Geographic patterns of genetic differentiation within the restricted rangeof the endangered Stephens' kangaroo rat Dipodomys stephensi

Using mtDNA variation in the kangaroo rat Dipodomys stephensi, we found no support for the hypothesis that a species with an historically restricted r ange will exhibit low levels of genetic polymorphism and little genetic str ucture. Dipodomys stephensi has long been restricted to a few interior coas tal valleys in southern California encompassing an area of approximately 70 x 40 km; however, we found high levels of genetic variation over much of i ts range and significant genetic structure both within and between regions. We also found evidence for a recent range expansion. Dipodomys stephensi i s a federally endangered species that is separated from D. panamintinus, it s presumed sister taxon, by a mountain range to the north. We assessed gene tic variation by sequencing 645 bases of the mitochondrial d-loop from 61 i ndividuals sampled from 16 locations across the species range and rooted th eir relationship using two D. panamintinus individuals. Despite its limited geographic range, the level of mtDNA variation in D. stephensi is comparab le to that of other rodents, including that of the more widely distributed D. panamintinus. This variation revealed significant regional differentiati on. The northern, central, and southern regions of the range differ in both the level and the distribution of genetic variation. Phylogenetic analysis revealed that the center of the range contains the most diversity of linea ges, including the most basal. In this region and in the north, most haplot ypes were found at only a single location (25/29), or at a pair of nearby l ocations (3/29). In addition, related haplotypes clustered geographically. These results are consistent with long-term demographic stability character ized by limited dispersal and high local effective population size. Further support for this conclusion is the finding of unique diversity in two nort hern peripheral populations, Norco and Potrero Creek (PC). However, in shar p contrast, one haplotype (CC) was found at five of ii central and northern locations and comprised 18% of individuals sampled. The atypical distribut ion of the CC haplotype reflected a pattern seen more strongly in the south ern region. Here the CC haplotype comprised 69% of the sample and was found at all five sampling locations. Consequently, the southern region had very low genetic variability. We propose that this dominance of CC was probably due to a local population bottleneck that occurred during a recent range e xpansion into the southern region.