Referee 2's Review:

**********
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.
*********

The manuscript "Paternal Genetic Structure of Hainan Aborigines Isolated at the Entrance to East Asia" presents some interesting and relevant Y-chromosome data from a population that was not previously characterized for the Y-chromosome, the Hainan Aborigines. The data can help us to understand the history of East Asian populations. The authors propose that the absence (or near absence) of O3 in these populations and predominance of O1 and O2 reflect different histories of these clades. O1 and O2 expanded through the coast from mainland Southeast Asia into East Asia while O3 expanded through an earlier offshoot in the West. The Hainan population became isolated after the sea-level rises and were not affected significantly by the Han expansion that brought the high frequency of O3 to other South Chinese populations. The paper should be published but it requires some minor to major changes and a better argumentation for some of its reasoning.

Major points:

The paper is partly based on the notion that O3 emerged in Sino-Tibetan speaking populations and its presence on other populations is mainly due to later expansions from these Sino-Tibetan speaking populations. The argument is based mainly on frequencies of O3. However O3 is more frequent in Hmong-Mien populations than in Sino-Tibetan speaking populations. Can the authors justify their argument on that aspect? Additionally, the idea that O3 was carried by Sino-Tibetan ancestors through a western route is not really supported in any way since, even assuming that O3 was brought to South China populations during the Han expansion, O3 could have emerged in the same and possibly single eastern route but later after the time of emergence of O1 and O2.

In the description of the building of the networks it would be useful to have more information on the actual weighting used in the networks. Moreover it seems unlikely that networks without any reticulation were obtained using a 7 STR system unless the threshold was reduced significantly which could cause many probable links to disappear and any conclusion obtained should be cautiously inferred. Information on that would also be useful. The authors mention that the age estimates obtained in network were confirmed by BATWING, although they do not describe the assumptions in those analyses. Moreover a table of age estimates of the calculated clades would be useful comparing both methods.

Minor points:

The terms "stained" and "unstained" when referring to presence or absence of genetic input from one population into another seem highly inappropriate. Could the authors please rephrase it?

It is not clear if the classification of the Hainan aborigines is strictly linguistic or ethnic. The authors should make it clear in the introduction.

The nature of the referred resemblances between Hainan aborigines and Malaysians is not clear and there is no reference to it.

As the authors point out in the introduction "time and route of expansion of modern humans into eastern Asia remains controversial", so what are exactly the bases for the expansions (arrows) in figure 1? Moreover the position of Taiwan "rather far from the entrance to East Asia" is not entirely clear due to the same reasoning.

The reference to the frequency of O3 in Taiwanese populations should be an available published one (Capelli et al.2001?). Additionally the frequency of O3 diverges greatly between Taiwanese groups and at least a minimum and maximum value should be mentioned.

The Ice Age peak in East Asia and Southeast Asia is not between 12 and 14 thousand years as mentioned, but before. At that time the sea level was rising and a significant tract of land in South China-Southeast Asia was already drowned.

Could the authors rephrase vague sentences like "quite a long time" (abstract) and "really old haplogroup" (results and discussion)?

The general Figure 1 legend ("Geographic distributions of the Hainan Island and the Hainan aborigines") does not make sense. Could the authors rephrase it?

In the age estimates the authors referred to population ages when they are referring to the age of clades. As a suggestion the authors could round the values to multiples of 100 or at least of 10 instead of placing the precise value.

Some minor corrections:
...and lay on one of the ways... instead of ... and lay in one of the ways... (page 4)
...have remained isolated... instead of ...have kept isolated... (page 4)
... cannot... instead of ... can not... (page 5 and 8)
...genetic studies... instead of "...genetics studies..." (page 10 and 11)
There is a missing space in ...Network4.201."

Reference:
Capelli, C, Wilson, JF, Richards, M, Stumpf, MPH, Gratrix, F, Oppenheimer, S, Underhill, P, Pascali, VL, Ko, T-M, Goldstein, DB. 2001. A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania. American Journal of Human Genetics 68:432-443.