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1. The impact of socioeconomic and phenotypic traits on self-perception of ethnicity in Latin America

Author

Francisco Rothhammer, Mirsha Emmanuel Quinto Sánchez, Gabriel Bedoya, Andres Ruiz-Linares, Orlando Pérez, Carolina Paschetta, Celia Cintas, Soledad de Azevedo, M. Catira Bortolini, Giovanni Poletti Ferrara, Virginia Ramallo, Víctor Acuña Alonzo, Carla Gallo, Kaustubh Adhikari, Rolando González-José, Pablo E. Navarro, Lucas M. Bandieri, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
Adult, Male, 0301 basic medicine, 050402 sociology, Science, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ethnic group, Identity (social science), Context (language use), ETHNIC SELF-PERCEPTION, Human physical appearance, Affect (psychology), Article, GENOMIC ANCESTRY, purl.org/becyt/ford/1 [https], 03 medical and health sciences, Medical research, 0504 sociology, Ethnicity, Genetics, Humans, purl.org/becyt/ford/1.6 [https], 10. No inequality, Socioeconomic status, Aged, Multidisciplinary, 05 social sciences, 1. No poverty, Phenotypic trait, Middle Aged, Self Concept, Latin America, Phenotype, 030104 developmental biology, Socioeconomic Factors, Trait, Medicine, Educational Status, Female, Psychology, Genetic Background, Demography
Abstract

Self-perception of ethnicity is a complex social trait shaped by both, biological and non-biological factors. We developed a comprehensive analysis of ethnic self-perception (ESP) on a large sample of Latin American mestizos from five countries, differing in age, socio-economic and education context, external phenotypic attributes and genetic background. We measured the correlation of ESP against genomic ancestry, and the influence of physical appearance, socio-economic context, and education on the distortion observed between both. Here we show that genomic ancestry is correlated to aspects of physical appearance, which in turn affect the individual ethnic self-perceived ancestry. Also, we observe that, besides the significant correlation among genomic ancestry and ESP, specific physical or socio-economic attributes have a strong impact on self-perception. In addition, the distortion among ESP and genomic ancestry differs across age ranks/countries, probably suggesting the underlying effect of past public policies regarding identity. Our results indicate that individuals’ own ideas about its origins should be taken with caution, especially in aspects of modern life, including access to work, social policies, and public health key decisions such as drug administration, therapy design, and clinical trials, among others. Fil: Paschetta, Carolina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: de Azevedo, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Cintas, Celia. Ibm Research; Estados Unidos Fil: Pérez, Orlando Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Navarro, Jose Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Bandieri, Lucas Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Quinto Sánchez, Mirsha Emmanuel. Universidad Nacional Autónoma de México; México Fil: Adhikari, Kaustubh. Colegio Universitario de Londres; Reino Unido Fil: Bortolini, Maria Catira. Universidade Federal do Rio Grande do Sul; Brasil Fil: Poletti Ferrara, Giovanni. Universidad Peruana de Ciencias Aplicadas (upc); Perú Fil: Gallo, Carla. Universidad Peruana de Ciencias Aplicadas (upc); Perú Fil: Bedoya Berrío, Gabriel. Universidad de Antioquia; Colombia Fil: Rothhammer, Francisco. Universidad de Tarapacá; Chile Fil: Alonzo, Victor Acuña. Universidad Nacional Autónoma de México; México Fil: Ruiz Linares, Andrés. Colegio Universitario de Londres; Reino Unido Fil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina

Published
2021
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2. How natural selection shapes genetic differentiation in the MHC region: A case study with Native Americans

