The authors propose to perform a quantitative viability analysis of Columbia River Chinook salmon. The technical background section implies in several places that the viability analyses of NOAA Fisheries were based on unrealistic assumptions (e.g., independent populations), thus not accounting for straying, interbreeding, etc. It is certainly the case that the metapopulation structure can play a critical role in the viability of a species and that spatial structure plays a dominant role in the dynamics of Chinook salmon. Therefore, it must be included in any serious viability analysis. On this basis, perhaps more complete analyses are justified.

The ISRP has reservations about the proposed analysis and consequently give it a "response requested" rating. Our impressions for consideration by the sponsors follow:

The stated objective is to perform an analysis. The objective should be to explore (or determine) the effects of stock diversity on the long-term persistence and cumulative abundance across stocks within strata and ESUs. The analysis is the task to reach the objective.

The proposal makes the interesting comment that life history types within regions are more similar than life history types among regions. How this statement accommodates the development of the "reservoir" life history type in fall Chinook, which contains elements of both stream and ocean life history strategies, is not explained. How will life history variation within regions be factored into viability analyses?

The proposal sponsors make two observations about the current status of population viability assessments for Columbia River Basin Chinook salmon and steelhead. The first is that the methods used by Holmes and McClure can be improved upon by performing a hierarchical analysis of contiguous populations which recognizes a dependence (in the analysis) on migration and interbreeding among spatially discrete populations. Although not entirely clear, presumably at least one portion of the hierarchy would be the populations presented on a line in Table 1. For example Catherine Creek, Wallowa/Lostine R., Minam River would be contiguous populations of spring Chinook in the Grande Ronde subbasin. The second is that quantitative methods of incorporating spatial structure and diversity (which along with abundance and productivity are the four VSP parameters proposed by McElhany et al. 2000) are not yet treated quantitatively in extinction analysis, and they should be.

The proposal needs to provide a more compelling case that they can rectify the limitations of the anticipated TRT, and Holmes and McClure analyses, and that this updated analysis can meaningfully alter the interpretation of management options. Somewhat of a case is made for improving the Holmes and McClure analysis, but the argument is not clear in terms familiar to mathematicians. The case is not made for diversity. It is not clear that the data needed to perform this analysis are available.

Granted, the Bayesian approach that is proposed here is tricky to explain, but Figures 1 and 2 did not help very much. Aside from the computational issues, there were questions of how data would be obtained, how missing data would be treated, and other practical issues that the proposal did not address.

The Bayesian approach may be the best available approach for this viability analysis and that the inclusion of spatial considerations and straying is absolutely necessary to make the results significant. However, the authors do not provide convincing evidence that the data are available to pull this off or if it is available that they know where to find it.

The first element is to estimate effective population size, or if the data is not available to assess that, probabilistic frequency of catastrophic decline. Sponsors state that it is challenging to measure an abundance threshold of a population below which the population goes extinct. The problem is not just measuring it. The problem is deciding what it should be based on our understanding of the demography of the species. It is not clear how an estimate of Ne will be made, the number of units for which this can be estimated, what data is required to estimate the catastrophic decline, how many populations can be evaluated for this parameter - or what this will be used for.

The structure of the hierarchical analysis needs to be clarified. Is there to be two hierarchies - populations and ESUs? In any case, how is the ESU hierarchy to be interpreted? That is the challenge facing the TRTs (and the tribes, states, and nation for that matter). For example, is it acceptable if an analysis of an entire ESU concludes it is viable for 1000 years, because some individuals remain in one subbasin (spring Chinook for example the Tucannon) but the ESU is extirpated in all others (Grande Ronde, Salmon, Imnaha)? It is not clear that this improvement in analysis necessarily solves the essential policy and management dilemma.

The sponsors seem to consider only gene diversity measured by allozymes, microsatellites, etc. in there assessment of diversity; whereas McElhany considers population variability in habitat and life history attributes that may not be reflected in genes that we can measure at this time. The methods to describe genetic diversity were essentially lacking, other than a few sentences and some references. Statements such as "Genetic diversity, population structure, effective population size, and gene flow among populations will be analyzed" (page 10) need to be followed with at least some details. There is an expanding universe of analytical approaches to determining population parameters (like migration rates) from genetic data. Sponsors need to provide convincing details of their intentions to be able to conclude they are on the right track.

There is no explanation of how much more genetic analysis will need to be performed. The budget for genetic and demographic analyses is the same…to the penny.