It is certainly a very good thing to reignite the debate, even though I do believe that Y-SNP based dating in the age of whole genome sequencing will solve many dating problems, especially for old clades of the tree. I have argued at length why the evolutionary mutation rate is wrong, but the more serious problem is the fact that different sets of Y-STRs lead to different age estimates (with slower-mutating ones producing much older ages than fast-mutating ones).
Microsatellite choice and Y chromosome variation: attempting to select the best STRs to date human Y chromosome lineages
G. B. J. Busby, C. Capelli
Recently the debate on the origins of the major European Y chromosome haplogroup R-M269 has reignited, and opinion has moved away from Paleolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. We investigate the young, STR-based Time to the Most Recent Common Ancestor estimates proposed so far for R-M269 related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. We further expand our analysis to include a worldwide dataset of over 60 STRs which differ in their molecular attributes. This analysis shows that by taking into account the intrinsic molecular characteristics of Y chromosome STRs, one can arrive at a more reliable estimate for the age of Y chromosome lineages. Subsequently, we suggest that most STR-based Y chromosome dates are likely to be underestimates due to the molecular characteristics of the markers commonly used, such as their mutation rate and the range of potential alleles that STR can take, which potentially leads to a loss of time-linearity. As a consequence, we update the STR-based age of important nodes in the Y chromosome tree, showing that credible estimates for the age of lineages can be made once these STR characteristics are taken into consideration. Finally we show that the STRs that are most commonly used to explore deep ancestry are not able to uncover ancient relationships, and we propose a set of STRs that should be used in these cases.