Author

Andres Ruiz-Linares, Francisco Rothhammer, Richard M. Single, Maria Helena Thomaz Maia, Eduardo José Melo dos Santos, Diogo Meyer, Giovanni Poletti, Gabriel Bedoya, João Farias Guerreiro, Elena Llop, Kelly Nunes, Sidney Santos, Maria Cátira Bortolini, Carla Gallo, Maria Luiza Petzl-Erler, Luiza T. Tsuneto, Jorge Rocha, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Immunology, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Human leukocyte antigen, POLIMORFISMO, Balancing selection, Major histocompatibility complex, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, HLA Antigens, Native Americans, Humans, Immunology and Allergy, Selection, Genetic, Allele, education, American Indian or Alaska Native, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, education.field_of_study, Polymorphism, Genetic, Natural selection, biology, Genetic Variation, Genomics, General Medicine, Populational differentiation, purl.org/pe-repo/ocde/ford#3.01.03 [https], HLA, Genetics, Population, 030104 developmental biology, Evolutionary biology, biology.protein, Microsatellite, MHC, Microsatellite Repeats, 030215 immunology
Abstract

The Human Leukocyte Antigen (HLA) loci are extremely well documented targets of balancing selection, yet few studies have explored how selection affects population differentiation at these loci. In the present study we investigate genetic differentiation at HLA genes by comparing differentiation at microsatellites distributed genomewide to those in the MHC region. Our study uses a sample of 494 individuals from 30 human populations, 28 of which are Native Americans, all of whom were typed for genomewide and MHC region microsatellites. We find greater differentiation in the MHC than in the remainder of the genome (F(ST-MHC) = 0.130 and F(ST-Genomic) = 0.087), and use a permutation approach to show that this difference is statistically significant, and not accounted for by confounding factors. This finding lies in the opposite direction to the expectation that balancing selection reduces population differentiation. We interpret our findings as evidence that selection favors different sets of alleles in distinct localities, leading to increased differentiation. Thus, balancing selection at HLA genes simultaneously increases intra-population polymorphism and inter-population differentiation in Native Americans.

Published
2021
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3. Prediction of eye, hair and skin colour in Latin Americans

