Appendix K Chinook and Coho Salmon Fishery Modeling Approach for Application to the Mitchell Act EIS

Transcription

1 Appendix K Chinook and Coho Salmon Fishery Modeling Approach for Application to the Mitchell Act EIS July 2009 Submitted to ICF Jones & Stokes Vashon Island, WA Prepared by Larry Lestelle 1 Gary Morishima 2 1/ Biostream Environmental Fjord Drive NE STE AA Poulsbo, WA / MORI-ko, L.L.C. P.O. Box 1563 Mercer Island, WA 98040

2 Table of Contents Table of Contents... i 1.0 Introduction General Approach EIS Chinook Model Model Formulation Overview Marine Fisheries Formulation Columbia River Fisheries Modeling Results EIS Coho Model Model Formulation Overview Marine Fisheries Formulation Columbia River Fisheries Modeling Results Literature Cited Appendices Appendix A README Sections of the EIS Chinook Model Appendix B README Section of the EIS Coho Model Appendix C - Chinook Populations Modeled and Number of Juveniles Arriving to Below Bonneville Dam Appendix D - PSC Chinook Model Stock Groups Appendix E - PSC Chinook Model Fisheries EIS Harvest Model Final Report i

3 Appendix F - PSC Chinook Model Incidental Mortality Rates Appendix G - Sliding Scale Harvest Rate Regimes for Upriver Spring Chinook and Upper Columbia Summer Chinook in the Columbia River Appendix H - Derivation of Chinook Contribution Rates Taking into Account Incidental Mortality Rates Appendix I - Coho Populations Modeled and Number of Juveniles Arriving to Below Bonneville Dam Appendix J - FRAM Coho Model Stock Groups Appendix K - FRAM Coho Model Fisheries Appendix L - FRAM Coho Model Incidental Mortality Rates List of Figures Figure 1. Application of exploitation rates (ERs) applied in an annual time step for simulating ocean fishery impacts in the EIS harvest models. Application for chinook is illustrated. Age specific contribution rates (rt) are used to estimate the post-natural mortality cohort sizes by age in the chinook model Figure 2. Application of gauntlet type impacts for simulating in-river catches and dam losses in the EIS harvest models Figure 3. EIS Chinook Model flow chart Figure 4. Harvest rate scalars in SEAK, NBC, WCVI fisheries Figure 5. EIS Coho Model flow chart List of Tables Table 1. Modeling results for chinook in ocean fisheries for five scenarios using the EIS Chinook Model (based on inputs applied in February 2009). Results are shown as values normalized to Scenario 1 (raw output for scenario divided by output for Scenario 1) and as differences from Scenario Table 2. Modeling results for chinook in Columbia River fisheries for five scenarios using the EIS Chinook Model (based on inputs applied in February 2009). Results are shown as values normalized to Scenario 1 (raw output for scenario divided by output for Scenario 1) and as differences from Scenario Table 3. Modeling results for coho in ocean fisheries for five scenarios using the EIS Coho Model (based on inputs applied in March 2009). Results are shown as values normalized to Scenario 1 (raw output for scenario divided by output for Scenario 1) and as differences from Scenario EIS Harvest Model Final Report ii

4 Table 4. Modeling results for coho in Columbia River fisheries for five scenarios using the EIS Coho Model (based on inputs applied in March 2009). Results are shown as values normalized to Scenario 1 (raw output for scenario divided by output for Scenario 1) and as differences from Scenario EIS Harvest Model Final Report iii

5 Chinook and Coho Salmon Fishery Modeling Approach for Application to the Mitchell Act EIS 1.0 Introduction Chinook and coho salmon produced by Mitchell Act hatcheries are harvested by fisheries in the Columbia River and in ocean areas over a geographic area extending from California to Alaska. This document describes the modeling approach used to assess fishery impacts of hatchery production alternatives in the Mitchell Act Environmental Impact Statement (EIS). One aspect of the EIS is to evaluate how possible changes to the Mitchell Act hatchery program would affect fisheries within the Columbia River system and in coastal waters. Changes in production levels or other production characteristics in Mitchell Act hatcheries are being considered as part of the Columbia River Hatchery Reform process or in response to funding changes. The modeling approach described herein was used to evaluate how the range of alternatives being analyzed within the Mitchell Act EIS would be expected to impact fishery harvests. Model output consisting of summarized projections of catches for commercial, recreational, and tribal fishery sectors of relevance to the EIS were provided to other members of the project team for analysis and incorporation into the EIS. Relatively simple, steady-state models were employed to project marine fishery catch levels and run sizes to the mouth of the Columbia River for chinook and coho. These models were based on more complex models used to support annual fishery planning processes of the Pacific Fisheries Management Council (PFMC) and Pacific Salmon Commission (PSC). Steady state models were developed in part to simplify evaluation and comparison of EIS alternatives, and in part due to the budget and time limitations to complete the analysis. Impacts of EIS alternatives on both marine and Columbia River fisheries were modeled within the context of exploitation rate constraints established to protect comingled naturally-produced stocks listed under the Endangered Species Act (ESA) under guidance given by NOAA Fisheries in recent years (NMFS 2005, PFMC 2006, and ODFW/WDFW 2006a and 2006b). These ESA exploitation rate limits have remained generally consistent since This document is organized into four sections: 1. Introduction; 2. General approach; 3. EIS Chinook Model; and 4. EIS Coho Model. EIS Harvest Model Final Report 1

