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Pleistocene vicariance is often invoked to explain the disjunct populations of animals in habitat refugia throughout the southwestern United States. The combined effects of small population size and isolation from the rest of the contiguous range are thought to result in genetic differentiation of relict organisms.

Here, we describe a relict population of dusky-footed woodrats (Neotoma fuscipes Baird) found in a pinyon-juniper-oak community in a small mountain range within the Mojave Desert. We compare morphological and genetic data for these individuals with two populations within the contiguous range, and with another species of woodrat (Neotoma lepida). We also examine the distributional overlap between contemporary oak species and dusky-footed woodrats, and estimate the potential oak woodland habitat available during the late Quaternary.

As expected, both the morphological and generic analysis confirm that the relict population is N. fuscipes. Within the limitations of our data, we detect no evidence of differentiation, Instead, the relict population forms a paraphyletic group with the nearest population within the contiguous range. This may be explained by the combined influences of a shorter period of isolation and a greater effective population size than was originally expected.

The linkage between contemporary oak and dusky-footed woodrat distributions is very tight, reinforcing the idea of an obligate relationship between the two.

We estimate that at similar to 8000 ybp, pinyon-juniper-oak woodlands may have covered similar to 53% of the central Mojave, forming large contiguous areas of habitat. Although considerably more fragmented, at present similar to 12% of the area consists of relict woodlands.

Our results suggest that there may be numerous other woodrat refugia, with a relatively high degree of connectiveness between the larger ones. Animals within them may effectively function as a single metapopulation, buffering against occasional stochastic extinction events.