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Hünemeier T. Biogeographic Perspectives on Human Genetic Diversification. Mol Biol Evol 2024; 41:msae029. [PMID: 38349332 PMCID: PMC10917211 DOI: 10.1093/molbev/msae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024] Open
Abstract
Modern humans originated in Africa 300,000 yr ago, and before leaving their continent of origin, they underwent a process of intense diversification involving complex demographic dynamics. Upon exiting Africa, different populations emerged on the four other inhabited continents, shaped by the interplay of various evolutionary processes, such as migrations, founder effects, and natural selection. Within each region, continental populations, in turn, diversified and evolved almost independently for millennia. As a backdrop to this diversification, introgressions from archaic species contributed to establishing different patterns of genetic diversity in different geographic regions, reshaping our understanding of our species' variability. With the increasing availability of genomic data, it has become possible to delineate the subcontinental human population structure precisely. However, the bias toward the genomic research focused on populations from the global North has limited our understanding of the real diversity of our species and the processes and events that guided different human groups throughout their evolutionary history. This perspective is part of a series of articles celebrating 40 yr since our journal, Molecular Biology and Evolution, was founded (Russo et al. 2024). The perspective is accompanied by virtual issues, a selection of papers on human diversification published by Genome Biology and Evolution and Molecular Biology and Evolution.
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Affiliation(s)
- Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
- Population Genetics Department, Institute of Evolutionary Biology (IBE - CSIC/Universitat Pompeu Fabra), 08003 Barcelona, Spain
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2
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Fam BSDO, Feira MF, Cadore NA, Sbruzzi R, Hünemeier T, Abel L, Zhang Q, Casanova JL, Vianna FSL. Human genetic determinants of COVID-19 in Brazil: challenges and future plans. Genet Mol Biol 2024; 46:e20230128. [PMID: 38226654 DOI: 10.1590/1678-4685-gmb-2023-0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
COVID-19 pandemic represented a worldwide major challenge in different areas, and efforts undertaken by the scientific community led to the understanding of some of the genetic determinants that influence the different COVID-19 outcomes. In this paper, we review the studies about the role of human genetics in COVID-19 severity and how Brazilian studies also contributed to those findings. Rare variants in genes related to Inborn Errors of Immunity (IEI) in the type I interferons pathway, and its phenocopies, have been described as being causative of severe outcomes. IEI and its phenocopies are present in Brazil, not only in COVID-19 patients, but also in autoimmune conditions and severe reactions to yellow fever vaccine. In addition, studies focusing on common variants and GWAS studies encompassing worldwide patients have found several loci associated with COVID-19 severity. A GWAS study including only Brazilian COVID-19 patients identified a new locus 1q32.1 associated with COVID-19 severity. Thus, more comprehensive studies considering the Brazilian genomic diversity should be performed, since they can help to reveal not only what are the genetic determinants that contribute to the different outcomes for COVID-19 in the Brazilian population, but in the understanding of human genetics in different health conditions.
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Affiliation(s)
- Bibiana S de Oliveira Fam
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Marilea Furtado Feira
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Nathan Araujo Cadore
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Renan Sbruzzi
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas/Universitat Pompeu Fabra), Barcelona, Spain
| | - Laurent Abel
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Jean-Laurent Casanova
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Necker Hospital for Sick Children, Department of Pediatrics, Paris, France
| | - Fernanda Sales Luiz Vianna
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
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3
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Castro E Silva MA, Hünemeier T. A multidisciplinary overview on the Tupi-speaking people expansion. Am J Biol Anthropol 2023. [PMID: 37990807 DOI: 10.1002/ajpa.24876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
The cultural and biological diversity of South American indigenous groups represent extremes of human variability, exhibiting one of the highest linguistic diversities alongside a remarkably low within-population genetic variation and an extremely high inter-population genetic differentiation. On top of that, this region has seen some of the most dramatic demographic events in human history unleashed by the European colonization of the Americas. As a result of this process, the distribution of indigenous populations has been radically changed. In this review we focus on the Tupi, the largest and most widespread linguistic family in eastern South America. Tupi are believed to have originated in southwestern Amazon, from where some of its subfamilies expanded into other parts of the Amazon and, in the case of the Tupi-Guarani, beyond its borders. Recent evidence from archaeology, linguistics, and genetics aligns with José Brochado's Tupi Expansion model. He proposed that the gradual development of agricultural systems within the Amazon resulted in population growth and, eventually, territorial expansion. This model also supports separate Tupi Expansion branches: Tupinambá (Atlantic coast) and Guarani (south, midwest Brazil). Although being the most populous group on Brazil's Atlantic coast, which was the most affected by European colonization, the Tupi still account for roughly 20% of the country's overall indigenous population. Finally, despite its importance and more than a century of research on the Tupi and their expansion history, many key questions remain unanswered, which we attempt to summarize and explore here.
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Affiliation(s)
- Marcos Araújo Castro E Silva
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departament of Population Genetics, Institut de Biologia Evolutiva (CSIC/Universitat Pompeu Fabra), Barcelona, Spain
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Faux P, Ding L, Ramirez-Aristeguieta LM, Chacón-Duque JC, Comini M, Mendoza-Revilla J, Fuentes-Guajardo M, Jaramillo C, Arias W, Hurtado M, Villegas V, Granja V, Barquera R, Everardo-Martínez P, Quinto-Sánchez M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Poletti G, Gallo C, Rothhammer F, Rojas W, Schmid AB, Adhikari K, Bennett DL, Ruiz-Linares A. Neanderthal introgression in SCN9A impacts mechanical pain sensitivity. Commun Biol 2023; 6:958. [PMID: 37816865 PMCID: PMC10564861 DOI: 10.1038/s42003-023-05286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023] Open
Abstract
The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.
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Affiliation(s)
- Pierre Faux
- 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, 200438, Shanghai, China
- UMR ADES, Aix-Marseille Université, CNRS, EFS, 13005, Marseille, France
- UMR GenPhySE, INRAE, INP, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Li Ding
- 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, 200438, Shanghai, China
| | | | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, SE-1069, Stockholm, Sweden
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Maddalena Comini
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015, Paris, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, 1000000, Arica, Chile
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), 07745, Jena, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Mirsha Quinto-Sánchez
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), 06320, Mexico City, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, 4510, Mexico City, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, U9129ACD, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, U9129ACD, Puerto Madryn, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, 4510, Mexico City, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000000, Arica, Chile
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - Annina B Schmid
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, UK.
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK.
| | - Andrés Ruiz-Linares
- 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, 200438, Shanghai, China.
- UMR ADES, Aix-Marseille Université, CNRS, EFS, 13005, Marseille, France.
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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5
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Ferraz T, Suarez Villagran X, Nägele K, Radzevičiūtė R, Barbosa Lemes R, Salazar-García DC, Wesolowski V, Lopes Alves M, Bastos M, Rapp Py-Daniel A, Pinto Lima H, Mendes Cardoso J, Estevam R, Liryo A, Guimarães GM, Figuti L, Eggers S, Plens CR, Azevedo Erler DM, Valadares Costa HA, da Silva Erler I, Koole E, Henriques G, Solari A, Martin G, Serafim Monteiro da Silva SF, Kipnis R, Müller LM, Ferreira M, Carvalho Resende J, Chim E, da Silva CA, Borella AC, Tomé T, Müller Plumm Gomes L, Barros Fonseca D, Santos da Rosa C, de Moura Saldanha JD, Costa Leite L, Cunha CMS, Viana SA, Ozorio Almeida F, Klokler D, Fernandes HLA, Talamo S, DeBlasis P, Mendonça de Souza S, de Paula Moraes C, Elias Oliveira R, Hünemeier T, Strauss A, Posth C. Genomic history of coastal societies from eastern South America. Nat Ecol Evol 2023; 7:1315-1330. [PMID: 37524799 PMCID: PMC10406606 DOI: 10.1038/s41559-023-02114-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 06/08/2023] [Indexed: 08/02/2023]
Abstract
Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr BP) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr BP from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our analyses show genetic heterogeneity among contemporaneous Sambaqui groups from the southeastern and southern Brazilian coast, contrary to the similarity expressed in the archaeological record. The complex history of intercultural contact between inland horticulturists and coastal populations becomes genetically evident during the final horizon of Sambaqui societies, from around 2,200 yr BP, corroborating evidence of cultural change.
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Affiliation(s)
- Tiago Ferraz
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Renan Barbosa Lemes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Verônica Wesolowski
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Marcony Lopes Alves
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Murilo Bastos
- Departamento de Antropologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Jéssica Mendes Cardoso
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Géosciences Environnement Toulouse, Observatoire Midi Pyrénées, UMR 5563, CNRS, Toulouse, France
| | - Renata Estevam
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Andersen Liryo
- National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Geovan M Guimarães
- Grupo de Pesquisa em Educação Patrimonial e Arqueologia (Grupep), Universidade do Sul de Santa Catarina, Santa Catarina, Brazil
| | - Levy Figuti
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Cláudia R Plens
- Laboratory of Archaeological Studies, Department of History, Federal University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Ana Solari
- Fundação Museu do Homem Americano, Piauí, Brazil
| | | | | | | | - Letícia Morgana Müller
- Scientia Consultoria Científica, São Paulo, Brazil
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mariane Ferreira
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Scientia Consultoria Científica, São Paulo, Brazil
| | - Janine Carvalho Resende
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Eliane Chim
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Ana Claudia Borella
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Tiago Tomé
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lisiane Müller Plumm Gomes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - João Darcy de Moura Saldanha
- Universidade de Évora, Évora, Portugal
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Lúcio Costa Leite
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Claudia M S Cunha
- Federal University of Piauí, Piauí, Brazil
- Centro de Investigação em Antropologia e Saúde, Universidade de Coimbra, Coimbra, Portugal
| | - Sibeli Aparecida Viana
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Fernando Ozorio Almeida
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Arqueologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela Klokler
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Antropologia e Arqueologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henry Luydy Abraham Fernandes
- Programa de Pós-Graduação em Arqueologia e Patrimônio Cultural, Universidade Federal do Recôncavo da Bahia, Bahia, Brazil
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paulo DeBlasis
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - Rodrigo Elias Oliveira
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Tábita Hünemeier
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil.
- Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain.
| | - André Strauss
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
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6
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Li Q, Chen J, Faux P, Delgado ME, Bonfante B, Fuentes-Guajardo M, Mendoza-Revilla J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Wu S, Du S, Giardina A, Paria SS, Khokan MR, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Rojas W, Rothhammer F, Navarro N, Wang S, Adhikari K, Ruiz-Linares A. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape. Commun Biol 2023; 6:481. [PMID: 37156940 PMCID: PMC10167347 DOI: 10.1038/s42003-023-04838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.
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Affiliation(s)
- Qing Li
- 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, 200438, China
| | - Jieyi Chen
- 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, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Miguel Eduardo Delgado
- 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, 200438, China
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, República Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Buenos Aires, República Argentina
| | - Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, 75015, France
| | - J Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City, 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Sijie Wu
- 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, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrea Giardina
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Soumya Subhra Paria
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Mahfuzur Rahman Khokan
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica, 1000000, Chile
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, Dijon, 21000, France
- EPHE, PSL University, Paris, 75014, France
| | - Sijia Wang
- 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, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- 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, 200438, China.
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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7
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Prates L, Lemes RB, Hünemeier T, Leonardi F. Population-based change-point detection for the identification of homozygosity islands. Bioinformatics 2023; 39:7114026. [PMID: 37039826 PMCID: PMC10112956 DOI: 10.1093/bioinformatics/btad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/07/2023] [Accepted: 03/14/2023] [Indexed: 04/12/2023]
Abstract
MOTIVATION This work is motivated by the problem of identifying homozygosity islands on the genome of individuals in a population. Our method directly tackles the issue of identification of the homozygosity islands at the population level, without the need of analysing single individuals and then combine the results, as is made nowadays in state-of-the-art approaches. RESULTS We propose regularised offline change-point methods to detect changes in the parameters of a multidimensional distribution when we have several aligned, independent samples of fixed resolution. We present a penalised maximum likelihood approach that can be efficiently computed by a dynamic programming algorithm or approximated by a fast binary segmentation algorithm. Both estimators are shown to converge almost surely to the set of change-points without the need of specifying a priori the number of change-points. In simulation we observed similar performances from the exact and greedy estimators. Moreover, we provide a new methodology for the selection of the regularisation constant which has the advantage of being automatic, consistent and less prone to subjective analysis. AVAILABILITY The data used in the application is from the Human Genome Diversity Project (HGDP) and is publicly available. Algorithms were implemented using the R software R Core Team (2020) in the R package blockcpd, found at https://github.com/Lucas-Prates/blockcpd. SUPPLEMENTARY INFORMATION Supplementary material is available online at Bioinformatics.
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Affiliation(s)
- Lucas Prates
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Renan B Lemes
- Institute of Biological Sciences, University of São Paulo, São Paulo, Brazil
| | - Tábita Hünemeier
- Institute of Biological Sciences, University of São Paulo, São Paulo, Brazil
| | - Florencia Leonardi
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
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8
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Couto-Silva CM, Nunes K, Venturini G, Araújo Castro e Silva M, Pereira LV, Comas D, Pereira A, Hünemeier T. Indigenous people from Amazon show genetic signatures of pathogen-driven selection. Sci Adv 2023; 9:eabo0234. [PMID: 36888716 PMCID: PMC9995071 DOI: 10.1126/sciadv.abo0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Ecological conditions in the Amazon rainforests are historically favorable for the transmission of numerous tropical diseases, especially vector-borne diseases. The high diversity of pathogens likely contributes to the strong selective pressures for human survival and reproduction in this region. However, the genetic basis of human adaptation to this complex ecosystem remains unclear. This study investigates the possible footprints of genetic adaptation to the Amazon rainforest environment by analyzing the genomic data of 19 native populations. The results based on genomic and functional analysis showed an intense signal of natural selection in a set of genes related to Trypanosoma cruzi infection, which is the pathogen responsible for Chagas disease, a neglected tropical parasitic disease native to the Americas that is currently spreading worldwide.
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Affiliation(s)
- Cainã M. Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
| | - Gabriela Venturini
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Lygia V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
| | - David Comas
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Alexandre Pereira
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
- Institut de Biologia Evolutiva (CSIC/Universitat Pompeu Fabra), Barcelona 08003, Spain
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9
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Giudicelli GC, De Souza CMB, Veronese FV, Pereira LV, Hünemeier T, Vianna FSL. Precision medicine implementation challenges for APOL1 testing in chronic kidney disease in admixed populations. Front Genet 2022; 13:1016341. [PMID: 36588788 PMCID: PMC9797503 DOI: 10.3389/fgene.2022.1016341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic Kidney Disease (CKD) is a public health problem that presents genetic and environmental risk factors. Two alleles in the Apolipoprotein L1 (APOL1) gene were associated with chronic kidney disease; these alleles are common in individuals of African ancestry but rare in European descendants. Genomic studies on Afro-Americans have indicated a higher prevalence and severity of chronic kidney disease in people of African ancestry when compared to other ethnic groups. However, estimates in low- and middle-income countries are still limited. Precision medicine approaches could improve clinical outcomes in carriers of risk alleles in the Apolipoprotein L1 gene through early diagnosis and specific therapies. Nevertheless, to enhance the definition of studies on these variants, it would be necessary to include individuals with different ancestry profiles in the sample, such as Latinos, African Americans, and Indigenous peoples. There is evidence that measuring genetic ancestry improves clinical care for admixed people. For chronic kidney disease, this knowledge could help establish public health strategies for monitoring patients and understanding the impact of the Apolipoprotein L1 genetic variants in admixed populations. Therefore, researchers need to develop resources, methodologies, and incentives for vulnerable and disadvantaged communities, to develop and implement precision medicine strategies and contribute to consolidating diversity in science and precision medicine in clinical practice.
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Affiliation(s)
- Giovanna Câmara Giudicelli
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, RS, Brazil
| | - Celia Mariana Barbosa De Souza
- Departamento de Nefrologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Programa de Pós-graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francisco Veríssimo Veronese
- Departamento de Nefrologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Programa de Pós-graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lygia V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil,Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain
| | - Fernanda Sales Luiz Vianna
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, RS, Brazil,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil,Programa de Medicina Personalizada Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,*Correspondence: Fernanda Sales Luiz Vianna,
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ormond L, Wang K, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera R, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Badillo Rivera KM, Nieves-Colón MA, Gignoux CR, Wojcik GL, Moreno-Estrada A, Hünemeier T, Ramallo V, Schuler-Faccini L, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Fumagalli M, Adhikari K, Ruiz-Linares A, Hellenthal G. Disentangling Signatures of Selection Before and After European Colonization in Latin Americans. Mol Biol Evol 2022; 39:6565306. [PMID: 35460423 PMCID: PMC9034689 DOI: 10.1093/molbev/msac076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.
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Affiliation(s)
- Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Louise Ormond
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
| | - Ke Wang
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,National School of Anthropology and History, Mexico City, Mexico
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | - Maria A Nieves-Colón
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Christopher R Gignoux
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | | | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, Australia
| | - Matteo Fumagalli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
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12
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Abstract
South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.
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Affiliation(s)
- Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Ferraz
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Cainã M Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Renan B Lemes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - David Comas
- Departament de Ciències, Institut de Biologia Evolutiva, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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13
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Chen Y, André M, Adhikari K, Blin M, Bonfante B, Mendoza-Revilla J, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, de Cerqueira CCS, Hünemeier T, Ramallo V, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Tobin DJ, Wang S, Faux P, Ruiz-Linares A. A genome-wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans. Br J Dermatol 2021; 185:988-998. [PMID: 33959940 DOI: 10.1111/bjd.20436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans. OBJECTIVES To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America. METHODS Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome. RESULTS Genome-wide significant association was observed at four genome regions: two were associated with wrinkling (in 1p13·3 and 21q21·2), one with mole count (in 1q32·3) and one with both wrinkling and mole count (in 5p13·2). Associated SNPs in 5p13·2 and in 1p13·3 are intronic within SLC45A2 and VAV3, respectively, while SNPs in 1q32·3 are near the SLC30A1 gene, and those in 21q21·2 occur in a gene desert. Analyses of SNPs in IRF4 and MC1R are consistent with a role of these genes in skin ageing. CONCLUSIONS We replicate the association of wrinkling with variants in SLC45A2, IRF4 and MC1R reported in Europeans. We identify VAV3 and SLC30A1 as two novel candidate genes impacting on wrinkling and mole count, respectively. We provide the first evidence that SLC45A2 influences mole count, in addition to variants in this gene affecting melanoma risk in Europeans.
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Affiliation(s)
- Y Chen
- 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
| | - M André
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - K 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, London, WC1E 6BT, UK
| | - M Blin
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - B Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - J Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú.,Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, 75015, France
| | - M Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - S Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - J C Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - M Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - V Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - V Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - C Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - W Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - R B Lozano
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, 07745, Germany
| | - P Everardo-Martínez
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico
| | - J Gómez-Valdés
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico
| | - H Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, MC, 4510, Mexico
| | | | - T Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - V Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil.,Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - R Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - L Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - M-C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - V Acuña-Alonzo
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico
| | - S Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, MC, 4510, Mexico
| | - C Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - G Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - G Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - F Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000000, Chile
| | - D Balding
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - D J Tobin
- The Charles Institute of Dermatology, University College Dublin, Dublin, Ireland
| | - S Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, University of the Chinese Academy of Sciences, Shanghai, 200031, China
| | - P Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - A Ruiz-Linares
- 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.,UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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14
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Palmal S, Adhikari K, Mendoza-Revilla J, Fuentes-Guajardo M, Silva de Cerqueira CC, Bonfante B, Chacón-Duque JC, Sohail A, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, Hünemeier T, Ramallo V, Parolin ML, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Faux P, Ruiz-Linares A. Prediction of eye, hair and skin colour in Latin Americans. Forensic Sci Int Genet 2021; 53:102517. [PMID: 33865096 DOI: 10.1016/j.fsigen.2021.102517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.
