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Alfonso‐Sánchez MA, Gómez‐Pérez L, Dipierri JE, Peña JA. Paternal heritage in Jujuy province (Northwest Argentina): Evidence for sex‐biased gene flow and genetic drift effects. Am J Hum Biol 2019; 31:e23262. [DOI: 10.1002/ajhb.23262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/27/2019] [Accepted: 05/17/2019] [Indexed: 12/30/2022] Open
Affiliation(s)
- Miguel A. Alfonso‐Sánchez
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Bilbao Spain
| | - Luis Gómez‐Pérez
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Bilbao Spain
| | - José E. Dipierri
- Instituto de Biología de la AlturaUniversidad Nacional de Jujuy San Salvador de Jujuy Argentina
| | - José A. Peña
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Bilbao Spain
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2
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Measuring the impact of European colonization on Native American populations in Southern Brazil and Uruguay: Evidence from mtDNA. Am J Hum Biol 2019; 31:e23243. [DOI: 10.1002/ajhb.23243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/05/2019] [Accepted: 03/10/2019] [Indexed: 01/26/2023] Open
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Szathmáry EJE, Zegura SL, Hammer MF. Exceeding Hrdlička's aims: 100 Years of genetics in anthropology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:754-776. [PMID: 29574830 DOI: 10.1002/ajpa.23406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Emőke J E Szathmáry
- Department of Anthropology, St. Paul's College, University of Manitoba, 70 Dysart Road, Winnipeg, Manitoba, R3T 2M6, Canada
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Arias L, Barbieri C, Barreto G, Stoneking M, Pakendorf B. High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:238-255. [DOI: 10.1002/ajpa.23345] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/17/2017] [Accepted: 10/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Leonardo Arias
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Anthropology; Leipzig D-04103 Germany
- Laboratorio de Genética Molecular Humana; Universidad del Valle; Cali Colombia
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution; Max Planck Institute for the Science of Human History; Jena D-07745 Germany
| | - Guillermo Barreto
- Laboratorio de Genética Molecular Humana; Universidad del Valle; Cali Colombia
| | - Mark Stoneking
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Anthropology; Leipzig D-04103 Germany
| | - Brigitte Pakendorf
- Dynamique du Langage; UMR5596, CNRS & Université de Lyon; Lyon Cedex 07 69363 France
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Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
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Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
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Llamas B, Fehren-Schmitz L, Valverde G, Soubrier J, Mallick S, Rohland N, Nordenfelt S, Valdiosera C, Richards SM, Rohrlach A, Romero MIB, Espinoza IF, Cagigao ET, Jiménez LW, Makowski K, Reyna ISL, Lory JM, Torrez JAB, Rivera MA, Burger RL, Ceruti MC, Reinhard J, Wells RS, Politis G, Santoro CM, Standen VG, Smith C, Reich D, Ho SYW, Cooper A, Haak W. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. SCIENCE ADVANCES 2016; 2:e1501385. [PMID: 27051878 PMCID: PMC4820370 DOI: 10.1126/sciadv.1501385] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 03/21/2016] [Indexed: 05/16/2023]
Abstract
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Corresponding author. E-mail: (B.L.); (A.C.); (W.H.)
| | - Lars Fehren-Schmitz
- Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guido Valverde
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Julien Soubrier
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Susanne Nordenfelt
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Cristina Valdiosera
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Stephen M. Richards
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Adam Rohrlach
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | | | - Elsa Tomasto Cagigao
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru
| | - Lucía Watson Jiménez
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru
- Centro de Investigaciones Arqueológicas del Museo de Sitio de Ancón, Lima 38, Peru
| | - Krzysztof Makowski
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru
| | | | - Josefina Mansilla Lory
- Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico
| | | | | | - Richard L. Burger
- Peabody Museum of Archaeology and Ethnology at Harvard University, Boston, MA 02138, USA
| | - Maria Constanza Ceruti
- Instituto de Investigaciones de Alta Montaña, Universidad Católica de Salta, Salta 4400, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Cdad. Autónoma de Buenos Aires, Argentina
| | | | | | - Gustavo Politis
- Instituto de Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano–Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina
| | - Calogero M. Santoro
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
| | - Vivien G. Standen
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
| | - Colin Smith
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Corresponding author. E-mail: (B.L.); (A.C.); (W.H.)
