Communications Biology (May 2023)
Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape
- Qing Li,
- Jieyi Chen,
- Pierre Faux,
- Miguel Eduardo Delgado,
- Betty Bonfante,
- Macarena Fuentes-Guajardo,
- Javier Mendoza-Revilla,
- J. Camilo Chacón-Duque,
- Malena Hurtado,
- Valeria Villegas,
- Vanessa Granja,
- Claudia Jaramillo,
- William Arias,
- Rodrigo Barquera,
- Paola Everardo-Martínez,
- Mirsha Sánchez-Quinto,
- Jorge Gómez-Valdés,
- Hugo Villamil-Ramírez,
- Caio C. Silva de Cerqueira,
- Tábita Hünemeier,
- Virginia Ramallo,
- Sijie Wu,
- Siyuan Du,
- Andrea Giardina,
- Soumya Subhra Paria,
- Mahfuzur Rahman Khokan,
- Rolando Gonzalez-José,
- Lavinia Schüler-Faccini,
- Maria-Cátira Bortolini,
- Victor Acuña-Alonzo,
- Samuel Canizales-Quinteros,
- Carla Gallo,
- Giovanni Poletti,
- Winston Rojas,
- Francisco Rothhammer,
- Nicolas Navarro,
- Sijia Wang,
- Kaustubh Adhikari,
- Andrés Ruiz-Linares
Affiliations
- 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
- Jieyi Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University
- Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES
- Miguel Eduardo Delgado
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University
- Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES
- Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá
- Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- J. Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum
- Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia
- William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia
- Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History
- Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History
- Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México)
- Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History
- Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica
- Caio C. Silva de Cerqueira
- Scientific Police of São Paulo State
- Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo
- Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
- Sijie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University
- Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences
- Andrea Giardina
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University
- Soumya Subhra Paria
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University
- Mahfuzur Rahman Khokan
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University
- Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET
- Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
- Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
- Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History
- Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica
- Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia
- Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica
- Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne
- Sijia Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University
- Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University
- Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University
- DOI
- https://doi.org/10.1038/s42003-023-04838-7
- Journal volume & issue
-
Vol. 6,
no. 1
pp. 1 – 13
Abstract
Abstract We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10−8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.