A note on erroneous ethnolinguistic affiliations in genetic studies of southern Africa.

Abstract

In his review on the genetics and prehistory of South Africa, Mitchell (2010) makes a much needed critical assessment of the ethnolinguistic and geographic affiliation of individuals that have been used so far in genetic analyses of indigenous peoples of southern Africa. In referring to a recent work that I co-authored (Coelho et al., 2009), Dr. Mitchell criticizes the fact that in Additional file 4 we repeat a current mistake in considering southern Angolan mtDNA samples from !Xun/Khwe communities as South African. Another criticism is that, in treating Y chromosome data in Additional file 5 we make an “absurd” and “artificial” division between Omega and Sekele San, when both refer to !Xun speakers from Angola. While the general point raised about nomenclature imprecision in genetic literature is undisputable, I feel that some important details are missing about my own work. Therefore, I would like to provide the readers of JASs an additional explanation of what in fact was done in that paper. The Additional files 4 and 5 in Coelho et al. (2009), to which Mitchell (2010) refers, simply list the samples from published literature that were included in our data base. As is common-practice in many genetic studies using previously published data, we chose to provide sample provenances as described by the authors who originally generated the data. For example, a distinction between Omega and Sekele San is explicitly done in the Y chromosome short tandem repeat data available at http://pritch.bsd. uchicago.edu/dataArchive/ydata.html, which was generated by Pritchard et al. (1999), as indicated in our Additional File 5. We therefore wanted to make sure that, when consulting Pritchard et al’s. (1999) data, the readers had no doubts about the fact that both sets of “San” samples were included in our analyses. While we could have added footnotes to better clarify inconsistencies in nomenclature and ethnolinguistic affiliation, our major purpose was to provide traceable information that could help the reader to assess the sources of the data as straightforwardly as he could. Finally, I would like to apologize for the typographic error that led us to refer to the Khwe as “Kwe” in Additional file 5, which left Dr. Mitchell uncertain about which population we were referring to.