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Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

Gravel, S; Zakharia, F; Moreno-Estrada, A; Byrnes, JK; Muzzio, M; Rodriguez-Flores, JL; Kenny, EE; ... Bustamante, CD; + view all (2013) Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data. PLoS Genetics , 9 (12) , Article e1004023. 10.1371/journal.pgen.1004023. Green open access

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Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is [Formula: see text] in MXL, [Formula: see text] in CLM, and [Formula: see text] in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas [Formula: see text] thousand years ago (kya), supports that the MXL Ancestors split [Formula: see text]kya, with a subsequent split of the ancestors to CLM and PUR [Formula: see text]kya. The model also features effective populations of [Formula: see text] in Mexico, [Formula: see text] in Colombia, and [Formula: see text] in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.

Type: Article
Title: Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pgen.1004023
Publisher version: http://dx.doi.org/10.1371/journal.pgen.1004023
Language: English
Additional information: © 2013 Gravel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. PMCID: PMC3873240
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: http://discovery.ucl.ac.uk/id/eprint/1429904
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