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The Strength of Selection Against Neanderthal Introgression

Ivan Juric, Simon Aeschbacher, Graham Coop
doi: https://doi.org/10.1101/030148
Ivan Juric
1Center for Population Biology & Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
2Current address: 23andMe, Inc., Mountain View, CA 94043, USA
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Simon Aeschbacher
1Center for Population Biology & Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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Graham Coop
1Center for Population Biology & Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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Abstract

Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral—and segregating at high frequency—in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human–Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.

Footnotes

  • ↵† Supervised this work jointly.

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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 October 30, 2015.
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The Strength of Selection Against Neanderthal Introgression
Ivan Juric, Simon Aeschbacher, Graham Coop
bioRxiv 030148; doi: https://doi.org/10.1101/030148
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The Strength of Selection Against Neanderthal Introgression
Ivan Juric, Simon Aeschbacher, Graham Coop
bioRxiv 030148; doi: https://doi.org/10.1101/030148

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