Lucie A Bergeron1, Søren Besenbacher2, Jaco Bakker3, Jiao Zheng4,5, Panyi Li4, George Pacheco6, Mikkel-Holger S Sinding7,8, Maria Kamilari1, M Thomas P Gilbert6,9, Mikkel H Schierup10, Guojie Zhang1,4,11,12. 1. Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark. 2. Department of Molecular Medicine, Aarhus University, Brendstrupgårdsvej 21A, 8200 Aarhus N, Denmark. 3. Animal Science Department, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands. 4. BGI-Shenzhen, Shenzhen 518083, Guangdong, China. 5. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China. 6. Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark. 7. Department of genetics, Trinity College Dublin, 2 college green, D02 VF25, Dublin, Ireland. 8. Greenland Institute of Natural Resources, Kivioq 2, 3900 Nuuk, Greenland. 9. Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway. 10. Bioinformatics Research Centre, Aarhus University, C.F.Møllers Allé 8, 8000, Aarhus C, Denmark. 11. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. 12. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
Abstract
BACKGROUND: Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. RESULTS: Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate. CONCLUSIONS: When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.
BACKGROUND: Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. RESULTS: Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate. CONCLUSIONS: When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.
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