1
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Yang G, Chen Y, Li Q, Benítez D, Ramírez LM, Fuentes-Guajardo M, Hanihara T, Scott GR, Acuña Alonzo V, Gonzalez Jose R, Bortolini MC, Poletti G, Gallo C, Rothhammer F, Rojas W, Zanolli C, Adhikari K, Ruiz-Linares A, Delgado M. Dental size variation in admixed Latin Americans: Effects of age, sex and genomic ancestry. PLoS One 2023; 18:e0285264. [PMID: 37141293 PMCID: PMC10159210 DOI: 10.1371/journal.pone.0285264] [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: 06/28/2022] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
Dental size variation in modern humans has been assessed from regional to worldwide scales, especially under microevolutionary and forensic contexts. Despite this, populations of mixed continental ancestry such as contemporary Latin Americans remain unexplored. In the present study we investigated a large Latin American sample from Colombia (N = 804) and obtained buccolingual and mesiodistal diameters and three indices for maxillary and mandibular teeth (except third molars). We evaluated the correlation between 28 dental measurements (and three indices) with age, sex and genomic ancestry (estimated using genome-wide SNP data). In addition, we explored correlation patterns between dental measurements and the biological affinities, based on these measurements, between two Latin American samples (Colombians and Mexicans) and three putative parental populations: Central and South Native Americans, western Europeans and western Africans through PCA and DFA. Our results indicate that Latin Americans have high dental size diversity, overlapping the variation exhibited by the parental populations. Several dental dimensions and indices have significant correlations with sex and age. Western Europeans presented closer biological affinities with Colombians, and the European genomic ancestry exhibited the highest correlations with tooth size. Correlations between tooth measurements reveal distinct dental modules, as well as a higher integration of postcanine dentition. The effects on dental size of age, sex and genomic ancestry is of relevance for forensic, biohistorical and microevolutionary studies in Latin Americans.
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Affiliation(s)
- Guangrui Yang
- 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
| | - Yingjie 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, Shanghai, China
| | - 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, Shanghai, China
| | - Daniel Benítez
- Department of Anthropology, University of Kentucky, Lexington, Kentucky, United States of America
| | | | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - G Richard Scott
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, United States of America
| | - Victor Acuña Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Rolando Gonzalez Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Maria Catira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | | | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Andres 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
- Laboratory of Biocultural Anthropology, Law, Ethics, and Health (Centre National de la Recherche Scientifique and Etablissement Français du Sang, UMR-7268), Aix-Marseille University, Marseille, France
| | - Miguel 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, Shanghai, 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
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2
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Gouveia MH, Borda V, Leal TP, Moreira RG, Bergen AW, Kehdy FSG, Alvim I, Aquino MM, Araujo GS, Araujo NM, Furlan V, Liboredo R, Machado M, Magalhaes WCS, Michelin LA, Rodrigues MR, Rodrigues-Soares F, Sant Anna HP, Santolalla ML, Scliar MO, Soares-Souza G, Zamudio R, Zolini C, Bortolini MC, Dean M, Gilman RH, Guio H, Rocha J, Pereira AC, Barreto ML, Horta BL, Lima-Costa MF, Mbulaiteye SM, Chanock SJ, Tishkoff SA, Yeager M, Tarazona-Santos E. Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas. Mol Biol Evol 2021; 37:1647-1656. [PMID: 32128591 DOI: 10.1093/molbev/msaa033] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Transatlantic Slave Trade transported more than 9 million Africans to the Americas between the early 16th and the mid-19th centuries. We performed a genome-wide analysis using 6,267 individuals from 25 populations to infer how different African groups contributed to North-, South-American, and Caribbean populations, in the context of geographic and geopolitical factors, and compared genetic data with demographic history records of the Transatlantic Slave Trade. We observed that West-Central Africa and Western Africa-associated ancestry clusters are more prevalent in northern latitudes of the Americas, whereas the South/East Africa-associated ancestry cluster is more prevalent in southern latitudes of the Americas. This pattern results from geographic and geopolitical factors leading to population differentiation. However, there is a substantial decrease in the between-population differentiation of the African gene pool within the Americas, when compared with the regions of origin from Africa, underscoring the importance of historical factors favoring admixture between individuals with different African origins in the New World. This between-population homogenization in the Americas is consistent with the excess of West-Central Africa ancestry (the most prevalent in the Americas) in the United States and Southeast-Brazil, with respect to historical-demography expectations. We also inferred that in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates strongly with the peak of arrivals from Africa. This study contributes with a population genetics perspective to the ongoing social, cultural, and political debate regarding ancestry, admixture, and the mestizaje process in the Americas.
