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 for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review


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.

Original languageEnglish
Article number100274
JournalCell Genomics
Number of pages16
Publication statusPublished - Mar 2023


  • archaic admixture
  • evolution
  • meiotic drive
  • positive selection
  • selective sweeps
  • X chromosomes


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