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Uricoechea Patiño D, Collins A, Romero García OJ, Santos Vecino G, Aristizábal Espinosa P, Bernal Villegas JE, Benavides Benitez E, Vergara Muñoz S, Briceño Balcázar I. Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley. Genes (Basel) 2023; 14:2036. [PMID: 38002979 PMCID: PMC10670959 DOI: 10.3390/genes14112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | | | | | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.V.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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3
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Cardinali I, Bodner M, Capodiferro MR, Amory C, Rambaldi Migliore N, Gomez EJ, Myagmar E, Dashzeveg T, Carano F, Woodward SR, Parson W, Perego UA, Lancioni H, Achilli A. Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia. Front Genet 2022; 12:819337. [PMID: 35069708 PMCID: PMC8773455 DOI: 10.3389/fgene.2021.819337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/14/2021] [Indexed: 11/15/2022] Open
Abstract
Mongolia is located in a strategic position at the eastern edge of the Eurasian Steppe. Nomadic populations moved across this wide area for millennia before developing more sedentary communities, extended empires, and complex trading networks, which connected western Eurasia and eastern Asia until the late Medieval period. We provided a fine-grained portrait of the mitochondrial DNA (mtDNA) variation observed in present-day Mongolians and capable of revealing gene flows and other demographic processes that took place in Inner Asia, as well as in western Eurasia. The analyses of a novel dataset (N = 2,420) of mtDNAs highlighted a clear matrilineal differentiation within the country due to a mixture of haplotypes with eastern Asian (EAs) and western Eurasian (WEu) origins, which were differentially lost and preserved. In a wider genetic context, the prevalent EAs contribution, larger in eastern and central Mongolian regions, revealed continuous connections with neighboring Asian populations until recent times, as attested by the geographically restricted haplotype-sharing likely facilitated by the Genghis Khan’s so-called Pax Mongolica. The genetic history beyond the WEu haplogroups, notably detectable on both sides of Mongolia, was more difficult to explain. For this reason, we moved to the analysis of entire mitogenomes (N = 147). Although it was not completely possible to identify specific lineages that evolved in situ, two major changes in the effective (female) population size were reconstructed. The more recent one, which began during the late Pleistocene glacial period and became steeper in the early Holocene, was probably the outcome of demographic events connected to western Eurasia. The Neolithic growth could be easily explained by the diffusion of dairy pastoralism, as already proposed, while the late glacial increase indicates, for the first time, a genetic connection with western Eurasian refuges, as supported by the unusual high frequency and internal sub-structure in Mongolia of haplogroup H1, a well-known post-glacial marker in Europe. Bronze Age events, without a significant demographic impact, might explain the age of some mtDNA haplogroups. Finally, a diachronic comparison with available ancient mtDNAs made it possible to link six mitochondrial lineages of present-day Mongolians to the timeframe and geographic path of the Silk Route.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Edgar J Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States.,FamilySearch Int., Salt Lake City, UT, United States
| | - Erdene Myagmar
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tumen Dashzeveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Francesco Carano
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Scott R Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, State College, PA, United States
| | - Ugo A Perego
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.,Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States.,Department of Math and Science, Southeastern Community College, Burlington, IA, United States
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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Ongaro L, Molinaro L, Flores R, Marnetto D, Capodiferro MR, Alarcón-Riquelme ME, Moreno-Estrada A, Mabunda N, Ventura M, Tambets K, Achilli A, Capelli C, Metspalu M, Pagani L, Montinaro F. Evaluating the Impact of Sex-Biased Genetic Admixture in the Americas through the Analysis of Haplotype Data. Genes (Basel) 2021; 12:genes12101580. [PMID: 34680976 PMCID: PMC8535939 DOI: 10.3390/genes12101580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/30/2023] Open
Abstract
A general imbalance in the proportion of disembarked males and females in the Americas has been documented during the Trans-Atlantic Slave Trade and the Colonial Era and, although less prominent, more recently. This imbalance may have left a signature on the genomes of modern-day populations characterised by high levels of admixture. The analysis of the uniparental systems and the evaluation of continental proportion ratio of autosomal and X chromosomes revealed a general sex imbalance towards males for European and females for African and Indigenous American ancestries. However, the consistency and degree of this imbalance are variable, suggesting that other factors, such as cultural and social practices, may have played a role in shaping it. Moreover, very few investigations have evaluated the sex imbalance using haplotype data, containing more critical information than genotypes. Here, we analysed genome-wide data for more than 5000 admixed American individuals to assess the presence, direction and magnitude of sex-biased admixture in the Americas. For this purpose, we applied two haplotype-based approaches, ELAI and NNLS, and we compared them with a genotype-based method, ADMIXTURE. In doing so, besides a general agreement between methods, we unravelled that the post-colonial admixture dynamics show higher complexity than previously described.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
- Correspondence:
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Marco R. Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (M.R.C.); (A.A.)