Author

Maria Cátira Bortolini, Jorge Gómez-Valdés, Francisco Rothhammer, Andres Ruiz-Linares, Anood Sohail, Caio Cesar Silva de Cerqueira, Giovanni Poletti, Carla Gallo, William Arias, Paola Everardo-Martínez, Rodrigo Barquera Lozano, Javier Mendoza-Revilla, Rolando González-José, Tábita Hünemeier, Maria-Laura Parolin, Samuel Canizales-Quinteros, Sagnik Palmal, Claudia Jaramillo, Betty Bonfante, David J. Balding, Valeria Villegas, Victor Acuña-Alonzo, Pierre Faux, Virginia Ramallo, Hugo Villamil-Ramírez, Malena Hurtado, Kaustubh Adhikari, Lavinia Schuler-Faccini, Gabriel Bedoya, Vanessa Granja, Macarena Fuentes-Guajardo, Juan Camilo Chacón-Duque, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genotype, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Datasets as Topic, Skin Pigmentation, Quantitative trait locus, Biology, GENOMAS, Polymorphism, Single Nucleotide, Pathology and Forensic Medicine, purl.org/becyt/ford/1 [https], 03 medical and health sciences, 0302 clinical medicine, DNA PHENOTYPING, Statistics, Genetics, Eye color, PIGMENTATION PREDICTION, Humans, 030216 legal & forensic medicine, education, Hair Color, purl.org/becyt/ford/1.6 [https], Categorical variable, EYE-COLOUR, ComputingMilieux_MISCELLANEOUS, education.field_of_study, Eye Color, integumentary system, Contrast (statistics), Genetic architecture, Random forest, LATIN AMERICANS, ADMIXTURE, purl.org/pe-repo/ocde/ford#3.01.02 [https], 030104 developmental biology, Genetics, Population, Latin America, Logistic Models, Phenotype, HAIR-COLOUR, sense organs, SKIN-COLOUR, DNA phenotyping
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. Fil: Palmal, Sagnik. Centre National de la Recherche Scientifique; Francia. Aix-Marseille Université; Francia Fil: Kaustubh Adhikari. The Open University; Reino Unido. University College London; Estados Unidos Fil: Mendoza Revilla, Javier. Universidad Peruana Cayetano Heredia; Perú. Institut Pasteur de Paris.; Francia Fil: Fuentes Guajardo, Macarena. Universidad de Tarapacá; Chile Fil: Silva de Cerqueira, Caio Cesar. Scientific Police of São Paulo State; Brasil Fil: Bonfante, Betty. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia Fil: Chacón Duque, Juan Camilo. Natural History Museum; Reino Unido Fil: Sohail, Anood. Kinnaird College for Women. Department of Biotechnology; Pakistán Fil: Hurtadeo, Malena. Universidad Peruana Cayetano Heredia; Perú Fil: Villegas, Valeria. Universidad Peruana Cayetano Heredia; Perú Fil: Granja, Vanessa. Universidad Peruana Cayetano Heredia; Perú Fil: Jaramillo, Claudia. Kinnaird College for Women. Department of Biotechnology; Pakistán. Universidad de Antioquia; Colombia Fil: Arias, Williams. Universidad de Antioquia; Colombia Fil: Barquera Lozano, Rodrigo. Instituto Nacional de Antropología e Historia; México. Max Planck Institute for the Science of Human History. Department of Archaeogenetics; Alemania Fil: Everardo Martínez, Paola. Instituto Nacional de Antropología e Historia; México Fil: Gómez Valdés, Jorge. Instituto Nacional de Antropología e Historia; México Fil: Villamil Ramirez, Hugo. Universidad Nacional Autónoma de México; México Fil: Hünemeier, Tábita. Universidade de Sao Paulo; Brasil Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina. Universidade Federal do Rio Grande do Sul; Brasil Fil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina Fil: Gonzalez, Rolando Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Schüler-Faccini, Lavinia. Universidade Federal do Rio Grande do Sul, Porto Alegre; Brasil Fil: Bortolini, María Cátira. Universidade Federal do Rio Grande do Sul; Brasil Fil: Acuña Alonzo, Victor. Instituto Nacional de Antropología e Historia; México. Universidade Federal do Rio Grande do Sul; Brasil Fil: Canizales Quinteros, Samuel. Universidad Nacional Autónoma de México; México Fil: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú Fil: Poletti, Giovanni. Universidad Peruana Cayetano Heredia; Perú Fil: Bedoya, Gabriel. Universidad de Antioquia; Colombia Fil: Rothhammer, Francisco. Universidad de Tarapacá; Chile. Universidad de Chile; Chile Fil: Balding, David. University College London; Reino Unido. University of Melbourne; Australia Fil: Faux, Pierre. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia Fil: Ruiz Linares, Andrés. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia. University College London; Reino Unido. Fudan University; República de China

Published
2021
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4. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

