More Like this

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. 

   more » « less
2. 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. 

   more » « less
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. 

   more » « less
4. A whole-genome scan for evidence of positive and balancing selection in aye-ayes ( Daubentonia madagascariensis ) utilizing a well-fit evolutionary baseline model

   https://doi.org/10.1093/g3journal/jkaf078  

   Soni, Vivak; Terbot, John W; Versoza, Cyril J; Pfeifer, Susanne P; Jensen, Jeffrey D (April 2025, G3: Genes, Genomes, Genetics)

   Macdonald, S (Ed.)

   Abstract The aye-aye (Daubentonia madagascariensis) is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation within aye-aye populations, and the relative influences of neutral and selective processes in shaping that variation, is thus important for future conservation efforts. In this study, we performed the first whole-genome scans for positive and balancing selection in the species, utilizing high-coverage population genomic data from newly sequenced individuals. We generated null thresholds for our genomic scans by creating an evolutionarily appropriate baseline model that incorporates the demographic history of this aye-aye population, and identified a small number of candidate genes. Most notably, a suite of genes involved in olfaction—a key trait in these nocturnal primates—were identified as experiencing long-term balancing selection. We also conducted analyses to quantify the expected statistical power to detect positive and balancing selection in this population using site frequency spectrum–based inference methods, once accounting for the potentially confounding contributions of population history, mutation and recombination rate variation, as well as purifying and background selection. This work, presenting the first high-quality, genome-wide polymorphism data across the functional regions of the aye-aye genome, thus provides important insights into the landscape of episodic selective forces in this highly endangered species. 

   more » « less
5. A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model

   https://doi.org/10.1101/2024.11.08.622667  

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

   The aye-aye (Daubentonia madagascariensis) is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation within aye-aye populations, and the relative influences of neutral and selective processes in shaping that variation, is thus important for future conservation efforts. In this study, we performed the first whole-genome scans for recent positive and balancing selection in the species, utilizing high-coverage population genomic data from newly sequenced individuals. We generated null thresholds for our genomic scans by creating an evolutionarily appropriate baseline model that incorporates the demographic history of this aye-aye population, and identified a small number of candidate genes. Most notably, a suite of genes involved in olfaction — a key trait in these nocturnal primates — were identified as experiencing long-term balancing selection. We also conducted analyses to quantify the expected statistical power to detect positive and balancing selection in this population using site frequency spectrum-based inference methods, once accounting for the potentially confounding contributions of population history, recombination and mutation rate variation, and purifying and background selection. This work, presenting the first high-quality, genome-wide polymorphism data across the functional regions of the aye-aye genome, thus provides important insights into the landscape of episodic selective forces in this highly endangered species. 

   more » « less