Mutation rate variation in primates

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PROJECT SUMMARY Despite the critical importance of germline mutation in human genetics, we still lack the answer to basic questions, notably about how and why rates differ among individuals. We also lack a comparative context for interpreting findings, as, other than for one chimpanzee family, there are no direct estimates of germline mutation rates for non-human primates. These gaps in our understanding have important implications for evolutionary biology as well, leading in particular to considerable uncertainty about the steadiness of the “molecular clock” in primates. We therefore propose to obtain direct estimates of germline mutation rates within humans, in chimpanzees, and in three Old World monkey (OWM) species. In Aim 1, we will elucidate variation in human mutation rates with age, sex, and across families, separately for different mutation types. We will generate and analyze high-quality genome sequences for eight nuclear families of Hutterites (86 individuals) who belong to a single, 13-generation pedigree. Their relatively high consanguinity allows us to estimate mutation rates both in transmissions from parents to children and in autozygous segments descended from an older common ancestor. By relying on three-generation families with 3–6 children each, instead of the standard trio design, we can assign mutations to male or female germlines, verify transmission of putative mutations, and estimate rates of germline mosaicism. To these ends, we will also resequence a subset of mutations at deep coverage. In Aim 2, we will obtain the first direct estimate of mutation rates in an OWM species. Specifically, we will generate and analyze high- quality genome sequences for seven three-generation families of vervet monkeys (43 individuals, for which ages are known). These individuals belong to a colony of 2,000+ in an 11-generation pedigree, so the data are very similar in structure to that of the Hutterites, and will be analyzed by the same approaches, providing a well-matched comparison to humans. In Aim 3, we will examine the evolution of mutation rates across apes and OWMs. We will generate high-quality genome sequences for ten overlapping nuclear families of western chimpanzees (54 individuals), five families of rhesus macaques (22), and two families of olive baboons (13), for which parental ages are known. The genomic data will be generated using a uniform approach, and a subset of putative mutations will be resequenced to estimate error rates. This analysis will yield the first direct look at the evolution of mutation rates across a set of closely related species, and allow us to revisit the chronology of primate evolution with a more reliable molecular clock. Thus, this study will elucidate variation in the mutation process within human and among closely related species. As a byproduct, the data will enable primate evolutionary genomics and mapping efforts in primate model organisms.