Author

Tábita Hünemeier, Andres Ruiz-Linares, Samuel Canizales-Quinteros, Christel Thauvin-Robinet, Betty Bonfante, Juan Camilo Chacón-Duque, Laurence Duplomb, Charlotte Montillot, Sagnik Palmal, Javier Mendoza-Revilla, Justin Cotney, Laurence Faivre, Seth M. Weinberg, Victor Acuña-Alonzo, Emma Wentworth, Philip H. Jones, Claudia Jaramillo, Caroline Costedoat, Morgane Dubied, David J. Balding, Manfred Kayser, Pierre Faux, Francisco Rothhammer, Mirsha Sánchez-Quinto, Carla Gallo, Paola Everardo-Martínez, Macarena Fuentes-Guajardo, Evie Stergiakouli, Pirro G. Hysi, Ziyi Xiong, Giovanni Poletti, Ceferino Varón-González, Rodrigo Barquera, Maria Cátira Bortolini, Laurence J. Howe, Lauriane Poloni, Rolando González-José, Valeria Villegas, Malena Hurtado, Kaustubh Adhikari, William Arias, Vanessa Granja, Lavinia Schuler-Faccini, Virginia Ramallo, John R. Shaffer, Timothy C. Cox, Tim D. Spector, Gabriel Bedoya, Hugo Villamil-Ramírez, Caio Cesar Silva de Cerqueira, Fan Liu, Binnaz Yalcin, Jorge Gómez-Valdés, Nicolas Navarro, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Universidad Peruana Cayetano Heredia (UPCH), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Connecticut Health Center [Farmington], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University College of London [London] (UCL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Universidad de Tarapaca, The Natural History Museum [London] (NHM), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], National School of Anthropology and History [Mexico City, Mexico] (NSAH), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State [Ourinhos, Brazil], Universidade de São Paulo = University of São Paulo (USP), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Centro Nacional Patagónico (CENPAT), Beijing Genomics Institute [Shenzhen] (BGI), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), University of Bristol [Bristol], King‘s College London, FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), University of Melbourne, University of Missouri [Kansas City] (UMKC), University of Missouri System, The Open University [Milton Keynes] (OU), Fudan University [Shanghai], Work leading to this publication was funded by grants from the National Natural Science Foundation of China (#31771393), the Scientific and Technology Committee of Shanghai Municipality (18490750300), the Ministry of Science and Technology of China (2020YFE0201600), the Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), the Leverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative of Aix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program), Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos de Excelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, the National Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078, R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award. B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-Marseille Université., ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, École pratique des hautes études (EPHE), Laboratorios de Investigación y Desarrollo (LID), Unit of Human Evolutionary Genetics, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Department of Genetics and Genome Sciences, University of Connecticut (UCONN), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, Department of Genetic Identification, Departamento de Tecnología Médica, Division of Vertebrates and Anthropology, Genética Molecular (GENMOL), Molecular Genetics Laboratory, National School of Anthropology and History, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Forensic Science, Universidad Nacional Autónoma de México (UNAM), Unidad de Genomica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Patagónico de Ciencias Sociales y Humanas, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Key Laboratory of Genomic and Precision Medicine [Beijing, China], Beijing Genomics Institute [Shenzhen] (BGI)-University of Chinese Academy of Sciences [Beijing] (UCAS), Center for Craniofacial and Dental Genetics, University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Human Genetics, Department of Anthropology, Medical Research Council Integrative Epidemiology Unit, University of the West of England [Bristol] (UWE Bristol), School of Oral and Dental Sciences, Department of Twin Research & Genetic Epidemiology, King's College London, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne-University of Melbourne, Department of Oral and Craniofacial Sciences, University of Missouri System-University of Missouri System, School of Mathematics and Statistics [Milton Keynes], Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Work leading to this publication was funded by grantsfrom the National Natural Science Foundation of China (#31771393), the Scientific andTechnology Committee of Shanghai Municipality (18490750300), the Ministry ofScience and Technology of China (2020YFE0201600), the Shanghai Municipal Scienceand Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), theLeverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative ofAix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program),Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico,Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos deExcelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, theNational Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078,R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award.B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-MarseilleUniversité., and Genetic Identification

Subjects
haplotype, Latin Americans, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Vesicular Transport Proteins, Genome-wide association study, Genome-wide association studies, Regulatory sequences, purl.org/becyt/ford/1 [https], Mice, 0302 clinical medicine, Native Americans, single nucleotide polymorphism, GWAS, 10. No inequality, Two-dimensional profiles, Research Articles, Mammals, 0303 health sciences, Multidisciplinary, biology, adult, article, SciAdv r-articles, Genomic regions, Hispanic or Latino, craniofacial development, VPS13B, GENÉTICA, Phenotype, American Indian, regulatory sequence, HUMAN POPULATION, Research Article, Morphology, Latin americans, Genotype, animal experiment, introgression, Introgression, Polymorphism, Single Nucleotide, Homo denisovan, 03 medical and health sciences, male, Animals, Humans, controlled study, human, Craniofacial, Facial feature, purl.org/becyt/ford/1.6 [https], Denisovan, Gene, mouse, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, nonhuman, genome-wide association study, Haplotype, face, Human Genetics, Single nucleotide polymorphisms, biology.organism_classification, photography, thickness, purl.org/pe-repo/ocde/ford#3.01.02 [https], facies, DENOSIVAN HAPLOTYPE, Evolutionary biology, Anthropology, Face, 030217 neurology & neurosurgery, purl.org/pe-repo/ocde/ford#1.06.07 [https], Genome-Wide Association Study
Abstract

