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An interesting freely available study has just been published: Irma Silva-Solezzi et al. Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico. PNAS, 2009.
Results
We analyzed data from 300 nonrelated self-identified Mestizo individuals from 6 states located in geographically distant regions in Mexico: Sonora (SON) and Zacatecas (ZAC) in the north, Guanajuato (GUA) in the center, Guerrero (GUE) in the center–Pacific, Veracruz (VER) in the center–Gulf, and Yucatan (YUC)in the southeast. Considering that Zapotecos have been shown as a good ancestral population for predicting Amerindian (AMI) ancestry in Mexican Mestizos (16), we included 30 Zapotecos(ZAP) from the southwestern state of Oaxaca (Fig. 1). For comparative purposes, we included similar data sets from HapMap populations: northern Europeans (CEU), Africans (YRI), and East Asians (EA), including Chinese (CHB) and Japanese (JPT). A HapMap-like database with SNP frequencies in Mexicans and HapMap populations was generated (http://diversity.inmegen. gob.mx).
Results
We analyzed data from 300 nonrelated self-identified Mestizo individuals from 6 states located in geographically distant regions in Mexico: Sonora (SON) and Zacatecas (ZAC) in the north, Guanajuato (GUA) in the center, Guerrero (GUE) in the center–Pacific, Veracruz (VER) in the center–Gulf, and Yucatan (YUC)in the southeast. Considering that Zapotecos have been shown as a good ancestral population for predicting Amerindian (AMI) ancestry in Mexican Mestizos (16), we included 30 Zapotecos(ZAP) from the southwestern state of Oaxaca (Fig. 1). For comparative purposes, we included similar data sets from HapMap populations: northern Europeans (CEU), Africans (YRI), and East Asians (EA), including Chinese (CHB) and Japanese (JPT). A HapMap-like database with SNP frequencies in Mexicans and HapMap populations was generated (http://diversity.inmegen. gob.mx).
Some assorted images:
Fig.1. Map showing areas sampled and diversity compared to HapMap standard samples. All populations are Mestizos except ZAP who are Native American Zapotecos.
Fig. 2. Plots of the Mexican and HapMap samples: A includes YRI (Yorubans), B without YRI. 
Fig. 3A. Poulation structure of Mexicans and HapMap samples.No novel conclusions, I'd say. As is known (at least by Mexicans) Northwesterners (represented here by SON) are "whiter" than average. All Mestizo Mexicans are basically a mixture of Europeans and Native Americans with very small apportion of African ancestry (more notable in Guerrero and some Veracruz individuals).
It is interesting to see anyhow how when a true Amerindian sample is introduced, a clear distinction appears with the East Asian HapMap sample that, by itself, can only be a poor approximation to Native American genotype. To a lesser extent surely it could be argued that CEU may not represent well the SW European ancestry of Mexicans but guess the differences are much less extreme (Europeans in general cluster all very close to CEU when in intercontinental contexts).
For further references on medical genomics regarding Mexico check this article at Science Daily.
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It is interesting to see anyhow how when a true Amerindian sample is introduced, a clear distinction appears with the East Asian HapMap sample that, by itself, can only be a poor approximation to Native American genotype. To a lesser extent surely it could be argued that CEU may not represent well the SW European ancestry of Mexicans but guess the differences are much less extreme (Europeans in general cluster all very close to CEU when in intercontinental contexts).
For further references on medical genomics regarding Mexico check this article at Science Daily.
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