A global catalog of whole-genome diversity from 233 primate species

• 成果类型: Article
• 署名作者: Kuderna, Lukas F. K.; Gao, Hong; Janiak, Mareike C.; Kuhlwilm, Martin; Orkin, Joseph D.; Bataillon, Thomas; Manu, Shivakumara; Valenzuela, Alejandro; Bergman, Juraj; Rousselle, Marjolaine; Silva, Felipe Ennes; Agueda, Lidia; Blanc, Julie; Gut, Marta; de Vries, Dorien; Goodhead, Ian; Harris, R. Alan; Raveendran, Muthuswamy; Jensen, Axel; Chuma, Idrissa S.; Horvath, Julie E.; Hvilsom, Christina; Juan, David; Frandsen, Peter; Schraiber, Joshua G.; de Melo, Fabiano R.; Bertuol, Fabricio; Byrne, Hazel; Sampaio, Iracilda; Farias, Izeni; Valsecchi, Joao; Messias, Malu; da Silva, Maria N. F.; Trivedi, Mihir; Rossi, Rogerio; Hrbek, Tomas; Andriaholinirina, Nicole; Rabarivola, Clement J.; Zaramody, Alphonse; Jolly, Clifford J.; Phillips-Conroy, Jane; Wilkerson, Gregory; Abee, Christian; Simmons, Joe H.; Fernandez-Duque, Eduardo; Kanthaswamy, Sree; Shiferaw, Fekadu; Wu, Dongdong; Zhou, Long; Shao, Yong; Zhang, Guoji; Keyyu, Julius D.; Knauf, Sascha; Le, Minh D.; Lizano, Esther; Merker, Stefan; Navarro, Arcadi; Nadler, Tilo; Khor, Chiea Chuen; Lee, Jessica; Tan, Patrick; Lim, Weng Khong; Kitchener, Andrew C.; Zinner, Dietmar; Gut, Ivo; Melin, Amanda D.; Guschanski, Katerina; Schierup, Mikkel Heide; Beck, Robin M. D.; Umapathy, Govindhaswamy; Roos, Christian; Boubli, Jean P.; Rogers, Jeffrey; Farh, Kyle Kai-How; Bonet, Tomas Marques
• 署名单位: Pompeu Fabra University; Illumina; University of Salford; University of Vienna; University of Vienna; Universite de Montreal; Aarhus University; Academy of Scientific & Innovative Research (AcSIR); Council of Scientific & Industrial Research (CSIR) - India; CSIR - Centre for Cellular & Molecular Biology (CCMB); Aarhus University; Universite Libre de Bruxelles; Barcelona Institute of Science & Technology; Pompeu Fabra University; Centre de Regulacio Genomica (CRG); Baylor College of Medicine; Baylor College of Medicine; Uppsala University; University of North Carolina; North Carolina Central University; North Carolina State University; Duke University; University of North Carolina; University of North Carolina Chapel Hill; Universidade Federal de Vicosa; Universidade Federal de Amazonas; Utah System of Higher Education; University of Utah; Universidade Federal do Para; Universidade Federal de Rondonia; Institute Nacional de Pesquisas da Amazonia; Universidade Federal de Mato Grosso; Trinity University; New York University; Saint Louis University; Washington University (WUSTL); University of Texas System; UTMD Anderson Cancer Center; Yale University; Arizona State University; Arizona State University-Downtown Phoenix; Chinese Academy of Sciences; Kunming Institute of Zoology, CAS; Zhejiang University; University of Copenhagen; Chinese Academy of Sciences; Kunming Institute of Zoology, CAS; Liangzhu Laboratory; Zhejiang University; Zhejiang University; Friedrich Loeffler Institute; Vietnam National University Hanoi (VNU Hanoi) System; Vietnam National University Hanoi (VNU Hanoi) System; Autonomous University of Barcelona; Institut Catala de Paleontologia Miquel Crusafont (ICP); ICREA; Pompeu Fabra University; Barcelona Institute of Science & Technology; Pompeu Fabra University; Centre de Regulacio Genomica (CRG); Agency for Science Technology & Research (A*STAR); A*STAR - Genome Institute of Singapore (GIS); National University of Singapore; Leibniz Association; Deutsches Primatenzentrum (DPZ); University of Gottingen; University of Calgary; University of Calgary; University of Calgary; University of Edinburgh; Leibniz Association; Deutsches Primatenzentrum (DPZ)
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-11297
• DOI: 10.1126/science.abn7829
• 发表日期: 2023-06-02
• 页码: 906-912
• 关键词: coverage neanderthal genome; population genomics; mutation-rate; EVOLUTION; reveal; insights; reconstruction; hybridization; determinants; chimpanzee

摘要

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage wholegenome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.