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

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.We would like to dedicate this paper to the memory of L.L. Cavalli-Sforza, a wonderful mentor and a constant source of inspiration. We are grateful to the volunteers for supporting this research. We thank Alvaro Alvarado, William Arias, Mónica Ballesteros Romero, Ricardo Cebrecos, Miguel Ángel Contreras Sieck, Francisco de Ávila Becerril, Joyce De la Piedra, María Teresa Del Solar, Gastón Macín, William Flores, Martha Granados Riveros, Rosilene Paim, Ricardo Gunski, Sergeant João Felisberto Menezes Cavalheiro, Major Eugênio Correa de Souza Junior, Wendy Hart, Ilich Jafet Moreno, Claudia Jaramillo, Paola León-Mimila, Francisco Quispealaya, Diana Rogel Diaz, Ruth Rojas and Vanessa Sarabia, for assistance with volunteer recruitment, sample processing and data entry. We acknowledge the institutions that provided facilities for the assessment of volunteers: Escuela Nacional de Antropología e Historia and Universidad Nacional Autónoma de México (México); Universidade Federal do Rio Grande do Sul (Brazil); 13° Companhia de Comunicações Mecanizada do Exército Brasileiro (Brazil); Pontificia Universidad Católica del Perú, Universidad de Lima and Universidad Nacional Mayor de San Marcos (Perú). We also thank the National Laboratory for the Genetics of Israeli Populations (http://yoran.tau.ac.il/nlgip/) and Dr. David Gurwitz for making available DNA samples. We thank Chris Tyler-Smith and Caroline Costedoat for comments on the manuscript. Work leading to this publication was funded by grants from: 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 programme), Wellcome Trust/Royal Society (098386/Z/12/Z to G.H.), 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) and Fundação de Aperfeiçoamento de Pessoal de Nível Superior. V.G. is supported by Fundação para a Ciência e Tecnologia (FCT) and Programa Operacional Potencial Humano (POCH), through the grant SFRH/BPD/76207/2011. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. Y.X. was supported by The Wellcome Trust (098051). K.A. was supported by an UCL Global Engagement Fund, and a Wellcome Investigator Award WT107055AIA (to Prof. C.D. Stern). J.C.C.D. was supported by a doctoral scholarship from COLCIENCIAS (Colombia)