6 2.0 General Approach For some purposes, it may be desirable to attempt to produce projections of catches under the proposed EIS alternatives in a manner suitable for direct comparison with catches observed during some selected period in order to facilitate interpretation. However, it must be recognized that observed fishery catches are an outcome of the cumulative effects of a multitude of choices made in response to the status of the particular set of stocks, biological requirements for conservation, and agency and individual decisions. Managers choose when, where, and how to provide opportunity to harvest fish. Individuals decide to avail themselves of those opportunities according to their own interests and priorities, relying upon personal assessments of the costs and benefits that suit their needs. Any multi-year historical period would reflect the outcomes of several years of these types of decisions in response to annual variability in stock-age cohort abundances. The EIS analysis involves what if scenarios under production alternatives described in the EIS. No historical time period would be expected to result in the same relative abundances of all stocks under each EIS alternative. Nor is there any reason to expect that any set of historical regulations or fishing pattern observed as a response to a particular stock-abundance mix, conservation requirements, and management objectives would be well suited to simulate the expected response of managers and fishermen to different conditions envisioned under the variety of EIS production alternatives. Both the U.S. and Canada adopted a substantial variety of regulations designed to respond to domestic conservation concerns for chinook and coho stocks over time. For chinook, fishing patterns developed in response to forecasts of stock-age specific abundance and estimates of projected impacts on individual populations, many of which originate from outside the Columbia River. For example, fisheries in Puget Sound must comply with requirements of 4(d) rules and annual guidance provided during the PFMC planning process. These requirements established exploitation rate constraints on impacts on individual chinook stocks originating in Puget Sound; since concerns for individual stocks can vary from year to year due to the relative abundance in contributing cohorts, fishing patterns and catches can vary substantially from year to year. Chinook fisheries off the West Coast of Vancouver are another example. During the early 2000s, actual regulations of Canadian fisheries under PST regimes included changes in size limits, time-area closures to reduce impacts on Interior Fraser coho and WCVI, early run Fraser, and Strait of Georgia chinook stocks, and reductions in harvests below levels allowed under the PST Agreement to obtain information on stock presence/absence to help address domestic conservation concerns. In Puget Sound and Washington coastal areas, fisheries operated under annually negotiated plans, taking into account expectations for terminal abundance of hatchery and natural stocks of chinook, coho, pink, sockeye, chum, steelhead, and sturgeon. For coho, due to Canadian conservation concerns for the status of the Interior Fraser Management Unit, cumulative annual exploitation rates imparted by all Canadian fisheries on this unit have been capped at 3% (substantially below the maximum allowable impact allowable under recent PST Agreements). A variety of measures have been implemented since the mid- 1990s, including elimination of coho-directed commercial fishing, non-retention restrictions for unmarked coho encountered in commercial fisheries, mark-selective fisheries (MSF) in recreational fishing with a variety of time-area restrictions on bag limits. EIS Harvest Model Final Report 2

7 Each year in the area south of the Canadian-Washington border, annual abundances of individual stocks, conservation requirements, and societal fishery management objectives are considered within an intensive three-month planning process that concludes in April. During this period, complex negotiations are employed to constrain impacts on critical stocks in ocean fisheries regulated through the PFMC and by state and tribal managers for fisheries in inside waters. Each year, the combination of stocks, constraints, and management objectives results in different preseason regulatory packages. Pre-season regulations are frequently revised in-season as fishery information becomes available. It may be possible to produce an analysis of harvest impacts for the limited set of fisheries when catches are dominated by contributions from Columbia River stocks using abundance estimates associated with some historic time period. But, while catch levels for Columbia River and PFMC fisheries might be expected to be similar to observed levels during this time period, catch levels observed for other areas would be driven principally by the abundance of stocks originating outside the Columbia River and fishing patterns. The selection of any particular historic period or set of regulations would be arbitrary. There is no assurance that the package of regulations would be selected or appropriate in response to changes in relative abundance of individual stock-age cohorts in specific fisheries or management objectives under any of the EIS alternative production scenarios. And, there would be no assurance that individual behavior in response to those regulations would mirror what was observed. It is neither feasible nor practicable to attempt to produce an EIS harvest analysis that would generate catch projections that would be directly comparable to observed historical catch levels. Such an effort would involve an extremely complex modeling approach. There is an immense potential for a wide variety of stock conditions, fishing patterns, and regulations that could potentially occur in response to changes in production of Columbia River stocks under various EIS alternative scenarios. Justification would be required for myriad decisions that affect the distribution of harvest opportunity and assumptions regarding fisherman behavior. And, the results that would be produced would confound effects of fishing patterns and stock-age cohort abundance, greatly increasing the complexity of reporting and interpreting potential impacts of EIS alternatives. A simple steady-state analysis was employed to provide information on how fishery impacts would be expected to change under EIS alternatives. Simulation models were developed separately for chinook and coho using Microsoft Excel software. The models incorporate three major elements: (a) Variation in abundance only for Columbia River stocks under the EIS alternatives. The abundance of all stocks originating outside the Columbia River are fixed at levels associated with base periods used in fishery planning models employed by the PSC and PFMC; (b) Exploitation rates, patterns, and regulations characterized by base period data for the PSC and PFMC planning models; and EIS Harvest Model Final Report 3

