Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity

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Abstract
Comparisons of levels of variability on the autosomes and X chromosome can be used to test hypotheses about factors influencing patterns of genomic variation. While a tremendous amount of nucleotide sequence data from across the genome is now available for multiple human populations, there has been no systematic effort to examine relative levels of neutral polymorphism on the X chromosome versus autosomes. We analyzed ∼210 kb of DNA sequencing data representing 40 independent noncoding regions on the autosomes and X chromosome from each of 90 humans from six geographically diverse populations. We correct for differences in mutation rates between males and females by considering the ratio of within-human diversity to human-orangutan divergence. We find that relative levels of genetic variation are higher than expected on the X chromosome in all six human populations. We test a number of alternative hypotheses to explain the excess polymorphism on the X chromosome, including models of background selection, changes in population size, and sex-specific migration in a structured population. While each of these processes may have a small effect on the relative ratio of X-linked to autosomal diversity, our results point to a systematic difference between the sexes in the variance in reproductive success; namely, the widespread effects of polygyny in human populations. We conclude that factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability. Like many primate species, the mating system of humans is considered to be moderately polygynous (i.e., males exhibit a higher variance in reproductive success than females). As a consequence, males are expected to have a lower effective population size (Ne) than females, and the proportion of neutral genetic variation on the X chromosome (relative to the autosomes) should be higher than expected under the assumption of strict neutrality and an equal breeding sex ratio. We test for the effects of polygyny by measuring levels of neutral polymorphism at 40 independent loci on the X chromosome and autosomes in six human populations. To correct for mutation rate heterogeneity among loci, we divide our diversity estimates within human populations by divergence with orangutan at each locus. Consistent with expectations under a model of polygyny, we find elevated levels of X-linked versus autosomal diversity. While it is possible that multiple demographic processes may contribute to the observed patterns of genomic diversity (i.e., background selection, changes in population size, and sex-specific migration), we conclude that an historical excess of breeding females over the number of breeding males can by itself explain most of the observed increase in effective population size of the X chromosome.