekason A, Mabulla AZ, Mudenda GS, Ndiema EK, Nelson C, Robertshaw P, Kennett DJ, Manthi FK, Reich D | display-authors = 6 |title=Supplementary Materials for Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa |journal=Science | date = 5 July 2019 | volume = 365 | issue = 6448 | pages = eaaw6275 | doi = 10.1126/science.aaw6275 | pmid = 31147405 | pmc = 6827346 | bibcode = 2019Sci...365.6275P }}</ref>

At Ol Kalou, in Nyandarua County, Kenya, a pastoralist of the [[History:Pastoral Neolithic|Pastoral Neolithic]] carried haplogroups [[Biology:Haplogroup E-Z827#E-M293|E1b1b1b2b2a1/E-M293]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3d1d]].<ref name="Prendergast" /><ref name="Prendergast II" />

At Kokurmatakore, in Marsabit County, Kenya, a pastoralist of the Pastoral [[History:Iron Age#Sub-Saharan Africa|Iron Age]] carried haplogroups [[Biology:Haplogroup E-M35|E1b1b1/E-M35]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3a2a]].<ref name="Prendergast" /><ref name="Prendergast II" />

At White Rock Point, in Homa Bay County, Kenya, there were two foragers of the Later Stone Age; one carried haplogroups [[Biology:Haplogroup BT|BT (xCT)]], likely [[Biology:Haplogroup B-M60|B]], and [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a|L2a4]], and another probably carried [[Biology:Haplogroup L0#Distribution|haplogroup L0a2]].<ref name="Prendergast" /><ref name="Prendergast II" />

At Nyarindi Rockshelter, in Kenya, there were two individuals, dated to the Later Stone Age (3500 BP); one carried [[Biology:Haplogroup L4 (mtDNA)|haplogroup L4b2a]] and another carried [[Biology:Haplogroup E-M96|haplogroup E (E-M96, E-P162)]].<ref name="Wang" /><ref name="Wang II" />

At Lukenya Hill, in Kenya, there were two individuals, dated to the [[History:Pastoral Neolithic|Pastoral Neolithic]] (3500 BP); one carried haplogroups [[Biology:Haplogroup E-Z827#E-V1515|E1b1b1b2b (E-M293, E-CTS10880)]] and [[Biology:Haplogroup L4 (mtDNA)|L4b2a2b]], and another carried [[Biology:Haplogroup L0#Distribution|haplogroup L0f1]].<ref name="Wang" /><ref name="Wang II" />

At Hyrax Hill, in Kenya, an individual, dated to the [[History:Pastoral Neolithic|Pastoral Neolithic]] (2300 BP), carried haplogroups [[Biology:Haplogroup E-Z827#E-V1515|E1b1b1b2b (E-M293, E-M293)]] and [[Biology:Haplogroup L5 (mtDNA)|L5a1b]].<ref name="Wang" /><ref name="Wang II" />

At Molo Cave, in Kenya, there were two individuals, dated to the [[History:Pastoral Neolithic|Pastoral Neolithic]] (1500 BP); while one had haplogroups that went undetermined, another carried haplogroups [[Biology:Haplogroup E-Z827#E-V1515|E1b1b1b2b (E-M293, E-M293)]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3h1a2a1]].<ref name="Wang" /><ref name="Wang II" />

At Kakapel, in Kenya, there were three individuals, one dated to the Later Stone Age (3900 BP) and two dated to the Later [[History:Iron Age#Sub-Saharan Africa|Iron Age]] (300 BP, 900 BP); one carried haplogroups [[Biology:Haplogroup CT|CT (CT-M168, CT-M5695)]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3i1]], another carried [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a1|haplogroup L2a1f]], and the last carried [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a|haplogroup L2a5]].<ref name="Wang" /><ref name="Wang II" />

At Panga ya Saidi, in Kenya, an individual, estimated to date between 496 BP and 322 BP, carried haplogroups [[Biology:Haplogroup E-M35#E-Z830 (E1b1b1b2)|E1b1b1b2]] and [[Biology:Haplogroup L4 (mtDNA)|L4b2a2]].<ref name="Skoglund">{{cite journal | vauthors = Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, Heinze A, Olalde I, Ferry M, Harney E, Michel M, Stewardson K, Cerezo-Román JI, Chiumia C, Crowther A, Gomani-Chindebvu E, Gidna AO, Grillo KM, Helenius IT, Hellenthal G, Helm R, Horton M, López S, Mabulla AZ, Parkington J, Shipton C, Thomas MG, Tibesasa R, Welling M, Hayes VM, Kennett DJ, Ramesar R, Meyer M, Pääbo S, Patterson N, Morris AG, Boivin N, Pinhasi R, Krause J, Reich D | display-authors = 6 | title = Reconstructing Prehistoric African Population Structure | journal = Cell | volume = 171 | issue = 1 | pages = 59–71.e21 | date = September 2017 | pmid = 28938123 | pmc = 5679310 | doi = 10.1016/j.cell.2017.08.049 }}</ref>

