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The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

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  • The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

    by Sriram Sankararaman, Swapan Mallick, Nick Patterson, David Reich
    Current Biology 26, 1–7 May 9, 2016
    http://dx.doi.org/10.1016/j.cub.2016.03.037

    Highlights
    • Denisovan admixture into modern humans occurred after Neanderthal admixture
    • There is more Denisovan ancestry in South Asians than expected from current models
    • Denisovan ancestry has been subject to positive and negative selection after admixture
    • Male infertility most likely occurred after modern human interbreeding with Denisovans


    Summary
    Some present-day humans derive up to ∼5% of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.
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