8 (c) Prescriptive rules to govern conduct of fisheries. These prescriptive rules include: (1) Pacific Salmon Treaty agreements for chinook and coho in effect through 2008; (2) annual guidance for fishery management planning provided by the NMFS for ESA-listed chinook and coho stocks; (3) the Columbia River Interim Management Agreement in effect through 2007; (4) the PFMC Framework Management Plan; and (5) MSF for coho only in PFMC ocean and Columbia River in-river fisheries; MSF only for spring chinook fisheries in the Columbia River below Bonneville Dam. Models based on this approach provide catch projections that can be readily employed to compare potential fishery impacts of EIS alternative production levels for stocks originating in the Columbia River. The EIS harvest models were designed to be integrated with the All-H Analyzer Model (AHA). The AHA Model uses Beverton-Holt stock-production parameters to estimate population abundance levels at different life stages over the full life cycle for the species. The stockproduction parameters are derived by integrating habitat, hydro, hatchery, and harvest effects on population performance (Mobrand-Jones & Stokes Associates 2005). AHA Model data sets have been created for virtually all Columbia River populations of chinook and coho, whether they are entirely natural, entirely hatchery (segregated), or an integrated composite of natural and hatchery fish. In its original form, the AHA Model incorporates simple assumptions about overall harvest impacts, and includes that mortality into the derivation of the stock-production parameters. The model estimates the parameters for steady state conditions incorporating the effects of all of the H s. The harvest models developed for the EIS replace the AHA assumptions. The EIS Models rely on the same datasets that are employed by the PFMC and PSC Models to characterize stockspecific fishery exploitation patterns. Compared to the PFMC and PSC Models, the representation of fishing processes is simpler in the ocean components of the EIS Models, while providing for more complex population structure for salmon produced in the Columbia River. Fishery exploitation patterns from the PFMC and PSC Models were assigned to natural and hatchery production components of chinook and coho from the Columbia River. This approach provided consistency with the PFMC and PSC Models necessary to incorporate abundance-based management regimes adopted by the Pacific Salmon Commission, evaluate impacts of Mitchell Act production changes within the context of ESA exploitation rate constraints on natural stocks, and estimate mortalities in the various fisheries of interest for the EIS analysis. Elements of the PSC chinook and coho FRAM models were simplified and adapted for use in the EIS Models, as described under species-specific sections that follow. For both species, the abundances of populations produced outside the Columbia River were set to be equal to levels associated with base periods ( and for chinook and coho, respectively). Thus, the EIS Models isolate production changes for Columbia River populations associated with the five EIS alternatives for purposes of the fishery impact analysis. EIS Harvest Model Final Report 4

9 The AHA and EIS harvest models were linked with output from each providing input to the other. Population-specific estimates of juvenile production served as the input to the harvest model, and harvest impacts output from the harvest model then became the final input needed to complete the life cycle in the AHA Model. Both models assumed steady state conditions, requiring that several iterations be modeled to achieve output approaching equilibriums. Three iterations through AHA were found to be sufficient for this purpose. ICF Jones & Stokes (J&S) used the AHA Model to produce estimates of juvenile chinook and coho for all natural, hatchery segregated, and hatchery-natural integrated populations in the Columbia River basin under each of the five alternatives being evaluated. The estimates represented the number of juveniles arriving to the mainstem Columbia River downstream of Bonneville Dam for each EIS alternative. The combined total for all populations modeled represented the total number of juveniles for each species produced in the Columbia River basin to arrive to the head of the river s estuarine zone. 1 Each of the EIS harvest models, one for chinook and one for coho, consists of two components: (1) an ocean fishery component employing an annual time step with associated exploitation rates; and (2) a gauntlet-type impact component for Columbia River fisheries that includes dam losses. The conceptual differences between how harvest impacts were modeled in the ocean and river are illustrated in Figures 1 and 2. Besides estimating total mortality (landed catch and incidental loss due to drop off and release mortality), exploitation rates, and landed catches for all fisheries of interest (freshwater and marine), the harvest models estimate the number of adult salmon escaping mainstem Columbia River fisheries to return to terminal areas. Terminal areas are defined as starting at the mouths of the various subbasins or the Columbia River upstream of McNary Dam. Terminal area harvest rates on hatchery fish were estimated using AHA so that final escapements achieved production targets or escapement goals. The EIS models were formulated in Microsoft Excel with separate applications for each species. Each model is configured with rules as described herein. The models have not been structured for readily exploring changes to the rules to perform that type of investigation would require revisions to the models. As currently structured, the models can be used to analyze variations in alternatives representing different production scenarios following the instructions given in the README sections of the model files. The EIS Chinook Model consists of two separate files, one for the ocean component and another for the in-river component. Output from the ocean component is used as input for in-river component. The file names at the time of the preparation of this report are (1) CRHMchin_OcnModule - Apr6_09.xls and (2) CRHMchin_CRModule - Apr6_09.xls. The model does not require any macros to be run all inputs entered into the model by copying ranges from smolt input files generated by J&S. The README sections for each modeling component are provided in Appendix A. The EIS Coho Model consists of one file, which is structured to assess catches in both the ocean and in-river fisheries. The file name for the model at the time of the preparation of this report CRHMcoho - Apr3_09.xls. The model does not require any macros to be run all inputs are 1 / The estuarine zone of the Columbia River begins a short distance downstream of Bonneville Dam. EIS Harvest Model Final Report 5

