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Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

Melissa J. Hubisz, Amy L. Williams, Adam Siepel
doi: https://doi.org/10.1101/687368
Melissa J. Hubisz
1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
2Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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  • For correspondence: mt269@cornell.edu asiepel@cshl.edu
Amy L. Williams
1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
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Adam Siepel
2Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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  • For correspondence: mt269@cornell.edu asiepel@cshl.edu
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Abstract

The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present an extended version of the ARGweaver algorithm, ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topology and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. We also identify 1% of the Denisovan genome which was likely introgressed from an unsequenced hominin ancestor, and note that 15% of these regions have been passed on to modern humans through subsequent gene flow.

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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-NC-ND 4.0 International license.
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Posted June 30, 2019.
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Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Melissa J. Hubisz, Amy L. Williams, Adam Siepel
bioRxiv 687368; doi: https://doi.org/10.1101/687368
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Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Melissa J. Hubisz, Amy L. Williams, Adam Siepel
bioRxiv 687368; doi: https://doi.org/10.1101/687368

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