Publication Date



Open access

Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Biology (Arts and Sciences)

Date of Defense


First Committee Member

Michael S. Gaines

Second Committee Member

Carla Hurt

Third Committee Member

Barbara Whitlock

Fourth Committee Member

Wm. David Webster


Climatic and geographic events such as glaciations, island formation, river formation, and urbanization strongly affect habitat specialist species. By contrast, it is traditionally assumed that these events have little effect on habitat generalists but few studies have tested this assumption. In this study I sought to identify the effects of historic and contemporary biogeographic events on the genetic structure of a habitat generalist, the cotton mouse (Peromyscus gossypinus). This species is distributed throughout the southeastern United States, a region that has experienced dramatic geographic changes associated with both historic Pleistocene glacial cycles, as well as contemporary anthropogenic forces. In analyzing the genetic structuring in this species I took a telescopic approach, beginning with the patterns of variation throughout the species range from a phylogenetic standpoint. Using mitochondrial sequence data I identified three reciprocally monophyletic clades of the cotton mouse, a southeastern, northeaster, and western clade. Among these clades I identified eight distinct subspecies, four of which had previously not been identified using morphological characters. Of the four previously identified subspecies, this study resulted in a restructuring of the range of all except the Key Largo cotton mouse, which is restricted to northern Key Largo Florida. Secondly, I employed phylogeographic methods to examine the genetic patterns of the cotton mouse in a geographic context. Phylogeographic breaks in the cotton mouse are largely consistent with those observed in other taxa distributed throughout the southeastern United States. Geographic structuring in this species shows deep patterns associated with glacial maxima and minima of the Pleistocene period. Many of these patterns are maintained by contemporary geographic barriers to gene flow. Thirdly, I identified geographic structuring of genetic variation at a regional and local level. This structuring is partially due to the cotton mouse’s limited dispersal ability but is strengthened and reinforced by naturally occurring contemporary barriers to gene flow and contemporary anthropogenic forces which serve to limit dispersal in this species. Finally, I determined that urbanization has a dramatic negative effect on gene flow and genetic variation in this species on a local scale. Over a twenty year period populations in urban areas experienced a marked decrease in genetic variation while populations in non-urban areas experienced an increase in variation. During this time period, gene flow was effectively cut off among populations that had previously been panmictic. This study demonstrates that small mammal habitat generalists can be affected by both historic and contemporary climatic and geographic events at multiple geographic scales. These effects range from large scale geographic structuring throughout the species’ range to fine scale structuring associated with contemporary anthropogenic forces.


Phylogeography; Urbanization; Population Genetics; Systematics; Peromyscus gossypinus; Mammalogy