Extraordinary selection on the human X chromosome associated with archaic admixture

Laurits Skov; Moisès Coll Macià; Elise Anne Lucotte; Maria Izabel Alvez Cavassim; David Castellano; Mikkel Heide Schierup; Kasper Munch

doi:10.1016/j.xgen.2023.100274

Extraordinary selection on the human X chromosome associated with archaic admixture

Laurits Skov, Moisès Coll Macià, Elise Anne Lucotte, Maria Izabel Alvez Cavassim, David Castellano, Mikkel Heide Schierup, Kasper Munch^*

^*Corresponding author af dette arbejde

Institut for Molekylærbiologi og Genetik - Center for Bioinformatik (BiRC)

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

Abstract

The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes 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 selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.

Originalsprog	Engelsk
Artikelnummer	100274
Tidsskrift	Cell Genomics
Vol/bind	3
Nummer	3
Antal sider	16
ISSN	2666-979X
DOI	https://doi.org/10.1016/j.xgen.2023.100274
Status	Udgivet - mar. 2023

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10.1016/j.xgen.2023.100274Licens: CC BY-NC-ND

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title = "Extraordinary selection on the human X chromosome associated with archaic admixture",

abstract = "The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes 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 selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.",

keywords = "archaic admixture, evolution, meiotic drive, positive selection, selective sweeps, X chromosomes",

author = "Laurits Skov and {Coll Maci{\`a}}, Mois{\`e}s and Lucotte, {Elise Anne} and Cavassim, {Maria Izabel Alvez} and David Castellano and Schierup, {Mikkel Heide} and Kasper Munch",

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AU - Skov, Laurits

AU - Coll Macià, Moisès

AU - Lucotte, Elise Anne

AU - Cavassim, Maria Izabel Alvez

AU - Castellano, David

AU - Schierup, Mikkel Heide

AU - Munch, Kasper

PY - 2023/3

Y1 - 2023/3

N2 - The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes 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 selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.

AB - The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes 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 selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.

KW - archaic admixture

KW - evolution

KW - meiotic drive

KW - positive selection

KW - selective sweeps

KW - X chromosomes

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M3 - Journal article

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SN - 2666-979X

VL - 3

JO - Cell Genomics

JF - Cell Genomics

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ER -

Extraordinary selection on the human X chromosome associated with archaic admixture

Abstract

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