Thesis Defence: Development and testing of a genetic monitoring tool for American pikas (Ochotona princeps) to investigate spatial and temporal genetic variation in the Canadian Rocky Mountains

Kate Arpin, supervised by Dr. Michael Russello, will defend their thesis titled “Development and testing of a genetic monitoring tool for American pikas (Ochotona princeps) to investigate spatial and temporal genetic variation in the Canadian Rocky Mountains” in partial fulfillment of the requirements for the degree of Master of Science in Biology.

An abstract for Kate Arpin’s thesis is included below.

Defences 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

By monitoring population trends of indicator species, especially climate sentinel species, we may improve our understanding of the ecological responses to environmental change. Genetic tools for wildlife monitoring can provide particularly valuable information on spatiotemporal population trends and connectivity; however, many DNA sequencing approaches are dependent on the high quality and quantity of DNA acquired from invasive samples. Rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have recently demonstrated high efficacy with lower quality DNA from non-invasive and archival samples, facilitating broad-scale spatial and temporal research with minimal disturbance to the studied system. We developed a multi-purpose GT-seq panel of 307 single nucleotide polymorphisms for a climate sentinel mammal (the American pika, Ochotona princeps) for use as a genetic monitoring tool in the Canadian Rocky Mountains. We first optimized the panel using contemporary tissue samples (n=77) and subsequently applied it to archival tissue (n=17) and contemporary fecal pellet samples (n=129) to evaluate its effectiveness at identifying individuals and sex, estimating relatedness, and inferring population structure. We subsequently compared estimates of putatively neutral and putatively adaptive genetic variation between the archival tissue samples and both paired-site contemporary fecal pellet samples (n=25) and unpaired-site contemporary tissue samples (n=33) to assess temporal genetic variation in relation to a changing climate. The panel demonstrated high efficacy with contemporary and archival tissue samples (94.7% and 90.5% genotyping success, respectively) and negligible genotyping error (0.001% and 0.0%, respectively). Despite relatively high genotyping success for fecal pellet samples (79.7%), high genotyping error (28.4%) limited its power as a monitoring tool to assess genetic variation using non-invasive samples, highlighting the need for further optimization around sample and data collection. We found preliminary evidence of a slight loss of genetic variation between archival and contemporary tissue samples at unpaired sites; though this could be indicative of a historical population decline, further work is needed to assess and reduce the impact of spatial variation in this comparison. Overall, these findings highlight the need to consider genetic changes in alpine indicator species that reflect evolutionary processes, which may have impending ecological consequences in a rapidly changing climate.