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Corresponding author. E-mail: (B.L.); (A.C.); (W.H.)
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Kanthaswamy S, Smith DG. Genetic and ethnohistoric evidence suggest current Native American population datasets in the FBI's CODIS Database Are Not Sufficiently Representative. Forensic Sci Int Genet 2014; 13:e13-5. [DOI: 10.1016/j.fsigen.2014.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/12/2014] [Accepted: 05/09/2014] [Indexed: 11/27/2022]
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Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB, Owings AC, Schurr TG. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:352-68. [PMID: 25043798 DOI: 10.1002/ajpa.22569] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 01/05/2023]
Abstract
Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre-Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre-Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y-chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y-chromosomes, with 85% of them instead being European/Mediterranean and 15% sub-Saharan African in origin. West Eurasian Y-chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans.
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Affiliation(s)
- Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, 19104-6398
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Reconstructing the history of Mesoamerican populations through the study of the mitochondrial DNA control region. PLoS One 2012; 7:e44666. [PMID: 23028577 PMCID: PMC3446984 DOI: 10.1371/journal.pone.0044666] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 08/06/2012] [Indexed: 12/02/2022] Open
Abstract
The study of genetic information can reveal a reconstruction of human population’s history. We sequenced the entire mtDNA control region (positions 16.024 to 576 following Cambridge Reference Sequence, CRS) of 605 individuals from seven Mesoamerican indigenous groups and one Aridoamerican from the Greater Southwest previously defined, all of them in present Mexico. Samples were collected directly from the indigenous populations, the application of an individual survey made it possible to remove related or with other origins samples. Diversity indices and demographic estimates were calculated. Also AMOVAs were calculated according to different criteria. An MDS plot, based on FST distances, was also built. We carried out the construction of individual networks for the four Amerindian haplogroups detected. Finally, barrier software was applied to detect genetic boundaries among populations. The results suggest: a common origin of the indigenous groups; a small degree of European admixture; and inter-ethnic gene flow. The process of Mesoamerica’s human settlement took place quickly influenced by the region’s orography, which development of genetic and cultural differences facilitated. We find the existence of genetic structure is related to the region’s geography, rather than to cultural parameters, such as language. The human population gradually became fragmented, though they remained relatively isolated, and differentiated due to small population sizes and different survival strategies. Genetic differences were detected between Aridoamerica and Mesoamerica, which can be subdivided into “East”, “Center”, “West” and “Southeast”. The fragmentation process occurred mainly during the Mesoamerican Pre-Classic period, with the Otomí being one of the oldest groups. With an increased number of populations studied adding previously published data, there is no change in the conclusions, although significant genetic heterogeneity can be detected in Pima and Huichol groups. This result may be explained because populations historically assigned as belonging to the same group were, in fact, different indigenous populations.
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Georges L, Seidenberg V, Hummel S, Fehren-Schmitz L. Molecular characterization of ABO blood group frequencies in pre-Columbian Peruvian highlanders. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:242-9. [DOI: 10.1002/ajpa.22115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/15/2012] [Indexed: 12/28/2022]
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Native Americans experienced a strong population bottleneck coincident with European contact. Proc Natl Acad Sci U S A 2011; 108:20444-8. [PMID: 22143784 DOI: 10.1073/pnas.1112563108] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic and demographic impact of European contact with Native Americans has remained unclear despite recent interest. Whereas archeological and historical records indicate that European contact resulted in widespread mortality from various sources, genetic studies have found little evidence of a recent contraction in Native American population size. In this study we use a large dataset including both ancient and contemporary mitochondrial DNA to construct a high-resolution portrait of the Holocene and late Pleistocene population size of indigenous Americans. Our reconstruction suggests that Native Americans suffered a significant, although transient, contraction in population size some 500 y before the present, during which female effective size was reduced by ∼50%. These results support analyses of historical records indicating that European colonization induced widespread mortality among indigenous Americans.
