  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.
