Reviewer 2's Review

“I think that this is a superb piece of work on phylogeography. The structure of the manuscript is clear to the reader and the results obtained are of great interest. Finally, the discussion appears as an interesting contribution to the historical biogeography of the African continent.

Nevertheless, there are some minor issues that I would like point out.

Title: In my opinion, to mention the question of conservation in the title may appear a bit ambitious, because this is only a very minor point in the whole manuscript. I rather would change "conservation" for "historical biogeography".

Abstract: The authors should include the scientific name of the species they study. This would make easy to identify it for those readers that are not familiarized with the English name.

Introduction (page 5): The authors mention limitations of other methods used to partition biodiversity. I would not say so much. I think that it is not needed to build up your own results by diminishing other work. This paper is good enough to stand without that.
That is why I would propose that this kind of analysis is complementary of traditional biogeographical analyses, rather than "forms the basis for a shift from the classical taxonomical or phylogeographycal approach" (page13 -Key Biogeographic Regions-).

Results (Genetic structure, page 7): I would say that it is very interesting to note that the spliting date of the two main lines and the timing of the diversification within them are congruent with evidence derived from fields as different as paleoclimatology (Shackleton, 1995), tectonics (Partridge et al., 1995), ruminant phylogenetics (Hernández Fernández & Vrba, 2005) and faunal turnover (Vrba, 1995, 2000, 2005). In my opinion, the authors could get into it a little bit more deeply.
Related to this, in my opinion, it is important to change figure 2 in order to include the timeframe for the genetic diversification of the species. It would be also valuable for the discussion on ecological and evolutionary issues.

Results (Biogeographic models, page 8): It could be interesting to include a recent biogeographical sectorization of Subsaharan Africa made according to avian assemblages (Williams et al. 1999) as another model to compare. That is a very exhaustive biogeographic model exclusively centered in the African continent.

Discussion (Origins, page 10): In relation to the information on the Pliocene climate of north-east Africa, might be adequate to include some references more specific on the topic (e.g. Reed, 1997; Bobe & Eck, 2001; Hernández Fernández & Vrba, 2006). And it could be interesting to include a comparison of the diversification pattern with the pattern of climatic changes during the Plio-Pleistocene.

Discussion (Model testing, page 11): The authors say that coat color, patterning, horn and body size and hair length are not enough to discriminate the different genetic populations described for them. Could they propose some additional phenotypic characters that may help to morphologists?

Discussion (Connectivity..., page 12): It does not appear clear to me, from the text, the definition of ecological specialists and generalists. It seems that there are two different measures. Is that right? If it is like that, are they congruent? If they are congruent and more or less indicate the same, it might be better to stuck to only one measure, in order to simplify this part of the article. And to look at table 2 does not help... may be because there are core habitats, core ecoregions, and core biomes, which does not help to understand the measure of specialization. A more clear approach to this question is needed.


I hope that the authors of this interesting paper consider these suggestions interesting and adequate.


References:

Bobe, R., and Eck, G.G., 2001, Responses of African bovids to Pliocene climatic change.: Paleobiology, v. 27, p. 1-47.
Hernández Fernández, M., and Vrba, E.S., 2005, A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants.: Biological Reviews, v. 80, p. 269-302.
Hernández Fernández, M., and Vrba, E.S., 2006, Plio-Pleistocene climatic change in the Turkana Basin (East Africa): Evidence from large mammal faunas.: Journal of Human Evolution, v. 50, p. 595-626.
Reed, K.E., 1997, Early hominid evolution and ecological change through the African Plio-Pleistocene.: Journal of Human Evolution, v. 32, p. 289-322.
Shackleton, N.J., 1995, New data on the evolution of Pliocene climatic variability., in Vrba, E.S., Denton, G.H., Partridge, T.C., and Burckle, L.H., eds., Paleoclimate and Evolution, with Emphasis on Human Origins.: New Haven, Yale University Press, p. 242-248.
Vrba, E.S., 1995, On the connections between paleoclimate and evolution., in Vrba, E.S., Denton, G.H., Partridge, T.C., and Burckle, L.H., eds., Paleoclimate and Evolution, with Emphasis on Human Origins.: New Haven, Yale University Press, p. 24-45.
Vrba, E.S., 2000, Major features of Neogene mammalian evolution in Africa., in Partridge, T.C., and Maud, R.R., eds., The Cenozoic of Southern Africa.: Oxford, Oxford University Press, p. 277-304.
Vrba, E.S., 2005, Mass turnover and heterochrony events in response to physical change.: Paleobiology, v. 31, p. 157-174.
Williams, P.H., Klerk, H.M.d., and Crowe, T.M., 1999, Interpreting biogeographical boundaries among Afrotropical birds: spatial patterns in richness gradients and species replacement.: J. Biogeography, v. 26, p. 459-474.”

n.b. These are the general comments made by the reviewer when reviewing the originally submitted version of this paper. The manuscript was revised before publication. Specific minor points addressed during revision of the paper are not shown.