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Motti JMB, Pauro M, Scabuzzo C, García A, Aldazábal V, Vecchi R, Bayón C, Pastor N, Demarchi DA, Bravi CM, Reich D, Cabana GS, Nores R. Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181:216-230. [PMID: 36919783 DOI: 10.1002/ajpa.24727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVE This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes. MATERIALS AND METHODS We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis. RESULTS We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP. DISCUSSION The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.
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Affiliation(s)
- Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Quequén, Buenos Aires, Argentina
| | - Maia Pauro
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina
| | - Clara Scabuzzo
- Centro de Investigación Científica y de Transferencia a la Producción (CICyTTP)-CONICET, Provincia de Entre Ríos-Universidad Autónoma de Entre Ríos (UADER)-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Diamante, Entre Ríos, Argentina
| | - Angelina García
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Verónica Aldazábal
- Instituto Multidisciplinario de Historia y Ciencias Humanas, CONICET, Buenos Aires, Argentina
| | - Rodrigo Vecchi
- Departamento de Humanidades, Universidad Nacional del Sur, CONICET, Bahía Blanca, Buenos Aires, Argentina
| | - Cristina Bayón
- Departamento de Humanidades, Universidad Nacional del Sur, CONICET, Bahía Blanca, Buenos Aires, Argentina
| | - Nicolás Pastor
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina
| | - Darío A Demarchi
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular, Centro Científico Tecnológica (CCT) La Plata CONICET, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Broad Institute, Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Graciela S Cabana
- Molecular Anthropology Laboratories, Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Rodrigo Nores
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina
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Amaru R, Song J, Reading NS, Gordeuk VR, Prchal JT. "What We Know and What We Do Not Know about Evolutionary Genetic Adaptation to High Altitude Hypoxia in Andean Aymaras". Genes (Basel) 2023; 14:640. [PMID: 36980912 PMCID: PMC10048644 DOI: 10.3390/genes14030640] [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: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Three well-studied populations living at high altitudes are Tibetans, Andeans (Aymaras and Quechuas), and Ethiopians. Unlike Tibetans and Ethiopians who have similar hemoglobin (Hb) levels as individuals living at sea level, Aymara Hb levels increase when living at higher altitudes. Our previous whole genome study of Aymara people revealed several selected genes that are involved in cardiovascular functions, but their relationship with Hb levels was not elucidated. Here, we studied the frequencies of known evolutionary-selected variants in Tibetan and Aymara populations and their correlation with high Hb levels in Aymara. We genotyped 177 Aymaras at three different altitudes: 400 m (Santa Cruz), 4000 m (La Paz), and 5000 m (Chorolque), and correlated the results with the elevation of residence. Some of the Tibetan-selected variants also exist in Aymaras, but at a lower prevalence. Two of 10 Tibetan selected variants of EPAS1 were found (rs13005507 and rs142764723) and these variants did not correlate with Hb levels. Allele frequencies of 5 Aymara selected SNPs (heterozygous and homozygous) at 4000 m (rs11578671_BRINP3, rs34913965_NOS2, rs12448902_SH2B1, rs10744822_TBX5, and rs487105_PYGM) were higher compared to Europeans. The allelic frequencies of rs11578671_BRINP3, rs34913965_NOS2, and rs10744822_SH2B1 were significantly higher for Aymaras living at 5000 m than those at 400 m elevation. Variant rs11578671, close to the BRINP3 coding region, correlated with Hb levels in females. Variant rs34913965 (NOS2) correlated with leukocyte counts. Variants rs12448902 (SH2B1) and rs34913965 (NOS2) associated with higher platelet levels. The correlation of these SNPs with blood cell counts demonstrates that the selected genetic variants in Aymara influence hematopoiesis and cardiovascular effects.
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Affiliation(s)
- Ricardo Amaru
- Cell Biology Unit, School of Medicine, San Andres University, La Paz 0201, Bolivia
| | - Jihyun Song
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - N. Scott Reading
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
- Department of Pathology-ARUP Laboratories, University of Utah, Salt Lake City, UT 84132, USA
| | - Victor R. Gordeuk
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 61820, USA
| | - Josef T. Prchal
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
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Reyes-Madrid M, Flores-Alvarado S, Pezo-Valderrama P, Orellana-Soto M, Apata M, Moraga M, de Saint Pierre M. An approach on the migratory processes in the north of Chile based on Y chromosome analysis. Am J Hum Biol 2022; 34:e23736. [PMID: 35263492 DOI: 10.1002/ajhb.23736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/23/2021] [Accepted: 02/12/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Northern Chile is an area characterized by a complex cultural and demographic trajectory. During the last few centuries, this complex trajectory has become the destination of intra- and intercontinental migratory waves. In this study, we analyzed the Y chromosome to evaluate how migratory and admixture patterns have affected the genetic composition of the populations in northern Chile compared with other populations of the country. METHODS A total of 311 people from urban (Antofagasta and Calama), rural (Azapa and Camarones), and Native (Aymara and Atacameño) populations from northern Chile were characterized by 26 SNPs and the STR DYS393 of the Y chromosome, along with 69 individuals from Native populations (Mapuche, Pehuenche, and Huilliche) from southern Chile. In addition to characterizing the paternal lineages, multivariate analyses were performed to compare with published data from other Chilean populations. RESULTS Both the Antofagasta and Calama populations show differences compared with the rest of the Chilean population. On one side, Antofagasta shows a high diversity of non-Amerindian lineages, including the highest value for haplogroup I (12%) for all Chileans populations. Otherwise, Calama has the highest value of any Chilean urban population (31.9%) for Amerindian lineages, including the only Q-M3 sub-lineage detected in the entire sample. Regarding the Native population, Aymara presents the highest percentage of Q-M3 (94.4%). CONCLUSIONS The Y chromosome haplogroup distribution allowed us to identify recent migratory processes typical of the northern populations studied. These have shaped the demographic and cultural dynamics of local and migrant groups in the territory.
