Unveiling hidden diversity: Phylogenomics of Neotomine rodents and taxonomic implications for the genus Peromyscus

Neotomine rodents (Cricetidae, Neotominae) represent one of the most commonly encountered and diverse group of rodents in North America, yet phylogenetic relationships within this group remain uncertain. We used ultraconserved elements and mitogenomes to analyzed several species within Neotominae to resolve phylogenetic relationships within the subfamily, and to further explore their evolutionary history and taxonomic boundaries. Our analyses, including Maximum Likelihood and Bayesian Inference with both mitogemomes and UCEs, as well as the coalescent species-tree-based approach with UCEs, consistently recovered concordant and well-resolved phylogenies with high levels of nodal support.