BS, Kent State University, 2024, College of Arts and Sciences / Department of Biological Sciences

The American pika (Ochotona princeps) is an herbivorous mammal that inhabits rocky, mountainous regions across the western United States. Although they share a common ancestor with rabbits and other species in the order Lagomorpha, American pikas have a specialized diet due to an inability to migrate from their narrow habitat range. Gene families are made up of genes similar in sequence and function among species that share a common ancestor. Increases in gene copy number due to random duplication results in gene family expansion, whereas gene deletion results in family contraction. Evolutionary divergence can result in functional and genetic differences in the way that pikas and other lagomorphs digest their food with the help of enzymes. We hypothesized that American pikas have undergone lineage-specific expansions or contractions in gene families encoding enzymes (particularly digestive enzymes), allowing the species to digest available food in their narrow and changing habitat. Using the computational tool, OrthoFinder, protein sequences of the American pika were compared to seven distantly related taxa to identify gene families. CAFE5 analysis identified copy number evolution compared to the most recent common ancestor of all eight species. Functional enrichment analysis with PANTHER showed gene families related to digestive enzymes are significantly expanded in the American pika compared to other species. This indicates that protease digestive enzymes are more highly expressed in the American pika, possibly contributing to their metabolism of plants that inhabit their habitat.

Committee: Sangeet Lamichhaney PhD (Advisor); Rafaela Takeshita PhD (Committee Member); Mark Kershner PhD (Committee Member); Helen Piontkivska PhD (Committee Member) Subjects: Bioinformatics; Biology