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Affiliation(s)
- Margarita Reyes-Madrid
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Bioestadística, Instituto de Salud Pública, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Michael Orellana-Soto
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mario Apata
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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Di Corcia T, Scano G, Martínez-Labarga C, Sarno S, De Fanti S, Luiselli D, Rickards O. Uniparental Lineages from the Oldest Indigenous Population of Ecuador: The Tsachilas. Genes (Basel) 2021; 12:genes12081273. [PMID: 34440446 PMCID: PMC8391833 DOI: 10.3390/genes12081273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 12/02/2022] Open
Abstract
Together with Cayapas, the Tsachilas constitute the oldest population in the country of Ecuador and, according to some historians, they are the last descendants of the ancient Yumbos. Several anthropological issues underlie the interest towards this peculiar population: the uncertainty of their origin, their belonging to the Barbacoan linguistic family, which is still at the center of an intense linguistic debate, and the relations of their Yumbo ancestors with the Inca invaders who occupied their ancient territory. Our contribution to the knowledge of their complex past was the reconstruction of their genetic maternal and paternal inheritance through the sequencing of 70 entire mitochondrial genomes and the characterization of the non-recombinant region of the Y chromosome in 26 males. For both markers, we built comprehensive datasets of various populations from the surrounding geographical area, northwestern South America, NW, with a known linguistic affiliation, and we could then compare our sample against the overall variability to infer relationships with other Barbacoan people and with other NW natives. We found contrasting patterns of genetic diversity for the two markers, but generally, our results indicated a possible common origin between the Tsachilas, the Chachi, and other Ecuadorian and Colombian Barbacoans and are suggestive of an interesting ancient linkage to the Inca invaders in Yumbo country.
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Affiliation(s)
- Tullia Di Corcia
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica n. 1, 00173 Rome, Italy; (C.M.-L.); (O.R.)
- Correspondence: (T.D.C.); (G.S.)
| | - Giuseppina Scano
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica n. 1, 00173 Rome, Italy; (C.M.-L.); (O.R.)
- Correspondence: (T.D.C.); (G.S.)
| | - Cristina Martínez-Labarga
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica n. 1, 00173 Rome, Italy; (C.M.-L.); (O.R.)
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (S.S.); (S.D.F.)
| | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (S.S.); (S.D.F.)
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, 40126 Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage (DBC), University of Bologna, Via degli Ariani, 1, 40121 Ravenna, Italy;
| | - Olga Rickards
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica n. 1, 00173 Rome, Italy; (C.M.-L.); (O.R.)
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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Neyra-Rivera CD, Ticona Arenas A, Delgado Ramos E, Velasquez Reinoso MRE, Caceres Rey OA, Budowle B. Population data of 27 Y-chromosome STRS in Aymara population from Peru. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1882571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Andres Ticona Arenas
- Posgrado de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Ciudad Universitaria Cercado de Lima, Lima, Perú
| | - Edgardo Delgado Ramos
- Universidad Nacional Mayor de San Marcos, Ciudad Universitaria Cercado de Lima, Lima, Perú
| | | | | | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
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8
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Guevara EK, Palo JU, Översti S, King JL, Seidel M, Stoljarova M, Wendt FR, Bus MM, Guengerich A, Church WB, Guillén S, Roewer L, Budowle B, Sajantila A. Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru. PLoS One 2020; 15:e0244497. [PMID: 33382772 PMCID: PMC7774974 DOI: 10.1371/journal.pone.0244497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Many native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jívaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.
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Affiliation(s)
- Evelyn K. Guevara
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- * E-mail: (EKG); (AS)
| | - Jukka U. Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Genetics Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sanni Översti
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Stoljarova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Frank R. Wendt
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Psychiatry, Yale University School of Medicine and VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Magdalena M. Bus
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Anna Guengerich
- Eckerd College, Saint Petersburg, Florida, United States of America
| | - Warren B. Church
- Department of Earth and Space Sciences, Columbus State University, Columbus, Georgia, United States of America
| | | | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- * E-mail: (EKG); (AS)
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9
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Gómez-Carballa A, Pardo-Seco J, Brandini S, Achilli A, Perego UA, Coble MD, Diegoli TM, Álvarez-Iglesias V, Martinón-Torres F, Olivieri A, Torroni A, Salas A. The peopling of South America and the trans-Andean gene flow of the first settlers. Genome Res 2018; 28:767-779. [PMID: 29735605 PMCID: PMC5991523 DOI: 10.1101/gr.234674.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/27/2018] [Indexed: 11/25/2022]
Abstract
Genetic and archaeological data indicate that the initial Paleoindian settlers of South America followed two entry routes separated by the Andes and the Amazon rainforest. The interactions between these paths and their impact on the peopling of South America remain unclear. Analysis of genetic variation in the Peruvian Andes and regions located south of the Amazon River might provide clues on this issue. We analyzed mitochondrial DNA variation at different Andean locations and >360,000 autosomal SNPs from 28 Native American ethnic groups to evaluate different trans-Andean demographic scenarios. Our data reveal that the Peruvian Altiplano was an important enclave for early Paleoindian expansions and point to a genetic continuity in the Andes until recent times, which was only marginally affected by gene flow from the Amazonian lowlands. Genomic variation shows a good fit with the archaeological evidence, indicating that the genetic interactions between the descendants of the settlers that followed the Pacific and Atlantic routes were extremely limited.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Michael D Coble
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Toni M Diegoli
- Office of the Chief Scientist, Defense Forensic Science Center, Ft. Gillem, Georgia 30297, USA.,Analytical Services, Incorporated, Arlington, Virginia 22201, USA
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain
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10
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Genetic variation in populations from central Argentina based on mitochondrial and Y chromosome DNA evidence. J Hum Genet 2018; 63:493-507. [DOI: 10.1038/s10038-017-0406-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/06/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022]
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11
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Enclaves of genetic diversity resisted Inca impacts on population history. Sci Rep 2017; 7:17411. [PMID: 29234095 PMCID: PMC5727115 DOI: 10.1038/s41598-017-17728-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 11/08/2022] Open
Abstract
The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.
