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Extraordinary selection on the human X chromosome associated with archaic admixture

L. Skov, View ORCID ProfileM. Coll Macià, E. Lucotte, M.I.A. Cavassim, D. Castellano, M.H. Schierup, K. Munch
doi: https://doi.org/10.1101/2022.09.19.508556
L. Skov
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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M. Coll Macià
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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  • ORCID record for M. Coll Macià
E. Lucotte
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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M.I.A. Cavassim
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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D. Castellano
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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M.H. Schierup
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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K. Munch
1Bioinformatics Research Centre, Aarhus University, C. F. Universitetsbyen 81, 3., DK-8000 Aarhus, Denmark
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  • For correspondence: kaspermunch@birc.au.dk
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Abstract

The X chromosome in non-African human populations shows less diversity and less Neanderthal introgression than expected under the standard neutral model. We analyzed 162 X chromosomes from human males worldwide and discovered 14 chromosomal regions where haplotypes of several hundred kilobases rapidly rose to high frequencies in non-Africans. These observations cannot be explained by neutral genetic drift in realistic demographic scenarios and are only consistent with partial selective sweeps produced by strong selection. Using an approach for inferring individual Neanderthal-derived haplotypes, which do not rely on an archaic reference genome, we further discover that the swept haplotypes are devoid of the archaic ancestry otherwise typical of the affected chromosomal regions. The ancient Ust’-Ishim male carries its expected proportion of these haplotypes, implying that the sweeps must have occurred between 45,000 and 55,000 years ago. Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selection in great ape evolution. We propose that this puzzling combination of observations points to a general mechanism of positive selection unique to the X chromosome.

Competing Interest Statement

The authors have declared no competing interest.

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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 September 20, 2022.
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Extraordinary selection on the human X chromosome associated with archaic admixture
L. Skov, M. Coll Macià, E. Lucotte, M.I.A. Cavassim, D. Castellano, M.H. Schierup, K. Munch
bioRxiv 2022.09.19.508556; doi: https://doi.org/10.1101/2022.09.19.508556
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Extraordinary selection on the human X chromosome associated with archaic admixture
L. Skov, M. Coll Macià, E. Lucotte, M.I.A. Cavassim, D. Castellano, M.H. Schierup, K. Munch
bioRxiv 2022.09.19.508556; doi: https://doi.org/10.1101/2022.09.19.508556

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