Ubiquitous impact of natural selection on nucleotide diversity in 178 species of primates

BACKGROUND: Genetic diversity shows great variation across the genome. To investigate the major evolutionary forces causing this variation in primates, we analyse genomic diversity in 178 species in coordinates of the human genome reference to enable direct comparisons. RESULTS: Across species, we find that genetic diversity decreases with declining recombination rates, with an average difference of 40% between high and low recombination regions (ranging from 0.76% to 79%). The magnitude of this effect scales with the estimated effective population size (Ne), being more pronounced in species with larger Ne. Using forward-in-time simulations, we show that these patterns are consistent with the expectations under both background selection and genetic hitchhiking and cannot arise under neutrality. We observe a skew in the site frequency spectrum toward rare variants in low-recombination regions in all species where this could be assessed, which our simulations show is consistent with both forms of linked selection. CONCLUSIONS: Understanding the importance of linked selection across the genome and between species has important implications for how genetic variation is shaped and the assumptions we use to infer population structure, demography, and selection. Our results show that linked selection is pervasive across primate genomes and leaves very few regions to evolve neutrally, even in regions of high recombination.