We carried out a genome-wide association study in Latin Americans and identified novel face morphology loci.., 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.

Published
2021
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5. Demographic history and selection at HLA loci in Native Americans

Author

Giovanni Poletti, William Klitz, Rodrigo dos Santos Francisco, Francisco Rothhammer, Carla Gallo, Maria Luiza Petzl-Erler, Diogo Meyer, Elena Llop, Andres Ruiz-Linares, Richard M. Single, Tábita Hünemeier, Gabriel Bedoya, Carolyn Katovich Hurley, Kelly Nunes, Martin Maiers, Luiza T. Tsuneto, A. M. Hurtado, State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Heredity, Population genetics, Natural selection, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Balancing selection, 01 natural sciences, Homozygosity, Microsatellite Loci, HLA Antigens, Natural Selection, Ethnicities, ComputingMilieux_MISCELLANEOUS, education.field_of_study, Multidisciplinary, Heterozygosity, Geography, Population size, Homozygote, Population groupings, Native American people, Medicine, Microsatellite loci, Research Article, Heterozygote, Evolutionary Processes, purl.org/pe-repo/ocde/ford#5.04.02 [https], Demographic history, Genetic loci, purl.org/pe-repo/ocde/ford#1.06.03 [https], Science, Population, Biology, GENOMAS, 010603 evolutionary biology, 03 medical and health sciences, Gene Types, Genetic variation, Genetics, Humans, Selection, Genetic, education, Selection (genetic algorithm), Alleles, American Indian or Alaska Native, Demography, Evolutionary Biology, Population Biology, Genetic Variation, Biology and Life Sciences, South America, 030104 developmental biology, Haplotypes, Evolutionary biology, Genetic Loci, Sample Size, North America, People and places, Population Genetics, Microsatellite Repeats
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.

Published
2020
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6. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair

Author

Francisco Rothhammer, Giovanni Poletti, Fuduan Peng, Victor Acuña-Alonzo, Samuel Canizales-Quinteros, Charanya Muralidharan, Nicholas G. Martin, Rolando González-José, Pirro G. Hysi, Krystal Breslin, Li Jin, Susan Walsh, Gu Zhu, Maria C. Bortolini, Wojciech Branicki, Andres Ruiz-Linares, Tamar Nijsten, Kaustubh Adhikari, Ewelina Pośpiech, Sarah E. Medland, Changqing Zeng, M. Arfan Ikram, Shuhua Xu, Carla Gallo, Sijia Wang, Cornelia M. van Duijn, Manfred Kayser, André G. Uitterlinden, Tim D. Spector, Gabriel Bedoya, Merel A. Hamer, Fan Liu, Sijie Wu, Yan Chen, Department of Physics, National University of Singapore (NUS), King‘s College London, Central South University [Changsha], Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), University of Chinese Academy of Sciences [Beijing] (UCAS), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands, Department of Twin Research and Genetic Epidemiology, King's College London, London, Queensland Institute of Medical Research, Forensic Molecular Biology, ErasmusMC, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Genetic Identification, Dermatology, Epidemiology, and Internal Medicine