10 entered by copying ranges from smolt input files generated by J&S. The README section of the model is provided in Appendix B. Application of exploitation rates in ocean fisheries (shown for chinook) Stock component smolts to ocean Age 2 contribution rt Age 3 contribution rt Age 4 contribution rt Age 5 contribution rt Age 2 postnatural mortality cohort size Age 3 postnatural mortality cohort size Age 4 postnatural mortality cohort size Age 5 postnatural mortality cohort size Age 2 hrv impact Age specific ER applied Age 3 hrv impact Age specific ER applied Age 4 hrv impact Age specific ER applied Age 5 hrv impact Age specific ER applied Stock component adults to CR Figure 1. Application of exploitation rates (ERs) applied in an annual time step for simulating ocean fishery impacts in the EIS harvest models. Application for chinook is illustrated. Age specific contribution rates (rt) are used to estimate the post-natural mortality cohort sizes by age in the chinook model. EIS Harvest Model Final Report 6

11 Application of gauntlet type impacts in Columbia River fisheries Entry from ocean Aggregate run size to lower river by race and major group Hrv rate Hrv rate Hrv rate Buoy 10 catch LCR comm LCR spt Terminal area returns Terminal catch Term hrv rates Spawn esc Bonneville Dam Loss rate Passage loss Aggregate run size to between Bonneville & McNary Dams Hrv rate Hrv rate Zone 6 treaty Non-treaty spt Terminal area returns Terminal catch Term hrv rates Spawn esc The Dalles, John Day, McNary Dams Loss rate Passage losses Aggregate run size to above McNary Dam Terminal area returns Terminal catch Term hrv rates Spawn esc Figure 2. Application of gauntlet type impacts for simulating in-river catches and dam losses in the EIS harvest models. EIS Harvest Model Final Report 7

12 3.0 EIS Chinook Model This section describes the EIS Chinook Model. The model s formulation is presented, followed by a short summary of modeling results for the five EIS alternatives. 3.1 Model Formulation Model formulation is described in three sections: overview, marine fisheries formulation, and Columbia River fisheries formulation. The overview describes the approach conceptually, the next two sections provide the primary mathematical formulations Overview The EIS chinook harvest model relied heavily on the PSC Chinook Model. The PSC model provided the analytical basis for implementing abundance-based management under the 1999 PSC Chinook Agreement. A key feature of that model is the interaction between the annual abundance of all stocks that contribute to fisheries north of the Washington-British Columbia border and annual catch ceilings. Consequently, allowable harvest rates in marine fisheries that impact Columbia River chinook are affected by the relative changes in the abundance of contributing stocks. Since the population sizes for stocks originating outside the Columbia River were fixed in the EIS analysis, this feature provided the means to change ocean fishery impacts in response to the different population abundance levels of Columbia River populations by EIS alternative. The PSC Chinook Model focuses primarily on ocean troll and sport fisheries between Cape Falcon off northern Oregon and Southeast Alaska at a scale suitable for the EIS analysis. Columbia River chinook populations migrate predominantly northward from the Columbia River (Snake River fall chinook are also encountered to some degree southward to central California). Ocean fisheries south of Cape Falcon were not modeled as part of this analysis. Fisheries south of Cape Falcon are managed to protect ESA-listed Sacramento River winter and California coastal chinook and to achieve fall chinook spawning escapement goals for the Klamath, Sacramento, and Oregon coastal rivers (PFMC 2004, 2005, 2007). Since the abundance of those stocks was fixed in this analysis, and since the migration pattern of Columbia River chinook is predominantly northward, the potential impact of EIS alternatives on chinook fisheries south of Cape Falcon would be negligible. Elements of the PSC Chinook Model were simplified and adjusted to accommodate the steady state assumptions applied here. The PSC Model evaluates stock and fishery impacts over a multiyear period using an annual time step. Initial stock-age abundances are specified through input data and annual stock-age abundances are determined through a calibration process that incorporates observed levels of fishery catches and escapements. The initial seed values for stock-age abundance do not represent expectations under steady state conditions. Therefore, a method to estimate initial stock-age abundances for each production unit was formulated, as described below. EIS Harvest Model Final Report 8

