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Uricoechea Patiño D, Collins A, Romero García OJ, Santos Vecino G, Aristizábal Espinosa P, Bernal Villegas JE, Benavides Benitez E, Vergara Muñoz S, Briceño Balcázar I. Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley. Genes (Basel) 2023; 14:2036. [PMID: 38002979 PMCID: PMC10670959 DOI: 10.3390/genes14112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | | | | | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.V.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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Aqil A, Gill S, Gokcumen O, Malhi RS, Reese EA, Smith JL, Heaton TT, Lindqvist C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience 2023; 26:106581. [PMID: 37138779 PMCID: PMC10149335 DOI: 10.1016/j.isci.2023.106581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.
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Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Ripan S. Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Jane L. Smith
- USDA-Forest Service, Tongass National Forest, Petersburg, AK 99833, USA
| | - Timothy T. Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Corresponding author
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Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
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Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
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Mizuno F, Tokanai F, Kumagai M, Ishiya K, Sugiyama S, Hayashi M, Kurosaki K, Ueda S. Bioarchaeological study of ancient Teotihuacans based on complete mitochondrial genome sequences and diet isotopes. Ann Hum Biol 2023; 50:390-398. [PMID: 37812249 DOI: 10.1080/03014460.2023.2261844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND The Teotihuacan civilisation was the largest one in ancient Mesoamerica. The Teotihuacan city was born in the north-eastern Basin of Mexico around the second century BC, reached its peak in the fourth century AD, and had cultural influence throughout Mesoamerica. At its peak, the size of the city reached more than 20 km2, and the total population is estimated to have increased from 100,000 to 200,000. However, knowledge of the genetic background of the Teotihuacan people is still limited. AIM We aimed to determine the mitogenome sequences of the Teotihuacan human remains and compare the ancient and present Mesoamericans. In addition, we aimed to identify the food habits of ancient Teotihuacans. SUBJECTS AND METHODS We determined the mitogenome sequences of human remains dated to 250-636 cal AD using target enrichment-coupled next generation sequencing. We also performed stable isotope analysis. RESULTS We successfully obtained nearly full-length sequences newly unearthed from a civilian dwelling in the Teotihuacan site. Teotihuacan mitochondrial DNA was classified into the haplogroups in present and ancient Mesoamericans. In addition, Teotihuacan individuals had a diet dependent on C4 plants such as maize. CONCLUSION Genetic diversity varied among the Teotihuacans.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Fuyuki Tokanai
- Center for Accelerator Mass Spectrometry, Yamagata University Advanced Analysis Center, Yamagata, Japan
| | - Masahiko Kumagai
- National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Chiyoda, Japan
| | - Saburo Sugiyama
- Research Institute for the Dynamics of Civilizations, Okayama University, Okayama, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Resolving mitochondrial haplogroups B2 and B4 with next-generation mitogenome sequencing to distinguish Native American from Asian haplotypes. Forensic Sci Int Genet 2019; 43:102143. [DOI: 10.1016/j.fsigen.2019.102143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
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6
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Ross AH, Ubelaker DH. Complex Nature of Hominin Dispersals: Ecogeographical and Climatic Evidence for Pre-Contact Craniofacial Variation. Sci Rep 2019; 9:11743. [PMID: 31409847 PMCID: PMC6692499 DOI: 10.1038/s41598-019-48205-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/01/2022] Open
Abstract
Coordinate data analysis of ancient crania from the New World reveals complexity in interpretation when addressing ancient population dispersals. The results of this study generally support a geographic patterning for the New World; however, it also revealed a much more complex and multifactorial mechanism shaping craniofacial morphology that should be considered when investigating ecogeographic models for hominin dispersals. We show that craniofacial variation is not the result of a single mechanism but is a much more complex interaction of environmental and microevolutionary forces.
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Affiliation(s)
- Ann H Ross
- North Carolina State University, Department of Biological Sciences, Raleigh, 27695, United States. .,Smithsonian Institution, National Museum of Natural History, Washington, DC, 20560, United States.
| | - Douglas H Ubelaker
- Smithsonian Institution, National Museum of Natural History, Washington, DC, 20560, United States
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7
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Fregel R, Ordóñez AC, Santana-Cabrera J, Cabrera VM, Velasco-Vázquez J, Alberto V, Moreno-Benítez MA, Delgado-Darias T, Rodríguez-Rodríguez A, Hernández JC, Pais J, González-Montelongo R, Lorenzo-Salazar JM, Flores C, Cruz-de-Mercadal MC, Álvarez-Rodríguez N, Shapiro B, Arnay M, Bustamante CD. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands. PLoS One 2019; 14:e0209125. [PMID: 30893316 PMCID: PMC6426200 DOI: 10.1371/journal.pone.0209125] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/15/2019] [Indexed: 12/30/2022] Open
Abstract
The Canary Islands’ indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- * E-mail:
| | - Alejandra C. Ordóñez
- Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Vicente M. Cabrera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Javier Velasco-Vázquez
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Verónica Alberto
- Tibicena Arqueología y Patrimonio, Las Palmas de Gran Canaria, Spain
| | | | | | - Amelia Rodríguez-Rodríguez
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Spain
| | | | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Granadilla, Spain
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matilde Arnay
- Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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Grugni V, Raveane A, Ongaro L, Battaglia V, Trombetta B, Colombo G, Capodiferro MR, Olivieri A, Achilli A, Perego UA, Motta J, Tribaldos M, Woodward SR, Ferretti L, Cruciani F, Torroni A, Semino O. Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas. BMC Biol 2019; 17:3. [PMID: 30674303 PMCID: PMC6345020 DOI: 10.1186/s12915-018-0622-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America. RESULTS Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe. CONCLUSIONS We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Jorge Motta
- Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT), Panama City, Panama
| | - Maribel Tribaldos
- Department of Health Technology Assessment and Economic Evaluation, Panama City, Panama
| | | | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.
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9
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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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10
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Hamilton-Brehm SD, Hristova LT, Edwards SR, Wedding JR, Snow M, Kruger BR, Moser DP. Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA. PLoS One 2018; 13:e0194223. [PMID: 29522562 PMCID: PMC5844571 DOI: 10.1371/journal.pone.0194223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/27/2018] [Indexed: 12/27/2022] Open
Abstract
Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.
