Strong selective sweeps associated with ampliconic regions in great ape X chromosomes

TL;DR

This study reveals that strong selective sweeps, especially in ampliconic regions, have significantly shaped the evolution of great ape X chromosomes, driven by intra-genomic conflict.

Contribution

It demonstrates the prevalence of strong selective sweeps in ampliconic regions of great ape X chromosomes, highlighting a potential mechanism for their rapid evolution.

Findings

Reduced diversity around X-linked genes compared to autosomes

Multiple megabase regions with strong signatures of selective sweeps

Association of sweeps with ampliconic sequences and intra-genomic conflict

Abstract

The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes, and that a higher proportion of substitutions results from positive selection. Strikingly, the X exhibits several megabase long regions where diversity is reduced more than five fold. These regions overlap significantly among species, and have a higher singleton proportion, population differentiation, and nonsynonymous to synonymous substitution ratio. We rule out background selection and soft selective sweeps as explanations for these observations, and conclude that several strong selective sweeps have occurred independently in similar regions in several species. Since these regions are strongly associated with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution.