Keinan and his colleagues provide data that challenges Hammer’s argument. While Hammer and his colleagues have argued that female effective population size is larger than male effective population size largely due to polygynous practices, comparing X chromosome variation to autosomal variation, Keinan and his colleagues show that female effective population size was reduced outside of Africa (note that females carry two X chromosomes and males carry one, so X chromosome variation reflect female demographic history more than male).
Compared to Hammer et al., Keinan et al. used bigger genome data. They analyzed 130,000 SNPs using subset of the HapMap data, 1,087 additional SNPs that they discovered in two West African copies of X chromosomes, and sequence data consist of over a billion base pairs of DNA from five North Europeans, four East Asians, and five Africans.
First, using SNP data, they obtained the ratio of X chromosome and autosomes allele frequency differentiation between two populations (FST) to estimate the amount of genetic drift. The ratios obtained between North European and East Asian were not significantly different from expected ratio (3/4 = 0.75), but the ratios between African and non-African were reduced.
Second, they compared the X chromosome and autosomes SNP allele frequency distribution within each population. The shape of allele frequency distribution for X chromosome and autosomes was significantly different for non-Africans. Non-Africans have more high-frequency derived allele on X chromosome than expected and the X chromosome allele frequency distribution of non-Africans does not fit the expected distribution.
Third, they obtained the X-to-autosome sequence divergence ratios for each population. West African has ratio close to expected, but non-Africans have significantly smaller ratio than expected (0.635 for North European and 0.690 for East Asian).
They think that X chromosome experienced accelerated genetic drift and sex-biased demographic processes rather than natural selection is likely explanation. However, the data do not support that polygyny is one of the process, because polygyny increases the ratio, but they observed decreased ratios. Alternatively, they suggest that non-Africans received long-range male migration from Africa or females have longer generation time than males. Also, some females were reproductively more successful than the others during out-of-Africa dispersal.
Two different conclusions were obtained from different groups of researchers, maybe because of several factors. First, the samples used by two groups were different. Hammer et al. have more sample populations that Keinan et al did not use. Second, although Hammer et al have sequence data from more individuals than Keinan et al., they used much smaller genomic data. Third, two groups used very different analytical methods.