Autosomal DNA spends an equal amount of time in male and female bodies, while X chromosomes spend twice as long in female than in male bodies. In a polygynous society, many males don't have offspring while most women do. Hence, genetic variation in X chromosomes has a higher chance to arise (more bodies=>more mutations) and to be maintained (more bodies=>less drift).
This ties in quite nicely with my recent suggestion on reproductive inequality for human Y-chromosomes.
Related story in the New Scientist.
Hammer's team discovered more genetic differences in the X chromosome than would be expected if equal numbers of males and females tended to mate, over human history. The only explanation for this pattern is widespread, long-lasting polygyny, he says.
His team's analysis reflects all of human history, and modern monogamy has not even left a blip in our genomes. "I don't know how long monogamy has been with us," Hammer says. "It seems it hasn't been around long, evolutionarily."
PLoS Genetics doi:10.1371/journal.pgen.1000202
Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity
Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity et al.
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.