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Affiliation(s)
- Mateus H Gouveia
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil.,Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD
| | - Victor Borda
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thiago P Leal
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Estatística, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rennan G Moreira
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Genômica, Centro de Laboratórios Multiusuário (CELAM), ICB, UFMG, Belo Horizonte, MG, Brazil
| | - Andrew W Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Fernanda S G Kehdy
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Isabela Alvim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marla M Aquino
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gilderlanio S Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará - Campus Guamá, Belém, PA, Brazil
| | - Nathalia M Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vinicius Furlan
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Ciências Exatas e Tecnológicas, Universidade Federal de Viçosa, Campus UFV-Florestal, Florestal, MG, Brazil
| | - Raquel Liboredo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Moara Machado
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Wagner C S Magalhaes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Núcleo de Ensino e Pesquisas do Instituto Mário Penna - NEP-IMP, Bairro Luxemburgo, Belo Horizonte, MG, Brazil
| | - Lucas A Michelin
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maíra R Rodrigues
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Hanaisa P Sant Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Meddly L Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marília O Scliar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Giordano Soares-Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Roxana Zamudio
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Camila Zolini
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Beagle, Belo Horizonte, MG, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Catira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Michael Dean
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert H Gilman
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, Vairão, Portugal
| | | | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Maria F Lima-Costa
- Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Sarah A Tishkoff
- Department of Genetics and Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Estudos Avançados Transdisciplinares, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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3
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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4
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Liu F, Chen Y, Zhu G, Hysi PG, Wu S, Adhikari K, Breslin K, Pospiech E, Hamer MA, Peng F, Muralidharan C, Acuna-Alonzo V, Canizales-Quinteros S, Bedoya G, Gallo C, Poletti G, Rothhammer F, Bortolini MC, Gonzalez-Jose R, Zeng C, Xu S, Jin L, Uitterlinden AG, Ikram MA, van Duijn CM, Nijsten T, Walsh S, Branicki W, Wang S, Ruiz-Linares A, Spector TD, Martin NG, Medland SE, Kayser M. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair. Hum Mol Genet 2019; 27:559-575. [PMID: 29220522 PMCID: PMC5886212 DOI: 10.1093/hmg/ddx416] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 09/05/2017] [Accepted: 11/29/2017] [Indexed: 01/18/2023] Open
Abstract
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62–0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans.
