Aim To reconstruct the regional biogeographical history of the bushy-tailed woodrat, Neotoma cinerea (Rodentia: Cricetidae), across its distribution using multiple sources of information, including genetic data, ecological niche models and the palaeorecord.
Location Western North America.
Methods We analysed complete cytochrome b gene (1143 bp) sequences from 182 specimens of N. cinerea using Bayesian and coalescent methods to infer phylogenetic relationships, time of major divergences, and recent demographic trends. For comparison, we developed clade-specific ecological niche models for groups of interest and analysed spatial trends of N. cinerea in the palaeorecord as well as temporal frequency trends across strata of individual palaeomiddens.
Results We found two largely allopatric clades within N. cinerea, with several regionally distinct subclades showing contrasting recent population dynamics. Niche models showed consistent habitat at the Last Glacial Maximum (LGM) and modern times in the Rocky Mountains and northern United States, while the Great Basin may have been markedly less suitable at the LGM than today. The palaeorecord showed great spatio-temporal variability in the presence of N. cinerea, but documents broad-scale patterns of occupancy and regional population trends.
Main conclusions The Quaternary dynamics and evolutionary history of N. cinerea appear to have been shaped by both vicariant events associated with geographical barriers and the availability of suitable habitat through time. Divergence of the two major clades dates to the Pliocene–Pleistocene transition, with clades separated by the Green and Colorado rivers and northern Rocky Mountain Pleistocene glaciations. We found largely concordant genetic, niche model and palaeorecord patterns suggesting long-term population stability in the Rocky Mountains, while extant clades in the Great Basin and far north appear to have expanded or re-expanded into these regions relatively recently. Furthermore, disjunct haplotype distributions, regional demographic history, and historical distribution of suitable habitat suggest that the Great Basin has been a particularly dynamic region.