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Affiliation(s)
- Sagnik Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, 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, London WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú; Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | | | - Betty Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anood Sohail
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Claudia Jaramillo
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan; GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City 6600, Mexico; Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | | | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil; Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | | | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Arica 1000000, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Pierre Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France.
| | - Andrés Ruiz-Linares
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; 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.
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15
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Bonfante B, Faux P, Navarro N, Mendoza-Revilla J, Dubied M, Montillot C, Wentworth E, Poloni L, Varón-González C, Jones P, Xiong Z, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Liu F, Weinberg SM, Shaffer JR, Stergiakouli E, Howe LJ, Hysi PG, Spector TD, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Thauvin-Robinet C, Faivre L, Costedoat C, Balding D, Cox T, Kayser M, Duplomb L, Yalcin B, Cotney J, Adhikari K, Ruiz-Linares A. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. Sci Adv 2021; 7:eabc6160. [PMID: 33547071 PMCID: PMC7864580 DOI: 10.1126/sciadv.abc6160] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/17/2020] [Indexed: 05/25/2023]
Abstract
To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.
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Affiliation(s)
- Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Morgane Dubied
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
| | - Charlotte Montillot
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Emma Wentworth
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Lauriane Poloni
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, UA, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Philip Jones
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Sagnik Palmal
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100864, China
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica 1000000, Chile
| | - Christel Thauvin-Robinet
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Timothy Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Laurence Duplomb
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Binnaz Yalcin
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - 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, London WC1E 6BT, UK
| | - Andrés Ruiz-Linares
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- 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
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16
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Missaggia BO, Reales G, Cybis GB, Hünemeier T, Bortolini MC. Adaptation and co-adaptation of skin pigmentation and vitamin D genes in native Americans. Am J Med Genet C Semin Med Genet 2020; 184:1060-1077. [PMID: 33325159 DOI: 10.1002/ajmg.c.31873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 11/06/2022]
Abstract
We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.
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Affiliation(s)
- Bruna Oliveira Missaggia
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela B Cybis
- Statistics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cátira Bortolini
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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17
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Single RM, Meyer D, Nunes K, Francisco RS, Hünemeier T, Maiers M, Hurley CK, Bedoya G, Gallo C, Hurtado AM, Llop E, Petzl-Erler ML, Poletti G, Rothhammer F, Tsuneto L, Klitz W, Ruiz-Linares A. Demographic history and selection at HLA loci in Native Americans. PLoS One 2020; 15:e0241282. [PMID: 33147239 PMCID: PMC7641399 DOI: 10.1371/journal.pone.0241282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
The American continent was the last to be occupied by modern humans, and native populations bear the marks of recent expansions, bottlenecks, natural selection, and population substructure. Here we investigate how this demographic history has shaped genetic variation at the strongly selected HLA loci. In order to disentangle the relative contributions of selection and demography process, we assembled a dataset with genome-wide microsatellites and HLA-A, -B, -C, and -DRB1 typing data for a set of 424 Native American individuals. We find that demographic history explains a sizeable fraction of HLA variation, both within and among populations. A striking feature of HLA variation in the Americas is the existence of alleles which are present in the continent but either absent or very rare elsewhere in the world. We show that this feature is consistent with demographic history (i.e., the combination of changes in population size associated with bottlenecks and subsequent population expansions). However, signatures of selection at HLA loci are still visible, with significant evidence selection at deeper timescales for most loci and populations, as well as population differentiation at HLA loci exceeding that seen at neutral markers.
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Affiliation(s)
- Richard M. Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, Vermont, United States of America
- * E-mail:
| | - Diogo Meyer
- Departmento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Departmento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | | | - Tábita Hünemeier
- Departmento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Martin Maiers
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, United States of America
| | - Carolyn K. Hurley
- CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University, Washington, DC, United States of America
| | - Gabriel Bedoya
- Instituto de Biología, Universidad de Antioquia Medellín, Medellín, Colombia
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ana Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| | - Elena Llop
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Giovanni Poletti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Tarapacá University, Arica, Chile
| | - Luiza Tsuneto
- Department of Basic Health Sciences, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - William Klitz
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Andrés Ruiz-Linares
- 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, Shanghai, China
- CNRS, EFS, ADES, D Aix-Marseille University, Marseille, France
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18
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Patrinos GP, Pasparakis E, Koiliari E, Pereira AC, Hünemeier T, Pereira LV, Mitropoulou C. Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries. Am J Hum Genet 2020; 107:589-595. [PMID: 33007198 DOI: 10.1016/j.ajhg.2020.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.
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19
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Carratto TMT, Marcorin L, Debortoli G, Hünemeier T, Norton H, Parra EJ, Castelli EC, Mendes-Junior CT. Insights on hair, skin and eye color of ancient and contemporary Native Americans. Forensic Sci Int Genet 2020; 48:102335. [PMID: 32593164 DOI: 10.1016/j.fsigen.2020.102335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Ribeirão Preto, SP, Brazil
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto at Mississauga, L5L 1C6, Mississauga, ON, Canada
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, 45221, Cincinnati, OH, United States
| | - Esteban Juan Parra
- Department of Anthropology, University of Toronto at Mississauga, L5L 1C6, Mississauga, ON, Canada
| | - Erick C Castelli
- São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, SP, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil.
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20
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Mas-Sandoval A, Arauna LR, Gouveia MH, Barreto ML, Horta BL, Lima-Costa MF, Pereira AC, Salzano FM, Hünemeier T, Tarazona-Santos E, Bortolini MC, Comas D. Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry. Genome Biol Evol 2020; 11:2593-2604. [PMID: 31328768 PMCID: PMC6756188 DOI: 10.1093/gbe/evz161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 01/19/2023] Open
Abstract
After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.
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Affiliation(s)
- Alex Mas-Sandoval
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Center for Research on Genomics and Global Health, National Institutes of Health, Bethesda, Maryland
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil.,Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Rio Grande do Sul, Brazil
| | | | | | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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21
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Chacón-Duque JC, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin ML, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon JM, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nat Commun 2018; 9:5388. [PMID: 30568240 PMCID: PMC6300600 DOI: 10.1038/s41467-018-07748-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.
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Affiliation(s)
- Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000009, Chile
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Jorge Gómez-Valdés
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Paola Everardo Martínez
- Posgrado en Antropología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, 05508-090, Brazil
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andrés (UMSA), La Paz, 2070, Bolivia
| | - René Vásquez
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Autónoma Tomás Frías, Potosí, 53820, Bolivia
| | - Elena Llop
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, 12, Peru
| | | | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Karla Sandoval
- National Laboratory of Genomics and Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico
| | - Rosenda I Peñaloza-Espinosa
- Department of Biological Systems, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, 1115, Mexico
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Claudio Bravi
- Instituto Multidisciplinario de Biología Celular, CONICET, La Plata, B1906APO, Argentina
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, 01011, Guatemala
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Verónica Gomes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Carlos Resende
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Leonor Gusmão
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- DNA Diagnostic Laboratory (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 23968-000, Brazil
| | - Antonio Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique, Université Toulouse 3 Paul Sabatier, Toulouse, 31330, France
| | - Pedro Moral
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Universitat de Barcelona, Barcelona, 08007, Spain
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000009, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- 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, Shanghai, 200433, China.
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, 13007, France.
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22
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Posth C, Nakatsuka N, Lazaridis I, Skoglund P, Mallick S, Lamnidis TC, Rohland N, Nägele K, Adamski N, Bertolini E, Broomandkhoshbacht N, Cooper A, Culleton BJ, Ferraz T, Ferry M, Furtwängler A, Haak W, Harkins K, Harper TK, Hünemeier T, Lawson AM, Llamas B, Michel M, Nelson E, Oppenheimer J, Patterson N, Schiffels S, Sedig J, Stewardson K, Talamo S, Wang CC, Hublin JJ, Hubbe M, Harvati K, Nuevo Delaunay A, Beier J, Francken M, Kaulicke P, Reyes-Centeno H, Rademaker K, Trask WR, Robinson M, Gutierrez SM, Prufer KM, Salazar-García DC, Chim EN, Müller Plumm Gomes L, Alves ML, Liryo A, Inglez M, Oliveira RE, Bernardo DV, Barioni A, Wesolowski V, Scheifler NA, Rivera MA, Plens CR, Messineo PG, Figuti L, Corach D, Scabuzzo C, Eggers S, DeBlasis P, Reindel M, Méndez C, Politis G, Tomasto-Cagigao E, Kennett DJ, Strauss A, Fehren-Schmitz L, Krause J, Reich D. Reconstructing the Deep Population History of Central and South America. Cell 2018; 175:1185-1197.e22. [PMID: 30415837 PMCID: PMC6327247 DOI: 10.1016/j.cell.2018.10.027] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/15/2018] [Accepted: 10/11/2018] [Indexed: 01/16/2023]
Abstract
We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA.
