The geographic genetic structure, based on sequence variation of an 810 base pair fragment of the mitochondrial cytochrome b gene, is described for populations of five subspecies of the Little Pocket Mouse, Perognathus longimembris, from Southern California. One of these, P. l. pacificus (Pacific Pocket Mouse), is listed as Endangered by the U.S. Federal Government. Sixty-two unique haplotypes were recovered from 99 individuals sampled. Phylogenetic analyses of these variants do not identify regionally reciprocally monophyletic lineages concordant with the current subspecies designations, but most haplotypes group by subspecies in networks generated by either statistical parsimony or molecular variance parsimony.Moreover, a substantial proportion of the total pool of haplotype variation is attributed to these subspecies, or to local populations within geographic segments of each, indicating their relative evolutionary independence. The pooled extant populations of the endangered Pacific Pocket Mouse exhibit the same levels of nucleotide and haplotype diversity as other, presumptively less-impacted populations of adjacent subspecies, although the sample from Dana Point, Orange County, has markedly low haplotype diversity in comparison to all others. These populations also show a genetic signature of population expansion rather than one of decline. Both pieces of evidence are at odds with current empirical population estimates, which reinforces the fact that present-day patterns of genetic diversity are the product of coalescent history and will not necessarily reflect recent anthropogenic, or other, perturbations. Comparison of haplotype variation within and among extant populations of the Pacific Pocket Mouse with those obtained from museum samples collected more than 70 years ago suggests that the pattern of population differentiation and diversity was in place before the post-WorldWar II exponential urbanization of Southern California.

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