At Kilifi, Mtwapa, in Kenya, an individual, dated between 1250 CE and 1650 CE, carried [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|haplogroup L3b1a1a]].<ref name="Brielle">{{cite journal |last1=Brielle |first1=Esther S. |display-authors=0 |title=Supplementary Data Files for Entwined African and Asian genetic roots of medieval peoples of the Swahili coast |journal=Nature |date=March 29, 2023 |volume=615 |issue=7954 |pages=866–873 |doi=10.1038/s41586-023-05754-w |pmid=36991187 |issn=0028-0836 |pmc=10060156 |oclc=9819552636 |bibcode=2023Natur.615..866B |s2cid=250534036}}</ref>

=====Tanzania=====

At Mlambalasi rockshelter, in Tanzania, an individual, dated between 20,345 BP and 17,025 BP, carried undetermined haplogroups.<ref name="Lipson II">{{cite journal |last1=Lipson |first1=Mark |display-authors=0 |title=Extended Data Table 1 Ancient individuals analysed in this study: Ancient DNA and deep population structure in sub-Saharan African foragers |journal=Nature |date=23 February 2022 |volume=603 |issue=7900 |pages=290–296 |doi=10.1038/s41586-022-04430-9 |pmid=35197631 |issn=0028-0836 |pmc=8907066 |oclc=9437356581 |bibcode=2022Natur.603..290L |s2cid=247083477}}</ref>

At Gishimangeda Cave, in Karatu District, Tanzania, there were eleven pastoralists of the [[History:Pastoral Neolithic|Pastoral Neolithic]]; one carried haplogroups [[Biology:Haplogroup E-V68#Family tree|E1b1b1a1b2/E-V22]] and [[Biology:Haplogroup HV (mtDNA)#Tree|HV1b1]], another carried [[Biology:Haplogroup L0#Distribution|haplogroup L0a]], another carried haplogroup [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3x1]], another carried haplogroup [[Biology:Haplogroup L4 (mtDNA)|L4b2a2b]], another carried haplogroups [[Biology:Haplogroup E-Z827#E-M293|E1b1b1b2b2a1/E-M293]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3i2]], another carried haplogroup [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3h1a2a1]], another carried haplogroups [[Biology:Haplogroup E-Z827#E-V1515|E1b1b1b2b2/E-V1486]], likely [[Biology:Haplogroup E-Z827#E-M293|E-M293]] and [[Biology:Haplogroup L0#Distribution|L0f2a1]], and another carried haplogroups [[Biology:Haplogroup E-Z827#E-V1515|E1b1b1b2b2/E-V1486]], likely [[Biology:Haplogroup E-Z827#E-M293|E-M293]], and [[Biology:Haplogroup T (mtDNA)|T2+150]]; while most of the haplogroups among three pastoralists went undetermined, one was determined to carry [[Biology:Haplogroup BT|haplogroup BT]], likely [[Biology:Haplogroup B-M60|B]].<ref name="Prendergast" /><ref name="Prendergast II" />

At Kilwa, Coast, in Tanzania, an individual, dated between 1300 CE and 1600 CE, carried haplogroups [[Biology:Haplogroup J-M172#Subclade distribution|J2a2a1a1a2a~]] and [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a|L2a1h]].<ref name="Brielle" />

At Lindi, in Tanzania, an individual, dated between 1511 cal CE and 1664 cal CE, carried haplogroups [[Biology:Haplogroup E-M2#E1b1a1a1a|E1b1a1a1a2a1a3a1d~]] and [[Biology:Haplogroup L0#Distribution|L0a1a2]].<ref name="Brielle" />

At Makangale Cave, on Pemba Island, Tanzania, an individual, estimated to date between 1421 BP and 1307 BP, carried [[Biology:Haplogroup L0#Distribution|haplogroup L0a]].<ref name="Skoglund" />

At Songo Mnara, in Tanzania, an individual, dated between 1294 cal CE and 1392 cal CE, carried haplogroups [[Biology:Haplogroup R1a|R1a]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3e3a]].<ref name="Brielle" />

=====Uganda=====

At Munsa, in Uganda, an individual, dated to the Later [[History:Iron Age#Sub-Saharan Africa|Iron Age]] (500 BP), carried haplogroup [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3b1a1]].<ref name="Wang" /><ref name="Wang II" />

====Y-Chromosomal DNA====

As of 19,000 years ago, Africans, bearing [[Biology:Haplogroup E-V38|haplogroup E1b1a-V38]], likely traversed across the Sahara, from [[Place:East Africa|east]] to [[Place:West Africa|west]].<ref name="Shriner"/>

