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1. Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis)

   https://doi.org/10.1101/2024.12.28.630620  

   Soni, Vivak; Versoza, Cyril J; Terbot, John W; Jensen, Jeffrey D; Pfeifer, Susanne P (December 2024, bioRxiv)

   The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species, but also across individual genomes. Despite previous studies having demonstrated that failing to account for rate heterogeneity across the genome can bias the inference of both selective and neutral population genetic processes, mutation and recombination rate maps have to date only been generated for a relatively small number of organisms. Here, we infer such fine-scale maps for the aye-aye (Daubentonia madagascariensis) – a highly endangered strepsirrhine that represents one of the earliest splits in the primate clade, and thus stands as an important outgroup to the more commonly-studied haplorrhines – utilizing a recently released fully-annotated genome combined with high-quality population sequencing data. We compare our indirectly inferred rates to previous pedigree-based estimates, finding further evidence of relatively low mutation and recombination rates in aye-ayes compared to other primates. 

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2. Inferring Fine‐Scale Mutation and Recombination Rate Maps in Aye‐Ayes ( Daubentonia madagascariensis )

   https://doi.org/10.1002/ece3.72314  

   Soni, Vivak; Versoza, Cyril J; Terbot, John W; Jensen, Jeffrey D; Pfeifer, Susanne P (November 2025, Ecology and Evolution)

   ABSTRACT The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species but also across individual genomes. Despite previous studies having demonstrated that failing to account for rate heterogeneity across the genome can bias the inference of both selective and neutral population genetic processes, mutation and recombination rate maps have to date only been generated for a relatively small number of organisms. Here, we infer such fine‐scale maps for the aye‐aye (Daubentonia madagascariensis)—a highly endangered strepsirrhine that represents one of the earliest splits in the primate clade and thus stands as an important outgroup to the more commonly studied haplorrhines—utilizing a recently released fully annotated genome combined with high‐quality population sequencing data. We compare our indirectly inferred rates to previous pedigree‐based estimates, finding further evidence of relatively low mutation and recombination rates in aye‐ayes compared to other primates. 

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3. Inferring fine-scale rates of mutation and recombination in the coppery titi monkey (Plecturocebus cupreus)

   https://doi.org/10.64898/2026.01.13.699361  

   Soni, Vivak; Versoza, Cyril J; Terbot, John W; Spatola, Gabriella J; Bales, Karen L; Jensen, Jeffrey D; Pfeifer, Susanne P (January 2026, bioRxiv)

   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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4. Rapid Evolution of the Fine-scale Recombination Landscape in Wild House Mouse ( Mus musculus ) Populations

   https://doi.org/10.1093/molbev/msac267  

   Wooldridge, Lydia K; Dumont, Beth L (January 2023, Molecular Biology and Evolution)

   Falush, Daniel (Ed.)

   Abstract Meiotic recombination is an important evolutionary force and an essential meiotic process. In many species, recombination events concentrate into hotspots defined by the site-specific binding of PRMD9. Rapid evolution of Prdm9's zinc finger DNA-binding array leads to remarkably abrupt shifts in the genomic distribution of hotspots between species, but the question of how Prdm9 allelic variation shapes the landscape of recombination between populations remains less well understood. Wild house mice (Mus musculus) harbor exceptional Prdm9 diversity, with >150 alleles identified to date, and pose a particularly powerful system for addressing this open question. We employed a coalescent-based approach to construct broad- and fine-scale sex-averaged recombination maps from contemporary patterns of linkage disequilibrium in nine geographically isolated wild house mouse populations, including multiple populations from each of three subspecies. Comparing maps between wild mouse populations and subspecies reveals several themes. First, we report weak fine- and broad-scale recombination map conservation across subspecies and populations, with genetic divergence offering no clear prediction for recombination map divergence. Second, most hotspots are unique to one population, an outcome consistent with minimal sharing of Prdm9 alleles between surveyed populations. Finally, by contrasting aggregate hotspot activity on the X versus autosomes, we uncover evidence for population-specific differences in the degree and direction of sex dimorphism for recombination. Overall, our findings illuminate the variability of both the broad- and fine-scale recombination landscape in M. musculus and underscore the functional impact of Prdm9 allelic variation in wild mouse populations. 

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5. Interpreting Patterns of X Chromosomal Relative to Autosomal Diversity in Aye‐Ayes ( Daubentonia madagascariensis )

   https://doi.org/10.1002/ajp.70091  

   Terbot, John W; Soni, Vivak; Versoza, Cyril J; Milhaven, Mark; Calahorra‐Oliart, Adriana; Shah, Devangana; Pfeifer, Susanne P; Jensen, Jeffrey D (December 2025, American Journal of Primatology)

   ABSTRACT We here present high‐quality, population‐level sequencing data from the X chromosome of the highly‐endangered aye‐aye,Daubentonia madagascariensis. Using both polymorphism‐ and divergence‐based inference approaches, we quantify fine‐scale mutation and recombination rate maps, study the demographic and selective processes additionally shaping variation on the X chromosome, and compare these estimates to those recently inferred from the autosomes in this species. Results suggest that an equal sex ratio is most consistent with observed patterns of variation, and that no sex‐specific demographic patterns are needed to fit the empirical site frequency spectrum. Further, reduced rates of recombination were observed relative to the autosomes as would be expected, whereas mutation rates were inferred to be similar. Utilizing the estimated population history together with the mutation and recombination rate maps, we evaluated evidence for both recent and recurrent selective sweeps as well as balancing selection across the X chromosome, finding no significant evidence supporting the action of these episodic processes. Overall, these analyses provide new insights into the evolution of the X chromosome in this species, which represents one of the earliest splits in the primate clade. 

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