Mexican Native American mtDNA

Considering the sheer size of Mexican Native American population (6 million) it is good to get an idea of the mtDNA haplogroup frequencies of these populations. I do have problems with the ordination of Figure 2 (PCA population plot) and Figure 3 (haplogroup plot). This is not an uncommon problem in the literature. If you look the axes are different values which doesn't accurately discriminate the population because the Huichol (more than likely due to haplogroup X) are having such an effect as an outlier in the plot that the whole thing is skewed (they should have probably bootstrapped this and recalulated without haplogroup X). So when you plot this these two populations with small frequencies of haplogroup X (Huichol and Tarahumara) demonstrate a much larger effect than the other populations in the plot. This current calculation results in this weird bimodal looking plot, which should be more evenly distributed. Also, in figure 3, why use X2 and then only state haplogroups A, B, C, and D when in the text and Table 1 you list A1, A2, B1, B2, C1, C2, D1, D2, if you found them plot them. Also, if the PC plots are compatible then why is A pulling out the Huichol and not X? Overall, would have been better to use an R-matrix (standardized PCA) or MDS plot and measured stress. There is of course the whole how much information can you determine from just mtDNA haplogroup frequency data question but that can wait for another rant.

Characterization of mtDNA Haplogroups in 14 Mexican
Indigenous Populations

rosenda i. penaloza-espinosa, diego arenas-aranda, ricardo m. cerdaflores, leonor buentello-malo, gerardo gonzalez-valencia, javier torres, berenice alvarez, irma mendoza, mario flores, lucila sandoval, francisco loeza, irma ramos, leopoldo munoz, and fabio salamanca1

Human Biology, June 2007, v. 79, no. 3, pp. 313–320.

Abstract
In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca- Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua- Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua- Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua- Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups
found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.