Before the slave trade period, East Africans, who carried [[Biology:Haplogroup E-M2|haplogroup E1b1a-M2]], expanded into Arabia, resulting in various rates of inheritance throughout Arabia (e.g., 2.8% Qatar, 3.2% Yemen, 5.5% [[Place:United Arab Emirates|United Arab Emirates]], 7.4% Oman).<ref name="Fernandes">{{cite web | vauthors = Neves da Nova Fernandes VC |title=High-resolution characterization of genetic markers in the Arabian Peninsula and Near East |url=https://etheses.whiterose.ac.uk/6301/1/Vfernandes_PhD_thesis.pdf |website=White Rose eTheses Online |publisher=University of Leeds}}</ref>

====Mitochondrial DNA====
{{Further|Biology:Macro-haplogroup L (mtDNA)|Biology:Haplogroup M (mtDNA)|Biology:Haplogroup N (mtDNA)}}

In 150,000 BP, Africans (e.g., [[Place:Central Africa|Central Africa]]ns, [[Place:East Africa|East Africa]]ns) bearing [[Biology:Haplogroup L1 (mtDNA)|haplogroup L1]] diverged.<ref name="Sá" /> In 130,000 BP, Africans bearing [[Biology:Haplogroup L5 (mtDNA)|haplogroup L5]] diverged in [[Place:East Africa|East Africa]].<ref name="Sá" /> Between 130,000 BP and 75,000 BP, [[Philosophy:Behavioral modernity|behavioral modernity]] emerged among [[Place:Southern Africa|Southern Africa]]ns and long-term interactions between the regions of Southern Africa and Eastern Africa became established.<ref name="Sá" /> Between 75,000 BP and 60,000 BP, Africans bearing [[Biology:Haplogroup L3 (mtDNA)|haplogroup L3]] emerged in [[Place:East Africa|East Africa]] and eventually migrated into and became present in modern [[Place:West Africa|West Africa]]ns, [[Place:Central Africa|Central Africa]]ns, and non-Africans.<ref name="Sá" /> Amid the Holocene, including the Holocene Climate Optimum in 8000 BP, Africans bearing haplogroup L2 spread within West Africa and Africans bearing haplogroup L3 spread within East Africa.<ref name="Sá" /> As the largest migration since the Out of Africa migration, migration from Sub-Saharan Africa toward the North Africa occurred, by West Africans, Central Africans, and East Africans, resulting in migrations into [[Earth:Europe|Europe]] and [[Earth:Asia|Asia]]; consequently, Sub-Saharan African mitochondrial DNA was introduced into Europe and Asia.<ref name="Sá" /> During the early period of the [[Earth:Holocene|Holocene]], 50% of [[Biology:Macro-haplogroup L (mtDNA)|Sub-Saharan African mitochondrial DNA]] was introduced into [[Place:North Africa|North Africa]] by [[Place:West Africa#Demographics and languages|West Africans]] and the other 50% was introduced by [[Place:East Africa#Demographics|East Africans]].<ref name="Sá" /> During the modern period, a greater number of West Africans introduced Sub-Saharan African mitochondrial DNA into North Africa than East Africans.<ref name="Sá" /> Between 15,000 BP and 7000 BP, 86% of Sub-Saharan African mitochondrial DNA was introduced into Southwest Asia by [[Place:East Africa#Demographics|East Africans]], largely in the region of Arabia, which constitute 50% of Sub-Saharan African mitochondrial DNA in modern Southwest Asia.<ref name="Sá" /> In the modern period, 68% of Sub-Saharan African mitochondrial DNA was introduced by East Africans and 22% was introduced by West Africans, which constitutes 50% of Sub-Saharan African mitochondrial DNA in modern Southwest Asia.<ref name="Sá" />

====Autosomal DNA====

Across all areas of {{wipe|Madagascar}}, the average ancestry for the Malagasy people was found to be 4% West Eurasian, 37% Austronesian, and 59% Bantu.<ref name="Heiske">{{cite journal | vauthors = Heiske M, Alva O, Pereda-Loth V, Van Schalkwyk M, Radimilahy C, Letellier T, Rakotarisoa JA, Pierron D | display-authors = 6 | title = Genetic evidence and historical theories of the Asian and African origins of the present Malagasy population | journal = Human Molecular Genetics | volume = 30 | issue = R1 | pages = R72–R78 | date = April 2021 | pmid = 33481023 | doi = 10.1093/hmg/ddab018 | doi-access = free }}</ref>

