A global catalog of whole-genome diversity from 233 primate species
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, Fabrício; Byrne, Hazel; Sampaio, Iracilda; Farias, Izeni; Valsecchi, João; Messias, Malu; da Silva, Maria N. F.; Trivedi, Mihir; Rossi, Rogerio; Hrbek, Tomas; Andriaholinirina, Nicole; Rabarivola, Clément 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, Guojie; Keyyu, Julius D.; Knauff, 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, Rob M. D.; Umapathy, Govindhaswamy; Roos, Christian; Boubli, Jean P.; Rogers, Jeffrey; Farh, Kyle Kai-How; Bonet, Toma Marques Bonet
Date:
2023-06
Abstract:
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
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