| | - Marta E. Alarcón-Riquelme
- Department of Medical Genomics, GENYO, Centro Pfizer—Universidad de Granada—Junta de Andalucía de Genómica e Investigación Oncológica, Av de la Ilustración 114, Parque Tecnológico de la Salud (PTS), 18016 Granada, Spain;
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico;
| | - Nedio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N°1, Província de Maputo, Maputo 1120, Mozambique;
| | - Mario Ventura
- Department of Biology-Genetics, University of Bari, 70126 Bari, Italy;
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (M.R.C.); (A.A.)
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK;
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
- Department of Biology, University of Padua, 35131 Padua, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
- Department of Biology-Genetics, University of Bari, 70126 Bari, Italy;
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6
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Bodner M, Perego UA, Gomez JE, Cerda-Flores RM, Rambaldi Migliore N, Woodward SR, Parson W, Achilli A. The Mitochondrial DNA Landscape of Modern Mexico. Genes (Basel) 2021; 12:genes12091453. [PMID: 34573435 PMCID: PMC8467843 DOI: 10.3390/genes12091453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022] Open
Abstract
Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Ugo A. Perego
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- Department of Math and Science, Southeastern Community College, Burlington, IA 52655, USA
| | - J. Edgar Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- FamilySearch Int., Salt Lake City, UT 84150, USA
| | | | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
- Forensic Science Program, Penn State University, University Park, State College, PA 16802, USA
- Correspondence: (W.P.); (A.A.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Correspondence: (W.P.); (A.A.)
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7
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Smith-Guzmán NE. An isthmus of isolation: The likely elevated prevalence of genetic disease in ancient Panama and implications for considering rare diseases in paleopathology. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2021; 33:1-12. [PMID: 33581446 DOI: 10.1016/j.ijpp.2021.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/11/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVE This study considers the evidence for elevated frequencies of "rare" diseases in ancient Panama. Indications of population isolation by multidisciplinary sources allow for the possibility that rare inherited conditions may have been maintained at relatively high prevalences in the region due to gene flow restriction. MATERIALS A sample of 267 skeletal human remains with diverse demographical characteristics from Pre-Columbian archaeological sites throughout Panama. METHODS Remains were analyzed macroscopically and hard tissue developmental anomalies were documented. RESULTS Frequencies of developmental anomalies and hard tissue changes consistent with specific rare genetic diseases, such as osteogenesis imperfecta, on the comparatively few human remains recovered from pre-Columbian archaeological sites are elevated as compared with global averages. CONCLUSIONS The paleopathological evidence is concordant with a scenario of isolation in Pre-Columbian times and with an increased presence of genetic disorders in the population. SIGNIFICANCE This study advocates for the special consideration of rare diseases by paleopathologists in regions where populations may have experienced prolonged geographical or social isolation in the past. LIMITATIONS A dearth of local modern epidemiological data and low sample sizes of preserved human remains in certain regions of the country limited the possibilities of spatiotemporal comparisons of rare disease prevalence. SUGGESTIONS FOR FURTHER RESEARCH Further scrutiny of developmental anomalies of genetic origin on ancient Panamanian remains and biomolecular testing of remains for specific disorders should be pursued to confirm the findings of this study.
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Affiliation(s)
- Nicole E Smith-Guzmán
- Smithsonian Tropical Research Institute, Ancón, Panamá, Rep. of Panamá, Apartado 0843-03092, Panama.
