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. molecular clock | mutation rate | primate evolution | CpG transition rate | human-ape divergence time G ermline mutations are the ultimate source of genetic differences among individuals and species. They are thought to arise from a combination of errors in DNA replication (e.g., the chance misincorporation of a base pair) or damage that is unrepaired by the time of replication (e.g., the spontaneous deamination of methylated CpG sites) (1). If mutations are neutral (i.e., do not affect fitness), then the rate at which they arise will be equal to the substitution rate (2). A key consequence is that if mutation rates remain constant over time, substitution rates should likewise be constant.This assumption of constancy of substitution rates plays a fundamental role in evolutionary genetics by providing a molecular clock with which to date events inferred from genetic data (3). Notably, important events in human evolution for which there is no fossil record (e.g., when humans and chimpanzees split, or when anatomically modern humans left Africa) are dated using a mutation rate obtained from contemporary pedigrees or phylogenetic analysis, assuming the per year rate has remained unchanged for millions of years (4).However, we know from studies of mammalian phylogenies, as well as of other taxa, that there can be substantial variation in substitution rates per unit time (5-7). In particular, there is the well-known hypothesis of a "generation time effect" on substitution rates,...