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Affiliation(s)
- Scott D. Hamilton-Brehm
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States of America
| | - Lidia T. Hristova
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Department of Anthropology, University of Nevada, Las Vegas, NV, United States of America
| | - Susan R. Edwards
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
| | - Jeffrey R. Wedding
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, United States of America
| | - Brittany R. Kruger
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States of America
| | - Duane P. Moser
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, United States of America
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States of America
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11
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Mizuno F, Wang L, Sugiyama S, Kurosaki K, Granados J, Gomez-Trejo C, Acuña-Alonzo V, Ueda S. Characterization of complete mitochondrial genomes of indigenous Mayans in Mexico. Ann Hum Biol 2017; 44:652-658. [PMID: 28724311 DOI: 10.1080/03014460.2017.1358393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The authors have previously published the complete mitochondrial genome (mitogenome) sequences of two indigenous Mesoamerican populations, Mazahua (n = 25) and Zapotec (n = 88). METHODS This study determined the complete mitogenome sequences of nine unrelated individuals from the indigenous Maya population living in Mexico. RESULTS Their mitogenome sequences could be classified into either of the haplogroups A2 and C1. Surprisingly, there were no mitogenome sequences (haplotypes) that the Maya, Mazahua, and Zapotec people share in common. CONCLUSIONS This indicates that no genetic exchange, at least matrilineally, has occurred among them.
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Affiliation(s)
- Fuzuki Mizuno
- a Department of Legal Medicine , Toho University School of Medicine , Ota-ku , Tokyo , Japan.,b Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo , Japan
| | - Li Wang
- c School of Medicine, Hangzhou Normal University School of Medicine , Hangzhou , Zhejiang , China
| | - Saburo Sugiyama
- d Graduate School of International Cultural Studies, Cultural Symbiosis Research Institute , Aichi Prefectural University , Nagakute , Aichi , Japan
| | - Kunihiko Kurosaki
- a Department of Legal Medicine , Toho University School of Medicine , Ota-ku , Tokyo , Japan
| | - Julio Granados
- e Department of Transplants , Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Celta Gomez-Trejo
- f Molecular Genetics Laboratory , National Institute of Anthropology and History , Mexico City , Mexico
| | - Víctor Acuña-Alonzo
- f Molecular Genetics Laboratory , National Institute of Anthropology and History , Mexico City , Mexico
| | - Shintaroh Ueda
- b Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo , Japan.,c School of Medicine, Hangzhou Normal University School of Medicine , Hangzhou , Zhejiang , China
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Mizuno F, Kumagai M, Kurosaki K, Hayashi M, Sugiyama S, Ueda S, Wang L. Imputation approach for deducing a complete mitogenome sequence from low-depth-coverage next-generation sequencing data: application to ancient remains from the Moon Pyramid, Mexico. J Hum Genet 2017; 62:631-635. [PMID: 28202952 DOI: 10.1038/jhg.2017.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 12/19/2022]
Abstract
It is considered that more than 15 depths of coverage are necessary for next-generation sequencing (NGS) data to obtain reliable complete nucleotide sequences of the mitogenome. However, it is difficult to satisfy this requirement for all nucleotide positions because of problems obtaining a uniform depth of coverage for poorly preserved materials. Thus, we propose an imputation approach that allows a complete mitogenome sequence to be deduced from low-depth-coverage NGS data. We used different types of mitogenome data files as panels for imputation: a worldwide panel comprising all the major haplogroups, a worldwide panel comprising sequences belonging to the estimated haplogroup alone, a panel comprising sequences from the population most closely related to an individual under investigation, and a panel comprising sequences belonging to the estimated haplogroup from the population most closely related to an individual under investigation. The number of missing nucleotides was drastically reduced in all the panels, but the contents obtained by imputation were quite different among the panels. The efficiency of the imputation method differed according to the panels used. The missing nucleotides were most credibly imputed using sequences of the estimated haplogroup from the population most closely related to the individual under investigation as a panel.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Saburo Sugiyama
- Graduate school of International Cultural Studies, Cultural Symbiosis Research Institute, Aichi Prefectural University, Aichi, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,School of Medicine, Hangzhou Normal University School of Medicine, Zhejiang, China
| | - Li Wang
- School of Medicine, Hangzhou Normal University School of Medicine, Zhejiang, China
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Maley B. Examining biological continuity across the late holocene occupation of the Aleutian Islands using cranial morphometrics and quantitative genetic permutation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:71-85. [PMID: 27075865 DOI: 10.1002/ajpa.22944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/09/2015] [Accepted: 01/01/2016] [Indexed: 11/08/2022]
Abstract
OBJECTIVES The number of distinct human migrations into the Aleutian Islands during the Holocene has been a recurrent debate in the anthropological literature. Stemming from Hrdlička's sorting of the prehistoric remains into two distinct populations based on archaeological context and cranial measurements, the human occupation of the Aleutian Islands has long been thought to be the consequence of two distinct human migrations, a Paleo-Aleut migration that provided the initial settlement of the islands, and a Neo-Aleut migration that replaced the original settlers around 1000 BP. This study examines the relationship of the Aleut cranial assemblages in the context of greater Alaskan population variability to assess the evidence for a substantial migration into the Aleutian Islands during the late Holocene. MATERIALS AND METHODS A battery of 29 cranial measurements that quantify global cranial shape were analyzed using Euclidean morphometric methods and quantitative genetic permutation methods to examine the plausibility for two distinct Aleut occupations ("Paleo-Aleut" and "Neo-Aleut"), the latter of which is held to share closer phenetic affinities to mainland Alaskan populations than the former. The Aleut skeletal assemblages were arranged according to temporal association, geographic location, and cranial typology, and analyzed within a comparative framework of mainland Alaskan samples using principal coordinates, biological distance and random skewers permutation methods. RESULTS Regardless of how the Aleut assemblages are divided, they show greater similarity to each other than to any of the mainland Alaskan assemblages. These findings are consistent across the methodological approaches. DISCUSSION The results obtained in this study provide no support for a cranial morphology-based subdivision of the Aleuts into two distinct samples, Hence, there is no evidence for a substantial population migration of so-called Neo-Aleuts, nor for a population replacement event of an extant Paleo-Aleut population by a mainland-affiliated Neo-Aleuts population at or after 1000 BP.