13 The principal modeling steps are illustrated in Figure 3 (steps are identified in parentheses in flow chart boxes). A. Juvenile population levels passing Bonneville Dam: The estimated number of juveniles by population to survive downstream passage at Bonneville Dam (or entering the mainstem downstream of Bonneville) provides the input to the harvest model. The AHA Model was used to produce juvenile estimates for each of 145 chinook populations defined for the analysis. The total across all populations is intended to represent the total chinook production from the Columbia River under each of the alternatives. The number of juveniles in each population are also identified as to production type, i.e., whether they are natural or hatchery produced. Appendix C lists the populations, together with number of juveniles (final iteration input) under each alternative, and other relevant population-specific information. B. Estimation of estuarine survival: Estimates of estuarine survival are derived for each population and production type, then applied to the number of juveniles corresponding to each population and type arriving at the head of the Columbia River estuary. This step is done in conjunction with the following step because it requires that the populations also be classified by their representative PSC stock component. The PSC Chinook Model uses marine survival estimates that are applied to the number of juveniles departing the estuary. In combination, the estuarine and PSC ocean survivals (not including harvest mortality) comprise the total smolt to adult survival rate (SAR). J&S formulated recent year averages of SAR for each of the populations being modeled. The information used in deriving the rates was obtained through the course of numerous Hatchery Scientific Review Group (HSRG) workshops held with biologists from each subbasin. The rates were intended to be approximations of recent year average survival of a cohort from the point of entering the estuary (i.e., arriving below Bonneville Dam) and back to the same point as mature fish in the absence of all fishing. We assumed that these rates were reasonable approximations and applied them in the EIS harvest model. The PSC Chinook Model uses stock-specific maturity rates and a global set of marine survival rates applied to the cohort as it enters the ocean (i.e., departs the river estuary). The J&S SAR rates divided by the marine survival rates used in the PSC Chinook Model (by stock component) produce the estimates of estuarine survival by population and production type. The number of juveniles that depart the estuary is the Age 1 cohort size. EIS Harvest Model Final Report 9

14 Production by population passing Bonneville (AHA) (A) Ocean phase Mainstem Columbia adult phase Terminal area phase Estimate estuarine survival by population (B) Group populations by PSC stock component (C) Apply pre-recruitment marine survival (D) Estimate spawning escapement by component (P) Mainstem Columbia juvenile phase Apply contribution rates to estimate age class abundance under steady state conditions (E) Apply dam passage mortality (N) Estimate terminal area catch (O) Estimate Abundance Indexes for PSC Agreement (F) Estimate mortality and catch by Zone 6 fishery (M) Adjust BP exploitation rates per 1999 PSC agreement & ESA (G) Apply Bonneville passage mortality (L) Estimate spawning escapement by component (P) Estimate mortality and catch by ocean fishery (H) Estimate mortality and catch by lower river fishery (K) Estimate terminal area catch (O) Mature fish & project run size to Columbia River by PSC group (I) Ungroup PSC stock groups to population (J) Figure 3. EIS Chinook Model flow chart. EIS Harvest Model Final Report 10

15 C. Populations grouped by PSC stock component: This step assigns each Columbia River population (with exception as noted below) to a particular stock group or component represented in the PSC Chinook Model. These stocks have specific exploitation patterns during the base period, maturation rates, and relationships between initial specifications of stock size by age. A total of 30 stock groups are used in the PSC Chinook Model (Appendix D), of which 10 originate in the Columbia River. All Columbia River populations are assigned to one of these stock groups, with the exception of upriver spring chinook and Snake River summer chinook, which are assumed to behave like upriver springs. This group is assumed to have only negligible impacts by ocean fisheries due to a different ocean migration pattern that largely keeps it from being harvested in coastal waters. All modeling in the ocean from this point on uses the PSC stock components. D. Application of pre-fishing marine survival: For each age, a fixed survival rate is applied to the cohort sizes producing the number of fish alive prior to fishing. E. Application of contribution rates to estimate age class abundance: In the PSC model, initial abundance of stock-age complexes are specified through input data. The initial population sizes for the base period represent estimates of abundance in one year, that being 1979; since the fish in any given year come from several different broods with different initial abundances and survival rates, the PSC input data do not reflect steady state conditions. In this step, contribution rates are estimated, then applied, presuming base period exploitation rates and steady state conditions. The contribution rates are applied to cohort sizes that exist at the beginning of the year following entry into the ocean. The rates estimate the initial number of fish in each stock group recruited to the beginning of fishing for each age class. Since all marine fisheries operate on a single pool of fish, only the pre-fishing recruitment size needs to be computed. Under steady-state conditions, the initial abundance of each stock group could be determined by simply multiplying production component projections by these contribution rates. However, because the rates computed using base period data do not directly reflect steady state conditions, an adjustment is necessary. Therefore, the rates derived for the base period with PSC Model inputs were adjusted to mimic the relative age-specific abundances represented in the PSC Model input data. The resulting rates applied to cohort sizes give the number of pre-fishing recruits for each age class under steady state conditions. F. Estimation of Abundance Indices under PSC Agreement: Under the 1999 PSC Chinook Agreement, the total allowable catches in certain highly mixed stock fisheries are regulated with aggregate abundance management regimes. Exploitation rates under these regimes are determined through the use of abundance indices. Abundance indices of relevance here are for Southeast Alaska (SEAK), Northern British Columbia (NBC), and the West Coast of Vancouver Island (WCVI). The indices for these areas are affected by the abundance of populations produced in the Columbia River, in addition to the abundances of stocks produced in other regions. All non- Columbia River stock abundances were fixed at base period levels for purposes of our modeling. EIS Harvest Model Final Report 11

