Population history and genetic diversity in the Americas

This thesis aims to provide insights into the evolutionary history of populations from the Americas by studying patterns of genetic diversity in uniparental (Y-chromosome and mtDNA) and in biparental (X-chromosome and autosomes) marker systems in Native Americans and in populations of mixed ancestry (i.e. “Mestizos”) from Latin American countries. A novel aspect of this work, relative to previous studies, is that the same population samples were examined for all marker systems, thus allowing a more direct contrast of results obtained with the different markers used. I obtained in the laboratory the complete D-loop sequences (~1,200 bp) of 327 Native American mtDNAs from 22 populations sampled across the Americas and in 211 Mestizo individuals from 13 urban centres. I also genotyped 3 SNPs and 11 microsatellites on the Y-chromosome for 220 male individuals available. These data were analyzed together with unpublished data for 38 X-chromosome and 6 Y-chromosome STRs (collected by the Marshfield Foundation, USA) and with published data for 678 autosomal STRs obtained in the same population samples (Wang et al. 2007). Both, the Native and Mestizo populations show evidence of higher admixture with the Y-chromosome than with the mtDNA data. This indicates that admixture in these populations has been sex-biased and involved predominantly Native American women and immigrant men. This sex-biased admixture has thus influenced in a similar way the genetic makeup of both Native and Mestizo populations, which differ only in the extent of this admixture. Population structure analysis also indicates that the mtDNA lineages found in the Mestizo are of local origin, confirming the earlier proposal of a regional “genetic continuity” between Mestizo and native populations. This means that the Mestizo can, to some extent, allow the analysis of Native populations that do not exist anymore. For subsequent analyses I therefore considered the Native American mtDNA and Y-chromosome lineages identified in Mestizo populations as samples of from these presently unavailable native populations. These data demonstrate a lower diversity and higher differentiation among American populations, relative to other continental populations. In addition, a pattern of North to South decrease in population diversity (and increasing population differentiation) is observed across the American continent. These findings agree with the proposal that Native American ancestors came to the New World through the Bering Strait. These data also point to an important role of the coasts as facilitators of migration during the initial colonization of the continent. Phylogenetic, genetic structure and principal component analyses are broadly consistent with the geographic distribution of the populations examined and their proposed linguistic affinity. In addition, these data point to a differentiated demographic history between the various populations examined. Signals of population expansion were detected in the Meso American and Andean populations while populations from East and North West South American appear to have undergone population contractions