UPDATE (Oct 13):
The paper adds nothing to the issue of the appropriate mutation rate choice for TMRCA estimation. The revised Evolutionary Mutation Rates (rEMR) proposed in this paper are nothing more than an application of the Zhivotovsky et al. (Z. et al.) Evolutionary Mutation Rate (EMR) for markers not included in the original calibration by Z. et al. and exhibiting either higher or lower variance than those that are included. The use of a Z. et al.-like calibration is taken uncritically for granted.
Furthermore, the authors use BATWING to generate genealogies in order to infer TMRCA of lineages and populations, employing their rEMR for this purpose. This is wrong because both the "evolutionary mutation rate" and BATWING take into account genealogy. By using rEMR in conjunction with BATWING they are correcting for loss of Y-STR diversity due to genetic drift twice. This mistake was also done in another paper this Spring. I wrote:
Indeed, in this paper they attempt to use Batwing to estimate ages using the effective rate. Batwing employs a Bayesian method with coalescent simulations, and thus takes into account "population history", the effects of which are supposedly encapsulated in the effective mutation rate. Thus, they are "correcting" (inappropriately of course) for population history twice.In conclusion: the age estimates provided in this paper (which can be found in Supplementary Table S4) are useless. The paper is, nonetheless, useful, because it shows the relative ages of many haplogroups, even though the small sample sizes for many of them do not inspire confidence in their accuracy.
UPDATE II: The paper also completely ignores admixture as a source of genetic diversity.
Molecular Biology and Evolution, doi:10.1093/molbev/msp243
A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations
Wentao Shi et al.
We have investigated human male demographic history using 590 males from 51 populations in the HGDP-CEPH worldwide panel, typed with 37 Y-SNPs and 65 Y-STRs, and analyzed with the program BATWING. The general patterns we observe show a gradient from the oldest population TMRCAs and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously-documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan, and recent expansion of the Mozabites in North Africa.