Comparative phylogeography of Baileys' pocket mouse (Chaetodipus baileyi) and the Peromyscus eremicus species group: historical vicariance of the Baja California Peninsular Desert.

Phylogenetic analysis of 699 bp of the mitochondrial DNA (mtDNA) COIII and 450 bp of the cytochrome b genes among 14 species of coarse-haired pocket mice (Heteromyidae: Chaetodipus) corroborated previous indications that genetic divergence between species and species groups within the genus is generally very high, suggesting old times of divergence, and that the nominal species C. baileyi represents a highly divergent lineage within the genus, with no closely related extant sister species. Analysis of phylogeographic structure among 51 individuals from 12 localities throughout the geographic range of C. baileyi revealed three geographically separate mtDNA haplotype lineages. The oldest split separates populations east and west of the Colorado River, a pattern that is congruent with chromosomal and allozyme electrophoretic evidence. We consider the western populations to represent a distinct species, C. rudinoris. Within C. rudinoris, mtDNA haplotypes are further subdivided into northern and southern lineages along the Baja California Peninsula. Comparison of phylogeographic structure in the baileyi species group and the codistributed Peromyscus eremicus species group implies two points of codivergence and thus supports two historical vicariance hypotheses proposed for biotas distributed across the peninsular and continental warm deserts: a late Neogene (3 Ma) northern extension of the Sea of Cortéz and a mid-Pleistocene (1 Ma) midpeninsular seaway across Baja California.