Date of Award

August 2019

Degree Type


Degree Name

Doctor of Philosophy


Biological Sciences

First Advisor

Emily K Latch

Committee Members

Linda Whittingham, Peter Dunn, Filipe Alberto, Rafael Rodriguez Sevilla


conservation genomics, landscape genomics, Plague, population genomics, prairie dog, transmission


The transmission of vector-borne diseases involves complex interactions between vectors and their host species. These complex host-parasite interactions can be difficult to study with traditional, field-based methods. My dissertation aims to use a population genomics approach to elucidate transmission pathways of plague among prairie dog colonies. Plague is a flea-borne, zoonotic disease caused by the bacterium Yersinia pestis. It is infamous for causing the Black Death (1347-1353), one of the most devastating pandemics in human history. Since its emergence in North America around 1900, plague has spread to native rodents, thus creating a sylvatic cycle. Prairie dogs (Cynomys spp.) are highly susceptible to the disease, experiencing >90% mortality during outbreaks. Further, prairie dogs exacerbate the spread of plague by acting as an amplifying host, initiating epizootic events. In the first chapter of my dissertation, I examine how the landscape influences the connectivity of black-tailed prairie dog colonies in order to better understand the role of prairie dogs in plague transmission. I found that slope and bodies of water explain effective dispersal better than geographic distance alone. My second chapter describes patterns of connectivity for Oropsylla hirsuta, the main flea species found on prairie dogs and a known vector for plague. I compare those patterns of vector-mediated plague transmission to the host (prairie dogs) and potential alternative hosts [Northern grasshopper mice (Onychomys leucogaster) and deer mice (Peromyscus maniculatus)] to uncover alternative modes of transmission. I found that the best performing model used patterns of connectivity for prairie dogs and deer mice to explain patterns of connectivity for O. hirsuta. My third chapter uses both neutral and putatively adaptive loci to characterize patterns of genetic variation for the threatened Utah prairie dog in order to improve recovery efforts for this threatened species. I found low species-wide genetic variation and high population divergence among sampling sites, which suggests that this species is highly vulnerable to the effects of genetic drift. Overall, this dissertation not only improves the conservation and management of prairie dogs in light of devastating plague outbreaks, but also provides a more general population genomics framework suitable for elucidating transmission pathways of wildlife diseases.