UBC Theses and Dissertations
Patterns of population structure and genetic diversity among Western Rattlesnakes (Crotalus oreganus) in the Pacific Northwest Schmidt, Danielle Aimery
Advances in DNA sequencing technologies have enabled the collection of genome-wide data, facilitating a shift from population genetics to population genomics. This transition has greatly augmented the amount of data that can be collected from DNA samples as well as increased the scope of ecological and conservation studies. Historically, non-invasive or minimally-invasive sampling (MIS) has been widespread in wildlife studies, especially for those species of elevated conservation concern. Despite the benefits of MIS, the utility of these samples for collecting genomic information is limited. Low DNA quantity, degradation, and contamination by exogenous DNA make MIS challenging to use with modern genotyping-by-sequencing approaches, which have traditionally been developed for high quality DNA sources. Here, we demonstrate the utility of Genotyping-in-Thousands by sequencing (GT-seq), a targeted, multiplex amplicon approach, for genotyping minimally-invasive DNA samples from the Western Rattlesnake (Crotalus oreganus), a species-at-risk in British Columbia, Canada. Using a panel of 362 single nucleotide polymorphisms (SNPs) generated from high quality blood samples identified via restriction site-associated DNA sequencing (RADseq), we genotyped a total of 96 blood (n=68), minimally-invasive cloacal swab (n=9), and opportunistically collected roadkill tissue samples (n=19) across the distribution of Western Rattlesnakes in BC and Washington (USA). The targeted GT-seq panel yielded comparable estimates of within- and among-population variation to that of the larger RADseq dataset (n=9568 SNPs). We then applied this approach to a set of blood (n=68) and minimally-invasive samples (n =690) collected from across species the distribution. Hierarchical STRUCTURE analyses found evidence for population structure within and among all five geographic regions of C. oreganus occurrence in BC and Washington, as well as low levels of migration among groups of den sites across the distribution, with no evidence for a pattern of isolation-by-distance. These results provide evidence for population discreteness, as well as barriers to gene flow across the distribution suggesting that the single, recognized designatable unit for conservation for Western Rattlesnakes in BC should be re-assessed. More broadly, this thesis demonstrates the efficacy of combining genomic tools with MIS to investigate ecological and evolutionary processes impacting wild populations and better inform conservation management.
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