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Admixture Between Archaic and Modern Humans Fossils From Fossils From Vindija Cave, Croatia (38–44 kya) Admixture between Archaic and Modern Humans Alan R. Rogers September 23, 2021 1 / 64 2 / 64 Hominin tooth from Denisova Cave, Altai Mtns, southern Hominin finger from Denisova Cave Siberia (41 kya) 3 / 64 4 / 64 Sites yielding Archaic hominin DNA Outline I Estimating admixture from shared derived alleles I Deep separation plus extensive LD. I Selection against archaic DNA I Excess Neanderthal in Asia I Consequences of small population size I Multiple Denisovan populations 5 / 64 6 / 64 Nucleotide site patterns Population tree . Ancestral allele (0) is shared with . chimp. .. .. .... .... .... .... .... .... Nucleotide Derived allele (1) shared by two .... ......... .... .... .... .... .... Site Pattern .... .... .... .... human populations. .... ... .... .... ea en an .... .... .... .... .... .... .... .... .... .... .... .... Eur 1 1 0 .... ........ .... .... .... Pattern ea: most common; .... ........ .... .... .... Afr 1 0 1 .... .... .... .... .... .... reflects history of population .... .... .... .... .... .... .... .... .... .... .... .... Nea 0 1 1 splits. .... .... .... .... .... .... .... .... .... .... .... .... Chmp 0 0 0 .... ...... .... .... .... .... .... .... ........ .... .... .... .... .... .... .... .... .... .... .... .... .... # 303,340 103,612 95,347 Patterns en & an: how do they .... .... .......... .... .... .... .... arise? AENC A, Africa; E, Europe; N, Neanderthal; C, chimpanzee Why does en exceed an? 7 / 64 8 / 64 Embedded gene genealogy with mutation Incomplete lineage sorting Pattern an Pattern en . ... .... .......... .... I Genealogy of 4 genes shown . .... ..... ..... .... ... ........ ... ... ........ ... .... ..... ..... .... .... ..... ..... .... .... ..... ..... .... ... ..... ..... ... in color. ... ..... ..... ... ... ..... ..... ... .... ..... ........ ..... .... .... .... ..... .... .... ...... ..... .... .... ...... ........ .... .... .... ..... ... .... .... .... ....... ... .... .... .... ....... .... .... ..... .... Bullet ( ) marks mutation ... ...... ........ ..... ... ... ........ ........ ..... ... ... ....... ... .... ..... ... I .... .......... .... ..... .... .... ............ .... ..... .... .... ..... .... ... ..... .... • .... .............. ... ..... .... .... ........ .... ... ..... .... .... .... ... .... .... .... from allele 0 to allele 1. .... .....•........ .... .... .... .... ........... .... .... .... ... ..... ... .... .... ..... ... ... ............ .... .... ..... ... ... ...........•.... .... ..... ... .... ..... .... .... ... ..... .... .... .............. .... ... ..... .... .... .......... .... ... ..... .... .... .... ... ..... ... .... .... .... .... .......... ..... ... .... .... .... .... ......... ..... ... .... .... .... ... ..... ...... ..... .... .... ..... ... I Descendants of mutant have ... ........ .... .... ... ..... ... ... ......... ..... .... ... ..... ... .... ..... .... .... .... ... ... ..... .... .... ................ ..... ... .... .... .... .... ............... .... ... .... .... .... .... .... •... .... ..... .... .... .... .... .... ............... .... .... .... ..... .... .... ................. ..... .... .... ..... .... ... ....... .... ... .... .... .... ..... ... allele 1; others have 0. ... .............. ... ..... .... ... ..... ... ... ............. ... .... .... ... ..... ... .... ....... ... .... ..... ... ... ..... .... .... ............. .... ..... ... .... .... .... .... ............ .... ..... ... .... .... .... .... .... ..... .... .... ..... .... .... .... .... .... ........ ... .... .... .... .... ..... .... .... ......... ... .... ..... .... .... ..... .... .... ..... .... .... .... .... .... .... ..... .... .... .......... .... .... ..... .... .... ..... .... .... .......... .... .... .... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... I Gene genealogy matches .... ..... ..... .... .... ..... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... .... ..... .... ..... .... .... ..... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... .... ..... ........ ..... .... .... ..... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... phylogeny .... ..... ....... ..... .... .... ..... .... .... ..... .... .... ..... ....... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... ... .... ... ......... ... ......... ... ... .... ... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... I Mutant allele shared by .