The Comparative Survival Study (CSS) is a management-oriented, large scale, life-cycle monitoring study of spring/summer/fall Chinook, steelhead, and sockeye, utilizing PIT tags.  The CSS was designed to address several of the basin-wide monitoring needs and to provide demographic and other data for Snake River and Columbia River wild and hatchery salmon and steelhead populations.  One product of the CSS is annual estimates of SARs for Snake River hatchery and wild steelhead and salmon.  Estimation of the overall, aggregate SARs of fish that are transported and those that migrate entirely in-river is key to evaluation of avoidance of jeopardy (i.e., put at risk of extinction) as well as progress toward recovery goals.  Monitoring survival probability over the entire life-cycle can help identify where survival bottlenecks are occurring, which is critical input for informed management decisions (Good et al. 2007).  The CSS also examines environmental factors associated with life-cycle survival probability and evaluates the hypothesized mechanisms for variations in those probabilities.

An overall goal of CSS is to emphasize marking wild fish and to mark wild populations as representatively as possible.  Part of that effort involves marking wild fish at finer geographic scales by relying more on traps located in tributaries and reducing marking at mainstem traps.  This allows marking wild fish at the Major Population Group (MPG) level versus at the Ecologically Significant Unit (ESU) level.  Although truly representative marking is likely impossible, given constraints on fish handling, trapping operations during peak runoff and other limitations to sampling, the CSS has implemented changes to marking to attempt to improve representativeness of major population groups, transition toward finer geographic scale marking, and reduce the handling of listed hatchery stocks.  To accomplish these goals, CSS reduced or eliminated marking at mainstem traps in the Clearwater and Salmon rivers in 2015, and transitioned those tags to traps in tributaries higher up in the watersheds.  The foundational objectives of the CSS design translate these issues about the efficacy of transportation into key response variables.

The CSS uses the following two aspects for evaluating the efficacy of transportation:  (1) empirical SARs compared to those needed for survival and recovery of the ESU; and (2) SAR comparisons between transport and in-river migration routes.  In this broader context, the primary objective is to answer:  “Are the direct and delayed impacts of the configuration and operation of the FCRPS sufficiently low to ensure that cumulative life-cycle survival is high enough to recover threatened and endangered populations?”  The secondary objective is to answer:  “Is the survival of transported fish (SAR) higher than the survival (SAR) of fish migrating in-river?”  Beginning in 2003, the NPCC Fish and Wildlife Program adopted the goal to achieve smolt-to-adult survival probabilities (SARs) in the range of 2% to 6% (average 4%) for federal ESA-listed Snake and Upper Columbia river salmon and steelhead.  The objective continued through 2009 and most recently the amended 2014 Fish and Wildlife Program (NPCC 2003, 2009 2014).  Combining these objectives, effectiveness of transportation is assessed by whether (1) the overall SAR(LGR-to-LGR) meets the NPCC regional objective (2%–6% with 4% average) for the ESU and (2) the SAR of fish collected at Snake River dams and diverted into barges is higher than that of fish that migrate through reservoirs and pass these dams via the spillways and turbines.