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ABSTRACT Despite being a primate of considerable biomedical interest, particularly as a model for social behavior and neurobiology, the evolutionary processes shaping genetic variation in the coppery titi monkey (Plecturocebus cupreus) remain largely uncharacterized. Utilizing divergence and polymorphism data together with a recently published high-quality, annotated genome, we here infer the first fine-scale maps of mutation and recombination rates in this platyrrhine. We find a mean genome-wide mutation rate of between 0.93 × 10-8and 1.61 × 10-8per site per generation and a mean genome-wide recombination rate of 0.975 cM/Mb, in line with fine-scale rates estimated in other primates. In addition to providing novel biological insights into the mutation and recombination rates in this emerging model species for behavioral research, these fine-scale maps also improve our understanding of how the processes of mutation and recombination shape genetic variation in the coppery titi monkey genome, and their incorporation into evolutionary models will be a necessary aspect of future downstream inference of other evolutionary processes required to elucidate the genetic factors underlying the phenotypic traits studied in this species.
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Characterizing the rates and patterns of de novo germline mutations in coppery titi monkeys (Plecturocebus cupreus)
ABSTRACT Although recent advances in genomics have enabled the high-resolution study of whole genomes, our understanding of one of the key evolutionary processes, mutation, still remains limited. In primates specifically, studies have largely focused on humans and their closest evolutionary relatives, the great apes, as well as a handful of species of biomedical or conservation interest. Yet, as biological variation in mutation rates has been shown to vary across genomic regions, individuals, and species, a greater understanding of the underlying evolutionary dynamics at play will ultimately be illuminated by not only additional sampling across the Order, but also by a greater depth of sampling within-species. To address these needs, we here present the first population-scale genomic resources for a platyrrhine of considerable biomedical interest for both social behavior and neurobiology, the coppery titi monkey (Plecturocebus cupreus). Deep whole-genome sequencing of 15 parent-offspring trios, together with a computationalde novomutation detection pipeline based on pan-genome graphs, has provided a detailed picture of the sex-averaged mutation rate — 0.63 × 10-8(95% CI: 0.43 × 10-8– 0.90 × 10-8) per site per generation — as well as the effects of both sex and parental age on underlying rates, demonstrating a significant paternal age effect. Coppery titi monkey males exhibit long reproductive lifespans, afforded by long-term pair bonding in the species’ monogamous mating system, and our results have demonstrated that individuals reproducing later in life exhibit one of the strongest male mutation biases observed in any non-human primate studied to date. Taken together, this study thus provides an important piece of the puzzle for better comprehending the mutational landscape across primates.
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- Award ID(s):
- 2045343
- PAR ID:
- 10661940
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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ABSTRACT Along with germline mutations, meiotic recombination plays a fundamental role in shaping genetic diversity and thus directly influences a species’ potential adaptive response to environmental change, amongst other features. Despite the recombination landscape being of central importance for a variety of questions in molecular evolution, the genome-wide distribution and frequency of recombination remains to be elucidated in many non-human primate species. Utilizing novel high-coverage genomic data from three multi-sibling families, we here provide the first estimates of the rates and patterns of crossover and non-crossover recombination in coppery titi monkeys (Plecturocebus cupreus) — a socially monogamous, pair-bonded primate that serves as an important model in behavioral research. Consistent with haplorrhines, crossover and non-crossover recombination in this platyrrhine are frequently localized at PRDM9-mediated hotspots, characterized by a 15-mer binding motif with substantial similarities to the degenerate 13-mer motif found in humans. The sex-averaged crossover rate in coppery titi monkeys is comparable with those of other primates; however, no significant difference in recombination rates was observed between the sexes, despite a pronounced maternal age effect in the species. Similarities also exist with regards to the sex-specific genomic distribution of non-crossover events, though the minimal conversion tract lengths of extended events was observed to be considerably longer in maternally-inherited non-crossovers. Taken together, these similarities and differences in the recombination landscape relative to other primates highlight the importance of incorporating species-specific rates and patterns in evolutionary models, and the resources provided here will thus serve to aid future studies in this important primate model system.more » « less
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Given the many levels of biological variation in mutation rates observed to date in primates – spanning from species to individuals to genomic regions – future steps in our understanding of mutation rate evolution will be aided by both a greater breadth of species coverage across the primate clade, but also by a greater depth as afforded by an evaluation of multiple trios within individual species. In order to help bridge these gaps, we here present an analysis of a species representing one of the most basal splits on the primate tree (aye-ayes), combining whole-genome sequencing of seven parent-offspring trios from a three-generation pedigree with a novel computational pipeline that takes advantage of recently developed pan-genome graphs, thereby circumventing the application of (highly subjective) quality metrics that has previously been shown to result in notable differences in the detection of de novo mutations, and ultimately estimates of mutation rates. This deep sampling has enabled both a detailed picture of parental age effects as well as sex dependency in mutation rates which we here compare with previously studied primates, but has also provided unique insights into the nature of genetic variation in one of the most endangered primates on the planet.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Posted Content:
- https://doi.org/10.64898/2026.01.15.699688