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Affiliation(s)
- Blaine Maley
- Department of Biomedical Sciences, Marian University, Indianapolis, IN, 46222
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Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data. PLoS One 2015; 10:e0131791. [PMID: 26292226 PMCID: PMC4546282 DOI: 10.1371/journal.pone.0131791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022] Open
Abstract
The genetic characterization of Native American groups provides insights into their history and demographic events. We sequenced the mitochondrial D-loop region (control region) of 520 samples from eight Mexican indigenous groups. In addition to an analysis of the genetic diversity, structure and genetic relationship between 28 Native American populations, we applied Bayesian skyline methodology for a deeper insight into the history of Mesoamerica. AMOVA tests applying cultural, linguistic and geographic criteria were performed. MDS plots showed a central cluster of Oaxaca and Maya populations, whereas those from the North and West were located on the periphery. Demographic reconstruction indicates higher values of the effective number of breeding females (Nef) in Central Mesoamerica during the Preclassic period, whereas this pattern moves toward the Classic period for groups in the North and West. Conversely, Nef minimum values are distributed either in the Lithic period (i.e. founder effects) or in recent periods (i.e. population declines). The Mesomerican regions showed differences in population fluctuation as indicated by the maximum Inter-Generational Rate (IGRmax): i) Center-South from the lithic period until the Preclassic; ii) West from the beginning of the Preclassic period until early Classic; iii) North characterized by a wide range of temporal variation from the Lithic to the Preclassic. Our findings are consistent with the genetic variations observed between central, South and Southeast Mesoamerica and the North-West region that are related to differences in genetic drift, structure, and temporal survival strategies (agriculture versus hunter-gathering, respectively). Interestingly, although the European contact had a major negative demographic impact, we detect a previous decline in Mesoamerica that had begun a few hundred years before.
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Madrilejo N, Lombard H, Torres JB. Origins of marronage: Mitochondrial lineages of Jamaica's Accompong Town Maroons. Am J Hum Biol 2014; 27:432-7. [PMID: 25392952 DOI: 10.1002/ajhb.22656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 10/02/2014] [Accepted: 10/22/2014] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES The Accompong Town Maroons are descendants of enslaved Africans who successfully waged war against British colonial rule and established an independent community in western Jamaica. There are discrepancies regarding Accompong Town Maroon ancestry with some scholars noting ancestry from both Africans and Taínos, Jamaica's indigenous population, while other scholars only acknowledge African ancestry. We considered the mitochondrial lineages of contemporary Accompong Town Maroons to address the question of ancestral origins. METHODS We sequenced a section of the mitochondrial DNA control region (np 16,024-16,569) and genotyped a panel of hierarchically selected haplogroup diagnostic SNPs for 50 individuals with genealogical ties to Accompong Town. Mitochondrial haplotypes were also compared with publically available Jamaican mitochondrial haplotypes using an exact test as well as haplotypes within the EMPOP public database to further access biogeographic origins. RESULTS L-type mitochondrial haplogroups were observed in 96% of samples, and the remaining 4% belonged to haplogroup B2. Haplotype diversity was 0.922 (SD = 0.024) and not significantly different than the comparable Jamaican population. Of the two B2 haplotypes, one matched haplotypes throughout the Americas and East Asia and the other matched only in East Asia. These results suggest both African and indigenous American maternal ancestries within Accompong Town. CONCLUSIONS Our data suggested that the maternal ancestry of contemporary Accompong Town Maroons is predominantly African and, despite claims to suggest otherwise, also indigenous American. Our study complemented Maroon oral histories, archeological data, and illuminated how colonization shaped human genetic variation within the Caribbean.
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Affiliation(s)
- Nicole Madrilejo
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, 46556; Department of Pre-Professional Studies, University of Notre Dame, Notre Dame, Indiana, 46556
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Complete mitogenome analysis of indigenous populations in Mexico: its relevance for the origin of Mesoamericans. J Hum Genet 2014; 59:359-67. [PMID: 24804703 DOI: 10.1038/jhg.2014.35] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 11/08/2022]
Abstract
Mesoamerica has an important role in the expansion of Paleoamericans as the route to South America. In this study, we determined complete mitogenome sequences of 113 unrelated individuals from two indigenous populations of Mesoamerica, Mazahua and Zapotec. All newly sequenced mitogenomes could be classified into haplogroups A2, B2, C1 and D1, but one sequence in Mazahua was D4h3a, a subclade of haplogroup D4. This haplogroup has been mostly found in South America along the Pacific coast. Haplogroup X2a was not found in either population. Genetic similarity obtained using phylogenetic tree construction and principal component analysis showed that these two populations are distantly related to each other. Actually, the Mazahua and the Zapotec shared no sequences (haplotypes) in common, while each also showed a number of unique subclades. Surprisingly, Zapotec formed a cluster with indigenous populations living in an area from central Mesoamerica to Central America. By contrast, the Mazahua formed a group with indigenous populations living in external areas, including southwestern North America and South America. This intriguing genetic relationship suggests the presence of two paleo-Mesoamerican groups, invoking a scenario in which one group had expanded into South America and the other resided in Mesoamerica.
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Coutinho A, Valverde G, Fehren-Schmitz L, Cooper A, Barreto Romero MI, Espinoza IF, Llamas B, Haak W. AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas. PLoS One 2014; 9:e93292. [PMID: 24671218 PMCID: PMC3966882 DOI: 10.1371/journal.pone.0093292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 03/04/2014] [Indexed: 11/18/2022] Open
Abstract
Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.
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Affiliation(s)
- Alexandra Coutinho
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Guido Valverde
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- Historical Anthropology and Human Ecology, Johann-Friedrich-Blumenbach Department of Zoology and Anthropology, University Goettingen, Goettingen, Germany
- Department of Anthropology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JEL, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W. Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1. PLoS One 2014; 9:e87612. [PMID: 24503968 PMCID: PMC3913659 DOI: 10.1371/journal.pone.0087612] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/23/2013] [Indexed: 11/19/2022] Open
Abstract
The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined “C1f”. We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (CDS); (WH)
| | - Paul Brotherton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Jennifer E. L. Templeton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Julien Soubrier
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, Russia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (CDS); (WH)
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Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet 2013; 29:593-9. [PMID: 23972387 DOI: 10.1016/j.tig.2013.07.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/05/2013] [Accepted: 07/24/2013] [Indexed: 01/04/2023]
Abstract
Exome sequencing is one of the most cost-efficient sequencing approaches for conducting genome research on coding regions. However, significant portions of the reads obtained in exome sequencing come from outside of the designed target regions. These additional reads are generally ignored, potentially wasting an important source of genomic data. There are three major types of unintentionally sequenced read that can be found in exome sequencing data: reads in introns and intergenic regions, reads in the mitochondrial genome, and reads originating in viral genomes. All of these can be used for reliable data mining, extending the utility of exome sequencing. Large-scale exome sequencing data repositories, such as The Cancer Genome Atlas (TCGA), the 1000 Genomes Project, National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project, and The Sequence Reads Archive, provide researchers with excellent secondary data-mining opportunities to study genomic data beyond the intended target regions.
