Reconstructing native american migrations from whole-genome and whole-exome data

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 in MXL, in CLM, and 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 thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and 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.Fil: Gravel, Simon. Université du Québec a Montreal; Canadá. McGill University; CanadáFil: Zakharia, Fouad. University of Stanford; Estados UnidosFil: Moreno Estrada, Andrés. University of Stanford; Estados UnidosFil: Byrnes, Jake B.. University of Stanford; Estados UnidosFil: Muzzio, Marina. University of Stanford; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Rodriguez Flores, Juan L.. Weill Cornell Medical College; Estados UnidosFil: Kenny, Eimear E.. University of Stanford; Estados Unidos. Icahn School of Medicine at Mount Sinai; Estados UnidosFil: Gignoux, Christopher R.. University of California; Estados UnidosFil: Maples, Brian K.. University of Stanford; Estados UnidosFil: Guiblet, Wilfried. Universidad de Puerto Rico; Puerto RicoFil: Dutil, Julie. Universidad de Puerto Rico; Puerto RicoFil: Via, Marc. Universidad de Barcelona; España. University of California; Estados UnidosFil: Sandoval, Karla. University of Stanford; Estados UnidosFil: Bedoya, Gabriel. Universidad de Antioquía; ColombiaFil: Oleksyk, Taras K.. Universidad de Puerto Rico; Puerto RicoFil: Ruiz Linares, Andres. University College London; Estados UnidosFil: Burchard, Esteban G.. University of California; Estados UnidosFil: Martinez Cruzado, Juan Carlos. Universidad de Puerto Rico; Puerto RicoFil: Bustamante, Carlos. University of Stanford; Estados UnidosFil: The 1000 Genomes Project