====Medical DNA====

The genomes of Africans commonly found to undergo [[Biology:Adaptation|adaptation]] are [[Biology:Regulation of gene expression|regulatory DNA]], and many cases of adaptation found among Africans relate to [[Biology:Nutritional epigenetics|diet]], [[Biology:Physiology|physiology]], and [[Biology:Evolutionary pressure|evolutionary pressure]]s from pathogens.<ref name="Pfennig" /> Throughout [[Place:Sub-Saharan Africa|Sub-Saharan Africa]], genetic adaptation (e.g., rs334 mutation, Duffy blood group, increased rates of [[Medicine:Glucose-6-phosphate dehydrogenase deficiency|G6PD deficiency]], [[Medicine:Sickle cell disease|sickle cell disease]]) to [[Medicine:Malaria|malaria]] has been found among Sub-Saharan Africans, which may have initially developed in 7300 BP.<ref name="Pfennig" /> [[Place:Sub-Saharan Africa|Sub-Saharan Africa]]ns have more than 90% of the [[Biology:Duffy antigen system|Duffy-null]] genotype.<ref name="Wonkam" /> In the [[Earth:Ethiopian Highlands|highlands]] of Ethiopia, genetic adaptation (e.g., rs10803083, an [[Biology:Single-nucleotide polymorphism|SNP]] associated with the rate and function of [[Biology:Hemoglobin|hemoglobin]]; BHLHE41, a gene associated with [[Biology:Circadian rhythm|circadian rhythm]] and [[Medicine:Hypoxia (medical)|hypoxia]] response; EGNL1, a gene strongly associated with oxygen [[Homeostasis|homeostasis]] in mammals) to hypoxia and low [[Physics:Atmospheric pressure|atmospheric pressure]] has been found among the Amhara people, which may have developed within the past 5000 years.<ref name="Pfennig" /> In Tanzania, genetic adaptation (e.g., greater amount of [[Biology:Amylase|amylase]] genes than in African populations that consume low-starch foods) has been found in the Hadza people due to a food diet that especially includes consumption of tubers.<ref name="Pfennig" /> 

===Southern Africa===
{{Main|Biology:Genetic history of Southern Africa}}
{{Further|Biology:Genetic history of the African diaspora}}

From the region of Kenya and Tanzania to {{wipe|South Africa}}, eastern [[Social:Bantu languages|Bantu-speaking]] Africans constitute a north to south genetic [[Biology:Cline|cline]]; additionally, from eastern Africa to toward [[Place:Southern Africa|southern Africa]], evidence of genetic homogeneity is indicative of a [[Biology:Founder effect#Serial founder effect|serial founder effect]] and [[Biology:Genetic admixture|admixture]] events having occurred between Bantu-speaking Africans and [[History:Bantu expansion#Pre-expansion-era demography|other African populations]] by the time the Bantu migration had spanned into South Africa.<ref name="Pfennig" />

====Archaic Human DNA====

While [[History:Denisovan|Denisovan]] and [[Biology:Neanderthal|Neanderthal]] ancestry in non-Africans outside of Africa are more certain, archaic human ancestry in Africans is less certain and is too early to be established with certainty.<ref name="Bergström"/>

====Ancient DNA====

Three [[History:Later Stone Age|Later Stone Age]] hunter-gatherers carried ancient DNA similar to Khoisan-speaking hunter-gatherers.<ref name="Choudhury">{{cite journal | vauthors = Choudhury A, Sengupta D, Ramsay M, Schlebusch C | title = Bantu-speaker migration and admixture in southern Africa | journal = Human Molecular Genetics | volume = 30 | issue = R1 | pages = R56–R63 | date = April 2021 | pmid = 33367711 | pmc = 8117461 | doi = 10.1093/hmg/ddaa274 }}</ref> Prior to the Bantu migration into the region, as evidenced by ancient DNA from Botswana, [[Place:East Africa|East Africa]]n herders migrated into Southern Africa.<ref name="Choudhury" /> Out of four [[History:Iron Age|Iron Age]] Bantu agriculturalists of West African origin, two earlier agriculturalists carried ancient DNA similar to Tsonga and Venda peoples and the two later agriculturalists carried ancient DNA similar to Nguni people; this indicates that there were various movements of peoples in the overall Bantu migration, which resulted in increased interaction and admixing between [[Social:Bantu languages|Bantu-speaking]] peoples and Khoisan-speaking peoples.<ref name="Choudhury" />

=====Botswana=====

At Nqoma, in Botswana, an individual, dated to the Early [[History:Iron Age#Sub-Saharan Africa|Iron Age]] (900 BP), carried [[Biology:Haplogroup L2 (mtDNA)#Haplogroup L2a1|haplogroup L2a1f]].<ref name="Wang" /><ref name="Wang II" />

At Taukome, in Botswana, an individual, dated to the Early [[History:Iron Age#Sub-Saharan Africa|Iron Age]] (1100 BP), carried haplogroups [[Biology:Haplogroup E-M2#E1b1a1|E1b1a1 (E-M2, E-Z1123)]] and [[Biology:Haplogroup L0#Distribution|L0d3b1]].<ref name="Wang" /><ref name="Wang II" />

At Xaro, in Botswana, there were two individuals, dated to the Early [[History:Iron Age#Sub-Saharan Africa|Iron Age]] (1400 BP); one carried haplogroups [[Biology:Haplogroup E-M2#E1b1a1a1c|E1b1a1a1c1a]] and [[Biology:Haplogroup L3 (mtDNA)#Subclade distribution|L3e1a2]], and another carried haplogroups [[Biology:Haplogroup E-Z827#E-V1515|E1b1b1b2b (E-M293, E-CTS10880)]] and [[Biology:Haplogroup L0#Distribution|L0k1a2]].<ref name="Wang" /><ref name="Wang II" />

