Moorjani Priya, Amorim Carlos Eduardo G, Arndt Peter F, Przeworski Molly
Department of Biological Sciences, Columbia University, New York, NY 10027; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142;
Department of Biological Sciences, Columbia University, New York, NY 10027;
Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10607-12. doi: 10.1073/pnas.1600374113. Epub 2016 Sep 6.
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.
灵长类动物进化事件的年代通常是通过假设单位时间内恒定的替代率来确定的，但这一假设的有效性仍不明确。在哺乳动物中，众所周知，每年的替代率存在很大差异。这种差异是由生活史特征的不同所预期的，这表明在灵长类动物中也应该能发现这种差异。出于这些考虑，我们分析了10种灵长类动物的全基因组，包括旧世界猴（OWMs）、新世界猴（NWMs）和猿类，重点关注假定为中性的常染色体位点，并控制CpG位点上偏向基因转换和甲基化的可能影响。我们发现，从类人猿 - 新世界猴祖先到新世界猴的谱系中的替代率比到猿类的谱系高出64%。在猿类中，黑猩猩的替代率比人类高约2%，大猩猩的替代率比人类高约7%。受偏向基因转换影响的替代类型在物种间的差异并不比不受其影响的类型更大。然而，并非所有突变类型的行为都相似；特别是，CpG位点的转换比其他类型表现出更类似时钟的行为，大概是因为它们的非复制起源。因此，不仅总速率，而且突变谱在灵长类动物中也有所不同。这一发现表明，灵长类动物进化事件最可靠的年代测定是使用CpG转换。采用这种方法，我们估计人类和黑猩猩的分化时间为1210万年，人类和大猩猩的分化时间为1510万年。
