Migrations to the new world brought together individuals from Europe, Africa and the Americans. Inter-mating between these migrant and indigenous populations led to the subsequent formation of new admixed populations, such as African and Latino Americans. These unprecedented events brought together genomes that had evolved independently on different continents for tens of thousands of years and presented new environmental challenges for the indigenous and migrant populations, as well as their offspring. These circumstances provided novel opportunities for natural selection to occur that could be reflected in deviations at specific locations from the genome-wide ancestry distribution. Here we present an analysis examining European, Native American and African ancestry based on 284 microsatellite markers in a study of Mexican Americans from the Family Blood Pressure Program. We identified two genomic regions where there was a significant decrement in African ancestry (at 2p25.1...and 9p24.1...) and one region with a significant increase in European ancestry (at 1p33...). These locations may harbor genes that have been subjected to natural selection after the ancestral mixing giving rise to Mexicans.
After the great die-off of indigenous peoples in the New World in many regions such as Mexico and Venezuela mixed populations arose to become demographically preponderant. In places like Brazil and Argentina the persistence of Amerindian female lineages in populations of seemingly European and African ancestries suggests that even these regions experienced a transient period of Mestizo demographic dominance before immigration and the slave trade obscured it.
Obviously some of displacement of Amerindians by Mestizos can be explained by natural demographic processes as the latter reproduced a high rates to take advantage of the land surplus generated by the decrease in the population of the former (on the order of a 90% drop). Only in relatively isolated areas, such as the Guatemalan highlands, or in ecoregions where Amerindians had a physiological advantage such as the Andes, did native populations retain their demographic dominance (probably through a bounce back after the initial population drop). But it seems plausible that part of the displacement was simply due to the fact that the Mestizos were also resistant to many of the diseases to which their Amerindian relatives were vulnerable. Among the offspring of male Europeans and female Amerindians who mated to produce later generations segregation of alleles from their fathers which would confer immune resistance would exhibit variance within the population. Though almost everyone within the population of Mestizos would be about 1/2 European and 1/2 Amerindian, some would carry fewer of the European complement of alleles and so have reduced fitness. And so it might be that particular genomic regions from European ancestors might increase in frequency over time. As for the Africans, there are many disease adaptations for malaria that are obviously not useful anymore. The same process of purifying selection occurred among African Americans. Not all regions of the genome are subject to the same evolutionary dynamics. Or, at least the values of the parameters might vary.