May 07, 2009

Citation of my Y-STR mutation rate criticism

I was reading Tuuli Lappalainen Ph.D. dissertation, at the University of Helsinki: "Human genetic variation in the Baltic Sea region: Features of population history and natural selection," and, to my surprise, I noticed that my post on How Y-STR variance accumulates: a comment on Zhivotovsky, Underhill and Feldman (2006) was cited:
Estimating the age of haplogroups is important for connecting genetic patterns to historical phenomena. However, it is dependent on the correct estimation of the mutation rate, which has proven to be difficult. Rates calculated from pedigrees are 3-4 times higher than evolutionary rates (Parsons et al. 1997, Howell et al. 2003, Dupuy et al. 2004, Zhivotovsky et al. 2004, Zhivotovsky et al. 2006), and it is unclear which should be used for the calculation of the most recent common ancestor for major haplogroups in large geographic regions. It has recently been suggested (Pontikos 2008) that the widely used evolutionary rate of the Y chromosome (Zhivotovsky et al. 2004) is strongly underestimating the effective mutation rate due to not accounting for population growth and the bias of analyzing the biggest haplogroups that have grown at rates exceeding the general growth rate of the population. These analyses have not been published in a peer-reviewed journal, but they appear to correctly point out at least some problems of the commonly used models. Thus, the appropriate mutation rate to use for analyzing the temporal scale of the Y-chromosomal haplogroup variation may be a few times lower than was used in II – close to the pedigree rate. The same bias should apply to mitochondrial DNA, too. If the revised rates (Pontikos 2008) were used instead, TMRCAs for the main Y-chromosomal haplogroups I1a, N3 and R1a1 would be in the order of 3000-4000 years before present. These dates would imply that instead of the proposed Neolithic arrival of these haplogroups, their upper age limit would be in late Neolithic or early Bronze Age. Interestingly, the revised age of N3 variation in the Baltic Sea region would actually correspond nicely with the recently suggested Bronze Age arrival of the Finno-Ugric language (Häkkinen 2009). However, given the current uncertainty of the appropriate mutation rates, all time estimates should be used with great caution.
The cited post was the first one in the now extensive Y-STR series in which I have tried to dissect various aspects Y-STR based age estimation.


Kosmo said...

Congratulations on the citation! That's pretty cool.

pconroy said...

Yeah, congrats!

Are you going to publish your work in a "peer reviewed journal" anytime soon - or are you content to just have the research out there?

Maju said...

Yah, gratz. You made a good analysis in that post, even if I don't agree at all.