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8
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Capodiferro MR, Aram B, Raveane A, Rambaldi Migliore N, Colombo G, Ongaro L, Rivera J, Mendizábal T, Hernández-Mora I, Tribaldos M, Perego UA, Li H, Scheib CL, Modi A, Gòmez-Carballa A, Grugni V, Lombardo G, Hellenthal G, Pascale JM, Bertolini F, Grieco GS, Cereda C, Lari M, Caramelli D, Pagani L, Metspalu M, Friedrich R, Knipper C, Olivieri A, Salas A, Cooke R, Montinaro F, Motta J, Torroni A, Martín JG, Semino O, Malhi RS, Achilli A. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 2021; 184:1706-1723.e24. [PMID: 33761327 PMCID: PMC8024902 DOI: 10.1016/j.cell.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/20/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023]
Abstract
The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.
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Affiliation(s)
| | - Bethany Aram
- Department of Geography, History and Philosophy, the Pablo de Olavide University of Seville, Seville 41013, Spain
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy; Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Javier Rivera
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Tomás Mendizábal
- Patronato Panamá Viejo, Panama City 0823-05096, Panama; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Iosvany Hernández-Mora
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Hongjie Li
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alberto Gòmez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Gianluca Lombardo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Garrett Hellenthal
- UCL Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | | | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia 27100, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padua, Padua 35121, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ronny Friedrich
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Corina Knipper
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Bari 70125, Italy
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Juan Guillermo Martín
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Ripan Singh Malhi
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy.
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9
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Llanes A, Ortiz L, Moscoso J, Gutiérrez G, Blake E, Restrepo CM, Lleonart R, Cuero C, Vernaza-Kwiers A. HLA allele and haplotype frequencies in the Panamanian population. Hum Immunol 2020; 82:5-7. [PMID: 33303214 DOI: 10.1016/j.humimm.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 11/18/2022]
Abstract
In this study, we report for the first time HLA allele and haplotype frequencies in the modern Panamanian population at a two-field (four digits) resolution level. Reported frequencies were calculated from genotype data for the HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 loci of 462 healthy unrelated Panamanian adults of Hispanic ethnicity. In addition to providing new insights on the allelic structure of the Panamanian population and its origin, these data are critical for better planning of healthcare strategies in the country and for future research exploring the association with certain chronic and infectious diseases.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Clayton, Panama, Panama
| | - Luis Ortiz
- Laboratorio Nacional de Trasplante, Complejo Hospitalario Dr. Arnulfo Arias Madrid (CHDrAAM), Caja de Seguro Social, Panama, Panama
| | - Juan Moscoso
- Laboratorio Nacional de Trasplante, Complejo Hospitalario Dr. Arnulfo Arias Madrid (CHDrAAM), Caja de Seguro Social, Panama, Panama
| | - Gina Gutiérrez
- Laboratorio Nacional de Trasplante, Complejo Hospitalario Dr. Arnulfo Arias Madrid (CHDrAAM), Caja de Seguro Social, Panama, Panama
| | - Elena Blake
- Laboratorio Nacional de Trasplante, Complejo Hospitalario Dr. Arnulfo Arias Madrid (CHDrAAM), Caja de Seguro Social, Panama, Panama
| | - Carlos M Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Clayton, Panama, Panama
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Clayton, Panama, Panama
| | - Cesar Cuero
- Servicio de Nefrología, Complejo Hospitalario Dr. Arnulfo Arias Madrid (CHDrAAM), Caja de Seguro Social, Panama, Panama
| | - Alejandro Vernaza-Kwiers
- Laboratorio Nacional de Trasplante, Complejo Hospitalario Dr. Arnulfo Arias Madrid (CHDrAAM), Caja de Seguro Social, Panama, Panama.
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10
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Nieves-Colón MA, Pestle WJ, Reynolds AW, Llamas B, de la Fuente C, Fowler K, Skerry KM, Crespo-Torres E, Bustamante CD, Stone AC. Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities. Mol Biol Evol 2020; 37:611-626. [PMID: 31710665 DOI: 10.1093/molbev/msz267] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.
