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Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet 2013; 9:e1004023. [PMID: 24385924 PMCID: PMC3873240 DOI: 10.1371/journal.pgen.1004023] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
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 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. Populations of the Americas have a rich and heterogeneous genetic and cultural heritage that draws from a diversity of pre-Columbian Native American, European, and African populations. Characterizing this diversity facilitates the development of medical genetics research in diverse populations and the transfer of medical knowledge across populations. It also represents an opportunity to better understand the peopling of the Americas, from the crossing of Beringia to the post-Columbian era. Here, we take advantage sequencing of individuals of Colombian (CLM), Mexican (MXL), and Puerto Rican (PUR) origin by the 1000 Genomes project to improve our demographic models for the peopling of the Americas. The divergence among African, European, and Native American ancestors to these populations enables us to infer the continent of origin at each locus in the sampled genomes. The resulting patterns of ancestry suggest complex post-Columbian migration histories, starting later in CLM than in MXL and PUR. Whereas European ancestral segments show evidence of relatedness, a demographic model of synonymous variation suggests that the Native American Ancestors to MXL, PUR, and CLM panels split within a few hundred years over 12 thousand years ago. Together with early archeological sites in South America, these results support rapid divergence during the initial peopling of the Americas.
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Affiliation(s)
- Simon Gravel
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
- * E-mail:
| | - Fouad Zakharia
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Andres Moreno-Estrada
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jake K. Byrnes
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Ancestry.com DNA LLC, San Francisco, California, United States of America
| | - Marina Muzzio
- 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
| | | | - Eimear E. Kenny
- 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
| | - Christopher R. Gignoux
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Maples
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Wilfried Guiblet
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Marc Via
- 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
| | - Karla Sandoval
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | | | | | - Taras K. Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | | | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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Hünemeier T, Amorim CEG, Azevedo S, Contini V, Acuña-Alonzo V, Rothhammer F, Dugoujon JM, Mazières S, Barrantes R, Villarreal-Molina MT, Paixão-Côrtes VR, Salzano FM, Canizales-Quinteros S, Ruiz-Linares A, Bortolini MC. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution. PLoS One 2012; 7:e38862. [PMID: 22768049 PMCID: PMC3380856 DOI: 10.1371/journal.pone.0038862] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/12/2012] [Indexed: 12/26/2022] Open
Abstract
Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.
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Affiliation(s)
- Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Eduardo Guerra Amorim
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Soledad Azevedo
- Centro Nacional Patagónico, CONICET, U9120ACV, Puerto Madryn, Argentina
| | - Veronica Contini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Jean-Michel Dugoujon
- Laboratoire d′Anthropologie Moléculaire et d′Imagerie de Synthèse, UMR 5288 CNRS, Université Paul Sabatier (Toulouse3), Toulouse, France
| | - Stephane Mazières
- Anthropologie Bio-culturelle, Droit, Ethique et Santé (ADES), UMR 7268, Aix-Marseille-Université/CNRS/EFS, Marseille, France
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Vanessa Rodrigues Paixão-Côrtes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Canizales-Quinteros
- Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andres Ruiz-Linares
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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3
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Bisso-Machado R, Bortolini MC, Salzano FM. Uniparental genetic markers in South Amerindians. Genet Mol Biol 2012; 35:365-87. [PMID: 22888284 PMCID: PMC3389523 DOI: 10.1590/s1415-47572012005000027] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/12/2012] [Indexed: 12/25/2022] Open
Abstract
A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.
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Affiliation(s)
- Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet 2012; 90:229-46. [PMID: 22281367 DOI: 10.1016/j.ajhg.2011.12.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/06/2011] [Accepted: 12/19/2011] [Indexed: 11/20/2022] Open
Abstract
The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.
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Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Mazzotti G, Poletti G, Hill K, Hurtado AM, Labuda D, Klitz W, Barrantes R, Bortolini MC, Salzano FM, Petzl-Erler ML, Tsuneto LT, Llop E, Rothhammer F, Excoffier L, Feldman MW, Rosenberg NA, Ruiz-Linares A. Genetic variation and population structure in native Americans. PLoS Genet 2007; 3:e185. [PMID: 18039031 PMCID: PMC2082466 DOI: 10.1371/journal.pgen.0030185] [Citation(s) in RCA: 347] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 09/10/2007] [Indexed: 01/04/2023] Open
Abstract
We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.
