Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic

The northern Rocky Mountains have experienced a complex history of geologic al events and environmental fluctuation, including Pleistocene glaciation. To provide an initial assessment of the genetic impact of this history on t he regional biota we estimated phylogenetic relationships within Tamias ruf icaudus, a regional endemic, from cytochrome b sequence variation using par simony, maximum likelihood, and nested clade analysis. Analyses of sequence variation in 187 individuals from 43 localities across the distribution of T. ruficaudus indicate a history of vicariance events and range fluctuatio n consistent with successive periods of extensive Pleistocene glaciation in the northern Rocky Mountains. Intraspecific divergence levels (c. 4.7% unc orrected) and phylogenetic structure are consistent with a genealogical vic ariance initiated prior to the Late Pleistocene, whereas nested clade analy ses indicate more recent population history structured by both fragmentatio n and range expansion. A comparison of sequence variation with bacular morp hology indicates that the two genetically and morphologically differentiate d entities exhibit a zone of differential character introgression. Sequence data support a multiple refugia hypothesis and provide a phylogeographical case study for the ongoing synthesis of regional biogeography for northern Rocky Mountain endemics.