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Francis Crick Institute, London NW1 1AT, UK
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia 27100, Italy
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brendan J Culleton
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kelly Harkins
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology and Ethnology, Xiamen University, Xiamen 361005, China
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Mark Hubbe
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA; Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Región de Antofagasta, Antofagasta CP 1410000, Chile
| | - Katerina Harvati
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | | | - Judith Beier
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Michael Francken
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Peter Kaulicke
- Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru
| | - Hugo Reyes-Centeno
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | - Willa R Trask
- Central Identification Laboratory, Defense POW/MIA Accounting Agency, Department of Defense, Joint Base Pearl Harbor-Hickam, HI 96853, USA
| | - Mark Robinson
- Department of Archaeology, Exeter University, Exeter EX4 4QJ, UK
| | | | - Keith M Prufer
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87131, USA
| | - Domingo C Salazar-García
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany; Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Eliane N Chim
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | | | - Marcony L Alves
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Andersen Liryo
- Museu Nacional da Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil
| | - Mariana Inglez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Rodrigo E Oliveira
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Departamento de Estomatologia, Faculdade de Odontologia, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Danilo V Bernardo
- Laboratório de Estudos em Antropologia Biológica, Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande, Rio Grande do Sul 96203-900, Brazil
| | - Alberto Barioni
- Faculdade de Filosofia Ciencias e Letras, Universidade de São Paulo, São Paulo 05508-080, Brazil
| | - Veronica Wesolowski
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Nahuel A Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Mario A Rivera
- Comité Chileno del Consejo Internacional de Monumentos y Sitios, Santiago 8320000, Chile; Field Museum of Natural History, Chicago, IL 60605, USA; Universidad de Magallanes, Punta Arenas 6200000, Chile
| | - Claudia R Plens
- Escola De Filosofia, Letras E Ciências Humanas, Universidade Federal de São Paulo, São Paulo 07252-312, Brazil
| | - Pablo G Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Levy Figuti
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires y CONICET, Ciudad Autonoma de Buenos Aires, Junin 954, Argentina
| | - Clara Scabuzzo
- CONICET-División Arqueología, Facultad de Ciencias Naturales y Museo, La Plata 1900, Argentina
| | - Sabine Eggers
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Naturhistorisches Museum Wien, Vienna 1010, Austria
| | - Paulo DeBlasis
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Markus Reindel
- German Archaeological Institute, Commission for Archaeology of Non-European Cultures, Bonn 53173, Germany
| | - César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | | | - Douglas J Kennett
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - André Strauss
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil; Centro de Arqueologia Annette Laming Emperaire, Miguel A Salomão, Lagoa Santa, MG 33400-000, Brazil
| | - 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
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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23
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Jacovas VC, Couto-Silva CM, Nunes K, Lemes RB, de Oliveira MZ, Salzano FM, Bortolini MC, Hünemeier T. Selection scan reveals three new loci related to high altitude adaptation in Native Andeans. Sci Rep 2018; 8:12733. [PMID: 30143708 PMCID: PMC6109162 DOI: 10.1038/s41598-018-31100-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
The Andean Altiplano has been occupied continuously since the late Pleistocene, ~12,000 years ago, which places the Andean natives as one of the most ancient populations living at high altitudes. In the present study, we analyzed genomic data from Native Americans living a long-time at Andean high altitude and at Amazonia and Mesoamerica lowland areas. We have identified three new candidate genes - SP100, DUOX2 and CLC - with evidence of positive selection for altitude adaptation in Andeans. These genes are involved in the TP53 pathway and are related to physiological routes important for high-altitude hypoxia response, such as those linked to increased angiogenesis, skeletal muscle adaptations, and immune functions at the fetus-maternal interface. Our results, combined with other studies, showed that Andeans have adapted to the Altiplano in different ways and using distinct molecular strategies as compared to those of other natives living at high altitudes.
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Affiliation(s)
- Vanessa C Jacovas
- Genetics Departament, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cainã M Couto-Silva
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Renan B Lemes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | | | - Francisco M Salzano
- Genetics Departament, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Genetics Departament, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil.
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24
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Ferraz T, Rossoni DM, Althoff SL, Pissinatti A, Paixão-Cortês VR, Bortolini MC, González-José R, Marroig G, Salzano FM, Gonçalves GL, Hünemeier T. Contrasting patterns of RUNX2 repeat variations are associated with palate shape in phyllostomid bats and New World primates. Sci Rep 2018; 8:7867. [PMID: 29777172 PMCID: PMC5959863 DOI: 10.1038/s41598-018-26225-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
Establishing the genetic basis that underlies craniofacial variability in natural populations is one of the main topics of evolutionary and developmental studies. One of the genes associated with mammal craniofacial variability is RUNX2, and in the present study we investigated the association between craniofacial length and width and RUNX2 across New World bats (Phyllostomidae) and primates (Catarrhini and Platyrrhini). Our results showed contrasting patterns of association between the glutamate/alanine ratios (Q/A ratio) and palate shape in these highly diverse groups. In phyllostomid bats, we found an association between shorter/broader faces and increase of the Q/A ratio. In New World monkeys (NWM) there was a positive correlation of increasing Q/A ratios to more elongated faces. Our findings reinforced the role of the Q/A ratio as a flexible genetic mechanism that would rapidly change the time of skull ossification throughout development. However, we propose a scenario in which the influence of this genetic adjustment system is indirect. The Q/A ratio would not lead to a specific phenotype, but throughout the history of a lineage, would act along with evolutionary constraints, as well as other genes, as a facilitator for adaptive morphological changes.
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Affiliation(s)
- Tiago Ferraz
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Daniela M Rossoni
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | | | | | | | - Maria Cátira Bortolini
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Rolando González-José
- Patagonian Institute of Social and Human Sciences, National Council for Scientific and Technological Research-CONICET, U9120ACD, Puerto Madryn, Argentina
| | - Gabriel Marroig
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Francisco M Salzano
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Gislene L Gonçalves
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.,Department of Environmental Resources, Faculty of Agrarian Sciences, University of Tarapacá, Arica, Chile
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil.
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25
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Quinto-Sánchez M, Muñoz-Muñoz F, Gomez-Valdes J, Cintas C, Navarro P, Cerqueira CCSD, Paschetta C, de Azevedo S, Ramallo V, Acuña-Alonzo V, Adhikari K, Fuentes-Guajardo M, Hünemeier T, Everardo P, de Avila F, Jaramillo C, Arias W, Gallo C, Poletti G, Bedoya G, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Rosique J, Ruiz-Linares A, Gonzalez-Jose R. Developmental pathways inferred from modularity, morphological integration and fluctuating asymmetry patterns in the human face. Sci Rep 2018; 8:963. [PMID: 29343858 PMCID: PMC5772513 DOI: 10.1038/s41598-018-19324-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/15/2017] [Indexed: 01/25/2023] Open
Abstract
Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds. To do so, 4104 individuals were analyzed using 3D photogrammetry reconstructions and a set of 34 facial landmarks placed on each individual. We found a pattern of modularity and integration that is conserved across sub-samples differing in their genomic ancestry background. Specifically, a signal of modularity based on functional demands and organization of the face is regularly observed across the whole sample. Our results shed more light on previous evidence obtained from Genome Wide Association Studies performed on the same samples, indicating the action of different genomic regions contributing to the expression of the nose and mouth facial phenotypes. Our results also indicate that large samples including phenotypic and genomic metadata enable a better understanding of the developmental and genetic architecture of craniofacial phenotypes.
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Affiliation(s)
- Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Francesc Muñoz-Muñoz
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Avinguda de l'Eix Central, Edifici C, E-08193, Bellaterra (Cerdanyola del Vallès), Spain
| | - Jorge Gomez-Valdes
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
| | - Celia Cintas
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Pablo Navarro
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Caio Cesar Silva de Cerqueira
- Superintendência da Polícia Técnico-Científica do Estado de São Paulo. Equipe de Perícias Criminalísticas de Ourinhos, São Paulo, Brazil
| | - Carolina Paschetta
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
- Licenciatura en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Paola Everardo
- Licenciatura en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
- Posgrado en Antropología, Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco de Avila
- Licenciatura en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
| | | | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giovani Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Francisco Rothhammer
- Facultad Instituto de Alta Investigación Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
| | - Javier Rosique
- Departamento de Antropología, Facultad de Ciencias Sociales y Humanas. Universidad de Antioquia, Medellín, Colombia
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
- MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina.
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Quinto Sánchez ME, Cintas C, Ramallo V, Silva de Cerqueira CC, Gomez-Valdés J, Acuña-Alonzo V, Adhikari K, Everardo P, De Avila F, Jaramillo C, Arias W, Fuentes M, Hünemeier T, Gallo C, Poletti G, Rosique J, Schuler-Faccini L, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Ruiz-Linares A, Gonzalez-José R. Relación entre tratamiento hormonal, cirugía-ortodoncia maxilofacial, traumatismos y malformaciones craneofaciales y la asimetría fluctuante. Rev Arg Antrop Biol 2017. [DOI: 10.17139/raab.2018.0020.01.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
En este trabajo se evalúa la relación entre la asimetría fluctuante facial (AFF) y los tratamientos hormonales, cirugías maxilofaciales, ortodoncia, traumatismos y malformaciones. En el marco del proyecto CANDELA, se tomaron cinco fotografías faciales de 3162 voluntarios entre los 18 y 85 años. Por fotogrametría se colocaron 34 landmarks o puntos en 3D y mediante el método Procrustes ANOVA se obtuvieron valores individuales de asimetría fluctuante facial. Se realizó una prueba de ANOVA de una vía y la prueba de Welch y Levene para conocer las diferencias entre media y varianza de los valores de asimetría facial y las variables respuesta. También, se caracterizó la variación morfológica del componente asimétrico de la forma facial mediante técnicas multivariadas sobre los grupos que resultaran diferentes significativamente. Las mujeres que reportaron haber recibido algún tipo de tratamiento hormonal mostraron mayores valores de asimetría fluctuante facial respecto al grupo sin tratamiento. Esta asociación se mantuvo una vez removido el efecto de la ancestría genética y sin interactuar con el resto de variables incluidas en el análisis. Los cambios morfológicos asociados a este factor se concentran en el mentón, maxilar labio inferior, región perifrontal, región nasal y orejas. Algunos trabajos anteriores dieron cuenta de la posible relación entre la asimetría facial y los niveles de hormonas, pero no hay estudios que sustenten la relación causal o directa entre la asociación aquí planteada. El presente trabajo es una evidencia más de la asociación entre el consumo de hormonas y modificaciones de caracteres faciales en para poblaciones urbanas mestizas latinoamericanas.