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Affiliation(s)
- Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ.,National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - William J Pestle
- Department of Anthropology, University of Miami, Coral Gables, FL
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Kathleen Fowler
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ
| | - Katherine M Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ
| | - Edwin Crespo-Torres
- Forensic Anthropology and Bioarcheology Laboratory, University of Puerto Rico, Rio Piedras, Puerto Rico
| | | | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ
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11
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Epidemiologic Characteristics of Suicide in Panama, 2007–2016. Medicina (B Aires) 2020; 56:medicina56090442. [PMID: 32878148 PMCID: PMC7559330 DOI: 10.3390/medicina56090442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 11/17/2022] Open
Abstract
Background and objectives: We aim to describe the demographic characteristics associated with suicide in Panama, to estimate the suicide mortality rate and years of potential life lost (YPLL) to suicide, and to explore the correlation of suicide rates with the Multidimensional Poverty Index (MPI). We present a descriptive retrospective epidemiological report of suicide-related mortality (Panama, 2007–2016). Materials and Methods: Data were matched-merged to calculate unadjusted suicide mortality rates (overall, and by sex, age groups, and administrative region), YPLL, and coefficients (r) for the correlation of MPI and suicide rates. Results: There were 1475 deaths by suicide (86% among men, 47% between 20 and 39 years). The average mortality rate was estimated at 3.91 per 100,000 population with an average YPLL rate of 3.79 per 1000 population. There was a statistically significant trend to reduce YPLL over time (r = −0.93; p< 0.001). Exploratory analyses did not show a significant correlation between the MPI and suicide rates. Our study showed a 6:1 male-to-female ratio of suicide, mostly affecting the age groups of 20–29 and over 80 years. Conclusions: Exploratory analyses on the correlation of the MPI and the suicide rates did not achieve statistical significance, and alternative explanations, such as access to pesticides and alcohol, were further explored to inform potential interventions.
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12
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Quiel L, Moreno Velásquez I, Gómez B, Motta J, Herrera-Ballesteros V. Social determinants and cardiovascular disease mortality in Panama, 2012-2016. BMC Public Health 2019; 19:199. [PMID: 30770742 PMCID: PMC6377740 DOI: 10.1186/s12889-019-6508-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/04/2019] [Indexed: 12/30/2022] Open
Abstract
Background The aims of this study were to determine the geographic and time variation of social determinants of health (SDH) and cardiovascular disease (CVD) mortality in Panama from 2012 to 2016, and to identify which of the SDH has the strongest correlation with a socioeconomic index (SEI). Methods We conducted an ecological study obtaining mortality from the National Mortality Register and socioeconomic variables derived from the National Household Survey (NHS). The International Classification of Diseases 10th revision codes I20–I25 and I60–I69 were used for ischemic heart disease (IHD) and stroke, respectively. Standardized age-adjusted mortality rates were calculated by direct method. Mortality rates and socioeconomic variables were evaluated together in a panel data model. A SEI was developed from factorial analysis by principal components with a polychoric correlation matrix. Provinces and regions were categorized in tertiles according to median value of the SEI score. Results The NHS evaluated an average of 15,919 households per year. The mean of age throughout the study period was 41 years. The average monthly income increased, from US$ (SD) 331.94 (5.38) in 2012, to 406.24 (5.81) in 2016, whereas the social security health coverage remained in a range of 57–58%. The mean number of school years was twelve. Significant geographical and temporal variations in social determinants and mortality rates were observed throughout the country. Colon, categorized in the middle tertile according to the SEI, presented higher IHD mortality rates. Darién (in the lowest SEI tertile) Colón and Herrera had higher stroke mortality rates. The SEI categorized indigenous territories in the lowest tertile. Total years of education was the strongest correlated variable with the SEI, when we excluded the population living in indigenous territories. However, when this population was included, social security coverage had the strongest correlation with the SEI. Conclusion We observed geographical and temporal disparities in SDH and CVD mortality rates. Further epidemiological studies are warranted in the provinces of Colón, Darien, Herrera and Los Santos to explore in-depth the higher CVD mortality rates observed in these provinces. Electronic supplementary material The online version of this article (10.1186/s12889-019-6508-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Quiel
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | | | - Beatriz Gómez
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City, Panama.,National Secretariat for Science and Technology, Panama City, Panama
| | - Víctor Herrera-Ballesteros
- Gorgas Memorial Institute for Health Studies, Panama City, Panama. .,Department of Research and Health Technology Assessment,, Gorgas Memorial Institute for Health Studies, Panama City, Panama.
