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 evaluatedpopulation structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic historyusing a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum, LGM) environmentalsuitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify threeregionally distinct groups- 1) P. m. gambelii (southern California), 2) P. keeni (Pacific Northwest), 3) P. m. sonoriensis (a broad population spanningthe Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits betweenthe three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of theselineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in thepast. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacialperiods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period ledto population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscapetransformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distributionof biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.