16 This step estimates the index values for SEAK, NBC, and WCVI fisheries under each of the five EIS alternatives. G. Adjustment of base period exploitation rates per PSC Agreement and ESA requirements: In this step, the base period exploitation rates for specific marine fisheries are adjusted as called for under the 1999 PSC Chinook Agreement and to meet ESA requirements for U.S. fisheries. For Alaskan and Canadian fisheries of interest here (SEAK, NBC, WCVI), the abundance index is tied to a harvest impact index (HRI) to indicate the change in allowable fishery impact relative to the levels observed during the PSC Model base period (average of ). The HRI acts as a scalar on exploitation rate (Figure 4). Some simplification was necessary for our model because the index in our case could only be compared to one year during that four year period. Nonetheless, the relative change in a single year s abundance index is informative as a means to indicate the potential magnitude of change anticipated under the EIS alternatives. For PMFC fisheries north of Cape Falcon, a HRI was computed based on ESA jeopardy standards for the Snake River fall and Lower Columbia River (LCR) tule (i.e., Coweeman) fall chinook stocks. The maximum allowable HRI for each stock would be the smaller of the limit derived for each stock. For Snake River falls, the combined ocean fisheries are required to achieve a 30% reduction from the average exploitation rate for this population (NMFS 2005). Fisheries impacts have been lower than allowable limits in recent years. For LCR tules, the total exploitation rate for all fisheries combined is required to be below a 49% limit (NMFS 2005). Accounting for both of these limits, we determined that the LCR tule impact limit would be the more restrictive limit for our modeling. The HRIs as described above were used to adjust the base period exploitation rates (base period exploitation rate * HRI). H. Estimation of ocean fishery mortality and catch: Results from the previous step yield the total allowable exploitation rate by age for each stock in each fishery. These rates are for total impact, including drop-off and sub-legal release mortalities. Appendix E lists the complete set of fisheries modeled. Appendix F provides the incidental mortality rates applied for each fishery. Landed catches were estimated by applying these impact rates and subtracting off incidental mortalities. For PFMC fisheries, the combined total impact rate was allocated between the treaty and nontreaty troll and sport fisheries using the average division of catch over a five year period ( ).Resulting catches for each of these three fishery groups was then considered to be allocated between ports (north of Cape Falcon) based on the average proportion of catch in each port between Estimates of catch levels by fishery sector and port are needed for economic impact analysis for EIS alternatives. I. Projection of mature fish returning to Columbia River: The numbers of fish in each age group and each stock component surviving ocean fisheries represents the run sizes returning to EIS Harvest Model Final Report 12

17 the Columbia River mouth under steady state conditions. The sum across age groups is the total run size for each PSC stock component. 1.0 Exploitation rate scalar - SEAK 0.8 Scalar Abundance Index 1.0 Exploitation rate scalar - NBC 0.8 Scalar Abundance Index 1.0 Exploitation rate scalar - WCVI 0.8 Scalar Abundance Index Figure 4. Harvest rate scalars in SEAK, NBC, WCVI fisheries. J. Ungroup PSC stock components into populations: Ocean fishery impacts are evaluated using groups of individual populations as described in step (C). This step ungroups the PSC stock components into the 145 populations that comprise them. The relative abundance of populations EIS Harvest Model Final Report 13

18 within each group is assumed to be identical to the proportions that existed as juveniles departing the river. Run sizes of those populations that were assumed to not be harvested in coastal waters, i.e., upriver spring chinook and Snake River summer chinook, were estimated by applying the SARs reported by J&S. At this point in the modeling procedure, all populations are accounted for and run sizes back to the river mouth have been estimated. Steps that follow determine the impacts and catches made by the various in-river fisheries. K. Estimation of lower mainstem river (below Bonneville Dam) fishery mortality and catch: In-river fishery impacts were simulated as a sequential gauntlet of mortalities: lower river fisheries Bonneville Dam passage Zone 6 fisheries upper river dam passage mortalities terminal area tributary fisheries escapement. Specific fisheries modeled were: Downstream of Bonneville Dam Buoy 10 sport Lower river commercial Lower river sport Upstream of Bonneville Dam Zone 6 treaty Indian Zone 6 sport Terminal fisheries were defined as those in Select Area Fisheries Enhancement (SAFE) areas, all tributaries (including within the lower Willamette River), and the mainstem Columbia upstream of McNary Dam. Fishery regimes were driven principally by the projected in-river run sizes of the production components that constrain harvest impacts in accordance with the provisions of the Columbia River Interim Management Agreement 2 (in effect through 2007) and ESA requirements for fall chinook. Additional details for modeling fisheries were based on information contained in the Joint Staffs reports for spring-summer (ODFW/WDFW 2006a) and fall fisheries (ODFW/WDFW 2006b), and through communications with agency biologists. Spring and summer chinook fishery impacts in the mainstem Columbia River were modeled using sliding scales based on the abundances of upriver runs, as specified in the Interim Management Agreement. Modeling rules for these runs are detailed in Appendix G. Spring chinook fisheries downstream of Bonneville Dam are MSFs, requiring the release of all non-adipose clipped fish. This requirement applies both to the lower river commercial and sport fisheries. A mortality rate of 10% was applied to the release of sport caught unmarked fish. The lower river commercial fishery uses both tanglenet and 8-9 inch mesh gillnet, having expected mortality rates on released fish of 18.5% and 40% respectively (Guy Norman, WDFW, personal communications). We applied an average rate of 25% due to a mixed composition of nets that are apparently used. 2 / Columbia River Interim Management Agreement for Upriver Chinook, Sockeye, Steelhead, Coho and White Sturgeon. EIS Harvest Model Final Report 14