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13
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Casas-Vargas A, Romero LM, Rodríguez JV, Usaquén M W. Análisis de ADN mitocondrial en una muestra de restos óseos precolombinos de Norte de Santander, Colombia (Área Cultural Chitarera). ACTA BIOLÓGICA COLOMBIANA 2018. [DOI: 10.15446/abc.v23n3.65407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los análisis de ADN antiguo (ADNa) han incrementado en los últimos años permitiendo conocer la diversidad genética de las poblaciones precolombinas. En Colombia, existen pocos registros arqueológicos de la población prehispánica del Norte de Santander habitada en el siglo XVI por el grupo Chitarero. Por este motivo, nos propusimos analizar la diversidad genética a partir de secuencias de la región HVRI del ADNmt y determinar sus posibles relaciones con otras comunidades tanto antiguas como contemporáneas. Se analizaron siete individuos precolombinos asociados a este grupo prehispánico, recuperados en los municipios de Cácota y Silos en el departamento de Norte de Santander de los Andes Orientales colombianos, siguiendo criterios estrictos de autenticidad para el ADNa. En todos los individuos se logró identificar el haplogrupo B caracterizado por el polimorfismo en la posición 16217C, siendo éste uno de los más frecuentes en comunidades precolombinas y contemporáneas de los Andes Suramericanos. Este hallazgo indica que este grupo poblacional se encuentra estrechamente emparentado por línea materna, con posibles índices de endogamia, con una probable densidad demográfica baja y una baja diversidad genética, similares a lo observado en comunidades pertenecientes a periodos anteriores como el Formativo. Este grupo precolombino exhibe una de las diversidades genéticas más bajas reportadas en las poblaciones pertenecientes a la familia lingüistica Chibcha. Estos resultados genéticos coinciden con los planteamientos sobre el grupo Chitarero de pertenecer a comunidades pequeñas independientes, con asentamientos dispersos, apartados unos de otros.
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14
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Brandini S, Bergamaschi P, Cerna MF, Gandini F, Bastaroli F, Bertolini E, Cereda C, Ferretti L, Gómez-Carballa A, Battaglia V, Salas A, Semino O, Achilli A, Olivieri A, Torroni A. The Paleo-Indian Entry into South America According to Mitogenomes. Mol Biol Evol 2018; 35:299-311. [PMID: 29099937 PMCID: PMC5850732 DOI: 10.1093/molbev/msx267] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.
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Affiliation(s)
- Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Paola Bergamaschi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Servizio di Immunoematologia e Medicina Trasfusionale, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Fernando Cerna
- Biotechnology Laboratory, Salesian Polytechnic University of Ecuador, Quito, Ecuador
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | | | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Salas
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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15
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Morales-Arce AY, Hofman CA, Duggan AT, Benfer AK, Katzenberg MA, McCafferty G, Warinner C. Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico. Sci Rep 2017; 7:18100. [PMID: 29273718 PMCID: PMC5741722 DOI: 10.1038/s41598-017-18356-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022] Open
Abstract
The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800–1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200–1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively.
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Affiliation(s)
- Ana Y Morales-Arce
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Adam K Benfer
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - M Anne Katzenberg
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Geoffrey McCafferty
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, 73019, USA. .,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07743, Germany.
