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Bull trout (Salvelinus confluentus) are challenging to detect as a result of the species cryptic behavior and coloration, relatively low densities in complex habitats, and affinity for cold, high clarity, low conductivity waters. Bull trout are also closely associated with the stream bed, frequently conceal in substrate, and this concealment behavior is poorly understood. Consequently, population assessments are problematic and biologists and managers often lack quantitative information to accurately describe bull trout distributions, estimate abundance, and assess status and trends; particularly for stream-dwelling populations. During controlled laboratory trials, we recorded concealment, resting, and swimming behavior of juvenile wild bull trout in response to: (1) constant and fluctuating water temperature, (2) presence or absence of light, and (3) substrate size. Light level had the strongest influence on wild fish concealment and more fish concealed as light levels increased from darkness to daylight. Wild fish were 14.5 times less likely to conceal in constant darkness and 4.1 times more likely to conceal in 12 h light x 12 h darkness compared to constant light. Wild fish were 6.2 times less likely to conceal in small (26–51 mm) substrate compared to larger (52–102 mm) substrate. As water temperature increased, fewer wild fish concealed. Knowledge of wild bull trout concealment will improve field sampling protocols and increase detection efficiencies. These data also enhance knowledge of bull trout niche requirements which illuminates ecological differences among species and informs conservation and restoration efforts. [ABSTRACT FROM AUTHOR]

Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a diagnostic test can be advantageous as multiple pathogens can be examined and providing important information on associated pathological changes to the host. However, it is usually less sensitive than molecular or microbiological tests for specific pathogens. Our study objectives were to 1) develop a hierarchical occupancy model to examine pathogen prevalence in spring Chinook salmon Oncorhynchus tshawytscha and their distribution among host tissues 2) use the model to estimate pathogen-specific test sensitivities and infection rates, and 3) illustrate the effect of using replicate within host sampling on sample sizes required to detect a pathogen. We examined histological sections of replicate tissue samples from spring Chinook salmon O. tshawytscha collected after spawning for common pathogens seen in this population: Apophallus/echinostome metacercariae, Parvicapsula minibicornis, Nanophyetus salmincola/ metacercariae, and Renibacterium salmoninarum. A hierarchical occupancy model was developed to estimate pathogen and tissue-specific test sensitivities and unbiased estimation of host- and organ-level infection rates. Model estimated sensitivities and host- and organ-level infections rates varied among pathogens and model estimated infection rate was higher than prevalence unadjusted for test sensitivity, confirming that prevalence unadjusted for test sensitivity was negatively biased. The modeling approach provided an analytical approach for using hierarchically structured pathogen detection data from lower sensitivity diagnostic tests, such as histology, to obtain unbiased pathogen prevalence estimates with associated uncertainties. Accounting for test sensitivity using within host replicate samples also required fewer individual fish to be sampled. This approach is useful for evaluating pathogen or microbe community dynamics when test sensitivity is <100%. [ABSTRACT FROM AUTHOR]