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Masotti C, Brito L, Nica A, Ludwig K, Nunes K, Savastano C, Malcher C, Ferreira S, Kobayashi G, Bueno D, Alonso N, Franco D, Rojas-Martinez A, dos Santos S, Galante P, Meyer D, Hünemeier T, Mangold E, Dermitzakis E, Passos-Bueno M. MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach. J Dent Res 2017; 97:33-40. [DOI: 10.1177/0022034517735805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.
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Affiliation(s)
- C. Masotti
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
- Molecular Oncology Center, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - L.A. Brito
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - A.C. Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - K.U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - K. Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - C.P. Savastano
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - C. Malcher
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - S.G. Ferreira
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - G.S. Kobayashi
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - D.F. Bueno
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - N. Alonso
- Department of Plastic Surgery, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - D. Franco
- Department of Plastic Surgery, Hospital Clementino Braga Filho, Federal University of Rio de Janeiro Medical School, Rio de Janeiro, RJ, Brazil
| | - A. Rojas-Martinez
- Department of Biochemistry and Molecular Medicine, School of Medicine, and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - S.E. dos Santos
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - P.A. Galante
- Molecular Oncology Center, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - D. Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - T. Hünemeier
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - E. Mangold
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - E.T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - M.R. Passos-Bueno
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
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28
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Bampi GB, Bisso-Machado R, Hünemeier T, Gheno TC, Furtado GV, Veliz-Otani D, Cornejo-Olivas M, Mazzeti P, Bortolini MC, Jardim LB, Saraiva-Pereira ML. Haplotype Study in SCA10 Families Provides Further Evidence for a Common Ancestral Origin of the Mutation. Neuromolecular Med 2017; 19:501-509. [PMID: 28905220 DOI: 10.1007/s12017-017-8464-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 08/29/2017] [Indexed: 12/11/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder characterized by progressive cerebellar ataxia and epilepsy. The disease is caused by a pentanucleotide ATTCT expansion in intron 9 of the ATXN10 gene on chromosome 22q13.3. SCA10 has shown a geographical distribution throughout America with a likely degree of Amerindian ancestry from different countries so far. Currently available data suggest that SCA10 mutation might have spread out early during the peopling of the Americas. However, the ancestral origin of SCA10 mutation remains under speculation. Samples of SCA10 patients from two Latin American countries were analysed, being 16 families from Brazil (29 patients) and 21 families from Peru (27 patients) as well as 49 healthy individuals from Indigenous Quechua population and 51 healthy Brazilian individuals. Four polymorphic markers spanning a region of 5.2 cM harbouring the ATTCT expansion were used to define the haplotypes, which were genotyped by different approaches. Our data have shown that 19-CGGC-14 shared haplotype was found in 47% of Brazilian and in 63% of Peruvian families. Frequencies from both groups are not statistically different from Quechua controls (57%), but they are statistically different from Brazilian controls (12%) (p < 0.001). The most frequent expanded haplotype in Quechuas, 19-15-CGGC-14-10, is found in 50% of Brazilian and in 65% of Peruvian patients with SCA10. These findings bring valuable evidence that ATTCT expansion may have arisen in a Native American chromosome.
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Affiliation(s)
- Giovana B Bampi
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350, Porto Alegre, Rio Grande do Sul, 90035-903, Brazil.,Laboratory of Genetics Identification - Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Rafael Bisso-Machado
- Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tailise C Gheno
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350, Porto Alegre, Rio Grande do Sul, 90035-903, Brazil.,Laboratory of Genetics Identification - Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gabriel V Furtado
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350, Porto Alegre, Rio Grande do Sul, 90035-903, Brazil.,Laboratory of Genetics Identification - Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Diego Veliz-Otani
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Pillar Mazzeti
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | | | - Laura B Jardim
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350, Porto Alegre, Rio Grande do Sul, 90035-903, Brazil.,Laboratory of Genetics Identification - Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Luiza Saraiva-Pereira
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil. .,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350, Porto Alegre, Rio Grande do Sul, 90035-903, Brazil. .,Laboratory of Genetics Identification - Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil. .,Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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29
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Reales G, Rovaris DL, Jacovas VC, Hünemeier T, Sandoval JR, Salazar-Granara A, Demarchi DA, Tarazona-Santos E, Felkl AB, Serafini MA, Salzano FM, Bisso-Machado R, Comas D, Paixão-Côrtes VR, Bortolini MC. A tale of agriculturalists and hunter-gatherers: Exploring the thrifty genotype hypothesis in native South Americans. Am J Phys Anthropol 2017; 163:591-601. [PMID: 28464262 DOI: 10.1002/ajpa.23233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/06/2017] [Accepted: 04/06/2017] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations. MATERIALS AND METHODS 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed. RESULTS We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (FCT ) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals. DISCUSSION A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations.
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Affiliation(s)
- Guillermo Reales
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Diego L Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Vanessa C Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martin de Porres, Lima, Peru
| | | | - Darío A Demarchi
- Instituto de Antropología de Córdoba, CONICET, Universidad Nacional de Córdoba, Argentina
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Aline B Felkl
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Michele A Serafini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rafael Bisso-Machado
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de La Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Vanessa R Paixão-Côrtes
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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30
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Quinto-Sánchez M, Cintas C, Silva de Cerqueira CC, Ramallo V, Acuña-Alonzo V, Adhikari K, Castillo L, Gomez-Valdés J, Everardo P, De Avila F, Hünemeier T, Jaramillo C, Arias W, Fuentes M, Gallo C, Poletti G, Schuler-Faccini L, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Rosique J, Ruiz-Linares A, González-José R. Correction: Socioeconomic Status Is Not Related with Facial Fluctuating Asymmetry: Evidence from Latin-American Populations. PLoS One 2017; 12:e0172418. [PMID: 28192507 PMCID: PMC5305118 DOI: 10.1371/journal.pone.0172418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0169287.].
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31
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Quinto-Sánchez M, Cintas C, Silva de Cerqueira CC, Ramallo V, Acuña-Alonzo V, Adhikari K, Castillo L, Gomez-Valdés J, Everardo P, De Avila F, Hünemeier T, Jaramillo C, Arias W, Fuentes M, Gallo C, Poletti G, Schuler-Faccini L, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Rosique J, Ruiz-Linares A, González-José R. Socioeconomic Status Is Not Related with Facial Fluctuating Asymmetry: Evidence from Latin-American Populations. PLoS One 2017; 12:e0169287. [PMID: 28060876 PMCID: PMC5218465 DOI: 10.1371/journal.pone.0169287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/14/2016] [Indexed: 11/18/2022] Open
Abstract
The expression of facial asymmetries has been recurrently related with poverty and/or disadvantaged socioeconomic status. Departing from the developmental instability theory, previous approaches attempted to test the statistical relationship between the stress experienced by individuals grown in poor conditions and an increase in facial and corporal asymmetry. Here we aim to further evaluate such hypothesis on a large sample of admixed Latin Americans individuals by exploring if low socioeconomic status individuals tend to exhibit greater facial fluctuating asymmetry values. To do so, we implement Procrustes analysis of variance and Hierarchical Linear Modelling (HLM) to estimate potential associations between facial fluctuating asymmetry values and socioeconomic status. We report significant relationships between facial fluctuating asymmetry values and age, sex, and genetic ancestry, while socioeconomic status failed to exhibit any strong statistical relationship with facial asymmetry. These results are persistent after the effect of heterozygosity (a proxy for genetic ancestry) is controlled in the model. Our results indicate that, at least on the studied sample, there is no relationship between socioeconomic stress (as intended as low socioeconomic status) and facial asymmetries.
