Rapid evolution of fine-scale recombination during domestication

Abstract

ABSTRACTRecombination serves as a central force driving the evolution of genomic diversity in sexually reproducing organisms. Despite its fundamental role, the evolutionary dynamics of recombination rates remain largely elusive. The domestication of animals, characterized by dynamic selective pressures, provides a unique lens through which to investigate these phenomena. Here, we constructed a fine-scale recombination map using whole-genome data from domestic chickens, including both contemporary commercial breeds and their wild progenitor, the Red Junglefowl (RJF). Our analysis reveals a rapid evolution of the recombination landscape within and between chicken populations, and we find that the average recombination rate decreased during chicken domestication. Remarkably, this trend is further corroborated by re-analysis of the genomes of several domestic species including ducks, goats, pigs, and sheep. Contrary to the hypothesis that domestication leads to an increase in recombination rates, our results provide no support for such a scenario. We suggest that a low recombination rate is beneficial for maintaining uniform and stable phenotypes in domestic breeds during selective inbreeding. Furthermore, we find significant variation in recombination hotspots across chicken populations, which is particularly pronounced in commercial breeds despite their recent divergence. The rapid turnover of recombination hotspots and coldspots appears to be closely linked to selective sweeps. Interestingly, in contrast to prevailing observations in most species, we find that long-term selective inbreeding results in a negative correlation between recombination rates and the frequency of introgressed ancestry from other RJF subspecies. Our results provide insights into the complex interplay of evolutionary forces shaping the evolution of recombination.