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Affiliation(s)
- David C Samuels
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37232, USA
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20
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Mann PC, Cooper ME, Ryckman KK, Comas B, Gili J, Crumley S, Bream EN, Byers HM, Piester T, Schaefer A, Christine PJ, Lawrence A, Schaa KL, Kelsey KJ, Berends SK, Gadow E, Cosentino V, Castilla EE, Camelo JL, Saleme C, Day LJ, England SK, Marazita ML, Dagle JM, Murray JC, Murray JC. Polymorphisms in the fetal progesterone receptor and a calcium-activated potassium channel isoform are associated with preterm birth in an Argentinian population. J Perinatol 2013; 33:336-40. [PMID: 23018797 PMCID: PMC3719965 DOI: 10.1038/jp.2012.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To investigate genetic etiologies of preterm birth (PTB) in Argentina through evaluation of single-nucleotide polymorphisms (SNPs) in candidate genes and population genetic admixture. STUDY DESIGN Genotyping was performed in 389 families. Maternal, paternal and fetal effects were studied separately. Mitochondrial DNA (mtDNA) was sequenced in 50 males and 50 females. Y-chromosome anthropological markers were evaluated in 50 males. RESULT Fetal association with PTB was found in the progesterone receptor (PGR, rs1942836; P=0.004). Maternal association with PTB was found in small conductance calcium activated potassium channel isoform 3 (KCNN3, rs883319; P=0.01). Gestational age associated with PTB in PGR rs1942836 at 32-36 weeks (P=0.0004). MtDNA sequencing determined 88 individuals had Amerindian consistent haplogroups. Two individuals had Amerindian Y-chromosome consistent haplotypes. CONCLUSION This study replicates single locus fetal associations with PTB in PGR, maternal association in KCNN3, and demonstrates possible effects for divergent racial admixture on PTB.
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Affiliation(s)
- Paul C. Mann
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Margaret E. Cooper
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - Kelli K. Ryckman
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Belén Comas
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Juan Gili
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Suzanne Crumley
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Elise N.A. Bream
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Heather M. Byers
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Travis Piester
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Amanda Schaefer
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Paul J. Christine
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Amy Lawrence
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Kendra L. Schaa
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | | | - Susan K. Berends
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Enrique Gadow
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina
| | - Viviana Cosentino
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina
| | - Eduardo E. Castilla
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jorge López Camelo
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Capital Federal, Argentina,Instituto Multidisciplinario de Biología Celular, La Plata, Buenos Aires, Argentina
| | - Cesar Saleme
- Instituto de Maternidad y Ginecología Nuestra Señora de las Mercedes, San Miguel de Tucumán, Tucumán, Argentina
| | - Lori J. Day
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, Iowa, 52242
| | - Sarah K. England
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, Iowa, 52242,Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, 52242
| | - Mary L. Marazita
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - John M. Dagle
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242,Corresponding Author: Jeffrey C. Murray, MD Professor, Departments of Pediatrics, Epidemiology, and Biological Sciences University of Iowa Carver College of Medicine 500 Newton Road, 2182 ML, Iowa City, IA 52242-1181 319-335-6897 phone; 319-335-6970 fax
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Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes. PLoS One 2012; 7:e51311. [PMID: 23240014 PMCID: PMC3519775 DOI: 10.1371/journal.pone.0051311] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (mtDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11–13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.
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García A, Pauro M, Nores R, Bravi CM, Demarchi DA. Phylogeography of mitochondrial haplogroup D1: An early spread of subhaplogroup D1j from Central Argentina. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:583-90. [DOI: 10.1002/ajpa.22174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 09/13/2012] [Indexed: 12/16/2022]
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de Saint Pierre M, Bravi CM, Motti JMB, Fuku N, Tanaka M, Llop E, Bonatto SL, Moraga M. An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups. PLoS One 2012; 7:e43486. [PMID: 22970129 PMCID: PMC3438176 DOI: 10.1371/journal.pone.0043486] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/20/2012] [Indexed: 11/19/2022] Open
Abstract
After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ~15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.
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Affiliation(s)
- Michelle de Saint Pierre
- Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Rogalla U, Grzybowski T, Khusnutdinova E, Dambueva I, Zakharov I. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS One 2012; 7:e32179. [PMID: 22363811 PMCID: PMC3283723 DOI: 10.1371/journal.pone.0032179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/22/2012] [Indexed: 12/21/2022] Open
Abstract
With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes. Genome Res 2012; 22:811-20. [PMID: 22333566 PMCID: PMC3337427 DOI: 10.1101/gr.131722.111] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It is now widely agreed that the Native American founders originated from a Beringian source population ∼15–18 thousand years ago (kya) and rapidly populated all of the New World, probably mainly following the Pacific coastal route. However, details about the migration into the Americas and the routes pursued on the continent still remain unresolved, despite numerous genetic, archaeological, and linguistic investigations. To examine the pioneering peopling phase of the South American continent, we screened literature and mtDNA databases and identified two novel mitochondrial DNA (mtDNA) clades, here named D1g and D1j, within the pan-American haplogroup D1. They both show overall rare occurrences but local high frequencies, and are essentially restricted to populations from the Southern Cone of South America (Chile and Argentina). We selected and completely sequenced 43 D1g and D1j mtDNA genomes applying highest quality standards. Molecular and phylogeographic analyses revealed extensive variation within each of the two clades and possibly distinct dispersal patterns. Their age estimates agree with the dating of the earliest archaeological sites in South America and indicate that the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr. This study confirms that major sampling and sequencing efforts are mandatory for uncovering all of the most basal variation in the Native American mtDNA haplogroups and for clarification of Paleo-Indian migrations, by targeting, if possible, both the general mixed population of national states and autochthonous Native American groups, especially in South America.