19 Harvest rates in these fisheries, while governed by the sliding scale on upriver spring chinook in Appendix G, were also applied to Willamette and other lower river spring chinook. However, those rates were increased slightly to account for differences in run timing (impact rates average 2-4%, Guy Norman, WDFW, personal communications). The Interim Management Agreement allocates the non-treaty impact to areas above and below Bonneville Dam as follows: Downstream of Bonneville Dam 85% Upstream of Bonneville Dam 15% The allocation of the downriver impact between sport and commercial fisheries occurs as follows (Guy Norman, WDFW, personal communications): Sport 57% Commercial 43% Upper Columbia River summer chinook (originating upstream of Priest Rapids) are managed in a manner to allocate most of the fishery impact to fisheries upstream of Priest Rapids. These populations are not listed by the ESA. For combined run sizes of upriver summer chinook returning to the Columbia less than 50,000 in size, non-treaty impacts were allocated as follows (based on Bartlett and Tweit 2006): Below Priest Rapids 10% Above Priest Rapids 90% Larger run sizes provide a somewhat higher relative impact to non-treaty fisheries downstream of Priest Rapids. It should be noted from Appendix G, listing the sliding scale that governs overall impacts, that harvest rates on summer chinook are very small (~5%) on run sizes of less than 29,000. Rates rise as run sizes increase, jumping significantly at runs larger than 50,000. Allowable impacts in the mainstem Columbia River on fall chinook are determined by ESA requirements for Snake River wild falls and Lower River falls (Coweeman or LRH tule stock). Attention was primarily given to Snake River or Upriver Brights (URBs) in the Joint Staffs planning report for 2006, while it shifted to LRHs in their planning report for We applied the rates detailed for URBs as outlined in the Interim Management Agreement to simplify the modeling procedure. It turns out that the resulting rates on LRHs are very close to what they would have been had we modeled around that stock, and are in the lower end of the expected range reported by NMFS (2005) for LRHs. The Interim Management Agreement called for a 30% reduction from base period harvest rates on Snake River wild falls in combined non-indian and treaty Indian mainstem fisheries. The corresponding impact rate is 31.29% of the aggregate URB run. This impact rate is allocated as 23.04% to treaty Indian fisheries (Zone 6) and 8.25% for all non-indian fisheries. EIS Harvest Model Final Report 15

20 The allocation of the non-indian impact on URBs, as specified in ODFW/WDFW (2007), was modeled as follows: 3 Sport 51% Commercial 49% The allocated rate for sport fisheries was further divided between the Buoy 10, Lower River sport, and the sport fishery between Bonneville and McNary dams. The sport fishery upstream of McNary Dam is primarily located in the Hanford Reach, which does not impact Snake River falls. Therefore, impacts upstream of McNary Dam were not included in the 8.25% impact rate assigned to non-indian fisheries. We allocated the impact assigned to sport fisheries to achieve the pattern seen in recent years, as shown below: Buoy 10 20% Lower River sport Above Bonneville 76% 4% The harvest rates that result from using these allocations were applied to all fall chinook populations passing through the lower river with the exception of Lower River Wild (LRW) populations. The largest component of LRW populations is North Fork Lewis River wild falls. LRW fall chinook are somewhat later timed than LRHs and observed mainstem harvest rates since 2002 have been higher than on LRH fish (NMFS 2005). For LRW populations, we applied the average observed harvest rate between to the Lower River commercial fishery. L. Application of Bonneville Dam passage survival: A 97% passage rate was applied to populations destined for subbasins upstream of Bonneville Dam after all mortalities associated with downstream fisheries were subtracted. M. Estimation of Zone 6 fishery mortality and catch: Harvest impacts by treaty Indian fisheries on spring and summer chinook were modeled according to sliding scales based on population abundance as described in Step K. The impact rate on upriver fall chinook, as specified in the Interim Management Agreement, was modeled as 23.04%. These harvest impact rates were applied to the number of fish passing Bonneville Dam. The allowable harvest rates by treaty Indians include commercial as well as ceremonial and subsistence (C&S) catches. The percentages of the catches used for C&S purposes, based on averaging data for , are as follows (from PFMC database): Chinook race Spring % C&S 65.9% Summer 64.3% Fall 0.5% Small non-indian sport fisheries between Bonneville and McNary dams were assumed, as described in Joint Staff (2006a and 2006b). Allocations to these fisheries were described in Step K. 3 / We applied the allocation shown although the Interim Agreement called for a 50:50 split. EIS Harvest Model Final Report 16

