1. Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data
- Author
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Gravel, Simon, Zakharia, Fouad, Moreno Estrada, Andrés, Byrnes, Jake K., Muzzio, Marina, Rodriguez Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K., Ruiz Linares, Andrés, Burchard, Esteban G., Martinez Cruzado, Juan Carlos, Bustamante, Carlos D., The 1000 Genomes Project, and Universitat de Barcelona
- Subjects
Cancer Research ,Population genetics ,Amèrica ,Genoma humà ,92D25 ,purl.org/becyt/ford/1 [https] ,Effective population size ,Gene Frequency ,Models ,Human Genome Project ,Mexican Americans ,Sequencing ,Exome ,Aborígens ,Genetics (clinical) ,Native American Migrations ,Genetics ,0303 health sciences ,education.field_of_study ,Human migration ,Population size ,030305 genetics & heredity ,Chromosome Mapping ,Hispanic or Latino ,Bioquímica y Biología Molecular ,Full Genomes ,CIENCIAS NATURALES Y EXACTAS ,Research Article ,lcsh:QH426-470 ,Human Migration ,Population ,Black People ,America ,Biology ,White People ,Ciencias Biológicas ,03 medical and health sciences ,Pobles indígenes ,Migració de pobles ,Humans ,Ciencias Naturales ,Quantitative Biology - Genomics ,1000 Genomes Project ,purl.org/becyt/ford/1.6 [https] ,education ,Quantitative Biology - Populations and Evolution ,Molecular Biology ,Genotyping ,Allele frequency ,Mexico ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Genomics (q-bio.GN) ,Human genome ,business.industry ,Genome, Human ,Puerto Rico ,Racial Groups ,Native American ,Populations and Evolution (q-bio.PE) ,15. Life on land ,Migrations of nations ,lcsh:Genetics ,Genetics, Population ,Evolutionary biology ,FOS: Biological sciences ,Indians, North American ,Indigenous peoples ,business - 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 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 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., Facultad de Ciencias Naturales y Museo, Instituto Multidisciplinario de Biología Celular
- Published
- 2013