Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population. We evaluated genetic diversity, linkage disequilibrium patterns, and extent of haplotype sharing using genomewide data from Mexican Mestizos from regions with different histories of admixture and particular population dynamics. Ancestry was evaluated by including 1 Mexican Amerindian group and data from the HapMap. Our results provide evidence of genetic differences between Mexican subpopulations that should be considered in the design and analysis of association studies of complex diseases. In addition, these results support the notion that a haplotype map of the Mexican Mestizo population can reduce the number of tag SNPs required to characterize common genetic variation in this population. This is one of the first genomewide genotyping efforts of a recently admixed population in Latin America.
The basic issue here is that "Latino" or "Hispanic" is not a race in a genetic sense. There are Latinos of white, black and Amerindian origin, and every permutation of these three kinds. Population substructure is important for medical reasons because correlations between genetic variants & diseases might actually simply be due to the common relationship of these variants & diseases to a particular population. This is why research which shows how Ashkenazi Jews relate to other American whites is medically important; what might be typical of gentile whites might not be typical of Ashkenazi Jews (who have a history of population specific diseases).
In the case of Latin America the genetic complexity exists for an obvious historical reason: mass die off native populations due to disease and de facto polygyny on the part of Iberian males. Sex mediated gene flow results in the fact that among mixed populations Amerindian ancestry is tends to be found in the maternal lineage. This is almost certainly the case for Mexico. But, there is a variation in terms of the nature of Mestizo culture which likely tracks the ancestral quanta of European and Amerindian. In short, northern Mexico is more Spanish flavored due to both coincidences of climate and the relatively sparse populations of natives. The further south one goes the stronger the signal of native ancestry and impact of native culture. This we knew qualitatively, but studies like this give us a quantitative grasp. Here are the figures which tell the story rather well:
Nothing qualitatively surprising.
1) The balance between European and Amerindian ancestry varies as a function of latitude.
2) The proportion of African ancestry is highest in the very provinces one would expected based on historical records (Afro-Mexicans played a relatively large role in the colonial administration of particular coastal locales because of their robusticity in the face of diseases which took a toll on both Europeans and Amerindians).
3) Note that even in the relatively small sizes you see not too much variance in ancestral proportions in many of these states. That's because of the admixture event is many generations back, and the populations have now had time to mix thoroughly with each other.
4) There is a weakness in comparing to Utah whites and Zapotec Indians as proxies for the ancestral groups, as obviously the white ancestors of the Mestizos were mostly Iberian, not Northwest European. Additionally, some of the data from the Yucatan highlights the reality that the Zapotecs themselves differ from the Amerindian ancestors of Mestizos across regions of Mexico, and so are not perfect proxies.
Related: Genetic structure of Eastern European populations, Genetic map of Europe; genes vary as a function of distance , Genetic Map of East Asia, The Genetic Map of Europe, More genetic maps of Europe, Finns as European genetic outliers, Population substructure in Japan, Finns as European outliers, The genetics of Fenno-Scandinavia, Korean genetic relationships and Human population structure, part n.
OT, but have you posted about the Nature website "Scitable" yet? I've found it to be a very good resource and it'd be nice if everyone knew about it.