Biology subjects

Spatola, G. J.

Publications and source records attributed to Spatola, G. J..

4 recordsLinked to original sources

bioRxiv2026

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data

The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome, PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and non-model based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data, and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time [~]140,000 generations ago from an ancestral population of [~]65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of [~]220,000 individuals in the Chinese population and [~]14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.

evolutionary biology↗

bioRxiv2026

Comparing fine-scale mutation and recombination landscapes in rhesus macaque (Macaca mulatta) populations of Chinese and Indian descent inferred from both short- and long-read sequencing data

Genomic diversity amongst primates is fundamentally shaped by species- and population-specific rates of mutation and recombination. In this study, we infer fine-scale mutation and recombination rate maps for the rhesus macaque (Macaca mulatta) -- the most widely used non-human primate model in biomedical research -- leveraging both short-(Illumina) and long-(PacBio HiFi) read sequencing data from two distinct populations of Chinese and Indian descent. Thereby, we draw comparisons between the rates estimated from each dataset, highlighting both biologically meaningful variation between these populations as well as artefactual discrepancies likely arising from systematic biases and differences in the utilized sequencing technologies. Consistent with previous observations in humans, broad-scale features of the recombination landscape are well-conserved between the two populations, but significant differences exist at the finer scales. Notably, we find evidence for a high rate of turnover in recombination hotspots over a short evolutionary time span, resulting in population-specific recombination maps in which the vast majority of the >30,000 identified recombination hotspots in one population are inactive in the other population. Given that mutation and recombination rates are necessary components for the interpretation of other diversity-shaping processes and events, including those characterizing both the underlying demographic and selective histories, the incorporation of these population-specific maps into future models will improve our understanding of the evolutionary genomics of the species. Additionally, these maps will serve as a fundamental component of future genome-wide association and fine-mapping studies of disease traits in this biomedical model system.

evolutionary biology↗

bioRxiv2026

Inferring patterns of purifying, positive and balancing selection in the coppery titi monkey (Plecturocebus cupreus) utilizing a well-fit evolutionary baseline model

Despite the coppery titi monkey (Plecturocebus cupreus) being a model system for the study of neurodevelopment and behavior, the evolutionary forces shaping observed levels and patterns of genetic variation in the species have remained poorly studied. In order to illuminate the pervasive eCects of purifying and background selection, we have fit a distribution of fitness eCects of newly arising exonic mutations, utilizing patterns of polymorphism and divergence based on a recently published high-quality genome assembly. To further characterize episodically acting selective processes, we additionally performed the first whole-genome scans for recent positive and balancing selection in this species, reducing false-positive rates by incorporating the demographic history of the population into an evolutionary null model. These scans identified a small number of biomedically-relevant genes with strong statistical support for having experienced recent selective sweeps or long-term balancing selection. In addition, we identified four genomic deletions bearing the signatures of balancing selection. Taken together, this study provides the first insights into patterns of persistent and episodic selective processes in this species.

evolutionary biology↗

bioRxiv2026

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

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 x 10-8 and 1.61 x 10-8 per 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.

evolutionary biology↗