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Affiliation(s)
- Mirsha Quinto-Sánchez
- Grupo de Investigación en Biología Evolutiva Humana, Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET. Puerto Madryn, Chubut, Argentina
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Celia Cintas
- Grupo de Investigación en Biología Evolutiva Humana, Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET. Puerto Madryn, Chubut, Argentina
| | - Caio Cesar Silva de Cerqueira
- Grupo de Investigación en Biología Evolutiva Humana, Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET. Puerto Madryn, Chubut, Argentina
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- Superintendência da Polícia Técnico-Científica do Estado de São Paulo. Equipe de Perícias Criminalísticas de Ourinhos, São Paulo, Brazil
| | - Virginia Ramallo
- Grupo de Investigación en Biología Evolutiva Humana, Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET. Puerto Madryn, Chubut, Argentina
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
- Escuela Nacional de Antropología e Historia. Instituto Nacional de Antropología e Historia, Ciudad de México, México
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
| | - Lucía Castillo
- Grupo de Investigación en Biología Evolutiva Humana, Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET. Puerto Madryn, Chubut, Argentina
| | - Jorge Gomez-Valdés
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, México
| | - Paola Everardo
- Escuela Nacional de Antropología e Historia. Instituto Nacional de Antropología e Historia, Ciudad de México, México
| | - Francisco De Avila
- Escuela Nacional de Antropología e Historia. Instituto Nacional de Antropología e Historia, Ciudad de México, México
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo
| | | | | | - Macarena Fuentes
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
- Departamento de Técnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovani Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | | | | | - Javier Rosique
- Departamento de Antropología. Facultad de Ciencias Sociales y Humanas. Universidad de Antioquia, Medellín, Colombia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
- MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Rolando González-José
- Grupo de Investigación en Biología Evolutiva Humana, Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET. Puerto Madryn, Chubut, Argentina
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32
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Bisso-Machado R, Ramallo V, Paixão-Côrtes VR, Acuña-Alonzo V, Demarchi DA, Sandoval JRS, Granara AAS, Salzano FM, Hünemeier T, Bortolini MC. NAT2 gene diversity and its evolutionary trajectory in the Americas. Pharmacogenomics J 2015; 16:559-565. [DOI: 10.1038/tpj.2015.72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/21/2015] [Accepted: 09/08/2015] [Indexed: 01/26/2023]
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Skoglund P, Mallick S, Bortolini MC, Chennagiri N, Hünemeier T, Petzl-Erler ML, Salzano FM, Patterson N, Reich D. Genetic evidence for two founding populations of the Americas. Nature 2015. [PMID: 26196601 PMCID: PMC4982469 DOI: 10.1038/nature14895] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genetic studies have been consistent with a single common origin of Native American groups from Central and South America1-4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island southeast Asia)5-8. Here we analyze genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent or at all in present-day Northern and Central Americans or a ~12,600 year old Clovis genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
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Affiliation(s)
- Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Niru Chennagiri
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, 05508-090, SP, Brazil
| | | | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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de Azevedo S, Bortolini MC, Bonatto SL, Hünemeier T, Santos FR, González-José R. Ancient remains and the first peopling of the Americas: Reassessing the Hoyo Negro skull. Am J Phys Anthropol 2015; 158:514-21. [PMID: 26174009 DOI: 10.1002/ajpa.22801] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE A noticeably well-preserved ∼12.500 years-old skeleton from the Hoyo Negro cave, Yucatán, México, was recently reported, along with its archaeological, genetic and skeletal characteristics. Based exclusively on an anatomical description of the skull (HN5/48), Chatters and colleagues stated that this specimen can be assigned to a set of ancient remains that differ from modern Native Americans, the so called "Paleoamericans". Here, we aim to further explore the morphological affinities of this specimen with a set of comparative cranial samples covering ancient and modern periods from Asia and the Americas. METHODS Images published in the original article were analyzed using geometric morphometrics methods. Shape variables were used to perform Principal Component and Discriminant analysis against the reference samples. RESULTS Even thought the Principal Component Analysis suggests that the Hoyo Negro skull falls in a subregion of the morphospace occupied by both "Paleoamericans" and some modern Native Americans, the Discriminant analyses suggest greater affinity with a modern Native American sample. DISCUSSION These results reinforce the idea that the original population that first occupied the New World carried high levels of within-group variation, which we have suggested previously on a synthetic model for the settlement of the Americas. Our results also highlight the importance of developing formal classificatory test before deriving settlement hypothesis purely based on macroscopic descriptions.
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Affiliation(s)
- Soledad de Azevedo
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Bvd. Brown 2915, U9120ACD, Puerto Madryn, Argentina
| | - Maria C Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Sandro L Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul. Av. Ipiranga 6681, 90610-001, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Fabrício R Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-910, Belo Horizonte, MG, Brazil
| | - Rolando González-José
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Bvd. Brown 2915, U9120ACD, Puerto Madryn, Argentina
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Boquett J, Schüler-Faccini L, Jobim LF, Jobim M, Fagundes NJR, Hünemeier T. Self-assessment of color categories and its relationship with HLA profiling in Brazilian bone marrow donors. Biol Blood Marrow Transplant 2015; 21:1140-4. [PMID: 25704208 DOI: 10.1016/j.bbmt.2015.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
Abstract
The Brazil Ministry of Health maintains a Registry of Bone Marrow Donors that corresponds to approximately 12% of the Bone Marrow Donors Worldwide registry. This registry contains information on ethnicity (by self-assessment of color) and HLA-A, -B, and -DRB1 type. The self-assessment of color tool has been extensively used for admixed population characterization. In this context, Brazil represents a highly admixed population, resulting from 5 centuries of colonization and interbreeding, mainly, but not exclusively, among Native Americans, Europeans, and Africans. Here we evaluated self-assessed skin color and HLA genetic information from 71,291 bone marrow donors of southern Brazil to verify how likely is the HLA profiling correspondence within and between self-assessed color groups. We found that HLA itself was a better ancestry indicator than was self-assessed color. Therefore, self-assessment of color in highly admixed populations, such as that of Brazil, is not indicative of higher correspondence in the HLA profiles within skin color groups.
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Affiliation(s)
- Juliano Boquett
- Instituto Nacional de Genetica Medica Populacional, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schüler-Faccini
- Instituto Nacional de Genetica Medica Populacional, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luis Fernando Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Mariana Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Nelson Jurandi Rosa Fagundes
- Instituto Nacional de Genetica Medica Populacional, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tábita Hünemeier
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Quinto-Sánchez M, Adhikari K, Acuña-Alonzo V, Cintas C, Silva de Cerqueira CC, Ramallo V, Castillo L, Farrera A, Jaramillo C, Arias W, Fuentes M, Everardo P, de Avila F, Gomez-Valdés J, Hünemeier T, Gibbon S, Gallo C, Poletti G, Rosique J, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Ruiz-Linares A, González-José R. Facial asymmetry and genetic ancestry in Latin American admixed populations. Am J Phys Anthropol 2015; 157:58-70. [DOI: 10.1002/ajpa.22688] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 12/03/2014] [Accepted: 12/11/2014] [Indexed: 11/08/2022]
Affiliation(s)
| | - Kaustubh Adhikari
- Department of Genetics; Evolution and Environment; and UCL Genetics Institute; University College London; London UK
| | - Victor Acuña-Alonzo
- Department of Genetics; Evolution and Environment; and UCL Genetics Institute; University College London; London UK
- Escuela Nacional de Antropología e Historia; Instituto Nacional de Antropología e Historia; Distrito Federal Mexico
| | - Celia Cintas
- Centro Nacional Patagónico, CONICET; Puerto Madryn Argentina
| | | | | | - Lucia Castillo
- Centro Nacional Patagónico, CONICET; Puerto Madryn Argentina
| | - Arodi Farrera
- Posgrado en Antropología; Facultad de Filosofía y Letras; UNAM; México City Mexico
| | - Claudia Jaramillo
- Departamento de Antropología; Facultad de Ciencias Humanas y Sociales; Universidad de Antioquia; Medellín Colombia
| | - Williams Arias
- Departamento de Antropología; Facultad de Ciencias Humanas y Sociales; Universidad de Antioquia; Medellín Colombia
| | - Macarena Fuentes
- Instituto de Alta Investigación Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto; Arica Chile
| | - Paola Everardo
- Escuela Nacional de Antropología e Historia; Instituto Nacional de Antropología e Historia; Distrito Federal Mexico
| | - Francisco de Avila
- Escuela Nacional de Antropología e Historia; Instituto Nacional de Antropología e Historia; Distrito Federal Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética; Instituto de Biociências, Universidade Federal do Rio Grande do Sul; Porto Alegre Brasil
| | - Shara Gibbon
- Department of Anthropology; University College London; London UK
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo; Facultad de Ciencias y Filosofía; Universidad Peruana Cayetano Heredia; Lima Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo; Facultad de Ciencias y Filosofía; Universidad Peruana Cayetano Heredia; Lima Perú
| | - Javier Rosique
- Departamento de Antropología; Facultad de Ciencias Humanas y Sociales; Universidad de Antioquia; Medellín Colombia
| | - Maria Cátira Bortolini
- Departamento de Genética; Instituto de Biociências, Universidade Federal do Rio Grande do Sul; Porto Alegre Brasil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud; Facultad de Química; UNAM-Instituto Nacional de Medicina Genómica
| | - Francisco Rothhammer
- Instituto de Alta Investigación Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto; Arica Chile
| | - Gabriel Bedoya
- Departamento de Antropología; Facultad de Ciencias Humanas y Sociales; Universidad de Antioquia; Medellín Colombia
| | - Andres Ruiz-Linares
- Department of Genetics; Evolution and Environment; and UCL Genetics Institute; University College London; London UK
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de Cerqueira CCS, Hünemeier T, Gomez-Valdés J, Ramallo V, Volasko-Krause CD, Barbosa AAL, Vargas-Pinilla P, Dornelles RC, Longo D, Rothhammer F, Bedoya G, Canizales-Quinteros S, Acuña-Alonzo V, Gallo C, Poletti G, González-José R, Salzano FM, Callegari-Jacques SM, Schuler-Faccini L, Ruiz-Linares A, Cátira Bortolini M. Implications of the admixture process in skin color molecular assessment. PLoS One 2014; 9:e96886. [PMID: 24809478 PMCID: PMC4014568 DOI: 10.1371/journal.pone.0096886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/12/2014] [Indexed: 12/19/2022] Open
Abstract
The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice.
