More on Henn et al. on time-dependent evolutionary mutation rate

Brenna Henn, lead author of the recent study I commented on earlier has a guest post at the Spittoon on her paper. Here is the actionable bit:

To date, the timing of most population events in human evolutionary genetics was estimated has used a rate close to the slower one we see for older lineages, before the end of the Ice Age. So our understanding of the genetic history of early human evolution shouldn’t change very much. But the timing of the splits between mitochondrial lineages associated with relatively recent events, such as agricultural expansions, may need revision. Using our newly calibrated mitochondrial mutation rates, researchers will be better able to correlate genetic, archaeological and linguistic data, leading to a more accurate understanding of human prehistory.

Thus, event ages have been systematically underestimated in the literature whenever a slower "evolutionary" mutation rate, derived from calibration has been used.

For example, according to the recent paper on Soqotra:

For calculation of time to most recent common ancestor (TMRCA), q statistics (mean divergence from inferred ancestral haplotype) were used with a HVS-I mutation rate of one transition per 20,180 years (Forster et al., 1996).

Forster et al. (1996):

Therefore, we use ρ as an appropriate measure for time depth (table 2), yielding a rate of one transition per 20,180 + 1,000 years in the mtDNA control region (np 16090-16365).

Thus, this rate is equivalent to 0.28/bp/My (assuming a generation length of 20 years).

But from Henn et al.:

The average of ρ-based rate estimates for events younger than 5,000 years is 0.895/bp/My, virtually identical to the pedigree-based average and well within the confidence interval calculated by Howell et al. (2003).

Hence, the 6,000-year old estimate for the novel lineages identified by Cerny et al. for Soqotra should be downgraded to around ~2,000 years, making them more likely to be quite recent founder lineages, rather than Holocene lineages associated with the early settlement of the island.