Variation in the molecular clock of primates
Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from diff...
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2017
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| Online Access: | http://hdl.handle.net/1721.1/108808 |
| _version_ | 1826188820304887808 |
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| author | Moorjani, Priya Amorim, Carlos Eduardo G. Arndt, Peter F. Przeworski, Molly |
| author2 | Broad Institute of MIT and Harvard |
| author_facet | Broad Institute of MIT and Harvard Moorjani, Priya Amorim, Carlos Eduardo G. Arndt, Peter F. Przeworski, Molly |
| author_sort | Moorjani, Priya |
| collection | MIT |
| description | Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid–NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years, and the human and gorilla divergence time is 15.1 million years. |
| first_indexed | 2024-09-23T08:05:32Z |
| format | Article |
| id | mit-1721.1/108808 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:05:32Z |
| publishDate | 2017 |
| publisher | National Academy of Sciences (U.S.) |
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| spelling | mit-1721.1/1088082022-09-23T10:51:17Z Variation in the molecular clock of primates Moorjani, Priya Amorim, Carlos Eduardo G. Arndt, Peter F. Przeworski, Molly Broad Institute of MIT and Harvard Massachusetts Institute of Technology. Department of Biology Moorjani, Priya Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid–NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years, and the human and gorilla divergence time is 15.1 million years. United States. National Institutes of Health (F32 GM115006-01) 2017-05-11T14:37:39Z 2017-05-11T14:37:39Z 2016-09 2016-07 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/108808 Moorjani, Priya; Amorim, Carlos Eduardo G.; Arndt, Peter F. and Przeworski, Molly. “Variation in the Molecular Clock of Primates.” Proceedings of the National Academy of Sciences 113, no. 38 (September 2016): 10607–10612. © 2016 National Academy of Sciences en_US http://dx.doi.org/10.1073/pnas.1600374113 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Moorjani, Priya Amorim, Carlos Eduardo G. Arndt, Peter F. Przeworski, Molly Variation in the molecular clock of primates |
| title | Variation in the molecular clock of primates |
| title_full | Variation in the molecular clock of primates |
| title_fullStr | Variation in the molecular clock of primates |
| title_full_unstemmed | Variation in the molecular clock of primates |
| title_short | Variation in the molecular clock of primates |
| title_sort | variation in the molecular clock of primates |
| url | http://hdl.handle.net/1721.1/108808 |
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