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ..... .... AENC . .... .... closest relatives, A and E. AENC AENC 1 1 0 0 1 0 1 0 0 1 1 0 These two should be equally common 9 / 64 10 / 64 Nucleotide site patterns again Neanderthal admixture inflates en site pattern. Admixed locus Not admixed Nucleotide Site Pattern . ea en an . ... ........ ... ... ........ ... .... ..... ..... .... .... ..... ..... .... European 1 1 0 .... ..... ..... .... .... ..... ..... .... .... ..... ..... .... .... ..... ..... .... .... ..... ...... ..... .... .... ..... ...... ..... .... African 1 0 1 .... ..... ........ ..... .... .... ...... ........ ..... .... .... ..... .... .... ..... .... .... ........ .... .... ..... .... .... ...... .... .... ..... .... .... ....... .... .... ..... .... Neanderthal 0 1 1 .... ...... ... .... ..... .... .... ........•.... .... ..... .... ... ..... .... .... ..... ... ... ........... .... .... ..... ... .... ..... .. .... ... ..... .... .... ........... .... ... ..... .... Chimpanzee 0 0 0 .... .... ..... ... .... .... .... .... ......... ..... ... .... .... .... .... ..... .... .... .... ..... .... .... .......... ..... .... .... ..... .... .... ..... ........ ..... .... .... ..... .... .... .................. ..... .... .... ..... .... # sites 303,340 103,612 95,347 .... ..... ... .... ..... .... .... ..... .... .... ............. .... ..... .... .... ..... .... ... ..... .... ...•..... .... .... ..... ... ... ............. ... .... .... .... ..... ... .... ..... ... .... .... ... ... .... .... .... ............ .... ..... ... ... .... .... .... .... .. .... ..... .... .... ..... .... .... .......... .. .... ..... .... .... ..... .... .... ..... .... .... ...... .... .... ..... .... .... ..... .... .... .... .... .... .... ..... .... .... ..... .... .... ....... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... .... ..... .... .... ....... .... .... ..... .... .... ..... ..... .... .... ..... .... .... ..... .... Common pattern (ea) reflects history of population splits. .... ..... .... .... ........... .... .... ..... .... .... ..... .... ..... .... .... ..... .... .... ..... .... .... ..... ........ .... m...... ..... .... .... ..... .... .... ..... ........ ..... .... m.... ..... .... .... ..... .... .... ..... .... .... ............................................................................. .............................................................................................................................................................. ............... .... ..... .... .... ..... .... .... .... .............. .... ..... .... .... ..... .... .... ..... .... .... ..... .............. .... ..... .... .... ..... .... .... ..... .... ........... .... .... ..... .... .... ..... .... .... ..... .... ........... .... .... ..... .... .... ..... .... Absent admixture, the other two should be equally common AENC AENC 0 1 1 0 0 1 1 0 Why does en exceed an? Key: A, Africa; E, Europe; N, Neanderthal; C, chimpanzee. 11 / 64 12 / 64 Estimate from Neandertal DNA Eurasians share some derived alleles with archaics DNA of modern Eurasians is 1.5–2.1% Neandertal I Neanderthal matches French 4.6% more often than Yoruban (Pr¨uferet al 2014). (African). I Same is true for modern people of east Asia and Papua New Guinea, but not Africa. Green et al (2010) Denisova matches French 1.8% more often than Yoruban (African). I Admixture must have occurred after moderns left Africa but before they expanded throughout the world. Archaic component of Eurasian genome more Neanderthal than Denisovan. Eurasian introgressed segments most similar to Neanderthal I Green et al 2010; Reich et al. 2010. from Caucasus (Mezmaiskaya). (Pr¨uferet al 2014) 13 / 64 14 / 64 So do Asians and Papuans Apparent gradual decline in Neanderthal admixture Asians and Papuans carry as many Neanderthal alleles as Europeans do: 1.5–2.1%. 15 / 64 16 / 64 Apparent gradual decline in Neanderthal admixture Denisovan DNA most common in Australia, NG, and Oceania This turned out to be an artifact. The estimators of admixture were biased. Magnitude of bias differed in samples of different age. 17 / 64 18 / 64 Outline Another approach: look for deep separation plus extensive LD Estimating admixture from shared derived alleles ◦ Examine variation in modern human DNA. I Deep separation plus extensive LD. I Look for long segments of chromosome with many nucleotide I Selection against archaic DNA I differences. I Excess Neanderthal in Asia I Many nucleotide differences deep separation. I Consequences of small
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