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Casas-Vargas A, Gómez A, Briceño I, Díaz-Matallana M, Bernal JE, Rodríguez JV. High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:637-49. [PMID: 21990065 DOI: 10.1002/ajpa.21626] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 08/30/2011] [Indexed: 11/12/2022]
Abstract
Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate.
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Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:392-405. [PMID: 21994016 DOI: 10.1002/ajpa.21588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/17/2011] [Indexed: 11/09/2022]
Abstract
Discovered in the early 16th century by European colonists, Bermuda is an isolated set of islands located in the mid-Atlantic. Shortly after its discovery, Bermuda became the first English colony to forcibly import its labor by trafficking in enslaved Africans, white ethnic minorities, and indigenous Americans. Oral traditions circulating today among contemporary tribes from the northeastern United States recount these same events, while, in Bermuda, St. David's Islanders consider their histories to be linked to a complex Native American, European, and African past. To investigate the influence of historical events on biological ancestry and native cultural identity, we analyzed genetic variation in 111 members of Bermuda's self-proclaimed St. David's Island Native Community. Our results reveal that the majority of mitochondrial DNA (mtDNA) and Y-chromosome haplotypes are of African and West Eurasian origin. However, unlike other English-speaking New World colonies, most African mtDNA haplotypes appear to derive from central and southeast Africa, reflecting the extent of maritime activities in the region. In light of genealogical and oral historical data from the St. David's community, the low frequency of Native American mtDNA and NRY lineages may reflect the influence of genetic drift, the demographic impact of European colonization, and historical admixture with persons of non-native backgrounds, which began with the settlement of the islands. By comparing the genetic data with genealogical and historical information, we are able to reconstruct the complex history of this Bermudian community, which is unique among New World populations.
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Affiliation(s)
- Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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Moreau C, Vézina H, Jomphe M, Lavoie EM, Roy-Gagnon MH, Labuda D. When genetics and genealogies tell different stories-maternal lineages in Gaspesia. Ann Hum Genet 2010; 75:247-54. [PMID: 21058944 DOI: 10.1111/j.1469-1809.2010.00617.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Data from uniparentally inherited genetic systems were used to trace evolution of human populations. Reconstruction of the past primarily relies on variation in present-day populations, limiting historical inference to lineages that are found among living subjects. Our analysis of four population groups in the Gaspé Peninsula, demonstrates how this may occasionally lead to erroneous interpretations. Mitochondrial DNA analysis of Gaspesians revealed an important admixture with Native Americans. The most likely scenario links this admixture to French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century. However, in contrast to genetic data, analysis of genealogical record shows that Native American maternal lineages were brought to Gaspesia in the 18th century by Acadians who settled on the south-western coast of the peninsula. Intriguingly, within three generations, virtually all Métis Acadian families separated from their nonadmixed relatives and moved eastward mixing in with other Gaspesian groups, in which Native American maternal lines are present in relatively high frequencies. Over time, the carriers of these lines eventually lost memory of their mixed Amerindian-Acadian origin. Our results show that a reliable reconstruction of population history requires cross-verification of different data sources for consistency, thus favouring multidisciplinary approaches.