=====Malawi=====

At Fingira rockshelter, in Malawi, an individual, dated between 6179 BP and 2341 BP, carried haplogroups [[Biology:Haplogroup B-M60#B-M182|B2]] and [[Biology:Haplogroup L0#Distribution|L0d1]].<ref name="Lipson II" />

At Chencherere, in Malawi, an individual, estimated to date between 5400 BP and 4800 BP, carried [[Biology:Haplogroup L0#Distribution|haplogroup L0k2]].<ref name="Skoglund" />

At Hora 1 rockshelter, in Malawi, an individual, dated between 16,897 BP and 15,827 BP, carried haplogroups [[Biology:Haplogroup B-M60#B-M112|B2b]] and [[Biology:Haplogroup L5 (mtDNA)|L5b]].<ref name="Lipson II" />

=====South Africa=====

At Doonside, in {{wipe|South Africa}}, an individual, estimated to date between 2296 BP and 1910 BP, carried [[Biology:Haplogroup L0#Distribution|haplogroup L0d2]].<ref name="Schlebusch" /><ref name="Schlebusch II" />

At Ballito Bay, {{wipe|South Africa}}, an individual, estimated to date between 1986 BP and 1831 BP, carried haplogroups [[Biology:Haplogroup A (Y-DNA)#Structure & subclade distribution|A1b1b2]] and [[Biology:Haplogroup L0#Distribution|L0d2c1]].<ref name="Schlebusch">{{cite journal | vauthors = Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Edlund H, Munters AR, Vicente M, Steyn M, Soodyall H, Lombard M, Jakobsson M | display-authors = 6 | title = Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago | journal = Science | volume = 358 | issue = 6363 | pages = 652–655 | date = November 2017 | pmid = 28971970 | doi = 10.1126/science.aao6266 | s2cid = 206663925 | doi-access = free | bibcode = 2017Sci...358..652S }}</ref><ref name="Schlebusch II">{{cite journal | vauthors = Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Edlund H, Munters AR, Vicente M, Steyn M, Soodyall H, Lombard M, Jakobsson M | display-authors = 6 |title=Supplementary Materials for Southern African ancient genomes estimate modern human divergence to 350,000to 260,000years ago |journal=Science | date = 3 November 2017 | volume = 358 | issue = 6363 | pages = 652–655 | doi = 10.1126/science.aao6266 | pmid = 28971970 | bibcode = 2017Sci...358..652S | s2cid = 206663925 | doi-access = free }}</ref>

At Kalemba rockshelter, in Zambia, an individual, dated between 5285 BP and 4975 BP, carried [[Biology:Haplogroup L0#Distribution|haplogroup L0d1b2b]].<ref name="Lipson II" />

====Y-Chromosomal DNA====
[[File:Distribution of Y-Chromosome Haplogroup A in Africa.png|thumb|Distribution of Y-Chromosome Haplogroup A in Africa.]]
[[File:B haplogroup of Y-DNA.png|thumb|Distribution of haplogroup B (M60) of the human Y chromosome in native populations.]]

Various [[Biology:Y chromosome|Y chromosome]] studies show that the San carry some of the most divergent (oldest) [[Biology:Human Y-chromosome DNA haplogroup|human Y-chromosome haplogroup]]s. These haplogroups are specific sub-groups of haplogroups [[Biology:Haplogroup A (Y-DNA)|A]] and B, the two earliest branches on the human Y-chromosome [[Biology:Phylogenetic tree|tree]].<ref name=j1>{{cite journal | vauthors = Knight A, Underhill PA, Mortensen HM, Zhivotovsky LA, Lin AA, Henn BM, Louis D, Ruhlen M, Mountain JL | display-authors = 6 | title = African Y chromosome and mtDNA divergence provides insight into the history of click languages | journal = Current Biology | volume = 13 | issue = 6 | pages = 464–473 | date = March 2003 | pmid = 12646128 | doi = 10.1016/S0960-9822(03)00130-1 | s2cid = 52862939 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Hammer MF, Karafet TM, Redd AJ, Jarjanazi H, Santachiara-Benerecetti S, Soodyall H, Zegura SL | title = Hierarchical patterns of global human Y-chromosome diversity | journal = Molecular Biology and Evolution | volume = 18 | issue = 7 | pages = 1189–1203 | date = July 2001 | pmid = 11420360 | doi = 10.1093/oxfordjournals.molbev.a003906 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Naidoo T, Schlebusch CM, Makkan H, Patel P, Mahabeer R, Erasmus JC, Soodyall H | title = Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations | journal = Investigative Genetics | volume = 1 | issue = 1 | pages = 6 | date = September 2010 | pmid = 21092339 | pmc = 2988483 | doi = 10.1186/2041-2223-1-6 | doi-access = free }}</ref>