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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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Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, Curran JE. Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 2011; 11:293. [PMID: 21978175 PMCID: PMC3217880 DOI: 10.1186/1471-2148-11-293] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 10/07/2011] [Indexed: 01/07/2023] Open
Abstract
Background The Asian origin of Native Americans is largely accepted. However uncertainties persist regarding the source population(s) within Asia, the divergence and arrival time(s) of the founder groups, the number of expansion events, and migration routes into the New World. mtDNA data, presented over the past two decades, have been used to suggest a single-migration model for which the Beringian land mass plays an important role. Results In our analysis of 568 mitochondrial genomes, the coalescent age estimates of shared roots between Native American and Siberian-Asian lineages, calculated using two different mutation rates, are A4 (27.5 ± 6.8 kya/22.7 ± 7.4 kya), C1 (21.4 ± 2.7 kya/16.4 ± 1.5 kya), C4 (21.0 ± 4.6 kya/20.0 ± 6.4 kya), and D4e1 (24.1 ± 9.0 kya/17.9 ± 10.0 kya). The coalescent age estimates of pan-American haplogroups calculated using the same two mutation rates (A2:19.5 ± 1.3 kya/16.1 ± 1.5 kya, B2:20.8 ± 2.0 kya/18.1 ± 2.4 kya, C1:21.4 ± 2.7 kya/16.4 ± 1.5 kya and D1:17.2 ± 2.0 kya/14.9 ± 2.2 kya) and estimates of population expansions within America (~21-16 kya), support the pre-Clovis occupation of the New World. The phylogeography of sublineages within American haplogroups A2, B2, D1 and the C1b, C1c andC1d subhaplogroups of C1 are complex and largely specific to geographical North, Central and South America. However some sub-branches (B2b, C1b, C1c, C1d and D1f) already existed in American founder haplogroups before expansion into the America. Conclusions Our results suggest that Native American founders diverged from their Siberian-Asian progenitors sometime during the last glacial maximum (LGM) and expanded into America soon after the LGM peak (~20-16 kya). The phylogeography of haplogroup C1 suggest that this American founder haplogroup differentiated in Siberia-Asia. The situation is less clear for haplogroup B2, however haplogroups A2 and D1 may have differentiated soon after the Native American founders divergence. A moderate population bottle neck in American founder populations just before the expansion most plausibly resulted in few founder types in America. The similar estimates of the diversity indices and Bayesian skyline analysis in North America, Central America and South America suggest almost simultaneous (~ 2.0 ky from South to North America) colonization of these geographical regions with rapid population expansion differentiating into more or less regional branches across the pan-American haplogroups.
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Affiliation(s)
- Satish Kumar
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, 78227, USA.
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Figueiro G, Hidalgo PC, Sans M. Control region variability of haplogroup C1d and the tempo of the peopling of the Americas. PLoS One 2011; 6:e20978. [PMID: 21695136 PMCID: PMC3113844 DOI: 10.1371/journal.pone.0020978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/16/2011] [Indexed: 11/20/2022] Open
Abstract
Background Among the founding mitochondrial haplogroups involved in the peopling of the Americas, haplogroup C1d has been viewed as problematic because of its phylogeny and because of the estimates of its antiquity, apparently being much younger than other founding haplogroups. Several recent analyses, based on data from the entire mitochondrial genome, have contributed to an advance in the resolution of these problems. The aim of our analysis is to compare the conclusions drawn from the available HVR-I and HVR-II data for haplogroup C1d with the ones based on whole mitochondrial genomes. Methodology/Principal Findings HVR-I and HVR-II sequences defined as belonging to haplogroup C1d by standard criteria were gathered from the literature as well as from population studies carried out in Uruguay. Sequence phylogeny was reconstructed using median-joining networks, geographic distribution of lineages was analyzed and the age of the most recent common ancestor estimated using the ρ-statistic and two different mutation rates. The putative ancestral forms of the haplogroup were found to be more widespread than the derived lineages, and the lineages defined by np 194 were found to be widely distributed and of equivalent age. Conclusions/Significance The analysis of control region sequences is found to still harbor great potential in tracing microevolutionary phenomena, especially those found to have occurred in more recent times. Based on the geographic distributions of the alleles of np 7697 and np 194, both discussed as possible basal mutations of the C1d phylogeny, we suggest that both alleles were part of the variability of the haplogroup at the time of its entrance. Moreover, based on the mutation rates of the different sites stated to be diagnostic, it is possible that the anomalies found when analyzing the haplogroup are due to paraphyly.
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Affiliation(s)
- Gonzalo Figueiro
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay.
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Towards a reconciling model about the initial peopling of America. C R Biol 2011; 334:497-504. [PMID: 21784359 DOI: 10.1016/j.crvi.2011.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 12/16/2010] [Accepted: 03/16/2011] [Indexed: 01/04/2023]
Abstract
The last two decades have seen numerous debates in the field of the initial settlement of America and noteworthy was the disagreement between physical and molecular anthropologists. Recently, it has been pointed out that this discordance could partly originate from the description methods and classification labels used in craniometry, which did not account fairly for the within-sample and within-group variance. From there, a federative model for the initial peopling of America has been designed which could now explain the biological variability found at both the craniofacial and genetic level. This is a major step in the study of the initial settlement of America, which deserved to be highlighted. The present paper recalls the two conflicting models that prevailed for the last 20 years of anthropological studies in America before browsing the newly accepted hypothesis about the origin of the first Amerindians as seen by its authors. Lastly, the article evokes some areas of investigations, which could furnish significant fallouts about the dynamics of the peopling of Americas in the future.