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Affiliation(s)
- Claudia Moreau
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Côte Sainte-Catherine, Montréal, Québec, Canada
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Salas A, Lovo-Gómez J, Alvarez-Iglesias V, Cerezo M, Lareu MV, Macaulay V, Richards MB, Carracedo A. Mitochondrial echoes of first settlement and genetic continuity in El Salvador. PLoS One 2009; 4:e6882. [PMID: 19724647 PMCID: PMC2731219 DOI: 10.1371/journal.pone.0006882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 07/29/2009] [Indexed: 11/29/2022] Open
Abstract
Background From Paleo-Indian times to recent historical episodes, the Mesoamerican isthmus played an important role in the distribution and patterns of variability all around the double American continent. However, the amount of genetic information currently available on Central American continental populations is very scarce. In order to shed light on the role of Mesoamerica in the peopling of the New World, the present study focuses on the analysis of the mtDNA variation in a population sample from El Salvador. Methodology/Principal Findings We have carried out DNA sequencing of the entire control region of the mitochondrial DNA (mtDNA) genome in 90 individuals from El Salvador. We have also compiled more than 3,985 control region profiles from the public domain and the literature in order to carry out inter-population comparisons. The results reveal a predominant Native American component in this region: by far, the most prevalent mtDNA haplogroup in this country (at ∼90%) is A2, in contrast with other North, Meso- and South American populations. Haplogroup A2 shows a star-like phylogeny and is very diverse with a substantial proportion of mtDNAs (45%; sequence range 16090–16365) still unobserved in other American populations. Two different Bayesian approaches used to estimate admixture proportions in El Salvador shows that the majority of the mtDNAs observed come from North America. A preliminary founder analysis indicates that the settlement of El Salvador occurred about 13,400±5,200 Y.B.P.. The founder age of A2 in El Salvador is close to the overall age of A2 in America, which suggests that the colonization of this region occurred within a few thousand years of the initial expansion into the Americas. Conclusions/Significance As a whole, the results are compatible with the hypothesis that today's A2 variability in El Salvador represents to a large extent the indigenous component of the region. Concordant with this hypothesis is also the observation of a very limited contribution from European and African women (∼5%). This implies that the Atlantic slave trade had a very small demographic impact in El Salvador in contrast to its transformation of the gene pool in neighbouring populations from the Caribbean facade.
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Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.
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Ottoni C, Martínez-Labarga C, Loogväli EL, Pennarun E, Achilli A, De Angelis F, Trucchi E, Contini I, Biondi G, Rickards O. First genetic insight into Libyan Tuaregs: a maternal perspective. Ann Hum Genet 2009; 73:438-48. [PMID: 19476452 DOI: 10.1111/j.1469-1809.2009.00526.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Tuaregs are a semi-nomadic pastoralist people of northwest Africa. Their origins are still a matter of debate due to the scarcity of genetic and historical data. Here we report the first data on the mitochondrial DNA (mtDNA) genetic characterization of a Tuareg sample from Fezzan (Libyan Sahara). A total of 129 individuals from two villages in the Acacus region were genetically analysed. Both the hypervariable regions and the coding region of mtDNA were investigated. Phylogeographic investigation was carried out in order to reconstruct human migratory shifts in central Sahara, and to shed light on the origin of the Libyan Tuaregs. Our results clearly show low genetic diversity in the sample, possibly due to genetic drift and founder effect associated with the separation of Libyan Tuaregs from an ancestral population. Furthermore, the maternal genetic pool of the Libyan Tuaregs is characterized by a major "European" component shared with the Berbers that could be traced to the Iberian Peninsula, as well as a minor 'south Saharan' contribution possibly linked to both Eastern African and Near Eastern populations.
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Affiliation(s)
- Claudio Ottoni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, Italy
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Halverson MS, Bolnick DA. An ancient DNA test of a founder effect in Native American ABO blood group frequencies. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 137:342-7. [DOI: 10.1002/ajpa.20887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schultz Shook BA, Smith DG. Using ancient mtDNA to reconstruct the population history of northeastern North America. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 137:14-29. [DOI: 10.1002/ajpa.20835] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Melton PE, Briceño I, Gómez A, Devor EJ, Bernal JE, Crawford MH. Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 133:753-70. [PMID: 17340631 DOI: 10.1002/ajpa.20581] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present.