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Affiliation(s)
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jorge Gomez-Valdés
- Laboratorio de Antropología Física, Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Virgínia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Danaê Longo
- Instituto Federal de Educação, Ciência e Tecnologia Farroupilha, Alegrete, Brazil
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Facultad de Medicina, Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
| | | | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Carla Gallo
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Francisco Mauro Salzano
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sídia Maria Callegari-Jacques
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- INAGEMP – Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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Fernandes-Lima ZS, Paixão-Côrtes VR, Andrade AKMD, Fernandes AS, Coronado BNL, Monte Filho HP, Santos MJ, Omena Filho RLD, Biondi FC, Ruiz-Linares A, Ramallo V, Hünemeier T, Schuler-Faccini L, Monlleó IL. Ocular and craniofacial phenotypes in a large Brazilian family with congenital aniridia. Clin Genet 2014; 87:68-73. [PMID: 24266705 DOI: 10.1111/cge.12329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/28/2013] [Accepted: 11/22/2013] [Indexed: 11/27/2022]
Abstract
Congenital aniridia is a rare genetic disorder characterized by varying degrees of iris hypoplasia that are associated with additional ocular abnormalities. More than 90% of the causal mutations identified are found in the PAX6 gene, a transcription factor of critical importance in the process of neurogenesis and ocular development. Here, we investigate clinical, molecular, and craniofacial features of a large Brazilian family with congenital aniridia. Among the 56 eyes evaluated, phenotype variation encompassed bilateral total aniridia to mild iris defects with extensive variation between eyes of the same individual. PAX6 molecular screening indicated a heterozygous splice mutation (c.141 + 1G>A). Thus, we hypothesize that this splicing event may cause variation in the expression of the wild-type transcript, which may lead to the observed variation in phenotype. Affected individuals were more brachycephalic, even though their face height and cephalic circumference were not significantly different when compared to those of non-affected relatives. From this, we infer that the head shape of affected subjects may also be a result of the PAX6 splice-site mutation. Our data summarize the clinical variability associated with the ocular phenotype in a large family with aniridia, and help shed light on the role of PAX6 in neurocranial development.
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Affiliation(s)
- Z S Fernandes-Lima
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; gINAGEMP - Instituto Nacional de Genética Médica Populacional, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Hünemeier T, Gómez-Valdés J, De Azevedo S, Quinto-Sánchez M, Passaglia L, Salzano FM, Sánchez-Mejorada G, Alonzo VA, Martínez-Abadías N, Bortolini MC, González-José R. FGFR1 signaling is associated with the magnitude of morphological integration in human head shape. Am J Hum Biol 2013; 26:164-75. [DOI: 10.1002/ajhb.22496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 11/24/2013] [Accepted: 11/26/2013] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tábita Hünemeier
- Departamento de Genética; Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Caixa Postal 15053; 91501-970 Porto Alegre RS Brazil
| | - Jorge Gómez-Valdés
- Departamento de Anatomía; Facultad de Medicina; Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria; 04510 Distrito Federal México
| | - Soledad De Azevedo
- Centro Nacional Patagónico-CONICET; Bvd. Brown 2915, U9120ACD Puerto Madryn Argentina
| | - Mirsha Quinto-Sánchez
- Centro Nacional Patagónico-CONICET; Bvd. Brown 2915, U9120ACD Puerto Madryn Argentina
| | - Luciane Passaglia
- Departamento de Genética; Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Caixa Postal 15053; 91501-970 Porto Alegre RS Brazil
| | - Francisco M. Salzano
- Departamento de Genética; Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Caixa Postal 15053; 91501-970 Porto Alegre RS Brazil
| | - Gabriela Sánchez-Mejorada
- Departamento de Anatomía; Facultad de Medicina; Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria; 04510 Distrito Federal México
| | | | - Neus Martínez-Abadías
- EMBL-CRG Systems Biology Research Unit; Center for Genomic Regulation (CRG), Dr. Aiguader 88 08003 Barcelona Spain
| | - Maria-Cátira Bortolini
- Departamento de Genética; Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Caixa Postal 15053; 91501-970 Porto Alegre RS Brazil
| | - Rolando González-José
- Centro Nacional Patagónico-CONICET; Bvd. Brown 2915, U9120ACD Puerto Madryn Argentina
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Paixão-Côrtes VR, Viscardi LH, Salzano FM, Cátira Bortolini M, Hünemeier T. The cognitive ability of extinct hominins: bringing down the hierarchy using genomic evidences. Am J Hum Biol 2013; 25:702-5. [PMID: 23907779 DOI: 10.1002/ajhb.22426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 06/03/2013] [Accepted: 06/11/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The availability of the full genomes of Homo sapiens, Homo neanderthalensis, and Denisovans, as well as modern bioinformatic tools, are opening new possibilities for the understanding of the differences and similarities present in these taxa. METHODS We searched for cognitive genes, examined their status in the genomes of these three entities. All substitutions present among them were retrieved. RESULTS We found 93 nonsynonymous substitutions in 51 cognitive genes, in which the derived allele was present in archaic and modern humans and the ancestral allele in other nonhuman primates. CONCLUSIONS The general picture obtained is of similarity in cognitive genes between extinct and extant humans.
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Affiliation(s)
- Vanessa R Paixão-Côrtes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Bisso-Machado R, Ramallo V, Tarazona-Santos E, Salzano FM, Bortolini MC, Hünemeier T. Brief communication: 5-HTTLPR genetic diversity and mode of subsistence in Native Americans. Am J Phys Anthropol 2013; 151:492-4. [PMID: 23686378 DOI: 10.1002/ajpa.22286] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/04/2013] [Indexed: 11/10/2022]
Abstract
The relationship between the "individualism-collectivism" and the serotonin transporter functional polymorphism (5-HTTLPR), suggested in the previous reports, was tested in Native South Amerindian populations. A total of 170 individuals from 21 populations were genotyped for the 5-HTTLPR alleles. For comparative purposes, these populations were classified as individualistic (recent history of hunter-gathering) or collectivistic (agriculturalists). These two groups showed an almost identical S allele frequency (75 and 76%, respectively). The analysis of molecular variance showed no structural differences between them. Behavioral typologies like those suggested by JY Chiao and KD Blizinsky (Proc R Soc B 277 () 529-537) are always a simplification of complex phenomena and should be regarded with caution. In addition, classification of a whole nation in the individualist/collectivist dichotomy is controversial. The focus on modes of subsistence in preindustrial societies, as was tested here, may be a good alternative although the postulated association between the 5-HTTLPR S allele and the collectivist societies was not confirmed.
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Affiliation(s)
- Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Rio Grande do Sul, Brazil
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Amorim CEG, Bisso-Machado R, Ramallo V, Bortolini MC, Bonatto SL, Salzano FM, Hünemeier T. A bayesian approach to genome/linguistic relationships in native South Americans. PLoS One 2013; 8:e64099. [PMID: 23696865 PMCID: PMC3656118 DOI: 10.1371/journal.pone.0064099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/09/2013] [Indexed: 12/31/2022] Open
Abstract
The relationship between the evolution of genes and languages has been studied for over three decades. These studies rely on the assumption that languages, as many other cultural traits, evolve in a gene-like manner, accumulating heritable diversity through time and being subjected to evolutionary mechanisms of change. In the present work we used genetic data to evaluate South American linguistic classifications. We compared discordant models of language classifications to the current Native American genome-wide variation using realistic demographic models analyzed under an Approximate Bayesian Computation (ABC) framework. Data on 381 STRs spread along the autosomes were gathered from the literature for populations representing the five main South Amerindian linguistic groups: Andean, Arawakan, Chibchan-Paezan, Macro-Jê, and Tupí. The results indicated a higher posterior probability for the classification proposed by J.H. Greenberg in 1987, although L. Campbell's 1997 classification cannot be ruled out. Based on Greenberg's classification, it was possible to date the time of Tupí-Arawakan divergence (2.8 kya), and the time of emergence of the structure between present day major language groups in South America (3.1 kya).
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Affiliation(s)
- Carlos Eduardo Guerra Amorim
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro Luis Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
| | - Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Ramallo V, Bisso-Machado R, Bravi C, Coble MD, Salzano FM, Hünemeier T, Bortolini MC. Demographic expansions in South America: Enlightening a complex scenario with genetic and linguistic data. Am J Phys Anthropol 2013; 150:453-63. [DOI: 10.1002/ajpa.22219] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 12/05/2012] [Indexed: 11/10/2022]
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Gómez-Valdés J, Hünemeier T, Quinto-Sánchez M, Paschetta C, de Azevedo S, González MF, Martínez-Abadías N, Esparza M, Pucciarelli HM, Salzano FM, Bau CHD, Bortolini MC, González-José R. Lack of support for the association between facial shape and aggression: a reappraisal based on a worldwide population genetics perspective. PLoS One 2013; 8:e52317. [PMID: 23326328 PMCID: PMC3541377 DOI: 10.1371/journal.pone.0052317] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/16/2012] [Indexed: 12/03/2022] Open
Abstract
Antisocial and criminal behaviors are multifactorial traits whose interpretation relies on multiple disciplines. Since these interpretations may have social, moral and legal implications, a constant review of the evidence is necessary before any scientific claim is considered as truth. A recent study proposed that men with wider faces relative to facial height (fWHR) are more likely to develop unethical behaviour mediated by a psychological sense of power. This research was based on reports suggesting that sexual dimorphism and selection would be responsible for a correlation between fWHR and aggression. Here we show that 4,960 individuals from 94 modern human populations belonging to a vast array of genetic and cultural contexts do not display significant amounts of fWHR sexual dimorphism. Further analyses using populations with associated ethnographical records as well as samples of male prisoners of the Mexico City Federal Penitentiary condemned by crimes of variable level of inter-personal aggression (homicide, robbery, and minor faults) did not show significant evidence, suggesting that populations/individuals with higher levels of bellicosity, aggressive behaviour, or power-mediated behaviour display greater fWHR. Finally, a regression analysis of fWHR on individual's fitness showed no significant correlation between this facial trait and reproductive success. Overall, our results suggest that facial attributes are poor predictors of aggressive behaviour, or at least, that sexual selection was weak enough to leave a signal on patterns of between- and within-sex and population facial variation.
