Date of Award

Winter 1-1-2012

Document Type


Degree Name

Doctor of Philosophy (PhD)


Ecology & Evolutionary Biology

First Advisor

Andrew P. Martin

Second Advisor

Sharon K. Collinge

Third Advisor

Robert P. Guralnick

Fourth Advisor

Patrik Nosil

Fifth Advisor

Alan R. Templeton


Evolutionary biology seeks to understand the processes driving genetic diversity within species and phylogenetic divergence among species. Patterns of diversity may be dictated by both abiotic factors and community interactions. My dissertation research focuses on the processes that influence diversity and divergence in prairie dogs across spatial and temporal scales. At the macroevolutionary scale, habitat constraints influencing metabolism, reproductive period and growth rate may act as selective agents. Gunnison's prairie dogs (Cynomys gunnisoni) have been proposed to exist as two subspecies that occupy distinct habitats and are morphologically distinct in portions of their range. Using complementary approaches of phylogenetic analysis, genetic clustering, and spatial analysis of environment, I examine the contributions of different ecological selection pressures to genetic diversity of Gunnison's prairie dogs throughout their range. I find that elevation and temperature determine the distribution of two unique lineages of Gunnison's prairie dogs, and that plant communities differ between habitats occupied by each subspecies. At the local scale, landscape connectivity may interact with susceptibility to pathogens to influence population structure, particularly in social species such as prairie dogs. Although some land cover types, such as intense urbanization and water bodies, prevent dispersal across them, prairie dogs can travel across multiple land cover types such as grassland, shrubland and agricultural fields. Moreover, although large highways act as dispersal barriers, small roads can actually facilitate prairie dog dispersal, particularly across water bodies. Pathogen susceptibility is likely to influence genetic structure because prairie dogs suffer approximately 99% mortality during plague outbreaks. In Boulder County, re-colonization by black-tailed prairie dogs (C. ludovicianus) occurred 1 - 3 years after extirpation in well-connected colonies. Genetic diversity within the metapopulation was retained. Within some well-connected populations colonized by multiple source populations, genetic variation was maintained or increased, but diversity was lost in some isolated populations. Finally, individuals in recolonized populations had significantly higher heterozygosity than those present before plague. This dissertation will contribute to our understanding of the abiotic and biotic mechanisms of diversification in social species.