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PLoS Genet. 2013;9(12):e1004023. doi: 10.1371/journal.pgen.1004023. Epub 2013 Dec 26.

Reconstructing Native American migrations from whole-genome and whole-exome data.

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  • 1Department of Human Genetics, McGill University, Montréal, Québec, Canada ; McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada.
  • 2Department of Genetics, Stanford University, Stanford, California, United States of America.
  • 3Department of Genetics, Stanford University, Stanford, California, United States of America ; Ancestry.com DNA LLC, San Francisco, California, United States of America.
  • 4Department of Genetics, Stanford University, Stanford, California, United States of America ; Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE). CCT- CONICET-La Plata, Argentina and Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina.
  • 5Weill Cornell Medical College, New York, New York, United States of America.
  • 6Department of Genetics, Stanford University, Stanford, California, United States of America ; Department of Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, Center for Statistical Genetics, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
  • 7Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America.
  • 8Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
  • 9Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico.
  • 10Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America ; Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain.
  • 11Universidad de Antioquia, Medellín, Colombia.
  • 12Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.

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 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American 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 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 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.

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