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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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[Mitochondrial DNA diversity in prehispanic bone remains on the eastern Colombian Andes]. BIOMEDICA 2017; 37:548-560. [PMID: 29373774 DOI: 10.7705/biomedica.v37i4.3377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 01/23/2017] [Indexed: 12/16/2022]
Abstract
INTRODUCTION DNA extracted from ancient human bones allows to analyze the genetic makeup of pre-Columbian populations and to determine the dynamics that gave rise to the diversity of contemporary populations. OBJECTIVE To determine the genetic diversity of skeletal remains associated with the Templo del Sol (Sun Temple) and their relationship with other contemporary and ancient communities of America. MATERIALS AND METHODS We analyzed 13 individuals belonging to the pre-Columbian Muisca Period (IX-XVI centuries AD) from the vicinities of the Templo del Sol (Sun Temple) (Sogamoso, Boyacá) in the eastern Colombian Andes. Mitochondrial DNA was amplified and RFLPs were performed in order to type the four traditional Amerindian haplogroups (A, B, C and D). In addition, autosomal markers including amelogenin and Y-chromosome STRs were amplified. RESULTS Among the observed mitochondrial lineages, haplogroup A was the most frequent, followed by haplogroups B and C; no evidence of haplogroup D was found. The genetic variation analysis indicated a similar diversity of pre-ColumbianMuiscas to that of contemporary populations belonging to the Chibcha linguistic family from Colombia and Central America. Molecular sexing was accomplished and it was compared to osteological data. With only one exception, anthropological and molecular data were consistent. CONCLUSIONS Our results contribute new genetic elements supporting the hypothesis of Central American origin of the Chibcha groups of the Cundiboyacense plateau, and allowed sex typing and kinship evaluations.
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Novelletto A, Testa L, Iacovelli F, Blasi P, Garofalo L, Mingozzi T, Falconi M. Polymorphism in Mitochondrial Coding Regions of Mediterranean Loggerhead Turtles: Evolutionary Relevance and Structural Effects. Physiol Biochem Zool 2016; 89:473-486. [DOI: 10.1086/688679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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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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Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG. Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin. PLoS One 2015; 10:e0139192. [PMID: 26447794 PMCID: PMC4598113 DOI: 10.1371/journal.pone.0139192] [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: 07/13/2014] [Accepted: 09/10/2015] [Indexed: 11/18/2022] Open
Abstract
Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people's contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region's first peoples in shaping the genetic diversity seen in contemporary Caribbean populations.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
| | - Miguel G. Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Missions Programs, National Geographic Society, Washington, D.C., United States of America
| | - Gabriel A. Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jill B. Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Zoila E. Browne
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
| | - Marlon Stevenson
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
| | - Wendell Walters
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
- Sandy Bay Village, St. Vincent and the Grenadines
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Politis M, Higuera G, Chang LR, Gomez B, Bares J, Motta J. Trend Analysis of Cancer Mortality and Incidence in Panama, Using Joinpoint Regression Analysis. Medicine (Baltimore) 2015; 94:e970. [PMID: 26091467 PMCID: PMC4616533 DOI: 10.1097/md.0000000000000970] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and its incidence is expected to increase in the future. In Panama, cancer is also one of the leading causes of death. In 1964, a nationwide cancer registry was started and it was restructured and improved in 2012. The aim of this study is to utilize Joinpoint regression analysis to study the trends of the incidence and mortality of cancer in Panama in the last decade. Cancer mortality was estimated from the Panamanian National Institute of Census and Statistics Registry for the period 2001 to 2011. Cancer incidence was estimated from the Panamanian National Cancer Registry for the period 2000 to 2009. The Joinpoint Regression Analysis program, version 4.0.4, was used to calculate trends by age-adjusted incidence and mortality rates for selected cancers. Overall, the trend of age-adjusted cancer mortality in Panama has declined over the last 10 years (-1.12% per year). The cancers for which there was a significant increase in the trend of mortality were female breast cancer and ovarian cancer; while the highest increases in incidence were shown for breast cancer, liver cancer, and prostate cancer. Significant decrease in the trend of mortality was evidenced for the following: prostate cancer, lung and bronchus cancer, and cervical cancer; with respect to incidence, only oral and pharynx cancer in both sexes had a significant decrease. Some cancers showed no significant trends in incidence or mortality. This study reveals contrasting trends in cancer incidence and mortality in Panama in the last decade. Although Panama is considered an upper middle income nation, this study demonstrates that some cancer mortality trends, like the ones seen in cervical and lung cancer, behave similarly to the ones seen in high income countries. In contrast, other types, like breast cancer, follow a pattern seen in countries undergoing a transition to a developed economy with its associated lifestyle, nutrition, and body weight changes.
