Human pigmentation is a highly diverse and complex trait among populations, and has drawn particular attention from both academic and non-academic investigators for thousands of years. This diversity may be adapted for ultraviolet radiation and shaped by natural selection. Previous studies detected selection signals in several human pigmentation genes, but few studies have examined how multiple genes contributed to the evolution of human pigmentation. Moreover, none has quantified selective

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... sures on human pigmentation over epochs and between populations. Here, we dissect changes and differences of selective pressures during different periods and between distinct populations with new approaches. We propose a new model with multiple populations to estimate historical changes of selective pressures by summarizing selective pressures on multiple genes. We collected genotype data of 19 genes associated with human pigmentation from 15 datasets, and obtained data for 2498 individuals of five representative populations from worldwide. Our results reveal not only a recent incremental change of selective pressure (0.01332/generation) in modern Europeans, but also a significant historical increase of selective pressure (0.01460/generation) on light pigmentation shared by all Eurasians during the Out-of-Africa event. Our results also suggest that several derived alleles recently associated with human dark pigmentation may be under directional selection. Thus, directional selection not only affects light pigmentation in Eurasians, but also influences dark pigmentation in Africans. Our study provides quantitative information on the evolution of human pigmentation, and may facilitate studies of the evolution of other complex traits.