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Affiliation(s)
- Phillip E Melton
- Department of Anthropology, University of Kansas, Lawrence, KS 66045, USA.
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Kemp BM, Malhi RS, McDonough J, Bolnick DA, Eshleman JA, Rickards O, Martinez-Labarga C, Johnson JR, Lorenz JG, Dixon EJ, Fifield TE, Heaton TH, Worl R, Smith DG. Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:605-21. [PMID: 17243155 DOI: 10.1002/ajpa.20543] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.
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Affiliation(s)
- Brian M Kemp
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235-7703, USA.
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Marinho ANDR, Miranda NC, Braz V, Ribeiro-Dos-Santos AK, de Souza SMFM. Paleogenetic and taphonomic analysis of human bones from Moa, Beirada, and Zé Espinho Sambaquis, Rio de Janeiro, Brazil. Mem Inst Oswaldo Cruz 2006; 101 Suppl 2:15-23. [PMID: 17308804 DOI: 10.1590/s0074-02762006001000004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 10/16/2006] [Indexed: 11/22/2022] Open
Abstract
The present paper discusses mtDNA and taphonomy of human remains from Moa, Beirada, and Zé Espinho sambaquis of Saquarema, state of Rio de Janeiro, Brazil. New human bone dating by 14C-AMS for Moa archeological site (3810+50 BP - GX-31826-AMS) is included. Preservation of microscopic lamellae and DNA is not related to the macroscopic integrity of the bones. Results here suggest that the preservation of amplifiable DNA fragments may have relation to the preservation of the lamellar arrangement as indicated by optical microscopic examination (polarized light). In 13 human bone fragments from Moa, Beirada, and Zé Espinho it was possible to sequence mtDNA from the 3 individuals of Moa, and from 1 of 4 individuals of Beirada, whose bones also show extensive areas with preserved lamellar structures. The 6 human bone fragments of Zé Espinho and 3 of the 4 fragments of Beirada showed extensive destruction of cortical microstructure represented by cavities, intrusive minerals, and agglomerated microscopic bodies of fungi and bacteria; it was not possible to extract mtDNA from these samples. The results support the hypothesis that the preservation of the microscopic osteon organization is a good predictor for DNA preservation. It was also confirmed the C haplogroup antiquity in Brazil.
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Affiliation(s)
- Anderson Nonato do Rosario Marinho
- Laboratório de Genética Humana e Médica, Departamento de Patologia, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil.
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22
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Martínez-Cruzado JC, Toro-Labrador G, Viera-Vera J, Rivera-Vega MY, Startek J, Latorre-Esteves M, Román-Colón A, Rivera-Torres R, Navarro-Millán IY, Gómez-Sánchez E, Caro-González HY, Valencia-Rivera P. Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 128:131-55. [PMID: 15693025 DOI: 10.1002/ajpa.20108] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The haplogroup identities of 800 mtDNAs randomly and systematically selected to be representative of the population of Puerto Rico were determined by restriction fragment length polymorphism (RFLP), revealing maternal ancestries in this highly mixed population of 61.3% Amerindian, 27.2% sub-Saharan African, and 11.5% West Eurasian. West Eurasian frequencies were low in all 28 municipalities sampled, and displayed no geographic patterns. Thus, a statistically significant negative correlation was observed between the Amerindian and African frequencies of the municipalities. In addition, a statistically highly significant geographic pattern was observed for Amerindian and African mtDNAs. In a scenario in which Amerindian mtDNAs prevailed on either side of longitude 66 degrees 16' West, Amerindian mtDNAs were more frequent west of longitude 66 degrees 16' West than east of it, and the opposite was true for African mtDNAs. Haplogroup A had the highest frequency among Amerindian samples (52.4%), suggesting its predominance among the native Taínos. Principal component analysis showed that the sub-Saharan African fraction had a strong affinity to West Africans. In addition, the magnitudes of the Senegambian and Gulf of Guinea components in Puerto Rico were between those of Cape Verde and São Tomé. Furthermore, the West Eurasian component did not conform to European haplogroup frequencies. HVR-I sequences of haplogroup U samples revealed a strong North African influence among West Eurasian mtDNAs and a new sub-Saharan African clade.
