Multi-scale occupancy and species interactions of a desert amphibian

Matthew Michael Smith

Species occupancy is influenced by abiotic and biotic factors across multiple spatial scales. To estimate relationships between occupancy and covariates, sensitive methods are necessary to detect species and account for imperfect detection. Environmental DNA (eDNA) is an emerging tool to survey aquatic species and is effective in detecting elusive species. We used field and eDNA techniques to identify Columbia spotted frog (Rana luteiventris) (CSF) occupancy in the Great Basin, U.S.A. At each site, we filtered 250ml of water through a 0.45 !m cellulose nitrate filter for three samples and one negative control per site. DNA was extracted using DNeasy Blood and Tissue Kit in a lab dedicated to low quality DNA. We analyzed samples using quantitative PCR to amplify species-specific DNA fragment. In addition to analyzing samples for eDNA of CSF, we created a species-specific assay for American beaver (Castor canadensis), which has a potentially positive relationship with CSF presence and tested samples for the pathogen Batrachochytrium dendrobatidis (Bd). Environmental DNA increased the estimate of CSF at surveyed sites (naïve psi = 0.37) when compared to using traditional field methods alone (naïve psi = 0.20). We employed a multi-scale occupancy model that simultaneously estimated the probability of occupancy at a watershed and site scale while accounting for availability within the watershed and imperfect detection. The top two models had a combined AICc weight of 0.82. The top supported model (AICc weight = 0.51) included precipitation and temperature as covariates of watershed occupancy. We used two-species conditional occupancy model to determine if a species interaction existed between CSF and beavers and between CSF and Bd. For the two-species model between CSF and beavers, the top three models (combined AICc weight of 0.70) supported a species interaction. We found that CSF occupancy was higher at lower levels of annual precipitation when beaver was present then when absent. Additionally, Bd occupancy was strongly related to CSF being present (SIF = 2.63) and decreased as the distance to primary and secondary roads increased. Species interactions can have impacts on species occupancy that may influence species response to human impacts and climate change.

Multi-scale occupancy and species interactions of a desert amphibian

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