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Affiliation(s)
- Michael Politis
- From the The Gorgas Memorial Institute for Health Studies (MP, BG, JM); Santo Tomas Hospital (GH); MINSA (Ministry of Health, Panama) (LRC); and FUNDACANCER, Panama City, Panama (JB)
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Söchtig J, Álvarez-Iglesias V, Mosquera-Miguel A, Gelabert-Besada M, Gómez-Carballa A, Salas A. Genomic insights on the ethno-history of the Maya and the 'Ladinos' from Guatemala. BMC Genomics 2015; 16:131. [PMID: 25887241 PMCID: PMC4422311 DOI: 10.1186/s12864-015-1339-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs). Results Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America. Conclusions The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jens Söchtig
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Miguel Gelabert-Besada
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
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Indian signatures in the westernmost edge of the European Romani diaspora: new insight from mitogenomes. PLoS One 2013; 8:e75397. [PMID: 24143169 PMCID: PMC3797067 DOI: 10.1371/journal.pone.0075397] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
In agreement with historical documentation, several genetic studies have revealed ancestral links between the European Romani and India. The entire mitochondrial DNA (mtDNA) of 27 Spanish Romani was sequenced in order to shed further light on the origins of this population. The data were analyzed together with a large published dataset (mainly hypervariable region I [HVS-I] haplotypes) of Romani (N=1,353) and non-Romani worldwide populations (N>150,000). Analysis of mitogenomes allowed the characterization of various Romani-specific clades. M5a1b1a1 is the most distinctive European Romani haplogroup; it is present in all Romani groups at variable frequencies (with only sporadic findings in non-Romani) and represents 18% of their mtDNA pool. Its phylogeographic features indicate that M5a1b1a1 originated 1.5 thousand years ago (kya; 95% CI: 1.3-1.8) in a proto-Romani population living in Northwest India. U3 represents the most characteristic Romani haplogroup of European/Near Eastern origin (12.4%); it appears at dissimilar frequencies across the continent (Iberia: ≈ 31%; Eastern/Central Europe: ≈ 13%). All U3 mitogenomes of our Iberian Romani sample fall within a new sub-clade, U3b1c, which can be dated to 0.5 kya (95% CI: 0.3-0.7); therefore, signaling a lower bound for the founder event that followed admixture in Europe/Near East. Other minor European/Near Eastern haplogroups (e.g. H24, H88a) were also assimilated into the Romani by introgression with neighboring populations during their diaspora into Europe; yet some show a differentiation from the phylogenetically closest non-Romani counterpart. The phylogeny of Romani mitogenomes shows clear signatures of low effective population sizes and founder effects. Overall, these results are in good agreement with historical documentation, suggesting that cultural identity and relative isolation have allowed the Romani to preserve a distinctive mtDNA heritage, with some features linking them unequivocally to their ancestral Indian homeland.
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Phylogenetic relationships of three Italian merino-derived sheep breeds evaluated through a complete mitogenome analysis. PLoS One 2013; 8:e73712. [PMID: 24040036 PMCID: PMC3767607 DOI: 10.1371/journal.pone.0073712] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
In Italy, the crisis of the wool industry triggered the necessity to reconvert the two traditional Merino-derived breeds, Gentile di Puglia and Sopravissana, to meat production, by creating the Merinizzata Italiana. The aim of the present study was to assess the genetic diversity of these three Italian Merino-derived (IMd) breeds by examining the molecular information encoded in the maternally-inherited mitochondrial DNA (mtDNA). A parallel molecular investigation was performed on the putative paternal and maternal breeds, the Merino from Spain and the Appenninica from Italy, respectively, as well as on three unrelated dairy breeds (Sarda and Comisana from Italy, and Lacaune from France). Firstly, the mtDNA control region of 291 samples was analyzed. When comparing the overall genetic distances among the eight stocks, the three IMd breeds clustered together close to the Appenninica, thus confirming its parental role. Among the 90 IMd samples, 82 different haplotypes were observed, almost all belonging to haplogroup B, and only one to A. For 23 mtDNAs, including nine IMd, the analysis was then brought to the level of entire mitogenomes. Three distinct sub-haplogroups within B were found to encompass the IMd samples, with one clade (B1a2a1) apparently restricted to those sheep. Thus, despite experiencing a drastic reduction in number (mainly due to changes in breeding practices driven by the economy), the IMd breeds still represent a reservoir of distinctive mitochondrial variants, which could potentially contribute to the development of conservation and management programs of Italian sheep breeds.
