Novel genomic resources contribute to the systematics of threatened arboreal deer mice of the genus Hooper & Musser, 1964 (Cricetidae, Neotominae) within a neotomine-peromyscine phylogeny.

The Crested-tailed deer mouse, , is one of seven arboreal species within the genus . Species of this genus are monotypic, relatively rare, and occur in low densities. Their geographical distribution is highly fragmented due to being restricted to montane cloud forest in Mesoamerica and they are of conservation concern. All species are endemic to Mexico, except , which is also distributed in Guatemala and El Salvador. In this study, we obtained and characterized the first mitogenome and several thousand nuclear ultraconserved elements (UCEs) of to determine its phylogenetic position within neotomine-peromyscine mice. Its mitogenome sequence (16,509 bp) is only the second complete mitogenome obtained for this poorly known genus. We also obtained the first nuclear genomic data for , including 3,654 UCE loci, as well as a partial mitogenome of (6,349 bp), and 2,186 UCE for the outgroup . Phylogenetic analyses that included our newly generated genomic data coupled with previously published data from other neotomine-peromyscine mice confirm the placement of , , and within a highly supported clade. The clade was nested within a clade that also contains members of the genus and provides further support for the hypothesis of the paraphyly of . These genomic resources will contribute to future phylogenomic studies that aim to further elucidate the evolutionary history of this rare and critically endangered genus of rodents.