I am not quite sure what the analyses of this paper actually show. Neither migration nor admixture are mentioned in the text, and, in my opinion, these processes have shaped modern human Y chromosomal variation.
Migration may result in the expansion of a successful set of Y chromosome lineages, while admixture between divergent populations may inflate estimates of diversity in a population. The Complete Genomics data is dominated by two haplogroups representing vary recent expansions in Europe and West Africa. Is the expansion of R-M269 in Europe an example of selection or large-scale replacement? What does it mean to model "Europeans" or "Africans" as single evolving populations, when both of these were likely formed over the last few thousand years by admixture of divergent pre-existing populations.
PLoS Genetics doi:DOI: 10.1371/journal.pgen.1004064
Natural Selection Reduced Diversity on Human Y Chromosomes
Melissa A. Wilson Sayres et al.
The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.