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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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Reconciling migration models to the Americas with the variation of North American native mitogenomes. Proc Natl Acad Sci U S A 2013; 110:14308-13. [PMID: 23940335 DOI: 10.1073/pnas.1306290110] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study we evaluated migration models to the Americas by using the information contained in native mitochondrial genomes (mitogenomes) from North America. Molecular and phylogeographic analyses of B2a mitogenomes, which are absent in Eskimo-Aleut and northern Na-Dene speakers, revealed that this haplogroup arose in North America ∼11-13 ka from one of the founder Paleo-Indian B2 mitogenomes. In contrast, haplogroup A2a, which is typical of Eskimo-Aleuts and Na-Dene, but also present in the easternmost Siberian groups, originated only 4-7 ka in Alaska, led to the first Paleo-Eskimo settlement of northern Canada and Greenland, and contributed to the formation of the Na-Dene gene pool. However, mitogenomes also show that Amerindians from northern North America, without any distinction between Na-Dene and non-Na-Dene, were heavily affected by an additional and distinctive Beringian genetic input. In conclusion, most mtDNA variation (along the double-continent) stems from the first wave from Beringia, which followed the Pacific coastal route. This was accompanied or followed by a second inland migratory event, marked by haplogroups X2a and C4c, which affected all Amerindian groups of Northern North America. Much later, the ancestral A2a carriers spread from Alaska, undertaking both a westward migration to Asia and an eastward expansion into the circumpolar regions of Canada. Thus, the first American founders left the greatest genetic mark but the original maternal makeup of North American Natives was subsequently reshaped by additional streams of gene flow and local population dynamics, making a three-wave view too simplistic.
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Melton PE, Baldi NF, Barrantes R, Crawford MH. Microevolution, migration, and the population structure of five Amerindian populations from Nicaragua and Costa Rica. Am J Hum Biol 2013; 25:480-90. [PMID: 23559443 DOI: 10.1002/ajhb.22382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This research examines the coevolution of languages and uniparental genetic marker (mitochondrial DNA [mtDNA] and nonrecombining Y-chromosome [NRY]) variation within five Lower Central American (Rama, Chorotega, Maléku, Zapatón-Huetar, and Abrojo-Guaymí) Amerindian groups. This pattern occurred since European contact. METHODS We examined mtDNA sequence variation from the hypervariable region 1 (HVS-1) and NRY genetic variation using short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS439) and NRY haplogroups (Q1a3a, Q1a3*, C3b, R1b1b2, E1b1, G2a2, and I) identified through single-nucleotide polymorphisms. Phylogenetic analysis included multidimensional scaling (MDS), heterozygosity versus rii , and analysis of molecular variance (AMOVA). RESULTS Eighteen mtDNA haplotypes were characterized in 131 participants with 94.6% of these assigned to the Amerindian mtDNA subclades, A2 and B2. The Amerindian NRY haplogroup, Q1a3a, was present in all five groups and ranged from 85% (Zapatón-Huetar) to 35% (Chorotega). Four populations (Rama, Chorotega, Zapatón-Huetar, and Abrojo-Guaymí) were also characterized by the presence of NRY haplogroup R1b1b2 indicative of western European admixture. Seventy NRY STR haplotypes were identified of which 69 (97%) were population specific. MDS plots demonstrated genetic similarities between Mesoamericans and northern Chibchan Amerindian populations, absent in mtDNA analyses, which is further supported by heterozygosity versus rii results. CONCLUSIONS We conclude that although these linguistically related populations in geographic proximity demonstrate a high degree of paternal genetic differentiation, recent demographic events have dramatically altered the paternal genetic structure of the regions Amerindian populations.
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Affiliation(s)
- Phillip E Melton
- Centre for Genetic Origins of Health and Disease, University of Western Australia, Crawley, Australia.
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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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Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes. PLoS One 2012; 7:e51311. [PMID: 23240014 PMCID: PMC3519775 DOI: 10.1371/journal.pone.0051311] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (mtDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11–13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.
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