Dissertation Defence: Unravelling climate and high elevation adaptation in the American pika (Ochotona princeps) through a comparative genomics framework

Bryson Sjodin, supervised by Dr. Michael Russello, will defend their dissertation titled “Unravelling climate and high elevation adaptation in the American pika (Ochotona princeps) through a comparative genomics framework” in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology.

An abstract for Bryson Sjodin’s dissertation is included below.

Examinations are open to all members of the campus community as well as the general public. Please email michael.russello@ubc.ca to receive the Zoom link for this defence.

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ABSTRACT

Extreme environments offer great opportunities for studying local adaptation. For example, high elevation environments often have less oxygen, colder temperatures, and higher levels of solar radiation relative to lower elevation habitats. As such, species living at high elevations must adapt to these conditions to survive and thrive which can include genomic adaptations related to increased energy metabolism, increased oxidoreductase activity, and improvements in DNA repair. These adaptations can occur as both sequence and structural variation. Studying local adaptation can give us a clearer picture of how species respond to extreme environments. American pikas (Ochotona princeps) are high elevation specialists that are considered a sentinel species for the ecological effects of climate change. My research examined putative high elevation and climate adaptation in the American pika under a comparative genomics framework. I first developed a high-quality reference genome for the American pika, improving on both the contiguity and quality over the previous version, including the identification of chromosome-level scaffolds. Next, I identified putative regions under selection by comparing the American pika genome with eight other mammalian species. I identified orthologous gene groups across species and found that pika-specific groups and genes were functionally enriched in terms related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. Moreover, I detected 15 significantly expanded gene families displaying functionally enriched terms associated with hypoxia and cold adaptation. I found 41 positively selected genes associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. Lastly, I examined copy number variation within and among the major American pika lineages sampled from across their entire range to identify regions putatively linked to climate adaptation using genotype-environment association analyses. Adaptive divergence among climate-associated loci largely followed elevational and latitudinal gradients. Over 200 of these loci localized within 158 unique genes with several related to mitochondrial structure/function, hemoglobin function, hypoxia response, and DNA repair. This work expands our knowledge of environmental adaptation in the American pika genome and provides interesting targets for future research, including linking adaptive genomic variation to physiological and fitness advantages.