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

Nat Commun. 2018 Dec 19;9(1):5388. doi: 10.1038/s41467-018-07748-z. . Chacón-Duque JC1, Adhikari K1, Fuentes-Guajardo M1,2, Mendoza-Revilla J1,3, Acuña-Alonzo V1,4, Barquera R4,5, Quinto-Sánchez M6, Gómez-Valdés J7, Everardo Martínez P8, Villamil-Ramírez H9, Hünemeier T10, Ramallo V11,12, Silva de Cerqueira CC12, Hurtado M3, Villegas V3, Granja V3, Villena M13, Vásquez R14, Llop E15, Sandoval JR16, Salazar-Granara AA16, Parolin ML17, Sandoval K18, Peñaloza-Espinosa RI19, Rangel-Villalobos H20, Winkler CA21, Klitz W22, Bravi C23, Molina J24, Corach D25, Barrantes R26, Gomes V27,28, Resende C27,28, Gusmão L27,28,29, Amorim A27,28,30, Xue Y31, Dugoujon JM32, Moral P33, González-José R11, Schuler-Faccini L12, Salzano FM12, Bortolini MC12, Canizales-Quinteros S9, Poletti G3, Gallo C3, Bedoya G34, Rothhammer F15,35, Balding D1,36, Hellenthal G37, Ruiz-Linares A38,39. Author information 1 Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK. 2 Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000009, Chile. 3 Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru. 4 Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico. 5 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. 6 Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico. 7 Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico. 8 Posgrado en Antropología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico. 9 Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico. 10 Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, 05508-090, Brazil. 11 Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina. 12 Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil. 13 Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andrés (UMSA), La Paz, 2070, Bolivia. 14 Instituto Boliviano de Biología de Altura (IBBA), Universidad Autónoma Tomás Frías, Potosí, 53820, Bolivia. 15 Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile. 16 Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, 12, Peru. 17 Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina. 18 National Laboratory of Genomics and Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico. 19 Department of Biological Systems, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico. 20 Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, 1115, Mexico. 21 Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory, Frederick, MD, 21702, USA. 22 Integrative Biology, University of California, Berkeley, CA, 94720, USA. 23 Instituto Multidisciplinario de Biología Celular, CONICET, La Plata, B1906APO, Argentina. 24 Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, 01011, Guatemala. 25 Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina. 26 Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica. 27 Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal. 28 Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal. 29 DNA Diagnostic Laboratory (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 23968-000, Brazil. 30 Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal. 31 The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. 32 Centre National de la Recherche Scientifique, Université Toulouse 3 Paul Sabatier, Toulouse, 31330, France. 33 Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Universitat de Barcelona, Barcelona, 08007, Spain. 34 Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, 5001000, Colombia. 35 Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000009, Chile. 36 Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia. 37 Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK. g.hellenthal@ucl.ac.uk. 38 Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200433, China. andresruiz@fudan.edu.cn. 39 Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, 13007, France. andresruiz@fudan.edu.cn. 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. PMID: 30568240 DOI: 10.1038/s41467-018-07748-z