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Arpin, Kate

University of British Columbia

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 traditional sample sources. 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 contribute to genetic monitoring efforts of an alpine indicator species, which can ultimately help improve our understanding of the ecological consequences of rapid environmental change.

Text

2023-10-06

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/86088

Biology

University of British Columbia

UBCO

http://creativecommons.org/licenses/by-nc-nd/4.0/