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Affiliation(s)
- Fan Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sijie Wu
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Krystal Breslin
- Department of Biology, Indiana-University-Purdue-University-Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Ewelina Pospiech
- Institute of Zoology and Biomedical Research, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fuduan Peng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Charanya Muralidharan
- Department of Biology, Indiana-University-Purdue-University-Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Victor Acuna-Alonzo
- Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City, México
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City, México
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - 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
| | | | - Maria Catira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, CENPAT-CONICET, Puerto Madryn, Argentina
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Li Jin
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Susan Walsh
- Department of Biology, Indiana-University-Purdue-University-Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Sijia Wang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK.,Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,Laboratory of Biocultural Anthropology, Law, Ethics, and Health (Centre National de la Recherche Scientifique and Etablissement Français du Sang), Aix-Marseille Université, Marseille, France
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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5
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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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6
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Cintas C, Quinto‐Sánchez M, Acuña V, Paschetta C, de Azevedo S, Cesar Silva de Cerqueira C, Ramallo V, Gallo C, Poletti G, Bortolini MC, Canizales‐Quinteros S, Rothhammer F, Bedoya G, Ruiz‐Linares A, Gonzalez‐José R, Delrieux C. Automatic ear detection and feature extraction using Geometric Morphometrics and convolutional neural networks. IET BIOMETRICS 2017. [DOI: 10.1049/iet-bmt.2016.0002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Celia Cintas
- Instituto Patagónico de Ciencias Sociales y HumanasCentro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y TécnicasPuerto MadrynArgentina
| | | | - Victor Acuña
- Department of Genetics, Evolution and Environment, and UCL Genetics InstituteUniversity College LondonLondonUK
| | - Carolina Paschetta
- Instituto Patagónico de Ciencias Sociales y HumanasCentro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y TécnicasPuerto MadrynArgentina
| | - Soledad de Azevedo
- Instituto Patagónico de Ciencias Sociales y HumanasCentro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y TécnicasPuerto MadrynArgentina
| | | | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y HumanasCentro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y TécnicasPuerto MadrynArgentina
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y FilosofíaUniversidad Peruana Cayetano HerediaLimaPerú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y FilosofíaUniversidad Peruana Cayetano HerediaLimaPerú
| | - Maria Catira Bortolini
- Departamento de Genética, Instituto de BiociênciasUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | | | | | | | - Andres Ruiz‐Linares
- MOE Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
- Aix Marseille UnivCNRS, EFS, ADESMarseilleFrance
| | - Rolando Gonzalez‐José
- Instituto Patagónico de Ciencias Sociales y HumanasCentro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y TécnicasPuerto MadrynArgentina
| | - Claudio Delrieux
- Depto. de Ing. Eléctrica y ComputadorasUniversidad Nacional del Sur, and Consejo Nacional de Investigaciones Científicas y TécnicasBahía BlancaArgentina
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7
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Paré P, Paixão-Côrtes VR, Tovo-Rodrigues L, Vargas-Pinilla P, Viscardi LH, Salzano FM, Henkes LE, Bortolini MC. Oxytocin and arginine vasopressin receptor evolution: implications for adaptive novelties in placental mammals. Genet Mol Biol 2016; 39:646-657. [PMID: 27505307 PMCID: PMC5127151 DOI: 10.1590/1678-4685-gmb-2015-0323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 12/18/2015] [Accepted: 02/28/2016] [Indexed: 11/28/2022] Open
Abstract
Oxytocin receptor (OXTR) and arginine vasopressin receptors
(AVPR1a, AVPR1b, and AVPR2) are paralogous genes
that emerged through duplication events; along the evolutionary timeline, owing to
speciation, numerous orthologues emerged as well. In order to elucidate the
evolutionary forces that shaped these four genes in placental mammals and to reveal
specific aspects of their protein structures, 35 species were selected. Specifically,
we investigated their molecular evolutionary history and intrinsic protein disorder
content, and identified the presence of short linear interaction motifs.
OXTR seems to be under evolutionary constraint in placental
mammals, whereas AVPR1a, AVPR1b, and AVPR2 exhibit
higher evolutionary rates, suggesting that they have been under relaxed or
experienced positive selection. In addition, we describe here, for the first time,
that the OXTR, AVPR1a, AVPR1b, and AVPR2 mammalian orthologues preserve their
disorder content, while this condition varies among the paralogues. Finally, our
results reveal the presence of short linear interaction motifs, indicating possible
functional adaptations related to physiological and/or behavioral taxa-specific
traits.