====Mitochondrial DNA====

In 200,000 BP, Africans (e.g., Khoisan of Southern Africa) bearing [[Biology:Haplogroup L0|haplogroup L0]] diverged from other Africans bearing haplogroup L1′6, which tend to be northward of [[Place:Southern Africa|Southern Africa]].<ref name="Sá">{{cite journal |last1=Sá |first1=Luísa |display-authors=0 |title=Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade |journal=International Journal of Molecular Sciences |date=16 August 2022 |volume=23 |issue=16 |page=9219 |doi=10.3390/ijms23169219 |pmid=36012483 |issn=1661-6596 |pmc=9408831 |oclc=9627558751 |s2cid=251653686|doi-access=free }}</ref> Between 130,000 BP and 75,000 BP, [[Philosophy:Behavioral modernity|behavioral modernity]] emerged among Southern Africans and long-term interactions between the regions of Southern Africa and Eastern Africa became established.<ref name="Sá" />

[[Biology:Mitochondrial DNA|Mitochondrial DNA]] studies also provide evidence that the San carry high frequencies of the earliest [[Biology:Human mitochondrial DNA haplogroup|haplogroup]] branches in the human mitochondrial DNA tree. This DNA is inherited only from one's mother. The most divergent (oldest) mitochondrial haplogroup, [[Biology:Haplogroup L0|L0]]d, has been identified at its highest frequencies in the southern African San groups.<ref name=j1/><ref>{{cite journal | vauthors = Chen YS, Olckers A, Schurr TG, Kogelnik AM, Huoponen K, Wallace DC | title = mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations | journal = American Journal of Human Genetics | volume = 66 | issue = 4 | pages = 1362–1383 | date = April 2000 | pmid = 10739760 | pmc = 1288201 | doi = 10.1086/302848 }}</ref><ref>{{cite journal | vauthors = Tishkoff SA, Gonder MK, Henn BM, Mortensen H, Knight A, Gignoux C, Fernandopulle N, Lema G, Nyambo TB, Ramakrishnan U, Reed FA, Mountain JL | display-authors = 6 | title = History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation | journal = Molecular Biology and Evolution | volume = 24 | issue = 10 | pages = 2180–2195 | date = October 2007 | pmid = 17656633 | doi = 10.1093/molbev/msm155 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Schlebusch CM, Naidoo T, Soodyall H | title = SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa | journal = Electrophoresis | volume = 30 | issue = 21 | pages = 3657–3664 | date = November 2009 | pmid = 19810027 | doi = 10.1002/elps.200900197 | s2cid = 19515426 }}</ref>

====Autosomal DNA====

Henn et al. (2011) found that the ǂKhomani San, as well as the Sandawe and Hadza peoples of Tanzania, were the most genetically diverse of any living humans studied. This high degree of genetic diversity hints at the origin of anatomically modern humans.<ref>{{cite journal | vauthors = Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, Feldman MW | display-authors = 6 | title = Hunter-gatherer genomic diversity suggests a southern African origin for modern humans | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 13 | pages = 5154–5162 | date = March 2011 | pmid = 21383195 | pmc = 3069156 | doi = 10.1073/pnas.1017511108 | publisher = National Academy of Sciences | doi-access = free }}</ref><ref>{{cite journal |last=Kaplan |first=Matt |year=2011 |title=Gene Study Challenges Human Origins in Eastern Africa |journal=Scientific American|publisher=[[Company:Nature Publishing Group|Nature Publishing Group]] |url=http://www.scientificamerican.com/article/gene-study-challenges-human-origin-africa/ |access-date=22 June 2012}}</ref>

====Medical DNA====

Among the ancient DNA from three hunter-gatherers sharing genetic similarity with San people and four Iron Age agriculturalists, their SNPs indicated that they bore variants for resistance against sleeping sickness and [[Biology:Plasmodium vivax|Plasmodium vivax]].<ref name="Pfeiffer">{{cite journal | vauthors = Pfeiffer S | title = Disease as a Factor in the African Archaeological Record | journal = The African Archaeological Review | volume = 37 | issue = 3 | pages = 487–490 | year = 2020 | pmid = 32863518 | pmc = 7445818 | doi = 10.1007/s10437-020-09405-7 }}</ref> In particular, two out of the four Iron Age agriculturalists bore variants for resistance against sleeping sickness and three out of the four Iron Age agriculturalists bore [[Biology:Human genetic resistance to malaria#Duffy antigen receptor negativity|Duffy negative variants]] for resistance against [[Medicine:Malaria|malaria]].<ref name="Pfeiffer" /> In contrast to the Iron Age agriculturalists, from among the San-related hunter-gatherers, a six-year-old boy may have died from [[Medicine:Schistosomiasis|schistosomiasis]].<ref name="Pfeiffer" /> In Botswana, a man, who dates to 1400 BP, may have also carried the Duffy negative variant for resistance against malaria.<ref name="Pfeiffer" />

