Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population.

Although least chipmunks () are a widely distributed North American species of least concern, the southernmost population, (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the range to assess genomic differentiation and distinctiveness of the population. Additionally, we leveraged the historical component of sampling to conduct a temporal analysis of genetic diversity and also considered climate change effects on range persistence probability by projecting a species distribution model into the IPCC5 RCP 2.