On the same topic as the preceding post. I would add that a major cause for the higher informativeness of the human Y-chromosome is the fact that most of the presently dominant lineages in the world are fairly recent, and hence there has been less time for random diffusion of patrilineages on the map to wipe out pre-established patterns of Y-chromosomes associated with archaeologically or historically dominant patriarchal groups.
In the standard model, males are more static, and females more mobile, because they may move fairly long distances to settle in their husband's residence. This factor is counterbalanced, I think, by the excess organized migration of surplus males in societies where there is socio-economic/reproductive inequality.
Thus, the constant individualistic short-range migration of women, coupled with their greater reproductive equality, over long periods of time, evens out the distribution of mtDNA lineages, with the resulting distribution further obscured by (climate-related) selective factors acting on human mtDNA. On the contrary, the Y-chromosome landscape is established by patrilocal males staying by and defending their hearths, but is occasionally punctuated by long-range collective migration of patrilineally related males.
PLoS Genetics doi:10.1371/journal.pgen.1000200
Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study
Laure Ségurel et al.
In the last two decades, mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome (NRY) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations, and to infer sex-specific demography and history. Most studies converge towards the notion that among populations, women are genetically less structured than men. This has been mainly explained by a higher migration rate of women, due to patrilocality, a tendency for men to stay in their birthplace while women move to their husband's house. Yet, since population differentiation depends upon the product of the effective number of individuals within each deme and the migration rate among demes, differences in male and female effective numbers and sex-biased dispersal have confounding effects on the comparison of genetic structure as measured by uniparentally inherited markers. In this study, we develop a new multi-locus approach to analyze jointly autosomal and X-linked markers in order to aid the understanding of sex-specific contributions to population differentiation. We show that in patrilineal herder groups of Central Asia, in contrast to bilineal agriculturalists, the effective number of women is higher than that of men. We interpret this result, which could not be obtained by the analysis of mtDNA and NRY alone, as the consequence of the social organization of patrilineal populations, in which genetically related men (but not women) tend to cluster together. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter.