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Bravi CM, Motti JMB, García A. Letter to the editor: A Southern Cone origin rather than Peruvian affinities for ancient Patagonian B2 mitogenomes. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24934. [PMID: 38577959 DOI: 10.1002/ajpa.24934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 04/06/2024]
Affiliation(s)
- Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires. CONICET, CCT- Tandil, 7631 Quequén, Argentina
| | - Angelina García
- Instituto de Antropología de Córdoba, CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
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2
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Arencibia V, Muñoz M, Crespo CM, Russo MG, Vera P, Lia VV, García Guraieb S, Goñi RA, Avena S, Puebla A, Dejean CB. Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37548135 DOI: 10.1002/ajpa.24822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/23/2023] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVES The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.
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Affiliation(s)
- Valeria Arencibia
- Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marianne Muñoz
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Cristian M Crespo
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
| | - M Gabriela Russo
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Grupo de Investigación en Biología Evolutiva (GIBE), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Vera
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Solana García Guraieb
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael A Goñi
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio Avena
- Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrea Puebla
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Cristina B Dejean
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Instituto de Ciencias Antropológicas, Sección Antropología Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
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Salazar L, Burger R, Forst J, Barquera R, Nesbitt J, Calero J, Washburn E, Verano J, Zhu K, Sop K, Kassadjikova K, Ibarra Asencios B, Davidson R, Bradley B, Krause J, Fehren-Schmitz L. Insights into the genetic histories and lifeways of Machu Picchu's occupants. SCIENCE ADVANCES 2023; 9:eadg3377. [PMID: 37494435 PMCID: PMC11318671 DOI: 10.1126/sciadv.adg3377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.
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Affiliation(s)
- Lucy Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511-3707, USA
- Department of Archaeology, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru
| | - Richard Burger
- Department of Anthropology, Yale University, New Haven, CT 06511-3707, USA
| | - Janine Forst
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Jason Nesbitt
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
| | - Jorge Calero
- Department of Archaeology, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru
| | - Eden Washburn
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John Verano
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
| | - Kimberly Zhu
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Korey Sop
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kalina Kassadjikova
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bebel Ibarra Asencios
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
- Department of Archaeology, Universidad Nacional Santiago Antúnez de Mayolo, Huaraz 02002, Peru
| | - Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brenda Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
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Aquilano E, de la Fuente C, Rodríguez Golpe D, Motti JMB, Bravi CM. Sequencing errors in Native American mitogenomes: impact on clade definitions, haplogroup assignation, and beyond. Mitochondrion 2023; 70:54-58. [PMID: 37003527 DOI: 10.1016/j.mito.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
Available evidence allows the interpretation that some cases of absence of otherwise expected variation, based on phylogenetic expectations in mitogenomes of Native American origin, are due to artificial recombination rather than to homoplasy, while other more complex scenarios involving combination of original Cambridge Reference Sequence mistakes plus incomplete or incorrect scoring of variation are also showed. Several instances of mismatched control and coding regions as well as partially duplicated HV2 are observed in Peruvians, while intra-haplogroup chimaeras of different D1 subhaplogroups are referred to in Mexican Native Americans. A revised definition for haplogroup B2h is proposed, and preventive quality control measures are suggested.
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Affiliation(s)
- Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | | | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | - Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana (LEEH), Facultad de Ciencias Sociales (FACSO), Universidad Nacional del Centro de la Provincia de Buenos Aires-CONICET, Calle 508 #881, 7631 Quequén, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina.
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Segovia M, Schwabl P, Sueto S, Nakad CC, Londoño JC, Rodriguez M, Paiva M, Llewellyn MS, Carrasco HJ. Vector mapping and bloodmeal metabarcoding demonstrate risk of urban Chagas disease transmission in Caracas, Venezuela. PLoS Negl Trop Dis 2023; 17:e0010613. [PMID: 36930686 PMCID: PMC10057784 DOI: 10.1371/journal.pntd.0010613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 03/29/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Chagas disease is a significant public health risk in rural and semi-rural areas of Venezuela. Triatomine infection by the aetiological agent Trypanosoma cruzi is also observed in the Metropolitan District of Caracas (MDC), where foodborne T. cruzi outbreaks occasionally occur but active vector-to-human transmission (infection during triatomine bloodmeal) is considered absent. Citizen science-based domiciliary triatomine collection carried out between 2007 and 2013 in the MDC has advanced understanding of urban T. cruzi prevalence patterns and represents an important public awareness-building tool. The present study reports on the extension of this triatomine collection program from 2014 to 2019 and uses mitochondrial metabarcoding to assess feeding behavior in a subset of specimens. The combined, thirteen-year dataset (n = 4872) shows a high rate of T. cruzi infection (75.2%) and a predominance of Panstrongylus geniculatus (99.01%) among triatomines collected in domiciliary areas by MDC inhabitants. Collection also involved nymphal stages of P. geniculatus in 18 of 32 MDC parishes. Other collected species included Triatoma nigromaculata, Triatoma maculata, Rhodnius prolixus, and Panstrongylus rufotuberculatus. Liquid intestinal content indicative of bloodmeal was observed in 53.4% of analyzed specimens. Dissection pools representing 108 such visually blooded P. geniculatus specimens predominantly tested positive for human cytochrome b DNA (22 of 24 pools). Additional bloodmeal sources detected via metabarcoding analysis included key sylvatic T. cruzi reservoirs (opossum and armadillo), rodents, and various other synanthropic and domesticated animals. Results suggest a porous sylvatic-domiciliary transmission interface and ongoing adaptation of P. geniculatus to the urban ecotope. Although P. geniculatus defecation traits greatly limit the possibility of active T. cruzi transmission for any individual biting event, the cumulation of this low risk across a vast metropolitan population warrants further investigation. Efforts to prevent triatomine contact with human food sources also clearly require greater attention to protect Venezuela's capital from Chagas disease.
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Affiliation(s)
- Maikell Segovia
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Philipp Schwabl
- School of Biodiversity, One Health Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Salem Sueto
- School of Biodiversity, One Health Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Candy Cherine Nakad
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Juan Carlos Londoño
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Marlenes Rodriguez
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Manuel Paiva
- Escuela de Salud Pública, Universidad Central de Venezuela, Caracas, Venezuela
| | - Martin Stephen Llewellyn
- School of Biodiversity, One Health Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Hernán José Carrasco
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- * E-mail:
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6
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Motti JMB, Pauro M, Scabuzzo C, García A, Aldazábal V, Vecchi R, Bayón C, Pastor N, Demarchi DA, Bravi CM, Reich D, Cabana GS, Nores R. Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181:216-230. [PMID: 36919783 DOI: 10.1002/ajpa.24727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVE This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes. MATERIALS AND METHODS We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis. RESULTS We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP. DISCUSSION The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.
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Affiliation(s)
- Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Quequén, Buenos Aires, Argentina
| | - Maia Pauro
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina
| | - Clara Scabuzzo
- Centro de Investigación Científica y de Transferencia a la Producción (CICyTTP)-CONICET, Provincia de Entre Ríos-Universidad Autónoma de Entre Ríos (UADER)-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Diamante, Entre Ríos, Argentina
| | - Angelina García
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Verónica Aldazábal
- Instituto Multidisciplinario de Historia y Ciencias Humanas, CONICET, Buenos Aires, Argentina
| | - Rodrigo Vecchi
- Departamento de Humanidades, Universidad Nacional del Sur, CONICET, Bahía Blanca, Buenos Aires, Argentina
| | - Cristina Bayón
- Departamento de Humanidades, Universidad Nacional del Sur, CONICET, Bahía Blanca, Buenos Aires, Argentina
| | - Nicolás Pastor
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina
| | - Darío A Demarchi
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular, Centro Científico Tecnológica (CCT) La Plata CONICET, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Broad Institute, Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Graciela S Cabana
- Molecular Anthropology Laboratories, Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Rodrigo Nores
- Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina
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7
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Eisová S, Menéndez LP, Velemínský P, Bruner E. Craniovascular variation in four late Holocene human samples from southern South America. Anat Rec (Hoboken) 2023; 306:143-161. [PMID: 35684986 DOI: 10.1002/ar.25017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 01/29/2023]
Abstract
Craniovascular traits in the endocranium (traces of middle meningeal vessels and dural venous sinuses, emissary foramina) provide evidence of vascular anatomy in osteological samples. We investigate the craniovascular variation in four South American samples and the effect of artificial cranial modifications (ACM). CT scans of human adult crania from four archeological samples from southern South America (including skulls with ACM) are used for the analyses. The craniovascular features in the four samples are described, skulls with and without ACM are compared, and additionally, South Americans are compared to a previously analyzed sample of Europeans. Of the four South American samples, the Southern Patagonian differs the most, showing the most distinct cranial dimensions, no ACM, and larger diameters of the emissary foramina. Unlike previous studies, we did not find any major differences in craniovascular features between modified and non-modified skulls, except that the skulls with ACM present somewhat smaller foramina. South Americans significantly differed from Europeans, especially in the anteroposterior dominance of the middle meningeal artery, in the pattern of sinus confluence, in the occurrence of enlarged occipito-marginal sinuses, and in foramina frequencies and diameters. Craniovascular morphology is not affected by the cranial size, even in skulls with ACM, indicating a minor or null influence of structural topological factors. Concerning the samples from distinct geographic and climatic environments, it must be evaluated whether the craniovascular morphogenesis might be partially influenced by specific functions possibly associated with thermoregulation, intracranial pressure, and the maintenance of intracranial homeostasis.
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Affiliation(s)
- Stanislava Eisová
- Antropologické oddělení, Přírodovědecké muzeum, Národní muzeum, Prague, Czech Republic.,Katedra antropologie a genetiky člověka, Přírodovědecká fakulta, Univerzita Karlova, Prague, Czech Republic
| | - Lumila Paula Menéndez
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Department of Anthropology of the Americas, Universität Bonn, Bonn, Germany
| | - Petr Velemínský
- Antropologické oddělení, Přírodovědecké muzeum, Národní muzeum, Prague, Czech Republic
| | - Emiliano Bruner
- Programa de Paleobiología, Centro Nacional de Investigación sobre la Evolución Humana, Burgos, Spain
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Pardo-Seco J, Bello X, Gómez-Carballa A, Martinón-Torres F, Muñoz-Barús JI, Salas A. A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations. Int J Mol Sci 2022; 23:12899. [PMID: 36361690 PMCID: PMC9656715 DOI: 10.3390/ijms232112899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/02/2022] [Accepted: 10/18/2022] [Indexed: 08/30/2023] Open
Abstract
Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; tE-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10-3 substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the tE-QG estimates and narrow intervals of tE-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating tE-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings.
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Affiliation(s)
- Jacobo Pardo-Seco
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
| | - Xabier Bello
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
| | - Alberto Gómez-Carballa
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
| | - Federico Martinón-Torres
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
| | - José Ignacio Muñoz-Barús
- Department of Forensic Sciences, Pathology, Gynaecology and Obstetrics and Paediatrics, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Institute of Forensic Sciences (INCIFOR), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Grupo de Investigacion en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Comunidad de Madrid, Spain
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9
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Silva MACE, Ferraz T, Hünemeier T. A genomic perspective on South American human history. Genet Mol Biol 2022; 45:e20220078. [PMID: 35925590 PMCID: PMC9351327 DOI: 10.1590/1678-4685-gmb-2022-0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.
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Affiliation(s)
- Marcos Araújo Castro E Silva
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tiago Ferraz
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
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10
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Caro-Consuegra R, Nieves-Colón MA, Rawls E, Rubin-de-Celis V, Lizárraga B, Vidaurre T, Sandoval K, Fejerman L, Stone AC, Moreno-Estrada A, Bosch E. Uncovering signals of positive selection in Peruvian populations from three ecological regions. Mol Biol Evol 2022; 39:6647595. [PMID: 35860855 PMCID: PMC9356722 DOI: 10.1093/molbev/msac158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Perú hosts extremely diverse ecosystems which can be broadly classified into three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide SNP-array data from 286 Peruvians living across the three ecoregions and analysed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44 and ICAM1 in the coast; CBLB and PRDM1 in rainforest and the BRD2- HLA-DOA- HLA-DPA1 region in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Verónica Rubin-de-Celis
- Laboratorio de Genómica Molecular Evolutiva, Instituto de Ciencia y Tecnología, Universidad Ricardo Palma, Lima, Perú
| | - Beatriz Lizárraga
- Emeritus Professor, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Elena Bosch
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
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11
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Pezo P, Orellana-Soto M, de la Fuente C, Leiva X, Herrera L, Flores-Alvarado S, Galimany J, de Saint Pierre M, Bravi C, Moraga M. Native American mitochondrial lineages in admixed populations from Chile: Detecting recent migrations during post-Columbian times using geographically restricted lineages. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 178:504-512. [PMID: 36790622 DOI: 10.1002/ajpa.24513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVES To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population movement to Santiago (capital of Chile). The intensity of migration was quantified using three mitochondrial lineages restricted to South-Central native groups. METHODS D-loop sequences were genotyped in 550 unrelated individuals from San Felipe-Los Andes (n = 108), Santiago (n = 217), and Concepción (n = 225). Sequence processing, alignment, and haplogroup inference were carried out, and different genetic structure analyses were performed for haplogroup frequencies and D-loop sequences. RESULTS The Native lineages B2i2, C1b13, and D1g were the most frequent haplogroups, especially in Santiago (71.8%). Despite the distance, this city showed a high-genetic affinity with southern populations, including Concepción (~500 km distant) and native groups, rather than with those from San Felipe-Los Andes (<100 km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr = -0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepción, and other southern populations. Finally, we found lineages from Concepción acting as ancestral nodes in the northern clade. CONCLUSIONS Considering the geographic distances from these cities, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north-to-south migration during admixture onset in Concepción and in addition, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post-European contact.
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Affiliation(s)
- Patricio Pezo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michael Orellana-Soto
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Ximena Leiva
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Luisa Herrera
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Programa de Bioestadística, Instituto de Salud Poblacional, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jacqueline Galimany
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Claudio Bravi
- CCT La Plata, IMBICE, La Plata, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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12
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Nieves-Colón MA, Badillo Rivera KM, Sandoval K, Villanueva Dávalos V, Enriquez Lencinas LE, Mendoza-Revilla J, Adhikari K, González-Buenfil R, Chen JW, Zhang ET, Sockell A, Ortiz-Tello P, Hurtado GM, Condori Salas R, Cebrecos R, Manzaneda Choque JC, Manzaneda Choque FP, Yábar Pilco GP, Rawls E, Eng C, Huntsman S, Burchard E, Ruiz-Linares A, González-José R, Bedoya G, Rothhammer F, Bortolini MC, Poletti G, Gallo C, Bustamante CD, Baker JC, Gignoux CR, Wojcik GL, Moreno-Estrada A. Clotting factor genes are associated with preeclampsia in high-altitude pregnant women in the Peruvian Andes. Am J Hum Genet 2022; 109:1117-1139. [PMID: 35588731 PMCID: PMC9247825 DOI: 10.1016/j.ajhg.2022.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Preeclampsia is a multi-organ complication of pregnancy characterized by sudden hypertension and proteinuria that is among the leading causes of preterm delivery and maternal morbidity and mortality worldwide. The heterogeneity of preeclampsia poses a challenge for understanding its etiology and molecular basis. Intriguingly, risk for the condition increases in high-altitude regions such as the Peruvian Andes. To investigate the genetic basis of preeclampsia in a population living at high altitude, we characterized genome-wide variation in a cohort of preeclamptic and healthy Andean families (n = 883) from Puno, Peru, a city located above 3,800 meters of altitude. Our study collected genomic DNA and medical records from case-control trios and duos in local hospital settings. We generated genotype data for 439,314 SNPs, determined global ancestry patterns, and mapped associations between genetic variants and preeclampsia phenotypes. A transmission disequilibrium test (TDT) revealed variants near genes of biological importance for placental and blood vessel function. The top candidate region was found on chromosome 13 of the fetal genome and contains clotting factor genes PROZ, F7, and F10. These findings provide supporting evidence that common genetic variants within coagulation genes play an important role in preeclampsia. A selection scan revealed a potential adaptive signal around the ADAM12 locus on chromosome 10, implicated in pregnancy disorders. Our discovery of an association in a functional pathway relevant to pregnancy physiology in an understudied population of Native American origin demonstrates the increased power of family-based study design and underscores the importance of conducting genetic research in diverse populations.
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Affiliation(s)
- Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA; Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México
| | | | | | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, WC1E 6BT London, UK
| | - Ram González-Buenfil
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México
| | - Jessica W Chen
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Elisa T Zhang
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Gloria Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ramiro Condori Salas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ricardo Cebrecos
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | | | | | | | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Celeste Eng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Scott Huntsman
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Esteban Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, WC1E 6BT London, UK; Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico-CONICET y Programa Nacional de Referencia y Biobanco Genómico de la Población Argentina (PoblAr), Ministerio de Ciencia, Tecnología e Innovación, Puerto Madryn, Chubut, Argentina
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquía, Medellin, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación Universidad de Tarapacá, Tarapacá, Chile; Programa de Genética Humana, ICBM Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Carlos D Bustamante
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Genevieve L Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México.
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13
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Sturgess C, Montgomery H. Selection pressure at altitude for genes related to alcohol metabolism: A role for endogenous enteric ethanol synthesis? Exp Physiol 2021; 106:2155-2167. [PMID: 34487385 DOI: 10.1113/ep089628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/31/2021] [Indexed: 11/08/2022]
Abstract
NEW FINDINGS What is the topic of this review? Highland natives have undergone natural selection for genetic variants advantageous in adaptation to the hypobaric hypoxia experienced at high altitude. Why genes related to alcohol metabolism appear consistently selected for has not been greatly considered. We hypothesize that altitude-related changes in the gut microbiome offer one possible explanation. What advances does it highlight? Low intestinal oxygen tension might favour the production of ethanol through anaerobic fermentation by the gut microbiome. Subsequent increases in endogenous ethanol absorption could therefore provide a selection pressure for gene variants favouring its increased degradation, or perhaps reduced degradation if endogenously synthesized ethanol acts as a metabolic signalling molecule. ABSTRACT Reduced tissue availability of oxygen results from ascent to high altitude, where atmospheric pressure, and thus the partial pressure of inspired oxygen, fall (hypobaric hypoxia). In humans, adaptation to such hypoxia is necessary for survival. These functional changes remain incompletely characterized, although metabolic adaptation (rather than simple increases in convective oxygen delivery) appears to play a fundamental role. Those populations that have remained native to high altitude have undergone natural selection for genetic variants associated with advantageous phenotypic traits. Interestingly, a consistent genetic signal has implicated alcohol metabolism in the human adaptive response to hypobaric hypoxia. The reasons for this remain unclear. One possibility is that increased alcohol synthesis occurs through fermentation by gut bacteria in response to enteric hypoxia. There is growing evidence that anaerobes capable of producing ethanol become increasingly prevalent with high-altitude exposure. We hypothesize that: (1) ascent to high altitude renders the gut luminal environment increasingly hypoxic, favouring (2) an increase in the population of enteric fermenting anaerobes, hence (3) the synthesis of alcohol which, through systemic absorption, leads to (4) selection pressure on genes relating to alcohol metabolism. In theory, alcohol could be viewed as a toxic product, leading to selection of gene variants favouring its metabolism. On the contrary, alcohol is a metabolic substrate that might be beneficial. This mechanism could also account for some of the interindividual differences of lowlanders in acclimatization to altitude. Future research should be aimed at determining any shifts to favour ethanol-producing anaerobes after ascent to altitude.
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Affiliation(s)
- Connie Sturgess
- Institute for Human Health and Performance, Department of Medicine, University College London, London, UK
| | - Hugh Montgomery
- Institute for Human Health and Performance, Department of Medicine, University College London, London, UK
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14
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Silva Rochefort B, Root‐Bernstein M. History of canids in Chile and impacts on prey adaptations. Ecol Evol 2021; 11:9892-9903. [PMID: 34367547 PMCID: PMC8328442 DOI: 10.1002/ece3.7642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022] Open
Abstract
Artiodactyl prey species of Chile, especially guanacos (Lama guanicoe), are reported to be very susceptible to predation by pack-hunting feral dogs. It has been previously suggested that guanacos and endemic South American deer may have evolved in the absence of pack-hunting cursorial predators. However, the paleoecology of canid presence in southern South America and Chile is unclear. Here, we review the literature on South American and Chilean canids, their distributions, ecologies, and hunting behavior. We consider both wild and domestic canids, including Canis familiaris breeds. We establish two known antipredator defense behaviors of guanacos: predator inspection of ambush predators, for example, Puma concolor, and rushing at and kicking smaller cursorial predators, for example, Lycalopex culpaeus. We propose that since the late Pleistocene extinction of hypercarnivorous group-hunting canids east of the Andes, there were no native species creating group-hunting predation pressures on guanacos. Endemic deer of Chile may have never experienced group-hunting selection pressure from native predators. Even hunting dogs (or other canids) used by indigenous groups in the far north and extreme south of Chile (and presumably the center as well) appear to have been used primarily within ambush hunting strategies. This may account for the susceptibility of guanacos and other prey species to feral dog attacks. We detail seven separate hypotheses that require further investigation in order to assess how best to respond to the threat posed by feral dogs to the conservation of native deer and camelids in Chile and other parts of South America.
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Affiliation(s)
| | - Meredith Root‐Bernstein
- Center of Applied Ecology and SustainabilitySantiagoChile
- Institute of Ecology and BiodiversitySantiagoChile
- UMR CESCOCNRSMusée National d'Histoire NaturelleParisFrance
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15
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Roca-Rada X, Politis G, Messineo PG, Scheifler N, Scabuzzo C, González M, Harkins KM, Reich D, Souilmi Y, Teixeira JC, Llamas B, Fehren-Schmitz L. Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America. iScience 2021; 24:102553. [PMID: 34142055 PMCID: PMC8188552 DOI: 10.1016/j.isci.2021.102553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023] Open
Abstract
The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.
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Affiliation(s)
- Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Pablo G. Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Nahuel Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Clara Scabuzzo
- CICYTTP-CONICET, Provincia de Entre Ríos-UADER-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata. Dr. Materi y España (3105), Diamante, Entre Ríos Argentina
| | - Mariela González
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Kelly M. Harkins
- UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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16
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Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature 2021; 594:356-364. [PMID: 34135521 DOI: 10.1038/s41586-021-03499-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.
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Affiliation(s)
- Eske Willerslev
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Cambridge, UK.
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Anthropology, Southern Methodist University, Dallas, TX, USA.
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17
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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18
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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: 22] [Impact Index Per Article: 7.3] [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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19
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Davidson R, Fehren-Schmitz L, Llamas B. A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations. Genes (Basel) 2021; 12:215. [PMID: 33540755 PMCID: PMC7913103 DOI: 10.3390/genes12020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
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Affiliation(s)
- Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics (NCIG), Australian National University, Canberra, ACT 0200, Australia
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20
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Richalet JP. [Adaption to chronic hypoxaemia by populations living at high altitude]. Rev Mal Respir 2021; 38:395-403. [PMID: 33541755 DOI: 10.1016/j.rmr.2020.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/13/2020] [Indexed: 12/14/2022]
Abstract
Permanent life at high altitude induces important physiological stresses linked to the exposure to chronic hypoxia. Various strategies have been adopted by diverse populations living in the Andes, Tibet or East Africa. The main mechanism is an increase in red blood cell production, more marked in Andeans than in Tibetans or Ethiopians. Other changes are observed in the cardiovascular or respiratory systems, as well as in the utero-placental circulation. Sometimes, a de-adaptation process to hypoxia develops, when erythrocytosis becomes excessive and leads to haematological, vascular and cerebral complications (Monge's disease or chronic mountain sickness). Pulmonary hypertension may also appear. Therapeutic options are available but not sufficiently used. Genetic studies have recently been undertaken to try to better understand the evolution of the human genome in populations living in various high altitude regions of the world, as well as the genetic risk factors for chronic diseases. A new model has appeared, intermittent chronic hypoxia, due to the development of economic activities (mainly mining) in desert regions of the Altiplano.
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Affiliation(s)
- J-P Richalet
- Laboratoire « Hypoxie & Poumon », UMR Inserm U1272, Université Sorbonne Paris Nord 13, 74, rue Marcel-Cachin, 93017 Bobigny cedex, France.
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21
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Ribeiro-Dos-Santos AM, Vidal AF, Vinasco-Sandoval T, Guerreiro J, Santos S, Ribeiro-Dos-Santos Â, de Souza SJ. Exome Sequencing of Native Populations From the Amazon Reveals Patterns on the Peopling of South America. Front Genet 2020; 11:548507. [PMID: 33193622 PMCID: PMC7660019 DOI: 10.3389/fgene.2020.548507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/09/2020] [Indexed: 02/05/2023] Open
Abstract
Studies on the peopling of South America have been limited by the paucity of sequence data from Native Americans, especially from the east part of the Amazon region. Here, we investigate the whole exome variation from 58 Native American individuals (eight different populations) from the Amazon region and draw insights into the peopling of South America. By using the sequence data generated here together with data from the public domain, we confirmed a strong genetic distinction between Andean and Amazonian populations. By testing distinct demographic models, our analysis supports a scenario of South America occupation that involves migrations along the Pacific and Atlantic coasts. Occupation of the southeast part of South America would involve migrations from the north, rather than from the west of the continent.
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Affiliation(s)
| | - Amanda Ferreira Vidal
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil
| | - Tatiana Vinasco-Sandoval
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil
| | - João Guerreiro
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil
| | - Sidney Santos
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil.,Oncology and Medical Science Graduate Program, Núcleo de Pesquisas em Oncologica, UFPA, Belém, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Genetics and Molecular Biology Graduate Program, Instituto de Ciências Biológicas, UFPA, Belém, Brazil.,Oncology and Medical Science Graduate Program, Núcleo de Pesquisas em Oncologica, UFPA, Belém, Brazil
| | - Sandro J de Souza
- Instituto do Cérebro, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, UFRN, Natal, Brazil.,Institute of Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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22
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Mairbäurl H, Gassmann M, Muckenthaler MU. Geographical ancestry affects normal hemoglobin values in high-altitude residents. J Appl Physiol (1985) 2020; 129:1451-1459. [PMID: 33002380 DOI: 10.1152/japplphysiol.00025.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Increasing the hemoglobin (Hb) concentration is a major mechanism adjusting arterial oxygen content to decreased oxygen partial pressure of inspired air at high altitude. Approximately 5% of the world's population living at altitudes higher than 1,500 m shows this adaptive mechanism. Notably, there is a wide variation in the extent of increase in Hb concentration among different populations. This short review summarizes available information on Hb concentrations of high-altitude residents living at comparable altitudes (3,500-4,500 m) in different regions of the world. An increased Hb concentration is found in all high-altitude populations. The highest mean Hb concentration was found in adult male Andean residents and in Han Chinese living at high altitude, whereas it was lowest in Ethiopians, Tibetans, and Sherpas. A lower plasma volume in Andean high-altitude natives may offer a partial explanation. Indeed, male Andean high-altitude natives have a lower plasma volume than Tibetans and Ethiopians. Moreover, Hb values were lower in adult, nonpregnant females than in males; differences between populations of different ancestry were less pronounced. Various genetic polymorphisms were detected in high-altitude residents thought to favor life in a hypoxic environment, some of which correlate with the relatively low Hb concentration in the Tibetans and Ethiopians, whereas differences in angiotensin-converting enzyme allele distribution may be related to elevated Hb in the Andeans. Taken together, these results indicate different sensitivity of oxygen dependent control of erythropoiesis or plasma volume among populations of different geographical ancestry, offering explanations for differences in the Hb concentration at high altitude.
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Affiliation(s)
- Heimo Mairbäurl
- Departmment of Translational Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Max Gassmann
- Vetsuisse Faculty, Institute of Veterinary Physiology, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Martina U Muckenthaler
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany.,Departmment of Pediatric Hematology, Oncology and Immunology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg, Heidelberg, Germany.,German Centre for Cardiovascular Research, Partner Site Heidelberg/Mannheim, Germany
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23
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Prates L, Politis GG, Perez SI. Rapid radiation of humans in South America after the last glacial maximum: A radiocarbon-based study. PLoS One 2020; 15:e0236023. [PMID: 32697794 PMCID: PMC7375534 DOI: 10.1371/journal.pone.0236023] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 06/28/2020] [Indexed: 11/18/2022] Open
Abstract
The early peopling of the Americas has been one of the most hotly contested topics in American anthropology and a research issue that draws archaeologists into a multidisciplinary debate. In South America, although the background data on this issue has increased exponentially in recent decades, the core questions related to the temporal and spatial patterns of the colonization process remain open. In this paper we tackle these questions in the light of the quantitative analysis of a screened radiocarbon database of more than 1600 early dates. We explore the frequency of radiocarbon dates as proxies for assessing population growth; and define a reliable and statistically well supported lower chronological bound (not to the exact date) for the earliest human arrival. Our results suggest that the earliest chronological threshold for the peopling of South America should be between 16,600 and 15,100, with a mean estimated date ~ 15,500 cal BP (post Last Glacial Maximum). Population would have grown until the end of Antarctic Cold Reversal stadial ~12,500 cal BP at the time of the main extinctions of megafauna–, when the increase rate slows, probably as a result of the changes that occurred in the trophic niche of humans.
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Affiliation(s)
- Luciano Prates
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail:
| | - Gustavo G. Politis
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Instituto de Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano (CONICET), Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Argentina
| | - S. Ivan Perez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
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24
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Luisi P, García A, Berros JM, Motti JMB, Demarchi DA, Alfaro E, Aquilano E, Argüelles C, Avena S, Bailliet G, Beltramo J, Bravi CM, Cuello M, Dejean C, Dipierri JE, Jurado Medina LS, Lanata JL, Muzzio M, Parolin ML, Pauro M, Paz Sepúlveda PB, Rodríguez Golpe D, Santos MR, Schwab M, Silvero N, Zubrzycki J, Ramallo V, Dopazo H. Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina. PLoS One 2020; 15:e0233808. [PMID: 32673320 PMCID: PMC7365470 DOI: 10.1371/journal.pone.0233808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.
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Affiliation(s)
- Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Juan Manuel Berros
- Consejo Nacional de Investigaciones Científicas y Técnicas - Laboratorio de Análisis de Datos, Biocódices S.A., Buenos Aires, Argentina
| | - Josefina M B Motti
- Núcleo de Estudios Interdisciplinarios de Poblaciones Humanas de Patagonia Austral (NEIPHA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Centro de la Provincia de Buenos Aires, Quequén, Argentina
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Emma Alfaro
- Instituto de Ecorregiones Andinas (INECOA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Jujuy, Jujuy, Argentina.,Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Carina Argüelles
- Departamento de Genética, Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biología Subtropical (IBS)-Nodo Posadas, Universidad Nacional de Misiones (UNaM)-Consejo Nacional de Investigaciones Científicas y Técnicas, Posadas, Argentina.,Cátedra de Biología Molecular, Carrera de Medicina, Facultad de Ciencias de la Salud, Universidad Católica de las Misiones (UCAMI), Posadas, Argentina
| | - Sergio Avena
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Beltramo
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina.,Laboratorio de Análisis Comparativo de ADN, Corte Suprema de Justicia de la Provincia de Buenos Aires, La Plata, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariela Cuello
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Cristina Dejean
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | | | - Laura S Jurado Medina
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - José Luis Lanata
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio (IIDyPCa), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Río Negro, San Carlos de Bariloche, Argentina
| | - Marina Muzzio
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Paula B Paz Sepúlveda
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Rita Santos
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Marisol Schwab
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Natalia Silvero
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH) - Consejo Nacional de Investigaciones Científicas y Técnicas-Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Hernán Dopazo
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas - Biocodices S.A., Buenos Aires, Argentina
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25
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Mendes M, Alvim I, Borda V, Tarazona-Santos E. The history behind the mosaic of the Americas. Curr Opin Genet Dev 2020; 62:72-77. [PMID: 32659643 DOI: 10.1016/j.gde.2020.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes.
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Affiliation(s)
- Marla Mendes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Isabela Alvim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Victor Borda
- Laboratório de Bioinformática, LABINFO, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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26
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Tsosie KS, Begay RL, Fox K, Garrison NA. Generations of genomes: advances in paleogenomics technology and engagement for Indigenous people of the Americas. Curr Opin Genet Dev 2020; 62:91-96. [PMID: 32721847 PMCID: PMC7484015 DOI: 10.1016/j.gde.2020.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
For decades, scientists have collected genomic information from Indigenous peoples and their ancestors with the goal of elucidating human migration events, understanding ancestral origins, and identifying ancestral variants contributing to disease. However, such studies may not have offered much benefit to the Indigenous groups who contributed DNA, and many have instead perpetuated stereotypes and other harms. With recent advances in genomic technology facilitating the study of both ancient and present-day DNA, researchers and Indigenous communities have new opportunities to begin collaboratively addressing important questions about human health and history. Yet, while there are increased efforts to ethically engage Indigenous communities, more work is still needed as the discipline struggles to absolve itself of the racialized science and extractive biocolonialism that defined its past.
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Affiliation(s)
- Krystal S Tsosie
- Vanderbilt University, Nashville, TN 37325, USA; Native BioData Consortium, Eagle Butte, SD 57625, USA
| | - Rene L Begay
- Centers for American Indian and Alaska Native Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Keolu Fox
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Global Health, University of California, San Diego, La Jolla, CA 92093, USA; Indigenous Futures Lab, University of California, San Diego, La Jolla, CA 92093, USA; Native BioData Consortium, Eagle Butte, SD 57625, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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27
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Mojsiejczuk L, Torres C, Flichman D, Campos RH. Long-term evolution of hepatitis B virus genotype F: Strong association between viral diversification and the prehistoric settlement of Central and South America. J Viral Hepat 2020; 27:620-630. [PMID: 32052519 DOI: 10.1111/jvh.13273] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022]
Abstract
The genotype F (HBV-F) is an autochthonous Native American strain of the hepatitis B virus. In this study, we reconstruct the HBV-F long-term evolution under a hypothesis of co-divergence with humans in Central and South America, since their entry into the region 14.5-16 thousand years ago. The Bayesian phylogeographic reconstruction supported a virus-host co-expansion; however, two evolutionary scenarios would have been present. Whereas subgenotype F1 spreads along a Pacific coastal route and would have evolved associated with Central American and Andean cultures from the west of the continent, subgenotypes F2-F6 spread along the Atlantic coastline and inner pathways associated with communities inhabiting the tropical forest lowlands. Then, we propose a model for HBV-F evolution in which the selection of differential biological characteristics in these two main groups would be related to their evolution in host populations with different genetic backgrounds and dissimilar demographic conditions.
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Affiliation(s)
- Laura Mojsiejczuk
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina Torres
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Flichman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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28
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Nakatsuka N, Lazaridis I, Barbieri C, Skoglund P, Rohland N, Mallick S, Posth C, Harkins-Kinkaid K, Ferry M, Harney É, Michel M, Stewardson K, Novak-Forst J, Capriles JM, Durruty MA, Álvarez KA, Beresford-Jones D, Burger R, Cadwallader L, Fujita R, Isla J, Lau G, Aguirre CL, LeBlanc S, Maldonado SC, Meddens F, Messineo PG, Culleton BJ, Harper TK, Quilter J, Politis G, Rademaker K, Reindel M, Rivera M, Salazar L, Sandoval JR, Santoro CM, Scheifler N, Standen V, Barreto MI, Espinoza IF, Tomasto-Cagigao E, Valverde G, Kennett DJ, Cooper A, Krause J, Haak W, Llamas B, Reich D, Fehren-Schmitz L. A Paleogenomic Reconstruction of the Deep Population History of the Andes. Cell 2020; 181:1131-1145.e21. [PMID: 32386546 PMCID: PMC7304944 DOI: 10.1016/j.cell.2020.04.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/11/2020] [Accepted: 04/13/2020] [Indexed: 02/03/2023]
Abstract
There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA.
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chiara Barbieri
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
| | - Jannine Novak-Forst
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - José M Capriles
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Marta Alfonso Durruty
- Department of Sociology, Anthropology and Social Work, Kansas State University, Manhattan, KS 66506, USA
| | | | - David Beresford-Jones
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK
| | - Richard Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lauren Cadwallader
- Office of Scholarly Communication, Cambridge University Library, Cambridge CB3 9DR, UK
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru
| | - Johny Isla
- Peruvian Ministry of Culture, DDC Ica, Directos of the Nasca-Palpa Management Plan, Calle Juan Matta 880, Nasca 11401, Peru
| | - George Lau
- Sainsbury Research Unit, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Carlos Lémuz Aguirre
- Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia
| | - Steven LeBlanc
- Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA
| | - Sergio Calla Maldonado
- Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia
| | - Frank Meddens
- School of Archaeology, Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AH, UK
| | - Pablo G Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Brendan J Culleton
- Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jeffrey Quilter
- Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Reindel
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Berlin 14195, Germany
| | - Mario Rivera
- Universidad de Magallanes, Punta Arenas 6210427, Chile; Field Museum Natural History 1400 S Lake Shore Dr., Chicago, IL 60605, USA
| | - Lucy Salazar
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK
| | - José R Sandoval
- Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru
| | - Calogero M Santoro
- Instituto de Alta Investigation, Universidad de Tarapaca, Antafogasta 1520, Arica, 1000000, Chile
| | - Nahuel Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Vivien Standen
- Departamento de Antropología, Universidad de Tarapacá, Antafogasta 1520, Arica, 1000000, Chile
| | - Maria Ines Barreto
- Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru
| | - Isabel Flores Espinoza
- Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru
| | - Elsa Tomasto-Cagigao
- Department of Humanities, Pontifical Catholic University of Peru, San Miguel 15088, Peru
| | - Guido Valverde
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Douglas J Kennett
- Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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29
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Waters MR. Late Pleistocene exploration and settlement of the Americas by modern humans. SCIENCE (NEW YORK, N.Y.) 2020; 365:365/6449/eaat5447. [PMID: 31296740 DOI: 10.1126/science.aat5447] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
North and South America were the last continents to be explored and settled by modern humans at the end of the Pleistocene. Genetic data, derived from contemporary populations and ancient individuals, show that the first Americans originated from Asia and after several population splits moved south of the continental ice sheets that covered Canada sometime between ~17.5 and ~14.6 thousand years (ka) ago. Archaeological evidence shows that geographically dispersed populations lived successfully, using biface, blade, and osseous technologies, in multiple places in North and South America between ~15.5 and ~14 ka ago. Regional archaeological complexes emerged by at least ~13 ka ago in North America and ~12.9 ka ago in South America. Current genetic and archaeological data do not support an earlier (pre-17.5 ka ago) occupation of the Americas.
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Affiliation(s)
- Michael R Waters
- Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
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30
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Menéndez LP, Rademaker K, Harvati K. Revisiting East–West Skull Patterns and the Role of Random Factors in South America: Cranial Reconstruction and Morphometric Analysis of the Facial Skeleton from Cuncaicha Rockshelter (Southern Peru). ACTA ACUST UNITED AC 2019. [DOI: 10.1080/20555563.2019.1703167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lumila Paula Menéndez
- Konrad Lorenz Institute, Klosterneuburg, Austria, and DFG Centre for Advanced Studies “Words, Bones, Genes, Tools”, University of Tübingen, Tübingen, Germany
| | | | - Katerina Harvati
- Paleoanthropology, Senckenberg Centre for Human Evolution and Paleoenvironment, and DFG Centre for Advanced Studies “Words, Bones, Genes, Tools”, University of Tübingen, Tübingen, Germany
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31
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Carvalho Gontijo C, Porras-Hurtado LG, Freire-Aradas A, Fondevila M, Santos C, Salas A, Henao J, Isaza C, Beltrán L, Nogueira Silbiger V, Castillo A, Ibarra A, Moreno Chavez F, Söchtig J, Ruiz Y, Barreto G, Rondon F, Zabala W, Borjas L, de Oliveira SF, Carracedo A, Lareu MV, Phillips C. PIMA: A population informative multiplex for the Americas. Forensic Sci Int Genet 2019; 44:102200. [PMID: 31760353 DOI: 10.1016/j.fsigen.2019.102200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/01/2019] [Indexed: 11/26/2022]
Abstract
We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment In values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.
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Affiliation(s)
- C Carvalho Gontijo
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - L G Porras-Hurtado
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - A Freire-Aradas
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - C Santos
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - A Salas
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - J Henao
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - C Isaza
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - L Beltrán
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia; Health Science Faculty, Unidad Central del Valle del Cauca, Tulua, Colombia
| | - V Nogueira Silbiger
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, Brazil
| | - A Castillo
- Medical Genetic Laboratory, Industrial University of Santander (UIS), Colombia
| | - A Ibarra
- Medical Genetics Laboratory, University of Antioquia, Colombia
| | - F Moreno Chavez
- Servicio Médico Legal, Ministry of Justice and Human Rights of Chile, Santiago, Chile
| | - J Söchtig
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - Y Ruiz
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - G Barreto
- Human Molecular Genetics Research Group, University of Valle, Colombia
| | - F Rondon
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, Brazil; Human Molecular Genetics Research Group, University of Valle, Colombia
| | - W Zabala
- Molecular Genetics Laboratory, Medical Genetics Unit, University of Zulia, Venezuela
| | - L Borjas
- Molecular Genetics Laboratory, Medical Genetics Unit, University of Zulia, Venezuela
| | - S F de Oliveira
- Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil.
| | - A Carracedo
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, University of Santiago de Compostela, Spain.
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Resolving mitochondrial haplogroups B2 and B4 with next-generation mitogenome sequencing to distinguish Native American from Asian haplotypes. Forensic Sci Int Genet 2019; 43:102143. [DOI: 10.1016/j.fsigen.2019.102143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
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Gnecchi-Ruscone GA, Sarno S, De Fanti S, Gianvincenzo L, Giuliani C, Boattini A, Bortolini E, Di Corcia T, Sanchez Mellado C, Dàvila Francia TJ, Gentilini D, Di Blasio AM, Di Cosimo P, Cilli E, Gonzalez-Martin A, Franceschi C, Franceschi ZA, Rickards O, Sazzini M, Luiselli D, Pettener D. Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes-Amazonia Divide. Mol Biol Evol 2019; 36:1254-1269. [PMID: 30895292 PMCID: PMC6526910 DOI: 10.1093/molbev/msz066] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Extensive European and African admixture coupled with loss of Amerindian lineages makes the reconstruction of pre-Columbian history of Native Americans based on present-day genomes extremely challenging. Still open questions remain about the dispersals that occurred throughout the continent after the initial peopling from the Beringia, especially concerning the number and dynamics of diffusions into South America. Indeed, if environmental and historical factors contributed to shape distinct gene pools in the Andes and Amazonia, the origins of this East-West genetic structure and the extension of further interactions between populations residing along this divide are still not well understood. To this end, we generated new high-resolution genome-wide data for 229 individuals representative of one Central and ten South Amerindian ethnic groups from Mexico, Peru, Bolivia, and Argentina. Low levels of European and African admixture in the sampled individuals allowed the application of fine-scale haplotype-based methods and demographic modeling approaches. These analyses revealed highly specific Native American genetic ancestries and great intragroup homogeneity, along with limited traces of gene flow mainly from the Andes into Peruvian Amazonians. Substantial amount of genetic drift differentially experienced by the considered populations underlined distinct patterns of recent inbreeding or prolonged isolation. Overall, our results support the hypothesis that all non-Andean South Americans are compatible with descending from a common lineage, while we found low support for common Mesoamerican ancestors of both Andeans and other South American groups. These findings suggest extensive back-migrations into Central America from non-Andean sources or conceal distinct peopling events into the Southern Continent.
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Affiliation(s)
- Guido Alberto Gnecchi-Ruscone
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Laura Gianvincenzo
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alessio Boattini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Tullia Di Corcia
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Cesar Sanchez Mellado
- Faculty of Intercultural Education and Humanity, National Intercultural University of Amazon, Ucayali, Peru
| | | | - Davide Gentilini
- Center for Biomedical Research and Technologies, Italian Auxologic Institute IRCCS, Milan, Italy
| | - Anna Maria Di Blasio
- Center for Biomedical Research and Technologies, Italian Auxologic Institute IRCCS, Milan, Italy
| | | | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Antonio Gonzalez-Martin
- Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid, Spain
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Olga Rickards
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Davide Pettener
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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Biogeographical origin and timing of the founder ichthyosis TGM1 c.1187G > A mutation in an isolated Ecuadorian population. Sci Rep 2019; 9:7175. [PMID: 31073126 PMCID: PMC6509209 DOI: 10.1038/s41598-019-43133-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 04/11/2019] [Indexed: 11/22/2022] Open
Abstract
An unusually high frequency of the lamellar ichthyosis TGM1 mutation, c.1187G > A, has been observed in the Ecuadorian province of Manabí. Recently, the same mutation has been detected in a Galician patient (Northwest of Spain). By analyzing patterns of genetic variation around this mutation in Ecuadorian patients and population matched controls, we were able to estimate the age of c.1187G > A and the time to their most recent common ancestor (TMRCA) of c.1187G > A Ecuadorian carriers. While the estimated mutation age is 41 generations ago (~1,025 years ago [ya]), the TMRCA of Ecuadorian c.1187G > A carrier haplotypes dates to just 17 generations (~425 ya). Probabilistic-based inferences of local ancestry allowed us to infer a most likely European origin of a few (16% to 30%) Ecuadorian haplotypes carrying this mutation. In addition, inferences on demographic historical changes based on c.1187G > A Ecuadorian carrier haplotypes estimated an exponential population growth starting ~20 generations, compatible with a recent founder effect occurring in Manabí. Two main hypotheses can be considered for the origin of c.1187G > A: (i) the mutation could have arisen in Spain >1,000 ya (being Galicia the possible homeland) and then carried to Ecuador by Spaniards in colonial times ~400 ya, and (ii) two independent mutational events originated this mutation in Ecuador and Galicia. The geographic and cultural characteristics of Manabí could have favored a founder effect that explains the high prevalence of TGM1 c.1187G > A in this region.
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Human Genetic Adaptation to High Altitude: Evidence from the Andes. Genes (Basel) 2019; 10:genes10020150. [PMID: 30781443 PMCID: PMC6410003 DOI: 10.3390/genes10020150] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 12/31/2022] Open
Abstract
Whether Andean populations are genetically adapted to high altitudes has long been of interest. Initial studies focused on physiological changes in the O₂ transport system that occur with acclimatization in newcomers and their comparison with those of long-resident Andeans. These as well as more recent studies indicate that Andeans have somewhat larger lung volumes, narrower alveolar to arterial O₂ gradients, slightly less hypoxic pulmonary vasoconstrictor response, greater uterine artery blood flow during pregnancy, and increased cardiac O2 utilization, which overall suggests greater efficiency of O₂ transfer and utilization. More recent single nucleotide polymorphism and whole-genome sequencing studies indicate that multiple gene regions have undergone recent positive selection in Andeans. These include genes involved in the regulation of vascular control, metabolic hemostasis, and erythropoiesis. However, fundamental questions remain regarding the functional links between these adaptive genomic signals and the unique physiological attributes of highland Andeans. Well-designed physiological and genome association studies are needed to address such questions. It will be especially important to incorporate the role of epigenetic processes (i.e.; non-sequence-based features of the genome) that are vital for transcriptional responses to hypoxia and are potentially heritable across generations. In short, further exploration of the interaction among genetic, epigenetic, and environmental factors in shaping patterns of adaptation to high altitude promises to improve the understanding of the mechanisms underlying human adaptive potential and clarify its implications for human health.
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