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Arias L, Barbieri C, Barreto G, Stoneking M, Pakendorf B. High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:238-255. [DOI: 10.1002/ajpa.23345] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/17/2017] [Accepted: 10/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Leonardo Arias
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Anthropology; Leipzig D-04103 Germany
- Laboratorio de Genética Molecular Humana; Universidad del Valle; Cali Colombia
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution; Max Planck Institute for the Science of Human History; Jena D-07745 Germany
| | - Guillermo Barreto
- Laboratorio de Genética Molecular Humana; Universidad del Valle; Cali Colombia
| | - Mark Stoneking
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Anthropology; Leipzig D-04103 Germany
| | - Brigitte Pakendorf
- Dynamique du Langage; UMR5596, CNRS & Université de Lyon; Lyon Cedex 07 69363 France
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Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
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Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
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14
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Pardo-Seco J, Heinz T, Taboada-Echalar P, Martinón-Torres F, Salas A. Mapping the genomic mosaic of two 'Afro-Bolivians' from the isolated Yungas valleys. BMC Genomics 2016; 17:207. [PMID: 26956021 PMCID: PMC4784306 DOI: 10.1186/s12864-016-2520-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/24/2016] [Indexed: 12/13/2022] Open
Abstract
Background Unraveling the ancestry of ‘Afro-American’ communities is hampered by the complex demographic processes that took place during the Transatlantic Slave Trade (TAST) and the (post-)colonization periods. ‘Afro-Bolivians’ from the subtropical Yungas valleys constitute small and isolated communities that live surrounded by the predominant Native American community of Bolivia. By genotyping >580,000 SNPs in two ‘Afro-Bolivians’, and comparing these genomic profiles with data compiled from more than 57 African groups and other reference ancestral populations (n = 1,161 in total), we aimed to disentangle the complex admixture processes undergone by ‘Afro-Bolivians’. Results The data indicate that these two genomes constitute a complex mosaic of ancestries that is approximately 80 % of recent African origin; the remaining ~20 % being European and Native American. West-Central Africa contributed most of the African ancestry to ‘Afro-Bolivians’, and this component is related to populations living along the Atlantic coast (i.e. Senegal, Ghana, Nigeria). Using tract length distribution of genomic segments attributable to distinct ancestries, we could date the time of admixture in about 400 years ago. This time coincides with the maximum importation of slaves to Bolivia to compensate the diminishing indigenous labor force needed for the development of the National Mint of Potosí. Conclusions Overall, the data indicate that the genome of ‘Afro-Bolivians’ was shaped by a complex process of admixture occurring in America among individuals originating in different West-Central African populations; their genomic mosaics received additional contributions of Europeans and local Native Americans (e.g. Aymaras). Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2520-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, C.P. 15872, Galicia, Spain. .,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain.
| | - Tanja Heinz
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, C.P. 15872, Galicia, Spain.
| | - Patricia Taboada-Echalar
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, C.P. 15872, Galicia, Spain.
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain. .,Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain.
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, C.P. 15872, Galicia, Spain. .,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain.
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15
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Grugni V, Battaglia V, Perego UA, Raveane A, Lancioni H, Olivieri A, Ferretti L, Woodward SR, Pascale JM, Cooke R, Myres N, Motta J, Torroni A, Achilli A, Semino O. Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS One 2015; 10:e0144223. [PMID: 26636572 PMCID: PMC4670172 DOI: 10.1371/journal.pone.0144223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023] Open
Abstract
Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.