Subjects
0301 basic medicine, Otras Ciencias Biológicas, [SDV]Life Sciences [q-bio], Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Single-nucleotide polymorphism, Genome-wide association study, Biology, Genome, Polymorphism, Single Nucleotide, purl.org/becyt/ford/1 [https], Ciencias Biológicas, 03 medical and health sciences, Polymorphism (computer science), Native Americans, Genetics, Journal Article, Humans, Genetic Predisposition to Disease, purl.org/becyt/ford/1.6 [https], education, Molecular Biology, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Genetic association, education.field_of_study, Asian, Association Studies Articles, Regression analysis, General Medicine, 3. Good health, purl.org/pe-repo/ocde/ford#3.01.02 [https], 030104 developmental biology, Genes, Evolutionary biology, Meta-analysis, Single Nucleotide Polymorphism, native, CIENCIAS NATURALES Y EXACTAS, americans, Genome-Wide Association Study, Hair
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

Published
2018
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7. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Author

Juan C. Chacon-Duque, Hugo Villamil-Ramírez, Giovanni Poletti, Samuel Canizales-Quinteros, Mirsha Quinto-Sánchez, Maria Cátira Bortolini, Maria-Laura Parolin, Macarena Fuentes-Guajardo, Francisco Rothhammer, Rolando González-José, Valeria Villegas, Francisco Mauro Salzano, Javier Mendoza-Revilla, Verónica Gomes, Caio Cesar Silva de Cerqueira, Cheryl A. Winkler, José R. Sandoval, Carla Gallo, Elena Llop, Rosenda I. Peñaloza-Espinosa, Vanessa Granja, Daniel Corach, Lavinia Schuler-Faccini, Yali Xue, Garrett Hellenthal, Mercedes Villena, Virginia Ramallo, Victor Acuña-Alonzo, Gabriel Bedoya, Paola Everardo Martínez, Karla Sandoval, Andres Ruiz-Linares, David J. Balding, Claudio M. Bravi, Pedro Moral, Jean-Michel Dugoujon, Tábita Hünemeier, António Amorim, Malena Hurtado, Kaustubh Adhikari, René Vasquez, Julio Molina, Leonor Gusmão, Ramiro Barrantes, Carlos Resende, Jorge Gómez-Valdés, Alberto Salazar-Granara, Héctor Rangel-Villalobos, William Klitz, Rodrigo Barquera, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Boliviano de Biologıa de la Altura, Universidad Autonoma Tomas Frias, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, School of Human Evolution and Social Change, Arizona State University [Tempe] (ASU), Instituto Multidisciplinario de Biología Celular [La Plata] (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de la Plata [Argentine] (UNLP)-Comisión de Investigaciones Científicas [Buenos Aires] (CIC), Centro de Investigaciones Biomédicas de Guatemala, Servicio de Huellas Digitales Genéticas [Buenos Aires], Facultad de Farmacia y Bioquímica [Buenos Aires] (FFYB), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Escuela de Biologia, Universidad Nacional de Costa Rica, Population Genetics, Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Universidade de Lisboa (ULISBOA), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Barcelona, Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], University College of London [London] (UCL), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigação e Inovação em Saúde, Universidade de Lisboa = University of Lisbon (ULISBOA), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
haplotype, Latin Americans, Biología, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, purl.org/pe-repo/ocde/ford#1.03.00 [https], Human physical appearance, Colonialism, migration, CONVERSO JEWS, purl.org/becyt/ford/1 [https], Genética y Herencia, 0302 clinical medicine, genetics, Nose / anatomy & histology, East mediterranean, lcsh:Science, 0303 health sciences, Genealogy, Geography, Indians, South American / genetics, American Indian, Genetic structure, CIENCIAS NATURALES Y EXACTAS, Latin americans, Science, purl.org/pe-repo/ocde/ford#1.06.03 [https], Human Migration, Nose, Article, Ciencias Biológicas, 03 medical and health sciences, Indians, North American / genetics, parasitic diseases, Humans, human, purl.org/becyt/ford/1.6 [https], Mexico, Historical record, 030304 developmental biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Indians, South American, ANCESTRY INFORMATIVE, Environmental adaptation, South America, Converso jews, LATIN AMERICANS, Haplotypes, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Ancestry informative, purl.org/pe-repo/ocde/ford#1.04.00 [https], Indians, North American, lcsh:Q, 030217 neurology & neurosurgery, anatomy and histology
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., Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

