Extraordinary selection on the human X chromosome associated with archaic admixture

TY - JOUR

T1 - Extraordinary selection on the human X chromosome associated with archaic admixture

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

UR - http://www.scopus.com/inward/record.url?scp=85149687546&partnerID=8YFLogxK

U2 - 10.1016/j.xgen.2023.100274

DO - 10.1016/j.xgen.2023.100274

M3 - Journal article

C2 - 36950386

AN - SCOPUS:85149687546

SN - 2666-979X

VL - 3

JO - Cell Genomics

JF - Cell Genomics

IS - 3

M1 - 100274

ER -