Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America

The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse, Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify-three regionally distinct groups- 1) P. m. gambelii (southern California); 2) P. keeni (Pacific Northwest); 3) P. m. sonoriensis (a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.

A new mouse of the Peromyscus maniculatus species complex (Cricetidae) from the highlands of central Mexico

The Peromyscus maniculatus species complex is one of the most widespread group of small mammals in North America. However, the taxonomy and phylogenetic relationships among its constituent taxa remain unclear. As part of a revision of Peromyscus specimens from the highlands of the Trans-Mexican Volcanic Belt in central Mexico, we identified five individuals collected in 1968 that differed externally from other Peromyscus specimens, although morphologically similar to P. labecula and P. melanotis, both latter in the P. maniculatus species complex. Based on cranial measurements and mitochondrial DNA sequences, we aimed to more accurately determine the phylogenetic relationships and the taxonomic status of these individuals. Molecular phylogenetic analyses showed that the specimens formed a monophyletic clade sister to the P. maniculatus species complex. Pairwise genetic distances between those specimens and other species within the P. maniculatus species complex were greater than 7.91%. In addition, morphological analyses clearly distinguished the test specimens from P. melanotis and P. labecula. Based on the results of our molecular and morphological analyses, we conclude that these specimens represent an undescribed species of the P. maniculatus species complex, which we describe herein.