Phylogenetic Relationships and Geographic Structure in Pocket Gophers in the GenusThomomys

Abstract Phylogenetic relationships among pocket gophers were examined based on the complete sequence for the mitochondrial cytochrome b gene (1140 base pairs). The tribe Geomyini ( Geomys, Orthogeomys, Cratogeomys, and Pappogeomys ) was well differentiated from the tribe Thomomyini ( Thomomys ), using the heteromyid genera Dipodomys and Perognathus as the outgroup. Within the genus Thomomys, the species in the subgenus Thomomys ( T. talpoides, T. monticola, and T. mazama ) differed from those in the subgenus Megascapheus ( T. bottae, T. townsendii, and T. umbrinus ) by an average of 19.3% uncorrected sequence divergence. Extensive sampling within one species, T. bottae, revealed strongly differentiated geographic units, with a maximum difference among localities of 15.7%. The geographic units within T. bottae coincided with geographic regions based on allozyme data in some areas, but not at all boundaries. The geographic units within currently recognized species in the bottae group (subgenus Megascapheus ) were not grouped together with a high level of confidence. The pattern suggests a rapid radiation of the bottae group, followed by geographic subdivision.