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Referee Comments: Referee 2

Posted by PLOS_ONE_Group on 17 Mar 2008 at 23:55 GMT

Referee 2's Review:

The manuscript of Achilli et al. performs phylogenetic analyses on the complete mtDNA sequences of Native American haplogroups in order to identify and to date its founders. Besides collecting published sequences, the authors obtained 14 new complete sequences.

This subject was recently investigated in a paper by Tamm et al. (2007), published in PLOS One. As conclusions presented in this manuscript are different from the ones in that paper, I think that PLOS One should accept Achilli et al. manuscript. In fact, the different conclusions relate with a very important issue that is the calibration of the molecular clock. Tamm et al. use only coding synonymous substitutions for age estimations, while Achilli et al. use the conventional criteria of considering all variation in the coding region, and I agree with their argument "It is dubious whether the partial utilization of the coding-region information leads to more credible age estimates, taking into account the extremely low amount of synonymous mutation data characterizing younger clades such as the American ones, and the extreme discrepancies with ages based on control-region variation...".

So, as ages obtained by Achilli et al. are older, the hypothesis advanced by Tamm et al., that Asian ancestors of the first Native Americans paused in Beringia for a considerable period of time, is not favoured. But Tamm et al. also pointed out the absence of specific American mutations in Asian sister-clades as evidence supporting an isolation of the primitive population that eventually migrated to the New World. Do Achilli et al. agree with this last evidence? Are their "only six haplotypes might have been present in the Beringia founders" seen in nowadays Asian populations? Do they agree with a pause, although shorter, somewhere in Beringia?

N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.