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Affiliation(s)
- Viola Grugni
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Ancestry, Provo, Utah, United States of America
| | - Jorge Motta
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- * E-mail:
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16
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The Genomic Legacy of the Transatlantic Slave Trade in the Yungas Valley of Bolivia. PLoS One 2015; 10:e0134129. [PMID: 26263179 PMCID: PMC4532489 DOI: 10.1371/journal.pone.0134129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 07/06/2015] [Indexed: 11/23/2022] Open
Abstract
During the period of the Transatlantic Slave Trade (TAST) some enslaved Africans were forced to move to Upper Peru (nowadays Bolivia). At first they were sent to Potosí, but later to the tropical Yungas valley where the Spanish colonizers established a so-called “hacienda system” that was based on slave labor, including African-descendants. Due to their isolation, very little attention has been paid so far to ‘Afro-Bolivian’ communities either within the research field of TAST or in genetic population studies. In this study, a total of 105 individuals from the Yungas were sequenced for their mitochondrial DNA (mtDNA) control region, and mitogenomes were obtained for a selected subset of these samples. We also genotyped 46 Ancestry Informative Markers (AIM) in order to investigate continental ancestry at the autosomal level. In addition, Y-chromosome STR and SNP data for a subset of the same individuals was also available from the literature. The data indicate that the partitioning of mtDNA ancestry in the Yungas differs significantly from that in the rest of the country: 81% Native American, 18% African, and 1% European. Interestingly, the great majority of ‘Afro-descendant’ mtDNA haplotypes in the Yungas (84%) concentrates in the locality of Tocaña. This high proportion of African ancestry in the Tocaña is also manifested in the Y-chromosome (44%) and in the autosomes (56%). In sharp contrast with previous studies on the TAST, the ancestry of about 1/3 of the ‘Afro-Bolivian’ mtDNA haplotypes can be traced back to East and South East Africa, which may be at least partially explained by the Arab slave trade connected to the TAST.
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17
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Valverde G, Zhou H, Lippold S, de Filippo C, Tang K, López Herráez D, Li J, Stoneking M. A novel candidate region for genetic adaptation to high altitude in Andean populations. PLoS One 2015; 10:e0125444. [PMID: 25961286 PMCID: PMC4427407 DOI: 10.1371/journal.pone.0125444] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/12/2015] [Indexed: 02/07/2023] Open
Abstract
Humans living at high altitude (≥2,500 meters above sea level) have acquired unique abilities to survive the associated extreme environmental conditions, including hypoxia, cold temperature, limited food availability and high levels of free radicals and oxidants. Long-term inhabitants of the most elevated regions of the world have undergone extensive physiological and/or genetic changes, particularly in the regulation of respiration and circulation, when compared to lowland populations. Genome scans have identified candidate genes involved in altitude adaption in the Tibetan Plateau and the Ethiopian highlands, in contrast to populations from the Andes, which have not been as intensively investigated. In the present study, we focused on three indigenous populations from Bolivia: two groups of Andean natives, Aymara and Quechua, and the low-altitude control group of Guarani from the Gran Chaco lowlands. Using pooled samples, we identified a number of SNPs exhibiting large allele frequency differences over 900,000 genotyped SNPs. A region in chromosome 10 (within the cytogenetic bands q22.3 and q23.1) was significantly differentiated between highland and lowland groups. We resequenced ~1.5 Mb surrounding the candidate region and identified strong signals of positive selection in the highland populations. A composite of multiple signals like test localized the signal to FAM213A and a related enhancer; the product of this gene acts as an antioxidant to lower oxidative stress and may help to maintain bone mass. The results suggest that positive selection on the enhancer might increase the expression of this antioxidant, and thereby prevent oxidative damage. In addition, the most significant signal in a relative extended haplotype homozygosity analysis was localized to the SFTPD gene, which encodes a surfactant pulmonary-associated protein involved in normal respiration and innate host defense. Our study thus identifies two novel candidate genes and associated pathways that may be involved in high-altitude adaptation in Andean populations.
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Affiliation(s)
- Guido Valverde
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, Australia
| | - Hang Zhou
- Department of Computational Regulatory Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kun Tang
- Department of Computational Regulatory Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - David López Herráez
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- * E-mail: (DLH); (JL); (MS)
| | - Jing Li
- Department of Computational Regulatory Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
- * E-mail: (DLH); (JL); (MS)
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail: (DLH); (JL); (MS)
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18
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De Ferrari A, Miranda JJ, Gilman RH, Dávila-Román VG, León-Velarde F, Rivera-Ch M, Huicho L, Bernabé-Ortiz A, Wise RA, Checkley W. Prevalence, clinical profile, iron status, and subject-specific traits for excessive erythrocytosis in andean adults living permanently at 3,825 meters above sea level. Chest 2015; 146:1327-1336. [PMID: 24874587 DOI: 10.1378/chest.14-0298] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Excessive erythrocytosis (EE) is a prevalent condition in populations living at high altitudes (> 2,500 m above sea level). Few large population-based studies have explored the association between EE and multiple subject-specific traits including oxygen saturation, iron status indicators, and pulmonary function. METHODS We enrolled a sex-stratified and age-stratified sample of 1,065 high-altitude residents aged ≥ 35 years from Puno, Peru (3,825 m above sea level) and conducted a standardized questionnaire and physical examination that included spirometry, pulse oximetry, and a blood sample for multiple clinical markers. Our primary objectives were to estimate the prevalence of EE, characterize the clinical profile and iron status indicators of subjects with EE, and describe subject-specific traits associated with EE. RESULTS Overall prevalence of EE was 4.5% (95% CI, 3.3%-6.0%). Oxygen saturation was significantly lower among EE than non-EE group subjects (85.3% vs 90.1%, P < .001) but no difference was found in iron status indicators between both groups (P > .09 for all values). In multivariable logistic regression, we found that age ≥ 65 years (OR = 2.45, 95% CI, 1.16-5.09), male sex (3.86, 1.78-9.08), having metabolic syndrome (2.66, 1.27-5.75) or being overweight (5.20, 1.95-16.77), pulse oximetry < 85% (14.90, 6.43-34.90), and % predicted FVC < 80% (13.62, 4.40-41.80) were strongly associated with EE. Attributable fractions for EE were greatest for being overweight (26.7%), followed by male sex (21.5%), pulse oximetry < 85% (16.4%), having metabolic syndrome (14.4%), and % predicted FVC < 80% (9.3%). CONCLUSIONS We found a lower prevalence of EE than in previous reports in the Peruvian Andes. Although the presence of hypoxemia and decreased vital capacity were strongly associated with excessive erythrocytosis, being overweight or having metabolic syndrome were associated with an important fraction of cases in our study population.
