title: Reconstructing Native American migrations from whole-genome and whole-exome data.
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.
authors.affiliation: Department of Human Genetics, McGill University, Montréal, Québec, Canada ; McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada.
authors.forename: Simon
authors.initials: S
authors.lastname: Gravel
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America.
authors.forename: Fouad
authors.initials: F
authors.lastname: Zakharia
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America.
authors.forename: Andres
authors.initials: A
authors.lastname: Moreno-Estrada
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America ; Ancestry.com DNA LLC, San Francisco, California, United States of America.
authors.forename: Jake K
authors.initials: JK
authors.lastname: Byrnes
authors.affiliation: Department 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.
authors.forename: Marina
authors.initials: M
authors.lastname: Muzzio
authors.affiliation: Weill Cornell Medical College, New York, New York, United States of America.
authors.forename: Juan L
authors.initials: JL
authors.lastname: Rodriguez-Flores
authors.affiliation: Department 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.
authors.forename: Eimear E
authors.initials: EE
authors.lastname: Kenny
authors.affiliation: Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Gignoux
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America.
authors.forename: Brian K
authors.initials: BK
authors.lastname: Maples
authors.affiliation: Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
authors.forename: Wilfried
authors.initials: W
authors.lastname: Guiblet
authors.affiliation: Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico.
authors.forename: Julie
authors.initials: J
authors.lastname: Dutil
authors.affiliation: Department 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.
authors.forename: Marc
authors.initials: M
authors.lastname: Via
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America.
authors.forename: Karla
authors.initials: K
authors.lastname: Sandoval
authors.affiliation: Universidad de Antioquia, Medellín, Colombia.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Bedoya
authors.affiliation: Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
authors.forename: Taras K
authors.initials: TK
authors.lastname: Oleksyk
authors.affiliation: Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
authors.forename: Andres
authors.initials: A
authors.lastname: Ruiz-Linares
authors.affiliation: Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America.
authors.forename: Esteban G
authors.initials: EG
authors.lastname: Burchard
authors.affiliation: Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Martinez-Cruzado
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America.
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
mesh_terms: D044383:Black People / Q000235:genetics; D002874:Chromosome Mapping; D059472:Exome; D005787:Gene Frequency / Q000235:genetics*; D005828:Genetics, Population; D015894:Genome, Human; D006630:Hispanic or Latino / Q000235:genetics; D016045:Human Genome Project; D063426:Human Migration; D006801:Humans; D007198:Indians, North American / Q000235:genetics*; D017058:Mexican Americans / Q000235:genetics; D008800:Mexico; D011647:Puerto Rico; D044469:Racial Groups / Q000235:genetics; D044465:White People / Q000235:genetics