Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

Abstract

Fine-scale rates of meiotic recombination vary by several orders of magnitude across the genome, and are known to differ between species and even between populations. Studying the differences in recombination maps across populations has been stymied by the confounding effect of differences in demographic history. To address this problem, we developed a method that infers fine-scale recombination rates while taking demography into account and applied our method to infer population-specific recombination maps for each of 26 diverse human populations. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding an unexpected role for Polycomb-group proteins and the tri-methylation of H3K27 in elevating recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA-binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.