Published
2018
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8. Contrasting patterns of nuclear and mtDNA diversity in Native American populations

Author

Ning Ning, Yang, Stephane, Mazières, Claudio, Bravi, Nicolas, Ray, Sijia, Wang, Mari-Wyn, Burley, Gabriel, Bedoya, Winston, Rojas, Maria V, Parra, Julio A, Molina, Carla, Gallo, Giovanni, Poletti, Kim, Hill, Ana M, Hurtado, Maria L, Petzl-Erler, Luiza T, Tsuneto, William, Klitz, Ramiro, Barrantes, Elena, Llop, Francisco, Rothhammer, Damian, Labuda, Francisco M, Salzano, Maria-Cátira, Bortolini, Laurent, Excoffier, Jean Michel, Dugoujon, Andrés, Ruiz-Linares, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Instituto Multidisciplinario de Biología Celular [La Plata] (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de la Plata [Argentine] (UNLP)-Comisión de Investigaciones Científicas [Buenos Aires] (CIC), EnviroSPACE Laboratory - Forel Institute, Institute for Environmental Sciences [Geneva] (ISE), University of Geneva [Switzerland]-University of Geneva [Switzerland], Harvard FAS Center for Systems Biology, Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Centro de Investigaciones Biomédicas de Guatemala, School of Human Evolution and Social Change, Arizona State University [Tempe] (ASU), Departamento de Genética, Universidade Federal do Paraná (UFPR), Escuela de Biologia, Universidad Nacional de Costa Rica, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, CHU Sainte-Justine, Département de Pédiatrie, Université de Montréal (UdeM), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, CMPG, University of Bern, Programme AMAZONIE - Analyse, modélisation et ingénierie des systèmes amazoniens (programme interdisciplinaire du CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, Ameriindians, MtDNA, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Chromosomes, Human, Y/genetics, DNA, Mitochondrial, DNA, Mitochondrial/genetics, Ciencias Biológicas, Genética y Herencia, Chromosomes, Human, X/genetics, ddc:550, Humans, Ciencias Naturales, Y-chromosome, ddc:333.7-333.9, X-chromosome, Chromosomes, Human, X, Chromosomes, Human, Y, Indians, South American, Sequence Analysis, DNA, Emigration and Immigration, STRs, Indians, North American/genetics, Sequence Analysis, DNA/methods, Ciencias Médicas, Indians, North American, Indians, South American/genetics, Female, CIENCIAS NATURALES Y EXACTAS, Microsatellite Repeats
Abstract

We report an integrated analysis of nuclear (autosomal, X- and Y-chromosome) short tandem repeat (STR) data and mtDNA D-loop sequences obtained in the same set of 22 Native populations from across the Americas. A north to south gradient of decreasing population diversity was observed, in agreement with a settlement of the Americas from the extreme northwest of the continent. This correlation is stronger with "least cost distances," which consider the coasts as facilitators of migration. Continent-wide estimates of population structure are highest for the Y-chromosome and lowest for the autosomes, consistent with the effective size of the different marker systems examined. Population differentiation is highest in East South America and lowest in Meso America and the Andean region. Regional analyses suggest a deviation from mutation-drift equilibrium consistent with population expansion in Meso America and the Andes and population contraction in Northwest and East South America. These data hint at an early divergence of Andean and non-Andean South Americans and at a contrasting demographic history for populations from these regions., Instituto Multidisciplinario de Biología Celular

Published
2010
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