My position that Y-STRs are effectively dead for age estimation stands, but I thought it'd be a good exercise to do this, as my personal adieu to more than a decade of Y-STRs: they didn't live up to their promise, but, indirectly, they helped create an entire field of "genetic prehistory" that will live on after their demise.
The greatest contribution of the Busby et al. (2011) paper is that it has cured the naivete of some who bought into the "more STRs = more accuracy" scheme. After this paper all Y-STR based estimates (including my own, above) are suspect.
The non-linearity of the Y-STR mutation model is only one of the problems of Y-STRs. Over the last few years, I've examined many commonly held wrong assumptions about the way Y-STRs have been used:
- The "evolutionary" mutation rate and its inflated dates
- The lack of appreciation of the true confidence intervals of age estimates (even under a well-behaved, symmetric stepwise mutation model), which are wider than believed by many, once uncertainty about generation length, mutation rates, and the inherent stochasticity of the mutation process is taken into account
- A common conflation of haplogroup ages with migration events; a migration event may be actually much older or much younger than the Y-STR variance age, usually the latter, except in rare cases of the colonization of islands or remote regions of the world.
- Influence of foreigner contamination or relics in the estimation of population ages.
- Impact of population demography to age estimates, even "interclade" ones
But, on the whole, they are worse than useless for the prehistorian: not only do they produce estimates fraught with danger, but also, being the only game in town, are prone to over-interpretation and spurious associations.
Thankfully, it will only be a few years more until we can move past the Y-STR swamp, and into the more promising territory of well-behaved unique event polymorphisms that are currently too costly to type on a large number of samples. Archaeogenetics will also help, although that, too, has its own perils (namely contamination, and the inability to get data from the hot and humid regions of the world).
One way or another, we're bound to know more in the future, and destroying the Y-STR behemoth is the first step toward making some real progress in genetic prehistory.