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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Published in:Proceedings of the National Academy of Sciences - PNAS Vol. 113; no. 38; pp. 10607 - 10612
Main Authors: Moorjani, Priya, Amorim, Carlos Eduardo G, Arndt, Peter F, Przeworski, Molly
Format: Journal Article
Language:English
Published: United States 20.09.2016
Subjects:
Amino Acid Substitution - genetics
Animals
Biological Evolution
DNA Methylation - genetics
Evolution, Molecular
Gene Conversion - genetics
Genetic Variation
Genome - genetics
Gorilla gorilla - genetics
Humans
Pan troglodytes - genetics
Primates - genetics
CpG transition rate
human–ape divergence time
mutation rate
molecular clock
primate evolution
ISSN:1091-6490
Online Access:Get more information
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Summary: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​.
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ISSN:1091-6490
DOI:10.1073/pnas.1600374113