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Gayà-Vidal M, Moral P, Saenz-Ruales N, Gerbault P, Tonasso L, Villena M, Vasquez R, Bravi CM, Dugoujon JM. mtDNA and Y-chromosome diversity in Aymaras and Quechuas from Bolivia: Different stories and special genetic traits of the Andean Altiplano populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 145:215-30. [DOI: 10.1002/ajpa.21487] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/09/2010] [Indexed: 11/11/2022]
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Gonçalves VF, Parra FC, Gonçalves-Dornelas H, Rodrigues-Carvalho C, Silva HP, Pena SD. Recovering mitochondrial DNA lineages of extinct Amerindian nations in extant homopatric Brazilian populations. INVESTIGATIVE GENETICS 2010; 1:13. [PMID: 21122100 PMCID: PMC3014906 DOI: 10.1186/2041-2223-1-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 12/01/2010] [Indexed: 11/19/2022]
Abstract
Background Brazilian Amerindians have experienced a drastic population decrease in the past 500 years. Indeed, many native groups from eastern Brazil have vanished. However, their mitochondrial mtDNA haplotypes, still persist in Brazilians, at least 50 million of whom carry Amerindian mitochondrial lineages. Our objective was to test whether, by analyzing extant rural populations from regions anciently occupied by specific Amerindian groups, we could identify potentially authentic mitochondrial lineages, a strategy we have named 'homopatric targeting'. Results We studied 173 individuals from Queixadinha, a small village located in a territory previously occupied by the now extinct Botocudo Amerindian nation. Pedigree analysis revealed 74 unrelated matrilineages, which were screened for Amerindian mtDNA lineages by restriction fragment length polymorphism. A cosmopolitan control group was composed of 100 individuals from surrounding cities. All Amerindian lineages identified had their hypervariable segment HVSI sequenced, yielding 13 Amerindian haplotypes in Queixadinha, nine of which were not present in available databanks or in the literature. Among these haplotypes, there was a significant excess of haplogroup C (70%) and absence of haplogroup A lineages, which were the most common in the control group. The novelty of the haplotypes and the excess of the C haplogroup suggested that we might indeed have identified Botocudo lineages. To validate our strategy, we studied teeth extracted from 14 ancient skulls of Botocudo Amerindians from the collection of the National Museum of Rio de Janeiro. We recovered mtDNA sequences from all the teeth, identifying only six different haplotypes (a low haplotypic diversity of 0.8352 ± 0.0617), one of which was present among the lineages observed in the extant individuals studied. Conclusions These findings validate the technique of homopatric targeting as a useful new strategy to study the peopling and colonization of the New World, especially when direct analysis of genetic material is not possible.
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Affiliation(s)
- Vanessa F Gonçalves
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-910 Belo Horizonte, Brazil
| | - Flavia C Parra
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-910 Belo Horizonte, Brazil
| | - Higgor Gonçalves-Dornelas
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-910 Belo Horizonte, Brazil
| | | | - Hilton P Silva
- Museu Nacional do Rio de Janeiro, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Sergio Dj Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-910 Belo Horizonte, Brazil
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Uehara DT, Rincon D, Abreu-Silva RS, de Mello Auricchio MTB, Tabith A, Kok F, Mingroni-Netto RC. Role of the Mitochondrial Mutations, m.827A>G and the Novel m.7462C>T, in the Origin of Hearing Loss. Genet Test Mol Biomarkers 2010; 14:611-6. [DOI: 10.1089/gtmb.2010.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniela Tiaki Uehara
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel Rincon
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ronaldo Serafim Abreu-Silva
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Alfredo Tabith
- Divisão de Educação e Reabilitação de Distúrbios da Comunicação, Pontifícia Universidade Católica, São Paulo, Brazil
| | - Fernando Kok
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Neurologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Perego UA, Angerhofer N, Pala M, Olivieri A, Lancioni H, Hooshiar Kashani B, Carossa V, Ekins JE, Gómez-Carballa A, Huber G, Zimmermann B, Corach D, Babudri N, Panara F, Myres NM, Parson W, Semino O, Salas A, Woodward SR, Achilli A, Torroni A. The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia. Genome Res 2010; 20:1174-9. [PMID: 20587512 DOI: 10.1101/gr.109231.110] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d--the third subset of C1--looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geographically diverse, mixed, and indigenous American populations. The revised phylogeny not only brings the age of C1d within the range of that of its two sister clades, but reveals that there were two C1d founder genomes for Paleo-Indians. Thus, the recognized maternal founding lineages of Native Americans are at least 15, indicating that the overall number of Beringian or Asian founder mitochondrial genomes will probably increase extensively when all Native American haplogroups reach the same level of phylogenetic and genomic resolution as obtained here for C1d.
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Affiliation(s)
- Ugo A Perego
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah 84115, USA
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Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S, Herrmann B. Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 141:208-21. [PMID: 19639639 DOI: 10.1002/ajpa.21135] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups.
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Affiliation(s)
- Lars Fehren-Schmitz
- Johann-Friedrich-Blumenbach Department of Zoology and Anthropology, Historical Anthropology and Human Ecology, University of Goettingen, Germany.
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Sala A, Alechine E, Bobillo C, Merini LJ, Ayala CG, Ferreira JCA, Corach D. Mitochondrial DNA control region sequence analysis of Mataco–Guaicurú speaking tribes from Argentina. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Carnese FR, Mendisco F, Keyser C, Dejean CB, Dugoujon JM, Bravi CM, Ludes B, Crubézy E. Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 141:452-62. [DOI: 10.1002/ajpa.21165] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zlojutro M, Rubicz R, Crawford MH. Mitochondrial DNA and Y-chromosome variation in five eastern Aleut communities: evidence for genetic substructure in the Aleut population. Ann Hum Biol 2009; 36:511-26. [PMID: 19588274 DOI: 10.1080/03014460903103947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Since Russian contact in 1741, the Aleut communities of southwestern Alaska have undergone a series of demographic upheavals stemming from forced relocations, disease epidemics, population bottlenecks, and pervasive admixture with European populations. This study investigates the impact of key historical events on the genetic structure of the Aleut population through analysis of mitochondrial and Y-chromosome DNA variation in five eastern Aleut communities. Results from HVS-I sequencing and Y-chromosome typing reveal patterns of variability that exhibit east-west geographic differentiation for the major Aleut haplogroups. This finding is underscored by SAMOVA and Monmonier analyses that identify genetic discontinuities between eastern and western Aleut populations. The majority of Aleut Y-chromosomes were characterized to haplogroups of mostly Russian, Scandinavian and Western European origin (approximately 85%), which is in stark contrast to the 3.6% of Aleut mtDNA lineages identified as non-Native American, and thus indicating a large degree of asymmetrical gene flow between European men and Aleut women. Overall, this study identifies a significant relationship between geography and genetic variation in the Aleut population, with a distinct substructure along an east-west axis that reflects the combined effects of founder events in aggregate island communities, male-biased gene flow from European populations, and the original peopling of the Aleutian Archipelago.
