| Summary: | Understanding biodiversity is one of the driving foundations of evolutionary biology and researchers use a myriad of tools to uncover and understand the processes contributing to it. The evolutionary and ecological dynamics in a group of smooth-toothed pocket gophers, the <i>Thomomys umbrinus</i> species complex, is studied for this dissertation. This complex is distributed from south-central Arizona and southwestern New Mexico south to Veracruz, Mexico. The genetic complexity of <i>T. umbrinus</i> was initially discovered via allozymes and karyotypes, resulting in five genetic clades: three with one diploid number of chromosomes (2n = 76; two clades distributed in the Sierra Madre Occidental and 1 along the Pacific Coast) and two with a different diploid number (2n = 78; one in the Northern Desert and one in the Central Plateau).
Analyses of DNA sequences from 8 genes and genotype assignment tests for 21 allozyme loci establish the Sierra Madre clade within what was formerly <i>T. umbrinus</i> as a genetically isolated taxon. Accordingly, <i>Thomomys sheldoni</i> Bailey, 1915 is resurrected to recognize this divergent clade of pocket gophers with a diploid number of 2n = 76. A synonymy is provided for two subspecies within <i>T. sheldoni</i> based on a concordant genetic and morphological break.
Multi-locus genetic analyses reveal a previously undescribed species of pocket gopher (2n = 76) apparently restricted to the Sierra del Nayar of northeastern Nayarit. Molecular, chromosomal, and cranial morphometric data distinguish this new species from other members of the <i>T. umbrinus</i> species complex. This new taxon, <i>T. nayarensis</i>, is described and a key to distinguishing the 3 species of <i>Thomomys</i> in northeastern Nayarit is provided.
Subspecies relationships within <i>T. umbrinus</i> (2n = 78) are reevaluated using phylogenetic analyses, species tree analyses, allozymes, and morphology. Phylogenetic analyses confirm three genetic clades (Northern Desert, Central Plateau, and the Trans-Mexico Volcanic Belt [TMVB]). Reanalysis of published allozyme data shows no evidence of nuclear discordance among the three clades. Species tree analyses reveal four divergent lineages (two within the TMVB clade), which are recognized herein at the subspecies level.
Species distribution models were used to assess biotic and climatic factors that may influence how members of the <i>T. umbrinus</i> complex are distributed. <i>T. sheldoni</i> and <i>T. atrovarius</i> had well-predicted niches and climatic variables that differentiated them from the <i>T. umbrinus</i> clades. Niche equivalency tests were rejected and evidence of niche conservatism was found between some, but not all, members of the species complex, indicating a complex history of niche evolution, competition, and genetic differentiation in the <i>T. umbrinus</i> species complex.
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