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Affiliation(s)
- Sijia Wang
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - Cecil M Lewis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mattias Jakobsson
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sohini Ramachandran
- Department of Biological Sciences, Stanford University, Stanford, California, United States of America
| | - Nicolas Ray
- Computational and Molecular Population Genetics Lab, University of Bern, Bern, Switzerland
| | - Gabriel Bedoya
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Winston Rojas
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Maria V Parra
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Julio A Molina
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, United States of America
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Guido Mazzotti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Kim Hill
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Ana M Hurtado
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Damian Labuda
- Département de Pédiatrie, CHU Sainte-Justine, Université de Montréal, Montréal, Quebec, Canada
| | - William Klitz
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- Public Health Institute, Oakland, California, United States of America
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Luiza T Tsuneto
- Departamento de Genética, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Elena Llop
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, University of Bern, Bern, Switzerland
| | - Marcus W Feldman
- Department of Biological Sciences, Stanford University, Stanford, California, United States of America
| | - Noah A Rosenberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrés Ruiz-Linares
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
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Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. A genomewide admixture map for Latino populations. Am J Hum Genet 2007; 80:1024-36. [PMID: 17503322 PMCID: PMC1867092 DOI: 10.1086/518313] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/12/2007] [Indexed: 01/21/2023] Open
Abstract
Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.
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Affiliation(s)
- Alkes L Price
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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7
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Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. A genomewide admixture map for Latino populations. Am J Hum Genet 2007. [PMID: 17503322 DOI: 10.1086/538313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.
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Affiliation(s)
- Alkes L Price
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Bolnick DAW, Shook BAS, Campbell L, Goddard I. Problematic use of Greenberg's linguistic classification of the Americas in studies of Native American genetic variation. Am J Hum Genet 2004; 75:519-22. [PMID: 15284953 PMCID: PMC1182033 DOI: 10.1086/423452] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Bortolini MC, Salzano FM, Thomas MG, Stuart S, Nasanen SPK, Bau CHD, Hutz MH, Layrisse Z, Petzl-Erler ML, Tsuneto LT, Hill K, Hurtado AM, Castro-de-Guerra D, Torres MM, Groot H, Michalski R, Nymadawa P, Bedoya G, Bradman N, Labuda D, Ruiz-Linares A. Y-chromosome evidence for differing ancient demographic histories in the Americas. Am J Hum Genet 2003; 73:524-39. [PMID: 12900798 PMCID: PMC1180678 DOI: 10.1086/377588] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2003] [Accepted: 06/18/2003] [Indexed: 11/03/2022] Open
Abstract
To scrutinize the male ancestry of extant Native American populations, we examined eight biallelic and six microsatellite polymorphisms from the nonrecombining portion of the Y chromosome, in 438 individuals from 24 Native American populations (1 Na Dené and 23 South Amerinds) and in 404 Mongolians. One of the biallelic markers typed is a recently identified mutation (M242) characterizing a novel founder Native American haplogroup. The distribution, relatedness, and diversity of Y lineages in Native Americans indicate a differentiated male ancestry for populations from North and South America, strongly supporting a diverse demographic history for populations from these areas. These data are consistent with the occurrence of two major male migrations from southern/central Siberia to the Americas (with the second migration being restricted to North America) and a shared ancestry in central Asia for some of the initial migrants to Europe and the Americas. The microsatellite diversity and distribution of a Y lineage specific to South America (Q-M19) indicates that certain Amerind populations have been isolated since the initial colonization of the region, suggesting an early onset for tribalization of Native Americans. Age estimates based on Y-chromosome microsatellite diversity place the initial settlement of the American continent at approximately 14,000 years ago, in relative agreement with the age of well-established archaeological evidence.
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Carvajal-Carmona LG, Ophoff R, Service S, Hartiala J, Molina J, Leon P, Ospina J, Bedoya G, Freimer N, Ruiz-Linares A. Genetic demography of Antioquia (Colombia) and the Central Valley of Costa Rica. Hum Genet 2003; 112:534-41. [PMID: 12601469 DOI: 10.1007/s00439-002-0899-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2002] [Accepted: 11/26/2002] [Indexed: 10/25/2022]
Abstract
We report a comparative genetic characterization of two population isolates with parallel demographic histories: the Central Valley of Costa Rica (CVCR) and Antioquia (in northwest Colombia). The analysis of mtDNA, Y-chromosome and autosomal polymorphisms shows that Antioquia and the CVCR are genetically very similar, indicating that closely related parental populations founded these two isolates. In both populations, the male ancestry is predominantly European, whereas the female ancestry is mostly Amerind. In agreement with their isolation, the Amerindian mtDNA diversity of Antioquia and the CVCR is typical of ethnically-defined native populations and is markedly lower than in other Latin American populations. A comparison of linkage disequilibrium (LD) at 18 marker pairs in Antioquia and the CVCR shows that markers in LD in both populations are located at short genetic distances (<approximately 1 cM), whereas markers separated by greater distances are in LD only in the CVCR. This difference probably reflects stochastic variation of LD at the limited number of genome regions compared. The genetic similarity of the populations from Antioquia and the CVCR together with differences in LD between them should be exploitable for the identification and fine mapping of shared disease-related gene variants.
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