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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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Sex-specific landscapes of crossover and non-crossover recombination in coppery titi monkeys (Plecturocebus cupreus)
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.
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- Award ID(s):
- 2045343
- PAR ID:
- 10661941
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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.more » « less
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Gaining a better understanding of rates and patterns of meiotic recombination is crucial for improving evolutionary genomic modelling, with applications ranging from demographic to selective inference. Although previous research has provided important insights into the landscape of crossovers in humans and other haplorrhines, our understanding of both the considerably more common outcome of recombination (i.e., non-crossovers) as well as the landscapes in more distantly-related primates (i.e., strepsirrhines) remains limited owing to difficulties associated with both the identification of non-crossover tracts as well as species sampling. Thus, in order to elucidate recombination patterns in this under-studied branch of the primate clade, we here characterize crossover and non-crossover landscapes in aye-ayes utilizing whole-genome sequencing data from six three-generation pedigrees as well as three two-generation multi-sibling families, and in so doing provide novel insights into this important evolutionary process shaping genomic diversity in one of the world’s most critically endangered primate species.more » « less
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Guschanski, Katerina (Ed.)Abstract Gaining a better understanding of the rates and patterns of meiotic recombination is crucial for improving evolutionary genomic modeling, with applications ranging from demographic to selective inference. Although previous research has provided important insights into the landscape of crossovers in humans and other haplorrhines, our understanding of both the considerably more common outcome of recombination (i.e. noncrossovers) as well as the landscapes in more distantly related primates (i.e. strepsirrhines) remains limited owing to difficulties associated with both the identification of noncrossover tracts as well as species sampling. Thus, in order to elucidate recombination patterns in this understudied branch of the primate clade, we here characterize crossover and noncrossover landscapes in aye-ayes utilizing whole-genome sequencing data from six three-generation pedigrees and three two-generation multi-sibling families, and in so doing provide novel insights into this important evolutionary process shaping genomic diversity in one of the world's most critically endangered primate species.more » « less
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Coppery titi monkeys (Plecturocebus cupreus) are an important non-human primate model for studying neurobiology and social behavior, in part owing to their relatively unusual combination of social monogamy and paternal care. Despite this importance, relatively little is known regarding the underlying population genomics of this platyrrhine. This study presents high-coverage, whole-genome sequencing data from 26 individuals which, combined with a highly accurate multi-algorithm ensemble approach, was used to characterize the first map of structural variation in the species. This novel genomic resource includes over 13,000 structural variants, with the majority (>90%) being copy number variants. While many of these were found to be located in intergenic regions, several affected genes associated with disease, including an inversion predicted to impact a pathway implicated in early-onset Parkinson's disease. Furthermore, utilizing parent-offspring trios included within this study, the de novo structural variant rate was estimated to be one in every 1.5 births, similar to that reported in rhesus macaques but considerably higher than that observed in large human cohorts, as may be expected from underlying differences in life history traits amongst these species. Taken together, these insights into the structural variant landscape ofP. cupreuswill not only improve their utility as a behavioral model system, but will also contribute to our general understanding of the role of structural variation in both the evolution of the primate clade and disease-outcomes.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript
- Posted Content:
- https://doi.org/10.64898/2026.01.11.698870
