Abstract
Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.
Highlights
| | | | skin pigmentation polygenic selection complex traits evolution ancient DNA may have been selected independently or in parallel in one or more of these source populations or may instead only have been selected after admixture
Studies of present-day and ancient populations have revealed signatures of selection at skin pigmentation loci [5,6,7,8,9], and single-nucleotide polymorphisms (SNPs) associated with light skin pigmentation at some of these genes exhibit a signal of polygenic selection in Western Eurasians [10]
The majority of samples are from Western Eurasia, and we focus on that region, noting that a parallel process of selection for light skin pigmentation has acted in East Asian populations [9, 70]
Summary
| | | | skin pigmentation polygenic selection complex traits evolution ancient DNA may have been selected independently or in parallel in one or more of these source populations or may instead only have been selected after admixture. The impact of ancient shifts in ancestry is difficult to resolve using present-day data, but using ancient DNA, we can separate the effects of ancestry and selection and identify which loci were selected in which populations. We use ancient DNA to track the evolution of loci that are associated with skin pigmentation in present-day Europeans. We cannot make predictions about the phenotypes of ancient individuals or populations, we can assess the extent to which they carried the same light pigmentation alleles that are present today. This allows us to identify which pigmentationassociated variants have changed in frequency due to positive selection and the timing of these selective events. We present a systematic survey of the evolution of European skin pigmentationassociated variation, tracking over a hundred loci over 40,000 y of human history—almost the entire range of modern human occupation of Europe
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