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Affiliation(s)
- Mark Zlojutro
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78227, USA.
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Guardado-Estrada M, Juarez-Torres E, Medina-Martinez I, Wegier A, Macías A, Gomez G, Cruz-Talonia F, Roman-Bassaure E, Piñero D, Kofman-Alfaro S, Berumen J. A great diversity of Amerindian mitochondrial DNA ancestry is present in the Mexican mestizo population. J Hum Genet 2009; 54:695-705. [DOI: 10.1038/jhg.2009.98] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bobillo MC, Zimmermann B, Sala A, Huber G, Röck A, Bandelt HJ, Corach D, Parson W. Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database. Int J Legal Med 2009; 124:263-8. [DOI: 10.1007/s00414-009-0366-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
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Sandoval K, Buentello-Malo L, Peñaloza-Espinosa R, Avelino H, Salas A, Calafell F, Comas D. Linguistic and maternal genetic diversity are not correlated in Native Mexicans. Hum Genet 2009; 126:521-31. [PMID: 19495796 PMCID: PMC2762527 DOI: 10.1007/s00439-009-0693-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/25/2009] [Indexed: 11/30/2022]
Abstract
Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.
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Affiliation(s)
- Karla Sandoval
- Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, 08003 Barcelona, Catalonia, Spain
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41
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Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M, Olivieri A, Hooshiar Kashani B, Ritchie KH, Scozzari R, Kong QP, Myres NM, Salas A, Semino O, Bandelt HJ, Woodward SR, Torroni A. Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr Biol 2009; 19:1-8. [PMID: 19135370 DOI: 10.1016/j.cub.2008.11.058] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 11/25/2008] [Accepted: 11/26/2008] [Indexed: 11/15/2022]
Abstract
BACKGROUND It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western Hemisphere remain controversial because linguistic, archaeological, and genetic evidence have not yet provided coherent answers. Notably, most of the genetic evidence has been acquired from the analysis of the common pan-American mitochondrial DNA (mtDNA) haplogroups. In this study, we have instead identified and analyzed mtDNAs belonging to two rare Native American haplogroups named D4h3 and X2a. RESULTS Phylogeographic analyses at the highest level of molecular resolution (69 entire mitochondrial genomes) reveal that two almost concomitant paths of migration from Beringia led to the Paleo-Indian dispersal approximately 15-17 kya. Haplogroup D4h3 spread into the Americas along the Pacific coast, whereas X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets. The examination of an additional 276 entire mtDNA sequences provides similar entry times for all common Native American haplogroups, thus indicating at least a dual origin for Paleo- Indians. CONCLUSIONS A dual origin for the first Americans is a striking novelty from the genetic point of view, and it makes plausible a scenario positing that within a rather short period of time, there may have been several entries into the Americas from a dynamically changing Beringian source. Moreover, this implies that most probably more than one language family was carried along with the Paleo-Indians.
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Affiliation(s)
- Ugo A Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, 27100 Pavia, Italy
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Fagundes NJR, Kanitz R, Bonatto SL. A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia. PLoS One 2008; 3:e3157. [PMID: 18797501 PMCID: PMC2527677 DOI: 10.1371/journal.pone.0003157] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 08/08/2008] [Indexed: 11/18/2022] Open
Abstract
The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called "three-stage model" consisting of a very early expansion into Beringia followed by approximately 20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the "three-stage model", since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes.
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Affiliation(s)
- Nelson J. R. Fagundes
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ricardo Kanitz
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro L. Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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43
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Mulligan CJ, Kitchen A, Miyamoto MM. Updated three-stage model for the peopling of the Americas. PLoS One 2008; 3:e3199. [PMID: 18797500 PMCID: PMC2527656 DOI: 10.1371/journal.pone.0003199] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 08/11/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. approximately 40,000 years ago) expansion signal we had proposed for the proto-Amerind population. METHODOLOGY/FINDINGS Bayesian skyline plot analysis of a new dataset of Native American mitochondrial coding genomes confirms the absence of an early expansion signal for the proto-Amerind population and allows us to reduce the variation around our estimate of the New World founder population size. In addition, genetic variants that define New World founder haplogroups are used to estimate the amount of time required between divergence of proto-Amerinds from the Asian gene pool and expansion into the New World. CONCLUSIONS/SIGNIFICANCE The period of population isolation required for the generation of New World mitochondrial founder haplogroup-defining genetic variants makes the existence of three stages of colonization a logical conclusion. Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.
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Affiliation(s)
- Connie J. Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Andrew Kitchen
- Department of Anthropology, University of Florida, Gainesville, Florida, United States of America
| | - Michael M. Miyamoto
- Department of Zoology, University of Florida, Gainesville, Florida, United States of America
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Kong QP, Salas A, Sun C, Fuku N, Tanaka M, Zhong L, Wang CY, Yao YG, Bandelt HJ. Distilling artificial recombinants from large sets of complete mtDNA genomes. PLoS One 2008; 3:e3016. [PMID: 18714389 PMCID: PMC2515346 DOI: 10.1371/journal.pone.0003016] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 07/21/2008] [Indexed: 11/19/2022] Open
Abstract
Background Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high immanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable. Methodology/Principal Findings We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments. Conclusions We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments – fully concordant with the predictions from our data-analytical approach.
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Affiliation(s)
- Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
| | - Chang Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Noriyuki Fuku
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Masashi Tanaka
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China
| | - Cheng-Ye Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong-Gang Yao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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45
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Gender bias in the multiethnic genetic composition of central Argentina. J Hum Genet 2008; 53:662-674. [DOI: 10.1007/s10038-008-0297-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 04/15/2008] [Indexed: 10/24/2022]
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46
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Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, Bandelt HJ. The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PLoS One 2008; 3:e1764. [PMID: 18335039 PMCID: PMC2258150 DOI: 10.1371/journal.pone.0001764] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 02/09/2008] [Indexed: 11/18/2022] Open
Abstract
Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.
