Reconstructing Native American Population History

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Nature (Impact Factor: 41.46). 07/2012; 488(7411):370-4. DOI: 10.1038/nature11258
Source: PubMed


The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

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    • "The model does gain some support from the distribution of closely related modern native populations living along the coasts of North and South America that suggest an early single entry and distribution (Fagundes et al. 2008; Reich et al. 2012). The DNA of an early burial at On Your Knees Cave dating to ∼10.3 ka suggests it is linked to these coastal populations (Kemp et al. 2007). "
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    ABSTRACT: A substantial amount of archaeological data suggests groups with markedly different lithic technologies and subsistence adaptations were widespread throughout both American continents by ∼13–13.5 ka. While there are fewer archaeological sites credibly dated to ∼13.5–15.5 ka, they are sufficient to indicate human foragers occupied at least the Pacific coasts of both continents and probably interior continental locations as well. Assuming it required at least 500–2000 years for initial populations to expand throughout these regions, the first colonists must have begun to spread throughout the Americas south of the Laurentide and Cordilleran ice sheets well before post-glacial global warming at 14.5 ka resulted in the melting of the ice sheets and a rapid rise in sea levels. The European and Asian gateway regions to the Americas were occupied by ∼35 ka, and the initial colonization likely postdates this interval. Genetic data suggest the first colonists derive from populations that occupied the Altai Mountains area of central Asia sometime before ∼24 ka, but this hypothesis is based on the modern distribution of haplogroups, and the locations of their ancestral populations at the time they diverged from parent Eurasian populations is unknown. The Altai region is equidistant from both the Atlantic and Pacific gateways to the Americas, and the direction from which the first Americans arrived is a matter of speculation. There are no empirical data supporting the genetic-based hypothesis that there was a population " standstill " in interior Beringia for thousands of years. If there was such a standstill, it more likely occurred in coastal refugia or in other areas in northeast Asia. Scattered data suggest the possibility the Americas were initially occupied sometime prior to ∼17 ka, but these need to be confirmed before they are widely accepted. Of the three most viable hypotheses for the peopling of the Americas, a Clovis First – Ice-free Corridor model appears to be dead and buried; an Atlantic Ice Shelf – Solutrean Origin model is untested, with no empirical data either supporting or falsifying the model; a Pacific coastal model may be the most viable explanation for the initial peopling of the Americas, but also has limited empirical support. This model suggests that boat-using foragers, with an adaptation to the shorelines and estuaries of the Pacific Rim, moved around the margins of the northern Pacific into North and South America before expanding into interior continental regions. Such a migration likely occurred during or prior to the last full glacial.
    07/2015; 1(3):217-250. DOI:10.1179/2055557115Y.0000000006
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    • "Moreover, it is well recognized that native, Mestizos, or Hispanics in America are underrepresented in pharmacogenetic studies even more evidently than African Americans (Cavallari and P. MA, 2013). And although endeavors are currently ongoing, a complete characterization of the genetic diversity among diverse ethnic groups still encompasses a titanic task (Reich et al., 2012). Mexico is home of at least 60 different native groups, representing 7% of the country's over 100 million population, and of Mestizos which are known to be genetically different among the 30 states, with an Amerindian admixture ranging from 30 to 70%. "
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    ABSTRACT: The collection of pharmacogenetic variants in Mexican populations remains incomplete, thus, we aimed to characterize the genotype frequency of 11 SNP on CYP2C9 and VKORC1 in more than one-thousand individuals, and to explore their potential impact on coumarin dosing. In natives, genotype frequencies indicate that over 92% would reflect an extensive metabolism. For Mestizo populations, the proportion of CYP2C9 extensive (79%), intermediate (20.0%) and poor metabolizers (1.0%) was significantly different from that of natives, and varied among the different states of Mexico. Genotype frequencies of 7 SNP on VKORC1, were more homogenously distributed among natives and Mestizos. VKORC1 haplotype analysis revealed that most natives can be grouped into haplotypes H1 or H7-H8, while Mestizos showed a wider frequency distribution for other haplotypes. Our observations confirm previous reports on the genotype distribution of major CYP2C9 alleles, and contribute to the collection of genotype frequencies on relevant VKORC1 variants. Copyright © 2014. Published by Elsevier B.V.
    Gene 01/2015; 558(2). DOI:10.1016/j.gene.2014.12.068 · 2.14 Impact Factor
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    • "DNA evidence supports at least three migrations with the earliest 15–40,000 BP referred to generically as the Paleoindian and associated with the greatest distribution of language and cultural groups across North, Meso, and South America; the second 12–14,000 BP is the Na-Dene distributed in North America from Alaska to the Pacific Northwest and from Canada to the U.S. Southwest; and the third ca. 9000 BP is Eskimo-Aleut with circumpolar distribution [3], [4]. Linguists have classified Eskimo-Aleut and Na-Dene as separate language stocks, and the rest of the languages of the Americas as belonging to numerous stocks, but have otherwise been mostly silent on questions that connect Asian and the American populations because, with the exception of Eskimo-Aleut, the dates of these earlier connections lie beyond the traditionally accepted limit for comparative reconstruction. "
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    ABSTRACT: FULL TEXT HERE: Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America.
    PLoS ONE 12/2014; 9(3):e91722. DOI:10.1371/journal.pone.0091722 · 3.23 Impact Factor
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