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Affiliation(s)
- Pamela Paré
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Vanessa R Paixão-Côrtes
- Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Luciana Tovo-Rodrigues
- Laboratório de Fisiologia da Reprodução Animal, Universidade Federal de Santa Catarina (UFSC), Curitibanos, SC, Brazil
| | - Pedro Vargas-Pinilla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Lucas Henriques Viscardi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Francisco Mauro Salzano
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Luiz E Henkes
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas (UFPEL), Pelotas, RS, Brazil
| | - Maria Catira Bortolini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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8
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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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9
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Affiliation(s)
- T Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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10
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Mazières S, Guitard E, Crubézy E, Dugoujon JM, Bortolini MC, Bonatto SL, Hutz MH, Bois E, Tiouka F, Larrouy G, Salzano FM. Uniparental (mtDNA, Y-chromosome) polymorphisms in French Guiana and two related populations--implications for the region's colonization. Ann Hum Genet 2007; 72:145-56. [PMID: 17725814 DOI: 10.1111/j.1469-1809.2007.00392.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Blood samples collected in four Amerindian French Guiana populations (Palikur, Emerillon, Wayampi and Kali'na) in the early 1980s were screened for selected mtDNA and Y-chromosome length polymorphisms, and sequenced for the mtDNA hypervariable segment I (HVS-I). In addition, two other Amerindian populations (Apalaí and Matsiguenga) were examined for the same markers to establish the genetic relationships in the area. Strong dissimilarities were observed in the distribution of the founding Amerindian haplogroups, and significant p-values were obtained from F(ST) genetic distances. Interpopulation similarities occurred mainly due to geography. The Palikur did not show obvious genetic similarity to the Matsiguenga, who speak the same language and live in a region from where they could have migrated to French Guiana. The African-origin admixture observed in the Kali'na probably derives from historical contacts they had with the Bushinengue (Noir Marron), a group of escaped slaves who now lead independent lives in a nearby region. This analysis has identified significant clues about the Amerindian peopling of the North-East Amazonian region.
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Affiliation(s)
- S Mazières
- Laboratoire d'Anthropobiologie, FRE 2960 CNRS, Toulouse, France.
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11
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Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. A genomewide admixture map for Latino populations. Am J Hum Genet 2007; 80:1024-36. [PMID: 17503322 PMCID: PMC1867092 DOI: 10.1086/518313] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/12/2007] [Indexed: 01/21/2023] Open
Abstract
Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.
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Affiliation(s)
- Alkes L Price
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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12
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Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. A genomewide admixture map for Latino populations. Am J Hum Genet 2007. [PMID: 17503322 DOI: 10.1086/538313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.
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Affiliation(s)
- Alkes L Price
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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13
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Abstract
A sample of 103 randomly chosen healthy individuals from Alegrete, RS, Brazil, was tested for the CCR5delta32 allele, which is known to influence susceptibility to HIV-1 infection. The CCR5delta32 allele was identified by PCR amplification using specific primers flanking the region of deletion, followed by electrophoresis on a 3% agarose gel. The data obtained were compared to those reported for other populations and interpreted in terms of Brazilian history. The individuals studied came from a highly admixed population. Most of them were identified as white (N = 59), while blacks and browns (mulattoes) were N = 13 and N = 31, respectively. The observed frequencies, considering the white, black and brown samples (6.8, 3.8, and 6.4%, respectively), suggest an important European parental contribution, even in populations identified as black and brown. However, in Brazil as a whole, this allele shows gradients indicating a relatively good correlation with the classification based on skin color and other physical traits, used here to define major Brazilian population groups.
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Affiliation(s)
- A E Vargas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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14
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Mesa NR, Mondragón MC, Soto ID, Parra MV, Duque C, Ortíz-Barrientos D, García LF, Velez ID, Bravo ML, Múnera JG, Bedoya G, Bortolini MC, Ruiz-Linares A. Autosomal, mtDNA, and Y-chromosome diversity in Amerinds: pre- and post-Columbian patterns of gene flow in South America. Am J Hum Genet 2000; 67:1277-86. [PMID: 11032789 PMCID: PMC1288567 DOI: 10.1016/s0002-9297(07)62955-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2000] [Accepted: 09/06/2000] [Indexed: 11/29/2022] Open
Abstract
To evaluate sex-specific differences in gene flow between Native American populations from South America and between those populations and recent immigrants to the New World, we examined the genetic diversity at uni- and biparental genetic markers of five Native American populations from Colombia and in published surveys from native South Americans. The Colombian populations were typed for five polymorphisms in mtDNA, five restriction sites in the beta-globin gene cluster, the DQA1 gene, and nine autosomal microsatellites. Elsewhere, we published results for seven Y-chromosome microsatellites in the same populations. Autosomal polymorphisms showed a mean G(ST) of 6.8%, in agreement with extensive classical marker studies of South American populations. MtDNA and Y-chromosome markers resulted in G(ST) values of 0.18 and 0.165, respectively. When only Y chromosomes of confirmed Amerind origin were used in the calculations (as defined by the presence of allele T at locus DYS199), G(ST) increased to 0.22. G(ST) values calculated from published data for other South American natives were 0.3 and 0.29 for mtDNA and Amerind Y chromosomes, respectively. The concordance of these estimates does not support an important difference in migration rates between the sexes throughout the history of South Amerinds. Admixture analysis of the Colombian populations suggests an asymmetric pattern of mating involving mostly immigrant men and native women.
