Level-1 hypotheses sought to identify differences in trends among species/stocks, but did not propose mechanisms to explain those differences. Level-1 analyses completed by PATH included analyses of broad geographical and temporal trends in stock indicators such as recruits, spawners, and recruits/spawner (Deriso et al. 1996, in press, Schaller et al. 1999, Botsford and Paulsen 2000). An additional contribution of these analyses was the development of a comprehensive set of spawner-recruit data for 13 spring/summer stocks from the Snake River and other areas of the Columbia River basin (Beamesderfer et al. 1997). These analyses concluded that, while productivity and survival rate of all Columbia River spring/summer chinook stocks declined between the pre-1970 and post-1975 periods, Snake River and Upper Columbia stocks showed steeper patterns of decline over this time period than did lower Columbia stocks.

Level-2 hypotheses sought to explain trends in stock indicators during particular life history stages in terms of spatial/temporal contrasts in survival and candidate stressors that might be historically correlated with these survival patterns (i.e., hydropower, habitat, hatchery, harvest, and climate). Here the intent was to provide inferences from historical data on where to focus future management actions, in terms of both life history stages and stressors, and to elucidate gaps in the information required to distinguish among competing hypotheses. These analyses focused primarily on spring/summer chinook, including: regression analyses of recruits per spawner against various stressors (Paulsen 1996); assessments of the influence of spawning and rearing habitat (Petrosky and Schaller 1996, Paulsen et al. 1997, Petrosky et al. 2001); various analyses of the correlation between hatchery releases and survival/mortality rates (Wilson 1996, Budy et al. 1998, Paulsen and Hinrichsen 1998, Petrosky 1998, Williams et al. 1998); analyses of the role of climatic changes on salmon production (Anderson 1996, Hinrichsen et al. 1997, Paulsen and Fisher 1997); analyses of harvest impacts (Langness et al. 1998); and assessments of the effects of the hydrosystem (Deriso et al. 1996, in press, Schaller et al. 1999). Data sets developed for these analyses include survival indices for two phases of the spring/summer chinook life cycle: parr-smolt (Paulsen et al. 1997) and spawner-smolt (Petrosky and Schaller 1996). Major conclusions from Level-2 analyses were that hydrosystem, habitat, and climate conditions have all contributed to observed patterns of decline in Snake River stocks (although statistical power analyses showed that habitat changes alone were not sufficient to explain these patterns). PATH concluded that harvest effects did not contribute significantly to post-1974 declines, and that hatchery programs were probably also not a major factor.

Level-3 hypotheses sought to explain the specific mechanisms associated with observed trends in each life history stage identified at Level 2. These hypotheses link directly to key management decisions, which are affected by the quantitative magnitude of various effects (e.g., changes in survival with increased flow) rather than whether or not an effect merely exists. PATH completed a wide range of Level-3 analyses for spring/summer chinook and fall chinook, and a limited set of analyses for steelhead and sockeye. These analyses focused on the effects of specific hydrosystem actions on survival through the juvenile migratory corridor. For example, a PATH subgroup developed a detailed flowchart of the expected response of juvenile spring/summer chinook salmon to various operations and configurations of dams in the Snake and Columbia River (Toole et al. 1996). An important data set for Level-3 analyses was the mark–recapture experiments with PIT (Passive Induced Transponder) —tagged juvenile salmon conducted by NMFS (e.g., Muir et al. 1996). These data were useful for estimating reach- and project-specific survival rates of migrating salmon smolts, and for estimating smolt-adult survival rates of transported and nontransported fish. PATH conclusions from Level-3 hypotheses were that modifications to the existing hydropower system were not likely to improve juvenile survival rates. Transportation of smolts improves the direct survival of smolts, but there was insufficient information about delayed effects of transportation to say whether transporting smolts improves overall spawner-to-recruit survival rates. In addition, drawdown of Snake River dams can compensate for effects of the hydrosystem and improve juvenile survival rates.

The results of these retrospective analyses were ultimately condensed into a clearly written, 30-page Conclusions Document (Marmorek et al. 1996b). The tough internal and external review process led to 10 drafts of this document, but ensured that the strength of the conclusions was consistent with the available evidence.

FALL CHINOOK

Retrospective analyses for fall chinook were less comprehensive than for spring/summer chinook because of time constraints and limitations in available data (Peters et al. 1999, in press). For example, for fall chinook there is a shorter time series of spawner-recruit and juvenile passage survival data. Retrospective analyses for fall chinook generally focused on the consistency of different structures of stock-recruit models with spawner-recruit data developed for four fall chinook stocks from the Snake, Lewis, and Deschutes Rivers, and from the Hanford reach of the Columbia River. These models embodied different hypotheses about the importance of transportation, hatchery supplementation, and climate effects on historical trends in survival rates (these analyses were roughly analogous to Level-2 analyses in the spring/summer hypothesis framework). We also explored overall trends in spawner-recruit survival (analogous to Level-1 analyses), and reviewed evidence on the survival of smolts through various components of the hydrosystem such as survival through turbines and in spillways (analogous to Level-3 analyses).