https://www.biorxiv.org/content/10.1101/2023.04.24.538113v1.full.pdf
SLC24A5 is the dominant locus contributing to light skin pigmentation in Europeans
We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46).
https://www.cell.com/current-biology/pdf/S0960-9822(23)00189-6.pdf
The derived SLC24A5 allele, which is carried on the Neolithic ancestry back-
ground, is one of the two alleles which contributes most to light skin pigmentation in present-day West Eurasian-ancestry populations. 47 It has previously been shown to have been at relatively high frequency in the Neolithic population and absent in the Mesolithic hunter-gatherers, 5 and our results show that the selection removed hunter-gatherer ancestry at this locus in later admixed Neolithic groups.
We see significant evidence of correlation between trait scores and LAD in skin color (p = 1.2 3 104 ), consistent with adaptive admixture around SLC24A5. Indeed, this signal is solely driven by two loci (Figure 3B), wherein a HERC2 variant with a skew towards Mesolithic ancestry (Z = 1.8) also contributes to a lighter level of skin pigmentation alongside SLC24A5.
In contrast to SLC24A5, the second high-effect pigmentation variant in HERC displays an excess of Mesolithic ancestry (+10.79%, |Z| = 1.90). Together with the third high-effect pigmentation variant at SLC45A2, which arrived in Europe via later expansions from the steppe, selection on pigmentation in Europe thus targeted variants from each of the three major ancestral populations. 4
Arctic human gene OCA2 (50), while melanosome formation (i.e., melanogenesis) requires the Arctic-selected gene SLC24A5 (51). Mutations in either MLPH or RAB27A cause the hypopigmentation condition Griscelli syndrome (52, 53), while SLC24A5 and OCA2 variants are associated with albinism in humans (50, 54). In evolutionary terms, these “color” genes are functionally conserved across vertebrates, as polymorphisms in MLPH contribute to coat color in domestic cats (55) while muta-
tions in SLC24A5 and OCA2 result in the “golden” phenotype in zebrafish and cichlids, respectively (53, 56, 57).
https://www.biorxiv.org/content/10.1101/2022.08.24.505188v1.full.pdf
The strongest signal is at the allele rs16891982, in the gene SLC45A2, which is known to play a major role in light skin pigmentation, and for which there has been previous evidence for selection51. The second strongest signal based on our analysis is in the allele rs11636232 in OCA2/HERC2, which is a primary determinant of light eye color in Europeans4,5
In the Historical period, along with the LCT locus, we detect selection candidates in SH2B3 and
DHCR7—two genes that are directly related to vitamin D binding as well as a candidate in SLC45A2
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