Dataset Information

Reconstructing Native American population history.

ABSTRACT: The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

SUBMITTER: Reich D

PROVIDER: S-EPMC3615710 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

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Reconstructing Native American population history.

Reich David D Patterson Nick N Campbell Desmond D Tandon Arti A Mazieres Stéphane S Ray Nicolas N Parra Maria V MV Rojas Winston W Duque Constanza C Mesa Natalia N García Luis F LF Triana Omar O Blair Silvia S Maestre Amanda A Dib Juan C JC Bravi Claudio M CM Bailliet Graciela G Corach Daniel D Hünemeier Tábita T Bortolini Maria Cátira MC Salzano Francisco M FM Petzl-Erler María Luiza ML Acuña-Alonzo Victor V Aguilar-Salinas Carlos C Canizales-Quinteros Samuel S Tusié-Luna Teresa T Riba Laura L Rodríguez-Cruz Maricela M Lopez-Alarcón Mardia M Coral-Vazquez Ramón R Canto-Cetina Thelma T Silva-Zolezzi Irma I Fernandez-Lopez Juan Carlos JC Contreras Alejandra V AV Jimenez-Sanchez Gerardo G Gómez-Vázquez Maria José MJ Molina Julio J Carracedo Angel A Salas Antonio A Gallo Carla C Poletti Giovanni G Witonsky David B DB Alkorta-Aranburu Gorka G Sukernik Rem I RI Osipova Ludmila L Fedorova Sardana A SA Vasquez René R Villena Mercedes M Moreau Claudia C Barrantes Ramiro R Pauls David D Excoffier Laurent L Bedoya Gabriel G Rothhammer Francisco F Dugoujon Jean-Michel JM Larrouy Georges G Klitz William W Labuda Damian D Kidd Judith J Kidd Kenneth K Di Rienzo Anna A Freimer Nelson B NB Price Alkes L AL Ruiz-Linares Andrés A

Nature 20120801 7411

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siber ...[more]

PMID: 22801491

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Project description: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.

Project description:The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse--which today is reflected by shorter, older ancestry tracts--consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse--reflected by longer, younger tracts--is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

Dataset Information

Reconstructing Native American population history.

Publications

Reconstructing Native American population history.

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