The germline mutational process in rhesus macaque and its implications for phylogenetic dating
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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.
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Now published in GigaScience doi: 10.1093/gigascience/giab029
Lucie A. Bergeron 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucie A. BergeronFor correspondence: guojie.zhang@bio.ku.dk lucie.a.bergeron@gmail.comSøren Besenbacher 2Department of Molecular Medicine, Aarhus University, Aarhus, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJiao Zheng 4BGI-Shenzhen, Shenzhen 518083, Guangdong, China5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePanyi Li 4BGI-Shenzhen, …
Now published in GigaScience doi: 10.1093/gigascience/giab029
Lucie A. Bergeron 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucie A. BergeronFor correspondence: guojie.zhang@bio.ku.dk lucie.a.bergeron@gmail.comSøren Besenbacher 2Department of Molecular Medicine, Aarhus University, Aarhus, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJiao Zheng 4BGI-Shenzhen, Shenzhen 518083, Guangdong, China5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePanyi Li 4BGI-Shenzhen, Shenzhen 518083, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGeorge Pacheco 6Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMikkel-Holger S. Sinding 7Trinity College Dublin, Dublin, Ireland8Greenland Institute of Natural Resources, Nuuk, GreenlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMaria Kamilari 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM. Thomas P. Gilbert 6Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark9Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMikkel H. Schierup 10Bioinformatics Research Centre, Aarhus University, Aarhus, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuojie Zhang 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark4BGI-Shenzhen, Shenzhen 518083, Guangdong, China11State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China12Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: guojie.zhang@bio.ku.dk lucie.a.bergeron@gmail.com
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab029 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102718 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102719
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