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Affiliation(s)
- Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università degli Studi di Perugia, Perugia, Italy
| | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Claudio M. Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), La Plata, Argentina
| | - Michael D. Coble
- Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, Rockville, Maryland, United States of America
| | - Qing-Peng Kong
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Grupo de Medicina Xenómica, Hospital Clínico Universitario, Santiago de Compostela, Galicia, Spain
| | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- * To whom correspondence should be addressed. E-mail:
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47
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Fagundes NJ, Kanitz R, Eckert R, Valls AC, Bogo MR, Salzano FM, Smith DG, Silva WA, Zago MA, Ribeiro-dos-Santos AK, Santos SE, Petzl-Erler ML, Bonatto SL. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am J Hum Genet 2008; 82:583-92. [PMID: 18313026 PMCID: PMC2427228 DOI: 10.1016/j.ajhg.2007.11.013] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 11/13/2007] [Accepted: 11/29/2007] [Indexed: 11/24/2022] Open
Abstract
It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.
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Affiliation(s)
- Nelson J.R. Fagundes
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 91619-900, Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Ricardo Kanitz
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 91619-900, Brazil
| | - Roberta Eckert
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 91619-900, Brazil
| | - Ana C.S. Valls
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 91619-900, Brazil
| | - Mauricio R. Bogo
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 91619-900, Brazil
| | - Francisco M. Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - David Glenn Smith
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, Davis, CA 95616, USA
| | - Wilson A. Silva
- Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Marco A. Zago
- Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | | | - Sidney E.B. Santos
- Departamento de Patologia, Universidade Federal do Pará, Belém, PA, 66075-970, Brazil
| | | | - Sandro L. Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 91619-900, Brazil
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48
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Prieto L, Alonso A, Alves C, Crespillo M, Montesino M, Picornell A, Brehm A, Ramírez JL, Whittle MR, Anjos MJ, Boschi I, Buj J, Cerezo M, Cardoso S, Cicarelli R, Comas D, Corach D, Doutremepuich C, Espinheira RM, Fernández-Fernández I, Filippini S, Garcia-Hirschfeld J, González A, Heinrichs B, Hernández A, Leite FPN, Lizarazo RP, López-Parra AM, López-Soto M, Lorente JA, Mechoso B, Navarro I, Pagano S, Pestano JJ, Puente J, Raimondi E, Rodríguez-Quesada A, Terra-Pinheiro MF, Vidal-Rioja L, Vullo C, Salas A. 2006 GEP-ISFG collaborative exercise on mtDNA: reflections about interpretation, artefacts, and DNA mixtures. Forensic Sci Int Genet 2007; 2:126-33. [PMID: 19083807 DOI: 10.1016/j.fsigen.2007.10.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 09/11/2007] [Accepted: 10/02/2007] [Indexed: 11/29/2022]
Abstract
We report the results of the seventh edition of the GEP-ISFG mitochondrial DNA (mtDNA) collaborative exercise. The samples submitted to the participant laboratories were blood stains from a maternity case and simulated forensic samples, including a case of mixture. The success rate for the blood stains was moderate ( approximately 77%); even though four inexperienced laboratories concentrated about one-third of the total errors. A similar success was obtained for the analysis of mixed samples (78.8% for a hair-saliva mixture and 69.2% for a saliva-saliva mixture). Two laboratories also dissected the haplotypes contributing to the saliva-saliva mixture. Most of the errors were due to reading problems and misinterpretation of electropherograms, demonstrating once more that the lack of a solid devised experimental approach is the main cause of error in mtDNA testing.
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Affiliation(s)
- L Prieto
- Comisaría General de Policía Científica, DNA Laboratory, Madrid, Spain.
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Castrì L, Otárola F, Blell M, Ruiz E, Barrantes R, Luiselli D, Pettener D, Madrigal L. Indentured migration and differential gender gene flow: the origin and evolution of the East-Indian community of Limón, Costa Rica. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 134:175-89. [PMID: 17568447 DOI: 10.1002/ajpa.20652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
After the emancipation of African slaves in the Caribbean, the labor void left by out-migrating former slaves was filled by in-migrating indentured servants from prepartition India and China. In some areas of the Caribbean such as Trinidad, Suriname, and Guyana, the East-Indian migrants formed large communities. In this article, we report a study based on mtDNA and Y-chromosomal markers of a small East-Indian community from Limón, Costa Rica. The purpose of the project is to determine the place of origin in the Indian subcontinent of the ancestors of our group and the contributions to its gene pool through gene flow by members of other ethnic groups. Both Y-chromosome and mtDNA suggest that the Indo-Costa Ricans descend from migrants primarily from Central India. While both paternal and maternal markers indicate that this group is overwhelmingly of Indian origin, they also indicate that males and females of African, European, and Amerindian origin contributed to it differently. We discuss our results in the historical context of the virtual extinction of Amerindian Caribbean groups, the forced migration of African slaves to the Caribbean, and the gene flow between Amerindians, Europeans, East-Indians, and Africans that eventually produced the Caribbean's currently diverse gene pool.
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Affiliation(s)
- Loredana Castrì
- Dipartimento di Biologia Evoluzionistica Sperimentale, Area di Antropologia, Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
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50
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Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, Dorzhu C, Luzina F, Lee HK, Vanecek T, Villems R, Zakharov I. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 2007; 81:1025-41. [PMID: 17924343 DOI: 10.1086/522933] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 07/26/2007] [Indexed: 11/03/2022] Open
Abstract
To elucidate the human colonization process of northern Asia and human dispersals to the Americas, a diverse subset of 71 mitochondrial DNA (mtDNA) lineages was chosen for complete genome sequencing from the collection of 1,432 control-region sequences sampled from 18 autochthonous populations of northern, central, eastern, and southwestern Asia. On the basis of complete mtDNA sequencing, we have revised the classification of haplogroups A, D2, G1, M7, and I; identified six new subhaplogroups (I4, N1e, G1c, M7d, M7e, and J1b2a); and fully characterized haplogroups N1a and G1b, which were previously described only by the first hypervariable segment (HVS1) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings indicate that the southern Siberian mtDNA pool harbors several lineages associated with the Late Upper Paleolithic and/or early Neolithic dispersals from both eastern Asia and southwestern Asia/southern Caucasus. Moreover, the phylogeography of the D2 lineages suggests that southern Siberia is likely to be a geographical source for the last postglacial maximum spread of this subhaplogroup to northern Siberia and that the expansion of the D2b branch occurred in Beringia ~7,000 years ago. In general, a detailed analysis of mtDNA gene pools of northern Asians provides the additional evidence to rule out the existence of a northern Asian route for the initial human colonization of Asia.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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