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Affiliation(s)
- Aldo De Ferrari
- From the Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - J Jaime Miranda
- CRONICAS Centre of Excellence for Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru; Departamento de Medicina, Escuela de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Robert H Gilman
- CRONICAS Centre of Excellence for Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru; Departamento de Medicina, Escuela de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru; Program in Global Disease Epidemiology and Control, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Victor G Dávila-Román
- Cardiovascular Imaging and Clinical Research Core Laboratory, Cardiovascular Division, School of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Fabiola León-Velarde
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorio de Adaptación a la Altura, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Rivera-Ch
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorio de Adaptación a la Altura, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis Huicho
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorio de Adaptación a la Altura, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Antonio Bernabé-Ortiz
- CRONICAS Centre of Excellence for Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Robert A Wise
- From the Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - William Checkley
- From the Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, MD; CRONICAS Centre of Excellence for Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru; Departamento de Medicina, Escuela de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru.
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19
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Cárdenas JM, Heinz T, Pardo-Seco J, Álvarez-Iglesias V, Taboada-Echalar P, Sánchez-Diz P, Carracedo Á, Salas A. The multiethnic ancestry of Bolivians as revealed by the analysis of Y-chromosome markers. Forensic Sci Int Genet 2015; 14:210-8. [DOI: 10.1016/j.fsigen.2014.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/20/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
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20
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Parolin ML, Iudica CE, Lancelotti JL, Sambuco LA, Jaureguiberry SM, Avena SA, Carnese FR. Population data of 15 autosomal STR markers from Afro-Bolivians of Nor Yungas Province (Bolivia). Int J Legal Med 2014; 129:463-4. [PMID: 25217341 DOI: 10.1007/s00414-014-1080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022]
Abstract
Allele frequencies and forensic parameters for 15 autosomal loci included in the AmpFlSTR® Identifiler kit were estimated in a sample of 57 unrelated Afro-descendants from Nor Yungas (Bolivia). Buccal swabs samples were obtained from voluntary donors, after consent was given. All loci were in Hardy-Weinberg equilibrium after Bonferroni correction. D21S11 was the most informative locus, while the least discriminating locus was D3S1358. The combined power of discrimination and the combined probability of exclusion were >0.99999999 and >0.99997, respectively. The multidimensional scaling (MDS) plot generated by Rst matrix supported that Afro-Bolivians of Nor Yungas preserved a stronger African descent compared to other admixed Latin American populations. These results amplified the Bolivian databases of autosomal STR loci and may provide a useful tool for human identification tests and population genetic studies.
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Affiliation(s)
- María Laura Parolin
- Sistemática y Evolución, Laboratorio de Biología Molecular, Centro Nacional Patagónico-CONICET, Unidad de Diversidad, Bvd. Brown 2915, Puerto Madryn, Chubut, Argentina,
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Mendisco F, Keyser C, Seldes V, Rivolta C, Mercolli P, Cruz P, Nielsen AE, Crubezy E, Ludes B. Genetic diversity of a late prehispanic group of the Quebrada de Humahuaca, northwestern Argentina. Ann Hum Genet 2014; 78:367-80. [PMID: 24962720 DOI: 10.1111/ahg.12075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 05/13/2014] [Indexed: 11/29/2022]
Abstract
This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies whose cultural but especially biological diversity is still poorly understood. We analyzed the DNA extracted from 39 individuals who populated this upper valley during the Regional Development period (RDP) (between the 11th and 15th centuries CE), to determine their maternal and paternal genetic ancestry. Some mitochondrial and Y-chromosomal haplotypes specific to the Andean region are consistent with an origin in the highlands of Central Andes. On the other hand, a significant genetic affinity with contemporary admixed communities of the Chaco area was detected. Expectedly, recent demographic events, such as the expansion of the Inca Empire or the European colonization, have changed the original mitochondrial gene pool of the ancient Humahuaca Valley community. Finally, we identified a particular geographical organization of the prehispanic populations of Northwestern Argentina. Our results suggest that the communities of the region were divided between two different spheres of interaction, which is consistent with assumptions made by means of craniometric traits.
