Date of Award


Document Type


Degree Name


Organizational Unit

College of Natural Science and Mathematics, Biological Sciences

First Advisor

Erica L. Larson

Second Advisor

John R. Demboski

Third Advisor

Jonathan P. Velotta

Fourth Advisor

Scott A. Taylor

Fifth Advisor

Robin M. Tinghitella

Sixth Advisor

Scott A. Nichols


Genomics, Hybridization, Mammals, Reproduction, Speciation, Sterility


The natural recombination of divergent genomes within hybrid offspring provides windows through which we can study evolutionary processes and the dynamics of speciation. In this work, I use a combination of comparative and population genomics on both laboratory crosses of divergent rodent lineages and a hybrid zone of cottontail rabbits in the wild to study the causes and consequences of hybridization in mammals. Hybrid sterility is a common reproductive barrier between species that tends to preferentially manifest in the heterogametic sex and frequently genetically maps to the sex chromosomes. Thus, the sex chromosomes appear to play a special role in hybrid incompatibilities, and disrupted gene regulation of the X chromosome may contribute to their outsized role. Here, I investigate disrupted sex chromosome regulation in hybrid male sterility in two divergent rodent systems: (1) the Mus musculus musculus and M. m. domesticushouse mice subspecies and (2) Campbell’s dwarf hamster and the winter white dwarf hamster. I first establish the power of using Florescence Activated Cell Sorting to generate enriched spermatogenic cell populations in investigating disrupted gene expression in sterile hybrid males and then use this approach to examine common regulatory phenotypes associated with sterility. I show that misexpression does not universally tend towards overexpression in sterile hybrids and that misexpression tends to increase with the progression of spermatogenesis. Furthermore, I detected sex-chromosome specific overexpression in both systems but demonstrate that the overexpression phenotypes fundamentally differ between house mice and dwarf hamsters suggesting different underlying genomic architecture. I also used a contact zone of three species of cottontail rabbits in Colorado to investigate whether human disturbance in urban areas has led to hybridization among species. I generated mitochondrial haplotypes and ddRADSeq data from tissues from museum collections to show that (1) there are two main genetic linages of cottontails in Colorado (eastern and desert cottontails), (2) that both species are hybridizing in urban areas, and (3) that these species are occupying unexpected habitats consistent with contemporary range shifts. Collectively, I demonstrate the power of diverse mammalian hybrid systems in revealing the evolutionary processes underlying speciation.

Publication Statement

Copyright is held by the author. User is responsible for all copyright compliance.

Rights Holder

Kelsie E. Hunnicutt


Received from ProQuest

File Format




File Size

219 pgs


Evolution and development, Biology, Genetics

Available for download on Friday, August 01, 2025