Genetic structure among Mexican-Mestizo and Amerindian males

They examine the Y-chromosome among 314 Mexican male students at the Universidad de Guadalajara and 108 Amerindian males. They also compare their findings to published data on various other populations (other Amerindian populations and Spanish).
They do some interesting analyses relating genetic admixture to geography and population structure among the various pre-Hispanic Amerindian groups.

Genetic admixture, relatedness, and structure patterns among Mexican populations revealed by the Y-chromosome

H. Rangel-Villalobos, J.F. Muñoz-Valle, A. González-Martín, A. Gorostiza, M.T. Magaña, L.A. Páez-Riberos

American Journal of Physical Anthropology, Early view

Abstract: Y-linked markers are suitable loci to analyze genetic diversity of human populations, offering knowledge of medical, forensic, and anthropological interest. In a population sample of 206 Mestizo males from western Mexico, we analyzed two binary loci (M3 and YAP) and six Y-STRs, adding to the analysis data of Mexican Mestizos and Amerindians, and relevant worldwide populations. The paternal ancestry estimated in western Mexican-Mestizos was mainly European (60-64%), followed by Amerindian (25-21%), and African (15%). Significant genetic heterogeneity was established between Mestizos from western (Jalisco State) and northern Mexico (Chihuahua State) compared with Mexicans from the center of the Mexican Republic (Mexico City), this attributable to higher European ancestry in western and northern than in central and southeast populations, where higher Amerindian ancestry was inferred. This genetic structure has important implications for medical and forensic purposes. Two different Pre-Hispanic evolutionary processes were evident. In Mesoamerican region, populations presented higher migration rate (Nm = 24.76), promoting genetic homogeneity. Conversely, isolated groups from the mountains and canyons of the Western and Northern Sierra Madre (Huichols and Tarahumaras, respectively) presented a lower migration rate (Nm = 10.27) and stronger genetic differentiation processes (founder effect and/or genetic drift), constituting a Pre-Hispanic population substructure. Additionally, Tarahumaras presented a higher frequency of Y-chromosomes without Q3 that was explained by paternal European admixture (15%) and, more interestingly, by a distinctive Native-American ancestry. In Purepechas, a special admixture process involving preferential integration of non-Purepecha women in their communities could explain contrary genetic evidences (autosomal vs. Y-chromosome) for this tribe.