Analysis of contributions of archaic genome and their functions in modern non-Africans. Y. Hu1, Q. Ding1, Y. Wang1, H. Zheng1, L. Jin1,2 1) MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China; 2) Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Peoples Republic of China.

   Archaic hominin admixture with modern non-Africans was detected by genome wide analysis of Neanderthal and Denisovan individuals. Compared with Africans, non-Africans share excess derived alleles with Neanderthals. Especially, Europeans and East Asians are similarly related to Neanderthals, suggesting Neanderthal gene flow to Eurasians before their split. Additional Denisovan admixture was detected in Melanesian individuals. Several models were subsequently proposed regarding time and location of admixture events. To gain better understanding in demographic and evolutionary significance of archaic hominin admixture, we implemented an algorithm to identify archaic segments, i.e., carrying locally maximized number of alleles that are only observed in non-Africans, by analyzing 1K Genome Phase I data. Totally, we identified 410,683 archaic segments in 909 non-African individuals with averaged segment length 83,460bp. In the genealogy of each archaic segment with Neanderthal, Denisovan, African and chimpanzee segments, 77~81% archaic segment coalesced first with Neanderthal, 4~8% coalesced first with Denisovan, and 14% coalesced first with neither, validating the algorithm. Interestingly, a large proportion of all the archaic segments identified shared 88.9% similarity with Neanderthal, suggesting a single major admixture with Neanderthal at 82~121kya, right after the Africa exodus of the ancestors of modern humans. Furthermore, we found that several disease associated sites with alleles specific to archaic segments, suggesting a possible contribution of Neanderthal and Denisovans to human diseases.

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