Here, we favoured a
rate (1.0 x 10-9/bp/year) estimated directly from NGS analysis of MSY sequences in a deeprooting
pedigree (Xue et al. 2009). Though the direct nature of the analysis and the proven
transmission of newly arising variants are positive features, the study’s major disadvantage is
that its mutation rate rests on only four observations. These numbers will improve as other
resequencing studies are published, but meanwhile other studies (Mendez et al. 2013;
Scozzari et al. 2014) have taken the genome-wide de novo mutation rate (based on a larger
number of observations) and scaled it to account for male-specific transmission, thus inferring
slower rates of 0.62 x 10-9 (Mendez et al. 2013) or 0.64 x 10-9 (Scozzari et al. 2014). Criticism
of this approach (Elhaik et al. 2014) has been based on its indirect nature, and the fact that the
resulting rates are at odds with phylogenetic mutation rate estimates (1.5 – 2.1 x 10-9 /bp/year
(Skaletsky et al. 2003; Kuroki et al. 2006)) based on human-chimpanzee MSY comparisons.
Calibration based on archaeological dates and assumptions about colonisation history (such as
the peopling of the Americas (Poznik et al. 2013) or of Sardinia (Francalacci et al. 2013))
has also been applied, although it introduces other sources of uncertainty. Further analysis of
deep-rooting pedigrees, combined with accumulating data on well-dated ancient DNA, should
help to give more reliable mutation rate estimates in the near future.
I would favour the slower rates of 0.62 or 0.64