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Affiliation(s)
- Fanny Mendisco
- Institut de Médecine Légale, AMIS, CNRS UMR 5288, Université de Strasbourg, F-67085, Strasbourg, France; Université Paul Sabatier, AMIS, CNRS UMR 5288, F-31073, Toulouse, France
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Vullo C, Gomes V, Romanini C, Oliveira AM, Rocabado O, Aquino J, Amorim A, Gusmão L. Association between Y haplogroups and autosomal AIMs reveals intra-population substructure in Bolivian populations. Int J Legal Med 2014; 129:673-80. [PMID: 24878616 DOI: 10.1007/s00414-014-1025-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 05/15/2014] [Indexed: 12/24/2022]
Abstract
For the correct evaluation of the weight of genetic evidence in a forensic context, databases must reflect the structure of the population, with all possible groups being represented. Countries with a recent history of admixture between strongly differentiated populations are usually highly heterogeneous and sub-structured. Bolivia is one of these countries, with a high diversity of ethnic groups and different levels of admixture (among Native Americans, Europeans and Africans) across the territory. For a better characterization of the male lineages in Bolivia, 17 Y-STR and 42 Y-SNP loci were genotyped in samples from La Paz and Chuquisaca. Only European and Native American Y-haplogroups were detected, and no sub-Saharan African chromosomes were found. Significant differences were observed between the two samples, with a higher frequency of European lineages in Chuquisaca than in La Paz. A sample belonging to haplogroup Q1a3a1a1-M19 was detected in La Paz, in a haplotype background different from those previously found in Argentina. This result supports an old M19 North-south dispersion in South America, possibly via two routes. When comparing the ancestry of each individual assessed through his Y chromosome with the one estimated using autosomal AIMs, (a) increased European ancestry in individuals with European Y chromosomes and (b) higher Native American ancestry in the carriers of Native American Y-haplogroups were observed, revealing an association between autosomal and Y-chromosomal markers. The results of this study demonstrate that a sub-structure does exist in Bolivia at both inter- and intrapopulation levels, a fact which must be taken into account in the evaluation of forensic genetic evidence.
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Affiliation(s)
- Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team (EAAF), Córdoba, Argentina
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The Andean adaptive toolkit to counteract high altitude maladaptation: genome-wide and phenotypic analysis of the Collas. PLoS One 2014; 9:e93314. [PMID: 24686296 PMCID: PMC3970967 DOI: 10.1371/journal.pone.0093314] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/03/2014] [Indexed: 12/03/2022] Open
Abstract
During their migrations out of Africa, humans successfully colonised and adapted to a wide range of habitats, including extreme high altitude environments, where reduced atmospheric oxygen (hypoxia) imposes a number of physiological challenges. This study evaluates genetic and phenotypic variation in the Colla population living in the Argentinean Andes above 3500 m and compares it to the nearby lowland Wichí group in an attempt to pinpoint evolutionary mechanisms underlying adaptation to high altitude hypoxia. We genotyped 730,525 SNPs in 25 individuals from each population. In genome-wide scans of extended haplotype homozygosity Collas showed the strongest signal around VEGFB, which plays an essential role in the ischemic heart, and ELTD1, another gene crucial for heart development and prevention of cardiac hypertrophy. Moreover, pathway enrichment analysis showed an overrepresentation of pathways associated with cardiac morphology. Taken together, these findings suggest that Colla highlanders may have evolved a toolkit of adaptative mechanisms resulting in cardiac reinforcement, most likely to counteract the adverse effects of the permanently increased haematocrit and associated shear forces that characterise the Andean response to hypoxia. Regulation of cerebral vascular flow also appears to be part of the adaptive response in Collas. These findings are not only relevant to understand the evolution of hypoxia protection in high altitude populations but may also suggest new avenues for medical research into conditions where hypoxia constitutes a detrimental factor.
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Batai K, Williams SR. Mitochondrial variation among the Aymara and the signatures of population expansion in the central Andes. Am J Hum Biol 2014; 26:321-30. [PMID: 24449040 DOI: 10.1002/ajhb.22507] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 01/01/2014] [Accepted: 01/02/2014] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES The exploitation of marine resources and intensive agriculture led to a marked population increase early in central Andean prehistory. Constant historic and prehistoric population movements also characterize this region. These features undoubtedly affected regional genetic variation, but the exact nature of these effects remains uncertain. METHODS Mitochondrial DNA (mtDNA) hypervariable region I sequence variation in 61 Aymara individuals from La Paz, Bolivia, was analyzed and compared to sequences from 47 other South American populations to test hypotheses of whether increased female effective population size and gene flow influenced the mtDNA variation among central Andean populations. RESULTS The Aymara and Quechua were genetically diverse showing evidence of population expansion and large effective population size, and a demographic expansion model fits the mtDNA variation found among central Andean populations well. Estimated migration rates and the results of AMOVA and multidimensional scaling analysis suggest that female gene flow was also an important factor, influencing genetic variation among the central Andeans as well as lowland populations from western South America. mtDNA variation in south central Andes correlated better with geographic proximity than with language, and fit a population continuity model. CONCLUSION The mtDNA data suggests that the central Andeans experienced population expansion, most likely because of rapid demographic expansion after introduction of intensive agriculture, but roles of female gene flow need to be further explored.
