Genetic Variation and Population Structure in Native Americans

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Abstract
We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. Studies of genetic variation have the potential to provide information about the initial peopling of the Americas and the more recent history of Native American populations. To investigate genetic diversity and population relationships in the Americas, we analyzed genetic variation at 678 genome-wide markers genotyped in 29 Native American populations. Comparing Native Americans to Siberian populations, both genetic diversity and similarity to Siberians decrease with geographic distance from the Bering Strait. The widespread distribution of a particular allele private to the Americas supports a view that much of Native American genetic ancestry may derive from a single wave of migration. The pattern of genetic diversity across populations suggests that coastal routes might have been important during ancient migrations of Native American populations. These and other observations from our study will be useful alongside archaeological, geological, and linguistic data for piecing together a more detailed description of the settlement history of the Americas.