Long-time readers will remember my Y-STR series which was inspired by my desire to figure out why some papers used the directly observed mutation rate for Y-STRs while others used a 3-times slower "evolutionary" one. My conclusion was that the evolutionary rate was misapplied because its theoretical justification hinged on an assumption of constant population size that was wrong for modern humans and even modest amounts of growth led to a mutation rate that was closer to the genealogical one.
My enthusiasm for Y-STR based dating waned in 2011 when Busby et al. (2011) published a study which showed the effect of microsatellite choice on TMRCA estimates due to the fact that Y-STRs don't follow the the unconstrained strict symmetrical stepwise model (i.e., increase by +/- 1 steps per mutational event with equal probability). This meant that various published age estimates depended on the cocktail of slow/fast Y-STRs used as well as the age of the target node in the phylogeny (because deviations from linearity were more egregious for older nodes). Additionally, at that time it was clear that whole Y chromosome sequencing was around the corner and so the issue would soon be resolved by a new technology.
One comment to the authors is that the generation length of 25 years is not applicable to modern humans, but rather a male generation length of 31-32 years has been estimated across different cultures. The authors estimate the "super-Eurasian" CT clade at 56.26kya (using sequence data) which would correspond to ~71 thousand years if we apply a 31.5/25 multiplier. This would bring it closer to the age estimate for Eurasian M+N mtDNA which has been estimated without an assumption of generation length using ancient DNA. (There is of course no a priori reason that the two should match, but the dates seem to match with the drying up of the Sahara-Arabia zone c. 70kya. As I've argued before, the population contraction that must have accompanied such a traumatic event would be a good opportunity for drift to shed genetic lineages and leave the CT/M+N pair as the inheritors of Eurasia).
bioRxiv doi: 10.1101/004705
Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates
Chuan-Chao Wang, Li Hui
We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R. In addition, genealogical rates lead to more plausible time estimates for Neolithic coalescent sublineages compared with sequence-based dating.