The genomes of Africans commonly found to undergo [[Biology:Adaptation|adaptation]] are [[Biology:Regulation of gene expression|regulatory DNA]], and many cases of adaptation found among Africans relate to [[Biology:Nutritional epigenetics|diet]], [[Biology:Physiology|physiology]], and [[Biology:Evolutionary pressure|evolutionary pressure]]s from pathogens.<ref name="Pfennig" /> Throughout [[Place:Sub-Saharan Africa|Sub-Saharan Africa]], genetic adaptation (e.g., rs334 mutation, Duffy blood group, increased rates of [[Medicine:Glucose-6-phosphate dehydrogenase deficiency|G6PD deficiency]], [[Medicine:Sickle cell disease|sickle cell disease]]) to [[Medicine:Malaria|malaria]] has been found among Sub-Saharan Africans, which may have initially developed in 7300 BP.<ref name="Pfennig" /> [[Place:Sub-Saharan Africa|Sub-Saharan Africa]]ns have more than 90% of the [[Biology:Duffy antigen system|Duffy-null]] genotype.<ref name="Wonkam" /> In the Kalahari Desert region of Africa, various possible genetic adaptations (e.g., [[Biology:Adiponectin|adiponectin]], [[Body mass index|body mass index]], [[Biology:Metabolism|metabolism]]) have been found among the ǂKhomani people.<ref name="Pfennig" /> [[Place:Sub-Saharan Africa|Sub-Saharan Africa]]ns have more than 90% of the [[Biology:Duffy antigen system|Duffy-null]] genotype.<ref name="Wonkam" /> In {{wipe|South Africa}}, genetic adaptation (e.g., rs28647531 on [[Biology:Chromosome 4|chromosome 4q22]]) and [[Medicine:Tuberculosis#Risk factors|strong susceptibility to tuberculosis]] has been found among Coloureds.<ref name="Pfennig" />

==Recent African origin of modern humans==
{{Main|Biology:Recent African origin of modern humans}}
{{Further|Biology:Early human migrations|Biology:Basal Eurasian|Biology:Human genetic variation}}

Between 500,000 BP and 300,000 BP, anatomically modern humans may have emerged in Africa.<ref name="Pereira">{{cite journal | vauthors = Pereira L, Mutesa L, Tindana P, Ramsay M | title = African genetic diversity and adaptation inform a precision medicine agenda | journal = Nature Reviews. Genetics | volume = 22 | issue = 5 | pages = 284–306 | date = May 2021 | pmid = 33432191 | doi = 10.1038/s41576-020-00306-8 | publisher = Nature Reviews | s2cid = 231587564 }}</ref> As Africans (e.g., Y-Chromosomal Adam, [[Biology:Mitochondrial Eve|Mitochondrial Eve]]) have migrated from their places of origin in Africa to other locations in Africa, and as the time of divergence for [[Place:East Africa|East Africa]]n, [[Place:Central Africa|Central Africa]]n, and West African lineages are similar to the time of divergence for the Southern African lineage, there is insufficient evidence to identify a specific region for the origin of humans in [[Earth:Africa|Africa]].<ref name="Bergström" /> In 100,000 BP, anatomically modern humans migrated from [[Earth:Africa|Africa]] into [[Earth:Eurasia|Eurasia]].<ref name="Benton">{{cite journal | vauthors = Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA | title = The influence of evolutionary history on human health and disease | journal = Nature Reviews. Genetics | volume = 22 | issue = 5 | pages = 269–283 | date = May 2021 | pmid = 33408383 | pmc = 7787134 | doi = 10.1038/s41576-020-00305-9 }}</ref> Subsequently, tens of thousands of years after, the ancestors of all present-day Eurasians migrated from Africa into Eurasia and eventually became admixed with Denisovans and Neanderthals.<ref name="Benton" />

Archaeological and fossil evidence provide support for the [[Biology:Recent African origin of modern humans|African origin]] of homo sapiens and [[Philosophy:Behavioral modernity|behavioral modernity]].<ref name="Prendergast III">{{cite book |last1=Prendergast |first1=Mary E. |last2=Sawchuk |first2=Elizabeth A. |last3=Sirak |first3=Kendra A. |title=Oxford Research Encyclopedia of African History |date=19 October 2022 |publisher=Oxford University Press |isbn=9780190277734 |oclc=1013546425 |chapter-url=https://oxfordre.com/africanhistory/display/10.1093/acrefore/9780190277734.001.0001/acrefore-9780190277734-e-143 |chapter=Genetics and the African Past}}</ref> Models reflecting a pan-African origin (multiple locations of origin within Africa) and evolution of modern humans have been developed.<ref name="Prendergast III" /> As the idea of "modern" has become increasingly problematized, research has "begun to disentangle what is meant by "modern" genetic ancestry, skeletal morphology, and behavior, recognizing these are unlikely to form a single package."<ref name="Prendergast III" />