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Affiliation(s)
- Jorge Gómez-Valdés
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mirsha Quinto-Sánchez
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
| | - Carolina Paschetta
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
| | - Marina F. González
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
| | - Neus Martínez-Abadías
- EMBL-CRG Systems Biology Research Unit, Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mireia Esparza
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Héctor M. Pucciarelli
- División Antropología del Museo de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Claiton H. D. Bau
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rolando González-José
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
- * E-mail:
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Paixão-Côrtes VR, Viscardi LH, Salzano FM, Hünemeier T, Bortolini MC. Homo sapiens, Homo neanderthalensis and the Denisova specimen: New insights on their evolutionary histories using whole-genome comparisons. Genet Mol Biol 2012; 35:904-11. [PMID: 23413113 PMCID: PMC3571422 DOI: 10.1590/s1415-47572012000600003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
After a brief review of the most recent findings in the study of human evolution, an extensive comparison of the complete genomes of our nearest relative, the chimpanzee (Pan troglodytes), of extant Homo sapiens, archaic Homo neanderthalensis and the Denisova specimen were made. The focus was on non-synonymous mutations, which consequently had an impact on protein levels and these changes were classified according to degree of effect. A total of 10,447 non-synonymous substitutions were found in which the derived allele is fixed or nearly fixed in humans as compared to chimpanzee. Their most frequent location was on chromosome 21. Their presence was then searched in the two archaic genomes. Mutations in 381 genes would imply radical amino acid changes, with a fraction of these related to olfaction and other important physiological processes. Eight new alleles were identified in the Neanderthal and/or Denisova genetic pools. Four others, possibly affecting cognition, occured both in the sapiens and two other archaic genomes. The selective sweep that gave rise to Homo sapiens could, therefore, have initiated before the modern/archaic human divergence.
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Affiliation(s)
| | - Lucas Henrique Viscardi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Gómez-Valdés JA, Hünemeier T, Contini V, Acuña-Alonzo V, Macin G, Ballesteros-Romero M, Corral P, Ruiz-Linares A, Sánchez-Mejorada G, Canizales-Quinteros S, Martínez-Abadías N, Salzano FM, González-José R, Bortolini MC. Fibroblast growth factor receptor 1 (FGFR1) variants and craniofacial variation in Amerindians and related populations. Am J Hum Biol 2012; 25:12-9. [PMID: 23070782 DOI: 10.1002/ajhb.22331] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/17/2012] [Accepted: 09/10/2012] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The polymorphic site rs4647905 of the FGFR1 gene was previously associated with a decrease in cephalic index (CI). Here, we evaluate the relationships between genotypes and cephalometric measurements and indices in one Mexican Native and two mestizo Mexican populations using two haplotype-tag SNPs (rs4647905 and rs3213849) that represent >85% of the FGFR1 variability, plus three other SNPs (rs2293971, rs2304000, and rs930828) situated nearby. In addition, we genotyped five South American natives, two European, one African, and one Siberian populations to evaluate their intra and intercontinental population diversity. METHODS The five SNPs were tested and the craniofacial measurements and indices were collected using standardized procedures. Principal Component Analysis was used to verify individual/population comparisons. Associations were performed through the generalized linear model (GLM), coefficient of determination R(2) and linear regression tests. RESULTS We found a tendency for a decrease in CI in individuals homozygous for allele rs4647905C, regardless of the population to which they belong, though the effect is more pronounced in mestizo. When the GLM analyses were performed using the absolute/linear cephalometric measurements, a statistically significant association was found between four SNPs and head length in the mestizo population. CONCLUSIONS FGFR1 polymorphisms, especially rs4647905, can have an important role in the normal human skull variation, primarily due to their influence in head length, which would affect other cephalometric absolute/linear measures as well as indices like CI as a result of the pervasive nature of the morphological integration that characterizes the human skull.
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Affiliation(s)
- Jorge A Gómez-Valdés
- Laboratorio de Antropología Física, Departamento de Anatomía, Faculta de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
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Hünemeier T, Amorim CEG, Azevedo S, Contini V, Acuña-Alonzo V, Rothhammer F, Dugoujon JM, Mazières S, Barrantes R, Villarreal-Molina MT, Paixão-Côrtes VR, Salzano FM, Canizales-Quinteros S, Ruiz-Linares A, Bortolini MC. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution. PLoS One 2012; 7:e38862. [PMID: 22768049 PMCID: PMC3380856 DOI: 10.1371/journal.pone.0038862] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/12/2012] [Indexed: 12/26/2022] Open
Abstract
Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.
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Affiliation(s)
- Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Eduardo Guerra Amorim
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Soledad Azevedo
- Centro Nacional Patagónico, CONICET, U9120ACV, Puerto Madryn, Argentina
| | - Veronica Contini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Jean-Michel Dugoujon
- Laboratoire d′Anthropologie Moléculaire et d′Imagerie de Synthèse, UMR 5288 CNRS, Université Paul Sabatier (Toulouse3), Toulouse, France
| | - Stephane Mazières
- Anthropologie Bio-culturelle, Droit, Ethique et Santé (ADES), UMR 7268, Aix-Marseille-Université/CNRS/EFS, Marseille, France
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Vanessa Rodrigues Paixão-Côrtes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Canizales-Quinteros
- Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andres Ruiz-Linares
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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Cerqueira CCS, Paixão-Côrtes VR, Zambra FMB, Salzano FM, Hünemeier T, Bortolini MC. Predicting Homo pigmentation phenotype through genomic data: from Neanderthal to James Watson. Am J Hum Biol 2012; 24:705-9. [PMID: 22411106 DOI: 10.1002/ajhb.22263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 01/25/2012] [Accepted: 02/07/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Human pigmentation is regulated by several genes acting at different stages of melanin formation. Functional and association studies have elucidated the role of several of these genes in pigmentation phenotypes. Forensic and evolutionary studies can benefit from this knowledge. OBJECTIVES To evaluate the reliability of the prediction of pigmentation phenotypes using a large database of genetic markers in individuals with known phenotypes; and from this try to predict the pigmentation phenotype of prehistoric Homo specimens and of contemporary individuals whose visible phenotypes are not known. METHODS We compared predicted and observed phenotypic data through an analysis of 124 single nucleotide polymorphisms in 33 genic and seven intergenic regions of 30 subjects, five of them prehistoric, whose complete nuclear genomes are available in UCSC and PSU UCSC public databases. RESULTS For the molecular predicted versus observed phenotypes, the percentage of agreement was as follows: freckles: 91; skin: 64; hair: 44; eyes: 36; total: 59; while the molecular predicted versus probable (no visible observation available; inferences based on ethnic population characteristics) it was, respectively, 83, 60, 42, 67, and 63. The difference between two sets is statistically nonsignificant (P = 0.75). CONCLUSION To our knowledge, this is the first article to examine the effect of a large number of genetics markers for phenotype prediction. The approach could be useful for forensic applications, as well as for the determination of possible phenotypes of extinct prehistoric individuals.
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Affiliation(s)
- Caio C S Cerqueira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Hünemeier T, Ruiz-Linares A, Silveira Á, Paixão-Côrtes VR, Salzano FM, Bortolini MC. Brief communication: Population data support the adaptive nature of HACNS1 sapiens/neandertal-chimpanzee differences in a limb expression domain. Am J Phys Anthropol 2010; 143:478-81. [DOI: 10.1002/ajpa.21378] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Acuña-Alonzo V, Flores-Dorantes T, Kruit JK, Villarreal-Molina T, Arellano-Campos O, Hünemeier T, Moreno-Estrada A, Ortiz-López MG, Villamil-Ramírez H, León-Mimila P, Villalobos-Comparan M, Jacobo-Albavera L, Ramírez-Jiménez S, Sikora M, Zhang LH, Pape TD, Granados-Silvestre MDA, Montufar-Robles I, Tito-Alvarez AM, Zurita-Salinas C, Bustos-Arriaga J, Cedillo-Barrón L, Gómez-Trejo C, Barquera-Lozano R, Vieira-Filho JP, Granados J, Romero-Hidalgo S, Huertas-Vázquez A, González-Martín A, Gorostiza A, Bonatto SL, Rodríguez-Cruz M, Wang L, Tusié-Luna T, Aguilar-Salinas CA, Lisker R, Moises RS, Menjivar M, Salzano FM, Knowler WC, Bortolini MC, Hayden MR, Baier LJ, Canizales-Quinteros S. A functional ABCA1 gene variant is associated with low HDL-cholesterol levels and shows evidence of positive selection in Native Americans. Hum Mol Genet 2010; 19:2877-85. [PMID: 20418488 DOI: 10.1093/hmg/ddq173] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
It has been suggested that the higher susceptibility of Hispanics to metabolic disease is related to their Native American heritage. A frequent cholesterol transporter ABCA1 (ATP-binding cassette transporter A1) gene variant (R230C, rs9282541) apparently exclusive to Native American individuals was associated with low high-density lipoprotein cholesterol (HDL-C) levels, obesity and type 2 diabetes in Mexican Mestizos. We performed a more extensive analysis of this variant in 4405 Native Americans and 863 individuals from other ethnic groups to investigate genetic evidence of positive selection, to assess its functional effect in vitro and to explore associations with HDL-C levels and other metabolic traits. The C230 allele was found in 29 of 36 Native American groups, but not in European, Asian or African individuals. C230 was observed on a single haplotype, and C230-bearing chromosomes showed longer relative haplotype extension compared with other haplotypes in the Americas. Additionally, single-nucleotide polymorphism data from the Human Genome Diversity Panel Native American populations were enriched in significant integrated haplotype score values in the region upstream of the ABCA1 gene. Cells expressing the C230 allele showed a 27% cholesterol efflux reduction (P< 0.001), confirming this variant has a functional effect in vitro. Moreover, the C230 allele was associated with lower HDL-C levels (P = 1.77 x 10(-11)) and with higher body mass index (P = 0.0001) in the combined analysis of Native American populations. This is the first report of a common functional variant exclusive to Native American and descent populations, which is a major determinant of HDL-C levels and may have contributed to the adaptive evolution of Native American populations.
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Affiliation(s)
- Víctor Acuña-Alonzo
- Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Universidad Nacional Autónoma de México, Mexico City 14000, Mexico
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