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Fenner JN. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 128:415-23. [PMID: 15795887 DOI: 10.1002/ajpa.20188] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The length of the human generation interval is a key parameter when using genetics to date population divergence events. However, no consensus exists regarding the generation interval length, and a wide variety of interval lengths have been used in recent studies. This makes comparison between studies difficult, and questions the accuracy of divergence date estimations. Recent genealogy-based research suggests that the male generation interval is substantially longer than the female interval, and that both are greater than the values commonly used in genetics studies. This study evaluates each of these hypotheses in a broader cross-cultural context, using data from both nation states and recent hunter-gatherer societies. Both hypotheses are supported by this study; therefore, revised estimates of male, female, and overall human generation interval lengths are proposed. The nearly universal, cross-cultural nature of the evidence justifies using these proposed estimates in Y-chromosomal, mitochondrial, and autosomal DNA-based population divergence studies.
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Affiliation(s)
- Jack N Fenner
- Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA.
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Dornelles CL, Bonatto SL, De Freitas LB, Salzano FM. Is haplogroup X present in extant South American Indians? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 127:439-48. [PMID: 15624206 DOI: 10.1002/ajpa.20103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A total of 1,159 mitochondrial DNA samples from two Mongolian, two Siberian, and 25 South Native American populations was surveyed for the presence of the C16278T mutation, frequently found in haplogroup X. Material from 25 carriers of that mutation was then sequenced for the hypervariable segment I (HVS-I) control region, and those that still were not classifiable in classical Amerindian haplogroups were further studied. The tests involved all the control region, as well as the presence of characteristic mutations in seven coding fragments, totalling 5,760 base pairs. The results indicate that haplogroup X is not present in these samples.
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Affiliation(s)
- Cláudia L Dornelles
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
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Affiliation(s)
- Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6398;
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Schurr TG, Sherry ST. Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: Evolutionary and demographic evidence. Am J Hum Biol 2004; 16:420-39. [PMID: 15214060 DOI: 10.1002/ajhb.20041] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. While there is no complete agreement on the interpretation of the mitochondrial DNA (mtDNA) and Y chromosome (NRY) data from these groups, several generalizations can be made. To begin with, the primary migration of ancestral Asians expanded from south-central Siberia into the New World and gave rise to ancestral Amerindians. The initial migration seems to have occurred between 20,000-15,000 calendar years before present (cal BP), i.e., before the emergence of Clovis lithic sites (13,350-12,895 cal BP) in North America. Because an interior route through northern North America was unavailable for human passage until 12,550 cal BP, after the last glacial maximum (LGM), these ancestral groups must have used a coastal route to reach South America by 14,675 cal BP, the date of the Monte Verde site in southern Chile. The initial migration appears to have brought mtDNA haplogroups A-D and NRY haplogroups P-M45a and Q-242/Q-M3 to the New World, with these genetic lineages becoming widespread in the Americas. A second expansion that perhaps coincided with the opening of the ice-free corridor probably brought mtDNA haplogroup X and NRY haplogroups P-M45b, C-M130, and R1a1-M17 to North and Central America. Finally, populations that formerly inhabited Beringia expanded into northern North America after the LGM, and gave rise to Eskimo-Aleuts and Na-Dené Indians.
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MESH Headings
- Americas/epidemiology
- Anthropology, Physical
- Biological Evolution
- Chromosomes, Human, Y/genetics
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/history
- Demography
- Emigration and Immigration/history
- Genetic Variation
- Genetics, Population
- Haplotypes/genetics
- History, Ancient
- History, Early Modern 1451-1600
- Humans
- Indians, North American/genetics
- Indians, North American/history
- Siberia/ethnology
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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