In comparison to the non-African genome, the African genome features a ~25% greater number of [[Biology:Polymorphism|polymorphisms]],<ref name="Pfennig">{{cite journal |last1=Pfennig |first1=Aaron |display-authors=0 |title=Evolutionary Genetics and Admixture in African Populations |journal=Genome Biology and Evolution |date=March 29, 2023 |volume=15 |issue=4 |page=evad054 |doi=10.1093/gbe/evad054 |pmid=36987563 |url=https://academic.oup.com/gbe/article/15/4/evad054/7092825 |pmc=10118306 |oclc=9817135458 |s2cid=257803764}}</ref> or 
3 to 5 times as many,<ref name="Wonkam">{{cite journal |last1=Wonkam |first1=Ambroise |last2=Adeyemo |first2=Adebowale |title=Leveraging our common African origins to understand human evolution and health |journal=Cell Genomics |date=March 8, 2023 |volume=3 |issue=3 |page=100278 |doi=10.1016/j.xgen.2023.100278 |pmid=36950382 |url=https://www.cell.com/cell-genomics/pdf/S2666-979X(23)00038-1.pdf |pmc=10025516 |s2cid=257458855}}</ref> and [[Biology:Genetic variation|genetic variants]] that are rare outside of Africa are found to occur at an abundant rate within Africa.<ref name="Pfennig" /> Most of the genetic diversity found among non-Africans is found to be, at large, a subset of genetic diversity found among Africans.<ref name="Pfennig" /> The genomes of Africans commonly found to undergo [[Biology:Adaptation|adaptation]] are [[Biology:Regulation of gene expression|regulatory DNA]], and many cases of adaptation found among Africans relate to [[Biology:Nutritional epigenetics|diet]], [[Biology:Physiology|physiology]], and [[Biology:Evolutionary pressure|evolutionary pressure]]s from pathogens.<ref name="Pfennig" /> Throughout [[Place:Sub-Saharan Africa|Sub-Saharan Africa]], genetic adaptation (e.g., rs334 mutation, Duffy blood group, increased rates of [[Medicine:Glucose-6-phosphate dehydrogenase deficiency|G6PD deficiency]], [[Medicine:Sickle cell disease|sickle cell disease]]) to [[Medicine:Malaria|malaria]] has been found among Sub-Saharan Africans, which may have initially developed in 7300 BP.<ref name="Pfennig" /> Throughout Africa, various genetic adaptations (e.g., [[Biology:Apolipoprotein L1|apolipoprotein L1]] (APOL1): [[Biology:Apolipoprotein L1#Mutations|G1 and G2]] haplotype resistance to trypanosomiasis and increased risk of [[Medicine:Kidney disease|kidney disease]]; [[Biology:Human leukocyte antigen|human leukocyte antigen]] (HLA) genes; [[Biology:Major histocompatibility complex|major histocompatibility complex]] (MHC)) to HIV-1, [[Medicine:Smallpox|smallpox]], [[Medicine:Trypanosomiasis|trypanosomiasis]] (African sleeping sickness), and [[Medicine:Tuberculosis|tuberculosis]] has been found among [[Earth:Africa|Africa]]ns.<ref name="Pfennig" /> [[Medicine:Biomedical sciences|Biomedical]] [[Medicine:Medical test|tests]] for specific genetic variants (e.g., rs1799853 in the [[Biology:CYP2C9|CYP2C9]] gene), which have been approved by the U.S. [[Organization:Food and Drug Administration|Food and Drug Administration]] and are intended to indicate correct prescription of [[Chemistry:Warfarin|warfarin]], has been found to be increasingly irrelevant to Africans as the variants are rare in Africa.<ref name="Pfennig" /> As frequency rate factors into considering and deciding [[Biology:Allele|variant]] pathogenicity and generalizable [[Biology:Polygenic score|polygenic score]]s, modern clinical classifications of genetic variant pathogenicity are found to be inadequate due to a lack of genetic diversity in biomedical studies.<ref name="Pfennig" /> Fan et al (2023) recently found ~5.3 million [[Medicine:Rare variant (genetics)|unique genetic variants]] in 180 African hunter-gatherer populations, and among existing [[Philosophy:Variant of uncertain significance#Limitations of the classifications|classifications for variants]] determined to likely be “pathogenic”, ~29% (44/154) of these “pathogenic” classified variants were found to occur frequently among the African hunter-gatherers.<ref name="Pfennig" />

==See also==

* [[Biology:Genetic history of the African diaspora|Genetic history of the African diaspora]]

==Notes==

{{Notelist}}

==References==

{{reflist}}


[[Category:Genetic genealogy]]
[[Category:Human population genetics]]

{{Sourceattribution|Genetic history of Africa}}