Ancient West Eurasians evolved lighter skin from West African-like dark levels via sweeps at few large-effect loci.
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Polygenic score for dark skin alleles decreased significantly over 40,000 years in West Eurasians. Early Upper Paleolithic Europeans carried dark skin scores matching present-day West Africans. Mesolithic hunter-gatherers had fewer light skin alleles than Early Farmers or Steppe groups. Steppe ancestry showed strongest selection for lighter skin. Selection signals strongest at SLC45A2 rs16891982, TYR rs1126809, HERC2 rs12913832/rs1635168, GRM5 rs7109255. Removing top 5 largest-effect SNPs reduces selection signal by 78% and abolishes polygenic trend. No polygenic selection signal across all 170 SNPs in present-day Europeans. Large-effect SNPs explain most variance between Europeans and West Africans. Little PBS selection in source populations except SLC24A5 in Early Farmers and Steppe. Hunter-gatherers had high light allele frequency at OCA2 rs4778123 but lower overall scores. Selection continued post-admixture at SLC24A5. Dark alleles increased at some loci like EDEM2 rs6120849 and RALGPS1 rs7870409 due to selection or pleiotropy. Neanderthals and Denisovans had dark skin scores similar to early Europeans. No evidence of selection at MC1R in Europeans. Few pigmentation loci show divergent frequencies across ancient ancestry groups due to drift. UK Biobank SNPs with small effects neutral or constrained in evolution.

Evolution Skin color and pigmentation Genetics Science Cro-Magnon Homo Neanderthalensis Denisovans Europe and the EU Negroes Homo Sapiens

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