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Affiliation(s)
- Ken Batai
- Cancer Education and Career Development Program, Institute for Health Research and Policy, University of Illinois at Chicago (M/C 275), Chicago, Illinois, 60608; Institute of Human Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, 60607
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Sala A, Corach D. Analysis of admixture and genetic structure of two Native American groups of Southern Argentinean Patagonia. Mol Biol Rep 2014; 41:1533-43. [DOI: 10.1007/s11033-013-2999-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 12/28/2013] [Indexed: 12/20/2022]
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Pauro M, García A, Nores R, Demarchi DA. Analysis of Uniparental Lineages in Two Villages of Santiago del Estero, Argentina, Seat of Pueblos de Indios in Colonial Times. Hum Biol 2013; 85:699-720. [DOI: 10.3378/027.085.0504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2013] [Indexed: 11/05/2022]
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Sandoval JR, Lacerda DR, Jota MSA, Salazar-Granara A, Vieira PPR, Acosta O, Cuellar C, Revollo S, Fujita R, Santos FR. The genetic history of indigenous populations of the Peruvian and Bolivian Altiplano: the legacy of the Uros. PLoS One 2013; 8:e73006. [PMID: 24039843 PMCID: PMC3770642 DOI: 10.1371/journal.pone.0073006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
The Altiplano region of the South American Andes is marked by an inhospitable climate to which the autochthonous human populations adapted and then developed great ancient civilizations, such as the Tiwanaku culture and the Inca Empire. Since pre-Columbian times, different rulers established themselves around the Titicaca and Poopo Lakes. By the time of the arrival of Spaniards, Aymara and Quechua languages were predominant on the Altiplano under the rule of the Incas, although the occurrence of other spoken languages, such as Puquina and Uruquilla, suggests the existence of different ethnic groups in this region. In this study, we focused on the pre-Columbian history of the autochthonous Altiplano populations, particularly the Uros ethnic group, which claims to directly descend from the first settlers of the Andes, and some linguists suggest they might otherwise be related to Arawak speaking groups from the Amazon. Using phylogeographic, population structure and spatial genetic analyses of Y-chromosome and mtDNA data, we inferred the genetic relationships among Uros populations (Los Uros from Peru, Uru-Chipaya and Uru-Poopo from Bolivia), and compared their haplotype profiles with eight Aymara, nine Quechua and two Arawak (Machiguenga and Yanesha) speaking populations from Peru and Bolivia. Our results indicated that Uros populations stand out among the Altiplano populations, while appearing more closely related to the Aymara and Quechua from Lake Titicaca and surrounding regions than to the Amazon Arawaks. Moreover, the Uros populations from Peru and Bolivia are genetically differentiated from each other, indicating a high heterogeneity in this ethnic group. Finally, our results support the distinctive ancestry for the Uros populations of Peru and Bolivia, which are likely derived from ancient Andean lineages that were partially replaced during more recent farming expansion events and the establishment of complex civilizations in the Andes.
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Affiliation(s)
- José Raul Sandoval
- Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Universidad San Martin de Porres (USMP), Lima, Peru
| | | | | | | | | | - Oscar Acosta
- Universidad San Martin de Porres (USMP), Lima, Peru
| | | | | | | | - Fabrício R. Santos
- Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- * E-mail:
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Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, Woodward SR, Achilli A, Myres N, Torroni A, Semino O. The first peopling of South America: new evidence from Y-chromosome haplogroup Q. PLoS One 2013; 8:e71390. [PMID: 23990949 PMCID: PMC3749222 DOI: 10.1371/journal.pone.0071390] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/03/2013] [Indexed: 01/13/2023] Open
Abstract
Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.
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Affiliation(s)
- Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Viola Grugni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Norman Angerhofer
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Scott Ray Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
- * E-mail:
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Heinz T, Alvarez-Iglesias V, Pardo-Seco J, Taboada-Echalar P, Gómez-Carballa A, Torres-Balanza A, Rocabado O, Carracedo A, Vullo C, Salas A. Ancestry analysis reveals a predominant Native American component with moderate European admixture in Bolivians. Forensic Sci Int Genet 2013; 7:537-42. [PMID: 23948324 DOI: 10.1016/j.fsigen.2013.05.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 05/10/2013] [Accepted: 05/30/2013] [Indexed: 10/26/2022]
Abstract
We have genotyped 46 Ancestry Informative Markers (AIMs) in two of the most populated areas in Bolivia, namely, La Paz (Andean region; n=105), and Chuquisaca (Sub-Andean region; n=73). Using different analytical tools, we inferred admixture proportions of these two American communities by comparing the genetic profiles with those publicly available from the CEPH (Centre d'Etude du Polymorphisme Humain) panel representing three main continental groups (Africa, Europe, and America). By way of simulations, we first evaluated the minimum sample size needed in order to obtain accurate estimates of ancestry proportions. The results indicated that sample sizes above 30 individuals could be large enough to estimate main continental ancestry proportions using the 46 AIMs panel. With the exception of a few individuals, the results also indicated that Bolivians showed a predominantly Native American ancestry with variable levels of European admixture. The proportions of ancestry were statistically different in La Paz and Chuquisaca: the Native American component was 86% and 77% (Mann-Whitney U-test: un-adjusted P-value=2.1×10(-5)), while the European ancestry was 13% and 21% (Mann-Whitney U-test: un-adjusted P-value=3.6×10(-5)), respectively. The African ancestry in Bolivians captured by the AIMs analyzed in the present study was below 2%. The inferred ancestry of Bolivians fits well with previous studies undertaken on haplotype data, indicating a major proportion of Native American lineages. The genetic differences observed in these two groups suggest that forensic genetic analysis should be better performed based on local databases built in the main Bolivian areas.
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Affiliation(s)
- Tanja Heinz
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, 15872, Galicia, Spain
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Taboada-Echalar P, Álvarez-Iglesias V, Heinz T, Vidal-Bralo L, Gómez-Carballa A, Catelli L, Pardo-Seco J, Pastoriza A, Carracedo Á, Torres-Balanza A, Rocabado O, Vullo C, Salas A. The genetic legacy of the pre-colonial period in contemporary Bolivians. PLoS One 2013; 8:e58980. [PMID: 23527064 PMCID: PMC3604014 DOI: 10.1371/journal.pone.0058980] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 02/12/2013] [Indexed: 01/27/2023] Open
Abstract
Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1-2%) of a sub-Saharan component in Bolivians.
