Direct Mortality and System Capacity

a. Entrainment Mortality
Fish can become entrained in irrigation canal headworks and killed if not rescued before the canal is dewatered at the end of the irrigation season. Entrainment rates are expected to be variable between canals, however, there have been no recent studies to determine the total number of entrained fish and the overall effect on population sustainability. The primary data source to inform the potential severity of this threat is the Trout Unlimited Canada annual fish rescue program, which includes most but not all canal headworks within the current Bull Trout and Westslope Cutthroat Trout range. Typically, no or small numbers of entrained Bull Trout (<10) and Westslope Cutthroat Trout (<5) are rescued (Lindsey et al. 2015); however, it should be noted that the rescues are not designed to estimate entrainment rates so these numbers should be viewed as minimum values only. In contrast, entrainment at the Belly River canal prior to screening to exclude large fish was estimated at 15 – 20% of annual mortality (Clayton 2001). The majority of canal headworks within Alberta's eastern slopes do not have fish exclusion devices.
Fish can also become entrained in powerhouses for hydroelectric reservoirs where a portion are killed as they pass through the turbines. Various aspects of Bull Trout entrainment in hydroelectric reservoirs have been widely studied in both the U.S. and British Columbia (B.C.) (Martins et al. 2013, Ma et al. 2012, Underwood and Kramer 2007, Salow and Hostettler 2004, and FERC 1995). Entrainment and mortality rates are highly site-specific, varying with physical factors including reservoir size, dam height, fore bay configuration, depth of intake, turbine type, and operational timing as well as biological factors including fish size, seasonal and diurnal movements and density-dependent influences on fish movement.
No large-scale hydroelectric projects are currently in operation within the natural range of Athabasca Rainbow Trout. However, plans for hydroelectric and diversion dams are commonly proposed, such as proposals for dams on the Athabasca River and major tributaries (Hatch 2010).
For the Joe model, watersheds containing irrigation canal headworks were assigned an entrainment conditional mortality rate of 1% and those containing hydroelectric dams were assigned a rate of 4%, unless other data were available.

b. Research and Monitoring
Standard scientific methods for monitoring native trout populations typically involve the non-lethal capture, handling, and release of individual fish. Methods used to capture native trout include electrofishing, angling, trapping, and netting, with backpack and boat electrofishing being the most widely used in Alberta. After capture, fish are held for processing, often anesthetized, and measured. Depending on the project objectives, fish may also be marked (tagged), surgically implanted with telemetry transmitters, and/or have a small portion of a fin removed for genetic analysis. Lethal sampling of native trout is uncommon but may occur if information that cannot be collected using non-lethal means (e.g., maturity and age data) is required for management and assessment purposes. In these cases, the potential impacts on population sustainability are thoroughly reviewed by the appropriate regulatory agency(s) prior to project approval.
Alberta Fisheries Management has developed a series of standards including the Standard for the Ethical Use of Fish in Alberta (AESRD 2013a), Standard for Sampling Small Streams in Alberta (AESRD 2013b) and Electrofishing Policy Respecting Injuries to Fish (AFMD 2004) to minimize fish injury, stress and mortality during non-lethal collection and handling by research crews. These standards are included as conditions on Research Licences, which are mandatory licences issued to all agencies and organizations conducting fisheries-related work in the province. Research Licences also include a section detailing Best Management Practices relating to the processing of fish in cold and hot weather, proper handling techniques, and the use of anaesthetic. While the application of standards and best management practices does minimize fish injury, stress and mortality, some incidental mortality during fish collection and handling may occur. Incidental mortality is assumed to have negligible to very low population-level effects because the majority of native trout surveys are limited to small representative areas of a watershed and project time periods are typically short (1-5 years). Therefore, mortality due to scientific research and monitoring will not be included in the total annual mortality calculation unless there is evidence of a population-level impact within a particular watershed. Similarly, the U.S. Fish and Wildlife Service analyzed the effects of scientific research through a biological opinion survey (USFWS 2000) and determined that scientific collection does not jeopardize Bull Trout populations and is therefore not identified as a threat factor in the U.S. Bull Trout recovery plan (USFWS 2015). Similar to Bull Trout, we suspect that research and monitoring has little to no effect on Athabasca Rainbow Trout population sustainability, and at our most heavily studied systems (e.g. Tri-Creeks) have yet to detect any population-level effects of monitoring activities. Nonetheless, this parameter is included in the model and the level of research and monitoring mortality is included in the calculations.
For the Joe model the conditional rate of mortality due to research and monitoring was set to 0% unless other data were available. Values will be adjusted if new information becomes available suggesting otherwise.