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Affiliation(s)
- N R Mesa
- Laboratorio de Genética Molecular, Departamento de Fisiología y Bioquímica, Medellín, Colombia
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15
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Da Silva WA, Bortolini MC, Meyer D, Salzano FM, Elion J, Krishnamoorthy R, Schneider MP, De Guerra DC, Layrisse Z, Castellano HM, Weimer TD, Zago MA. Genetic diversity of two African and sixteen South American populations determined on the basis of six hypervariable loci. Am J Phys Anthropol 1999; 109:425-37. [PMID: 10423260 DOI: 10.1002/(sici)1096-8644(199908)109:4<425::aid-ajpa1>3.0.co;2-d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A total of 582 individuals (1,164 chromosomes) from two African, eight African-derived South American, five South American Amerindian, and three Brazilian urban populations were studied at four variable number of tandem repeat (VNTR) and two short tandem repeat (STR) hypervariable loci. These two sets of loci did not show distinct allele profiles, which might be expected if different processes promoted their molecular differentiation. The two African groups showed little difference between them, and their intrapopulational variation was similar to those obtained in the African-derived South American communities. The latter showed different degrees of interpopulation variability, despite the fact that they presented almost identical average degrees of non-African admixture. The F(ST) single locus estimates differed in the five sets of populations, probably due to genetic drift, indicating the need to consider population structure in the evaluation of their total variability. A high interpopulational diversity was found among Amerindian populations in relation to Brazilian African-derived isolated communities. This is probably a consequence of the differences in the patterns of gene flow and genetic drift that each of these semi-isolated groups experienced.
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Affiliation(s)
- W A Da Silva
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, 66075-900 Belém, PA, Brazil
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16
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Bortolini MC, da Silva-Júnior WA, Weimer TDA, Zago MA, de Guerra DC, Schneider MP, Layrisse Z, Castellano HM, Salzano FM. Protein and hypervariable tandem repeat diversity in eight African-derived South American populations: inferred relationships do not coincide. Hum Biol 1998; 70:443-61. [PMID: 9599938] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We compared data from individuals living in 4 African Venezuelan and 4 African Brazilian communities for 11 protein loci (551 subjects) and 8 hypervariable tandem repeat polymorphisms (252 subjects). There is heterogeneity in diversity within and between the two sets of loci. On the other hand, African-derived Brazilians and Venezuelans do not present marked variability differences between themselves. Although the hypervariable loci show gene diversities that are about four times higher than those obtained from the protein data, they are not more discriminative at the interpopulation level (averages 6% and 4%, respectively). Interpopulation differences do not strictly parallel the geographic distances between the groups, and population relationships obtained from the protein data are not the same as those indicated by hypervariable tandem repeat polymorphisms. Caution is needed in establishing relationships considering just one level of the biological hierarchy.
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Affiliation(s)
- M C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Bortolini MC, Baptista C, Callegari-Jacques SM, Weimer TA, Salzano FM. Diversity in protein, nuclear DNA, and mtDNA in South Amerinds--agreement or discrepancy? Ann Hum Genet 1998; 62:133-45. [PMID: 9759475 DOI: 10.1046/j.1469-1809.1998.6220133.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two sets of markers and populations were considered in this study: (a) the variability at 17 protein loci and in the sequences of the first hypervariable segment of the mitochondrial DNA (mtDNA) were compared in 10 South American Indian tribes, in a total 3016 and 241 individuals, respectively; and (b) a triple comparison was made, in relation to 17 protein, mtDNA and six hypervariable tandem repeat loci in four Brazilian Indian tribes, involving 1567, 56 and 194 persons, respectively. Both the intrapopulational diversities and the population relationships obtained in these groups with these different sets of markers showed no significant correlation. High levels of heterogeneity were observed both at the protein and hypervariable individual loci, as well between mtDNA sites. The different positions observed for the Yanomama (but not for the other nine tribes) in the trees which summarized the protein and mtDNA data suggest some degree of asymmetric interchange related to sex between them and neighbouring tribes.