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Affiliation(s)
- Patricia Taboada-Echalar
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Tanja Heinz
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Laura Vidal-Bralo
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Laura Catelli
- Equipo Argentino de Antropología Forense, Córdoba, Argentina
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ana Pastoriza
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Torres-Balanza
- Instituto de Investigaciones Forenses, Fiscalía General del Estado Plurinacional de Bolivia, La Paz, Bolivia
| | - Omar Rocabado
- Instituto de Investigaciones Forenses, Fiscalía General del Estado Plurinacional de Bolivia, La Paz, Bolivia
| | - Carlos Vullo
- Equipo Argentino de Antropología Forense, Córdoba, Argentina
- Laboratorio de Inmunogenética y Diagnóstico Molecular, Córdoba, Argentina
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
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Cardoso S, Palencia-Madrid L, Valverde L, Alfonso-Sánchez MA, Gómez-Pérez L, Alfaro E, Bravi CM, Dipierri JE, Peña JA, de Pancorbo MM. Mitochondrial DNA control region data reveal high prevalence of Native American lineages in Jujuy province, NW Argentina. Forensic Sci Int Genet 2013; 7:e52-5. [PMID: 23433579 DOI: 10.1016/j.fsigen.2013.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 12/29/2012] [Accepted: 01/29/2013] [Indexed: 10/27/2022]
Abstract
Mitochondrial control region (16024-576) sequences were generated from 180 individuals of four population nuclei from the province of Jujuy (NW Argentina), located at different altitudes above sea level. The frequency at which a randomly selected mtDNA profile would be expected to occur in the general population (random match probability) was estimated at 0.011, indicating a relatively high diversity. Analysis of the haplogroup distribution revealed that Native American lineages A2 (13.9%), B (56.7%), C1 (17.8%), D1 (8.9%) and D4h3a (1.1%) accounted for more than 98% of the total mtDNA haplogroup diversity in the sample examined. We detected a certain degree of genetic heterogeneity between two subpopulations located at different points along the altitudinal gradient (Valles and Puna), suggesting that altitude above sea level cannot be ruled out as a factor promoting divergences in mtDNA haplogroup frequencies, since altitude is closely associated with human living conditions, and consequently, with low demographic sizes and the occurrence of genetic drift processes in human communities. In all, mitochondrial DNA database obtained for Jujuy province strongly points to the need for creating local mtDNA databases, to avoid bias in forensic estimations caused by genetic substructuring of the populations.
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Affiliation(s)
- Sergio Cardoso
- BIOMICs Research Group, Centro de Investigación Lascaray Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
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Regueiro M, Alvarez J, Rowold D, Herrera RJ. On the origins, rapid expansion and genetic diversity of Native Americans from hunting-gatherers to agriculturalists. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:333-48. [PMID: 23283701 DOI: 10.1002/ajpa.22207] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/08/2012] [Indexed: 11/05/2022]
Abstract
Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.
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Affiliation(s)
- Maria Regueiro
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Simms TM, Wright MR, Martinez E, Regueiro M, McCartney Q, Herrera RJ. Y-STR diversity and sex-biased gene flow among Caribbean populations. Gene 2012. [PMID: 23178184 DOI: 10.1016/j.gene.2012.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures.
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Affiliation(s)
- Tanya M Simms
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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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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Gayà-Vidal M, Athanasiadis G, Carreras-Torres R, Via M, Esteban E, Villena M, Vasquez R, Dugoujon JM, Moral P. Apolipoprotein E/C1/C4/C2 gene cluster diversity in two native Andean populations: Aymaras and Quechuas. Ann Hum Genet 2012; 76:283-95. [PMID: 22681517 DOI: 10.1111/j.1469-1809.2012.00712.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The APOE/C1/C4/C2 gene cluster presents high relevance in lipid metabolism and, therefore, has important epidemiological implications. Here, we study for the first time the variation patterns of 25 polymorphisms (10 short tandem repeats, STRs, and 15 single nucleotide polymorphismas, SNPs) in two native Andean samples from Bolivia (45 Aymaras and 45 Quechuas) as well as one European sample (n = 41) as external reference. We estimated diversity parameters, linkage disequilibrium patterns, population structure, and possible selective effects. In general, diversity was low and could be partly attributed to selection (probably due to its physiological importance), since the APOE/C1/C4/C2 region was highly conserved compared to the flanking genes in both Bolivians and Europeans. Moreover, the lower gene diversity in Bolivians compared to Europeans for some markers might indicate different demographic histories. Regarding the APOE isoforms, in addition to ɛ3 (94%) and ɛ4 (5%), isoform ɛ2 (1%) was also detected in Bolivians. In relation to previous hypotheses, our results support that genetic drift or founder effects rather than selection for increased cholesterol absorption are the main factors that have shaped the distribution of APOE isoforms observed in South America.
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Affiliation(s)
- Magdalena Gayà-Vidal
- Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
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Simms TM, Wright MR, Hernandez M, Perez OA, Ramirez EC, Martinez E, Herrera RJ. Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:618-31. [DOI: 10.1002/ajpa.22090] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 04/04/2012] [Indexed: 11/06/2022]
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Bisso-Machado R, Bortolini MC, Salzano FM. Uniparental genetic markers in South Amerindians. Genet Mol Biol 2012; 35:365-87. [PMID: 22888284 PMCID: PMC3389523 DOI: 10.1590/s1415-47572012005000027] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/12/2012] [Indexed: 12/25/2022] Open
Abstract
A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.
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Affiliation(s)
- Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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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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