Publication Date

Spring 2023

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)

Department

Computer Science

First Advisor

Wendy Lee

Second Advisor

Jessica Castillo Vardaro

Third Advisor

William Andreopoulos

Keywords

Ochotana princeps, American pika, Whole Genome Sequencing, Evolution

Abstract

Climate change and rising temperatures pose a serious threat to the long-term survival of American pika (Ochotana princeps), emphasizing the interest in the adaptive capability of the pika. This project queried single nucleotide polymorphisms in a population of American pika in Yosemite National Park using Whole Genome Sequencing data, with a specific interest in metabolic variants. The sample data included temporally separated cohorts, comparing modern population data to historical data taken before rapid anthropogenic climate change. Statistically significant variants were identified under Approximate Bayesian Computation using a population decline model. Although population statistics indicated little change between the temporal cohorts, five intergenic SNPs were identified located about 20,000 base pairs upstream from DECR1, a gene that plays a key role in the metabolism of polyunsaturated fatty acids. Further work is needed to investigate any link between these SNPs and DECR1.

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