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Affiliation(s)
- M C Bortolini
- Genetics Department, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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Bortolini MC, Salzano FM, Zago MA, Da Silva Júnior WA, Weimer TDA. Genetic variability in two Brazilian ethnic groups: a comparison of mitochondrial and protein data. Am J Phys Anthropol 1997; 103:147-56. [PMID: 9209572 DOI: 10.1002/(sici)1096-8644(199706)103:2<147::aid-ajpa1>3.0.co;2-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sequence data from the first hypervariable segment of the mitochondrial DNA control region of 124 subjects belonging to three African-Brazilian and three Brazilian Indian populations were compared with information related to 12 protein genetic loci from 601 persons living in the same localities. There is high diversity among the mtDNA sites, and the most variable in one ethnic group are not the most variable in the other. No differences in gene diversity between populations within ethnic groups were observed, but the Indians showed a reduced variability. Much more interpopulation variation was observed in the mtDNA data than in the protein set. The relationships obtained for the six populations, however, are the same regardless whether mtDNA or protein loci are considered. African-Brazilians from Porto Alegre and Salvador, situated 3,000 km apart, are more similar to each other than both are to Paredão, despite the geographical proximity between Porto Alegre and Paredão, which are just 50 km apart. The tree topology in relation to the three Indians groups, on the other hand, is that expected when languages, culture, and geography are considered.
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Affiliation(s)
- M C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Bortolini MC, Zago MA, Salzano FM, Silva-Júnior WA, Bonatto SL, da Silva MC, Weimer TA. Evolutionary and anthropological implications of mitochondrial DNA variation in African Brazilian populations. Hum Biol 1997; 69:141-59. [PMID: 9057341] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The genetic diversity in three African Brazilian populations was analyzed using the 360-nucleotide sequences of the first hypervariable segment (HVS-I) of the mitochondrial DNA control region. Results from 42 individuals revealed 39 distinct lineages defined by 54 variable positions. Some of the sequence types were clearly African derived, but apparent Amerindian lineages also occurred. The lineage clusters did not show any association with place of residence of the individuals or with their morphological classification. Nucleotide diversity, however, seemed to be associated with degree of admixture. The mismatch distribution suggests a major human population expansion 60,000 years ago.
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Affiliation(s)
- M C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Bortolini MC, Weimer TDA, Salzano FM, Callegari-Jacques SM, Schneider H, Layrisse Z, Bonatto SL. Evolutionary relationships between black South American and African populations. Hum Biol 1995; 67:547-59. [PMID: 7649530] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Data related to ten protein genetic loci expressed in blood obtained from four South American black populations were compared with data from seven African countries. Estimates of admixture among South American blacks were revised, and several indexes of gene diversity and genetic distances between the 11 populations were calculated. The admixture values and genetic relationships observed among the South American black communities conform well with those expected on historical grounds, and they show only moderate reductions in genetic diversity.
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Affiliation(s)
- M C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Bortolini MC, Weimer TA, Franco MH, Salzano FM, Layrisse Z, Schneider H, Schneider MP, Harada ML. Genetic studies in three South American black populations. Gene Geogr 1992; 6:1-16. [PMID: 1299309] [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] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Twenty-one genetic systems were investigated in three relatively isolated South American Black populations. Unexpected allele frequencies were found in different systems in all populations, suggesting the occurrence of genetic drift and/or founder effects. The estimates of racial admixture indicate 50% to 79% of Black ancestry, with various degrees of White (18%-28%) and Amerindian (3%-32%) ancestry.
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Affiliation(s)
- M C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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