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The limits of long-term selection against Neandertal introgression

View ORCID ProfileMartin Petr, Svante Pääbo, Janet Kelso, Benjamin Vernot
doi: https://doi.org/10.1101/362566
Martin Petr
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Svante Pääbo
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Janet Kelso
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Benjamin Vernot
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Abstract

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans due to deleterious alleles that had accumulated in the Neandertals after they split from the modern human lineage. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45 thousand years. Here we show that this apparent decline is an artifact caused by gene flow between West Eurasians and Africans, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When applying a more robust statistic that takes advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Western Europe over the past 45 thousand years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters, and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular a depletion of Neandertal ancestry in conserved genomic regions that are likely to be of functional importance. Thus, we find that negative selection against Neandertal ancestry has not played as strong a role in recent human evolution as had previously been assumed.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 04, 2018.
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The limits of long-term selection against Neandertal introgression
Martin Petr, Svante Pääbo, Janet Kelso, Benjamin Vernot
bioRxiv 362566; doi: https://doi.org/10.1101/362566
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The limits of long-term selection against Neandertal introgression
Martin Petr, Svante Pääbo, Janet Kelso, Benjamin Vernot
bioRxiv 362566; doi: https://doi.org/10.1101/362566

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