Regular ArticlePhylogenetic Relationships and Geographic Structure in Pocket Gophers in the GenusThomomys

Phylogenetic relationships among pocket gophers were examined based on the complete sequence for the mitochondrial cytochromebgene (1140 base pairs). The tribe Geomyini (Geomys, Orthogeomys, Cratogeomys,andPappogeomys) was well differentiated from the tribe Thomomyini (Thomomys), using the heteromyid generaDipodomysandPerognathusas the outgroup. Within the genusThomomys,the species in the subgenusThomomys(T. talpoides, T. monticola,andT. mazama) differed from those in the subgenusMegascapheus(T. bottae, T. townsendii,andT. 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 withinT. bottaecoincided with geographic regions based on allozyme data in some areas, but not at all boundaries. The geographic units within currently recognized species in thebottaegroup (subgenusMegascapheus) were not grouped together with a high level of confidence. The pattern suggests a rapid radiation of thebottaegroup, followed by geographic subdivision.