21 N. Application of dam passage survivals: Fish surviving the Zone 6 fisheries in each population were then subjected to the fish passage rate specified by J&S as part of their data input to the harvest model. The rate accounted for all dams passed upstream of Bonneville Dam prior to arriving to terminal areas. Fish that pass dams associated with these rates are assumed to represent escapement to the subbasins (or to the mainstem upstream of McNary Dam). O. Estimation of terminal area run sizes and terminal area catches: Terminal area catches for each population were estimated by applying the terminal areas harvest rates provided by J&S as part of their data input to the harvest model. These rates include MSFs on hatchery fish where appropriate. P. Estimation of spawning escapements: Fish surviving terminal area fisheries were assumed to represent spawning escapements Marine Fisheries Formulation The primary formulas for understanding the modeling procedure are presented. The EIS Chinook Model utilizes the following types of input data: (1) stock-age-fishery specific exploitation rates; (2) stock-age specific maturation rates; (3) assumed age-specific survival rates; (4) fishery-age-specific release and drop off mortality rates; and (5) initial stock-age specific cohort sizes. Notation used is defined below. For clarification, individual populations within the Columbia River are denoted by the i subscript. These combine into the PSC stock groups (or components) denoted by the subscript c. AER Allowable Exploitation Rate for component c c AI Abundance Index for fishery f f AR Adjusted Contribution rate for component c at age a ca, BP Estimated average production level for component c age a ca, during the PSC Model Base Period BPER Base Period Exploitation Rate as it would be applied to the c, f, a 1 entire cohort size in fishery f for component c age a-1. Note: the BPER described here differs from that used in the PSC Model. In that model, the BPER represents the proportion of the vulnerable cohort that was harvested during the base period, i.e., not the proportion harvested of the entire cohort size. The BPERs as applied here are simply the PSC Chinook Model BPERS multiplied by age-specific proportions vulnerable to exploitation. COH c, Cohort size of component c at age a a CRRUN c, Run size back to the Columbia River of mature fish for a component c and age a EIS Harvest Model Final Report 17

22 DO Drop Off mortality rate for fishery f age a-1 fish ESA HRI f, a 1 c f ESA jeopardy standard for component c Harvest Rate Index for fishery f J i, k, Juvenile estuarine survival rate for population i of production c type k (natural or hatchery) associated with PSC stock component c M i, k, Number of migrants reaching the ocean in population i of c production type k (natural or hatchery) associated with PSC stock component c MR Maturation rate for component c at age a c, a 1 N c, Initial population size of component c age a fish input into the a PSC Chinook Model during the base period p i, k, Juveniles for population i of production type k (natural or c hatchery) associated with PSC stock component c R, Contribution rate for component c at age a c a RM Release mortality rate for fishery f age a-1 fish c a f, a 1 s, Pre-fishery survival rate for component c age a SAR i, k, Smolt (number entering estuary) to adult (number arriving to c head of estuary) survival rate for population i of production type k associated with component c SN Initial population size of age a fish estimated from production ca, component c The formulation is presented in the same steps used in the overview. A. Juvenile population levels passing Bonneville Dam: The juvenile production level for each population i (p i ) by production type k (natural or hatchery) is the number to arrive to the lower Columbia River downstream of Bonneville Dam. This is the point considered the upstream end of the estuarine zone. Each Columbia River population is classified as belonging to one of 10 PSC model stocks. B. Estimation of estuarine survival: Estimates of estuarine survival are derived for each population by production type (natural or hatchery) and applied to the number of juveniles arriving at the head of the Columbia River estuary to produce the number of migrants reaching the ocean by = (eq.1) M i, k, c pi, k, c J i, k, c Juvenile estuarine survival for each i, k, and c is derived by first estimating total marine survival (MS c ) of the Age 1 cohort (number departing the estuary) in the absence of fishing for each PSC stock component. This is the base period adult equivalent stock size (BPAEQ) divided by its Age 1 cohort size (COH 1 ) for each component c as follows: EIS Harvest Model Final Report 18

23 BPAEQ c MS c = (eq.2) COH c,1 Where BPAEQ is calculated as BPAEQ = COH s MR ) (eq.3) c ( c, a c, a c, a a Then juvenile estuarine survival for each i, k, and c is simply J MS c i, k, c = (eq.4) SARi, k, c C. Populations grouped by PSC stock component: All populations except upriver springs and Snake River summers are grouped according to their representative PSC stock component c; the Age 1 cohort size for each stock component is then COH c, 1 = M i, k, c (eq.5) i k E. Application of contribution rates to estimate age class abundance: Age specific contribution rates, presuming base period exploitation rates (BPER c,f,a ) and steady state conditions, are calculated as R = s (eq.6) c, 2 c,2 for age 2 and by the following for older ages R c, a = Rc, a 1 (1 BPERc, f, a 1) *(1 MRc, a 1) * sc, a f * (eq.7) Under steady-state conditions, the initial abundance of each stock group could be determined by simply multiplying production component projections by these contribution rates. However, because the rates computed using base period data do not directly reflect steady state conditions, an adjustment is necessary. Therefore, the rates derived for the base period with PSC Model inputs were adjusted to mimic the relative age-specific abundances represented in the PSC Model input data. The resulting rates applied to cohort sizes give the number of pre-fishing recruits for each age class under steady state conditions after accounting for pre-fishing natural mortality. It should be noted that the version of equation 7 shown above is actually a simplification of what was used in the model. We derived the contribution rates that were applied by taking into account release mortality of sub-legals and drop-off mortalities, which requires several more steps than shown in equation 7. The derivation of contribution rates taking these incidental mortality rates into account is given in Appendix H. EIS Harvest Model Final Report 19