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Referee Comments: Referee 1

Posted by PLOS_ONE_Group on 13 May 2008 at 23:50 GMT

Referee 1's Review:

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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.
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This manuscript presents a detailed study of mitochondrial DNA lineages belonging to the X haplogroup in an Israeli Druze population. X, an ancient and fascinating lineage distributed throughout western Eurasia and North America, has long been a mystery to population geenticists studying human migratory history. The hypothesis advanced in the manuscript by Shlush et al. is that the current distribution of X results from an expansion out of refugia that acted as a type of 'nursery' for the development of X diversity. The authors suggest that the Israeli Druze population, and in particular the population from the region of Galilee, represents such a population refugium.

I have several issue with the manuscript as a candidate for publication in PLoS One. First, it represents a very focused study on one particular mtDNA lineage in one particular population. As such, I feel that it's interest is mainly limited to specialists in the field of mtDNA population genetics, and that it may not appeal to the broader readership of PLoS One. Second, while the frequency of X lineages in the studied Druze population is quite high, the diversity - 2 and 5 distinct whole-genome lineages on the X1 and X2 branches, respectively - does not encompass the total range of variation found in haplogroup X, so the author's contention that such refugia account for the pattern of X diversity seen today is not strongly supported. I would, for instance, suggest that the present pattern is much more likely to have resulted from an ancient spread of X lineages during the Pleistocene which has since been subsumed under more recent Holocene migrations. Nonetheless, the pattern of X variation they see is interesting. I would have liked to have seen what the rest the mtDNA patterns looked like - if the Druze do truly represent a refugium, I would expect other lineages to exhibit similar patterns - or are the authors suggesting that the pattern of X diversity was preferentially maintained relative to that of other lineages? Finally, in general, it is unclear to me how a population that seems to have come into existence in the 12th-13th centuries from a diverse set of founders could be seen as a refugium for a mtDNA lineage that is perhaps 50,000 years old.

I would urge the authors to re-draft their manuscript, giving a more complete picture of the overall pattern of mtDNA diversity in their Druze sample (not just haplogroup X) and submit it to AJHG or another more specialized journal.