***Please Note*** April 3, Dear advisory committee members:

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1 April 3, 29 Dear advisory committee members: The fifth meeting of the CHF advisory committee will be held April 13 in Grants Pass from 6:-8:3 PM, and the purpose of this document is to help committee members prepare for that meeting. ***Please Note*** There is a lot of information included in this distribution packet. About half of this material will be presented during the course of the April 13 meeting. The other half is background information for those committee members who wish to learn more the finer points of technical estimation issues. Those of you who wish to focus on the primary information related to development of a draft statement of desired status, please focus on the information presented on pages The primary purposes of the April 13 meeting are: (1) Review and discuss boundaries chosen to delineate CHF populations in the Rogue River Basin. This is an important topic because individual populations must be covered by the conservation plan and biological data indicates that multiple populations are present in the basin. (2) Review and discuss development of a method to estimate the passage of adult CHF at Huntley Park. This is an important topic because a fishery assessment should be based on estimates of fish abundance, if reasonable estimates can be developed. (3) Review and discuss passage estimates of CHF at Huntley Park. This is an important topic because fish abundance should be a critical element of the desired status statement. (4) Review and discuss the stock-recruitment relationship for pooled CHF populations in the Rogue River Basin. This is an important topic because interpretation of the relationship will provide some guidance related to identification of a desired status element for fish abundance. (5) Based on information related to above items 4, the committee should be ready to initiate discussion needed to identify a desired status statement element(s) for fish abundance in the Rogue River Basin. The element(s) could be in directed towards freshwater escapement and/or spawning escapement. Thank you for your attention to this matter. Let me know if you have any questions related to the enclosed material. Tom Satterthwaite Oregon Department of Fish and Wildlife 5375 Monument Drive Grants Pass, OR Tom.D.Satterthwaite@state.or.us

2 Agenda Item 3 - CHF populations in the Rogue River Basin Based on CHF life history information, and some genetic data, there appears to be five significant populations of CHF in the Rogue River Basin: 1. Illinois River Basin; hereafter termed the Illinois population 2. Applegate River Basin; hereafter termed the Applegate population 3. Area between Rogue mouth and Mule Creek (includes tributaries except Illinois River Basin); hereafter termed the Lower Rogue population 4. Area between Gold Ray Dam and Mule Creek (includes tributaries except Applegate River Basin); hereafter termed the Middle Rogue population 5. Area upstream of Gold Ray Dam (includes tributaries) hereafter termed the Upper Rogue population Adult CHF that return to each of these areas tend to enter the Rogue River at different times and also tend to spawn at different times. Both of these life history traits have a genetic basis. Spawning time especially is highly heritable among Chinook salmon. Time of Freshwater Entry ODFW tagged a large number of CHF near the mouth of the Rogue River during and recovered tags during spawning surveys conducted throughout the basin. Results from the tagging study showed differences in time of freshwater entry for the various populations: Upper Rogue: primarily entered the Rogue in August Middle Rogue: primarily entered the Rogue in late August - early September Lower Rogue: primarily entered the Rogue in late September - early October Applegate: primarily entered the Rogue in September Illinois: primarily entered the Rogue in late September - early October The tagging study also found that CHF that spawned in two small tributaries of the lower Applegate (Slate and Waters creeks) entered freshwater an average of two weeks later as compared to counterparts that spawned in the lower portion of the mainstem of the Applegate River. This finding suggests that a small, yet distinct, population of CHF may be present in small tributary streams of the lower section of the Applegate River Basin. Time of Spawning ODFW estimated CHF spawning time within a number of spawning areas during Results showed differences in CHF spawning time for the various populations: Middle Rogue: primarily spawned during October Lower Rogue: primarily spawned during mid-november through mid-december Applegate: primarily spawned during late October through November Surveys also indicated that CHF spawning in two small tributaries of the lower Applegate (Slate and Waters creeks) spawned an average of two weeks later as compared to counterparts that spawned in the lower portion of the mainstem of the Applegate River. This finding suggests that a small, yet distinct, population of CHF may be present in small tributary streams of the lower section of the Applegate River Basin. Genetics Sampling for CHF genetic assessments has been conducted in various areas of the Rogue River Basin. The purpose of most of this work was to assess the relative difference of Rogue populations as compared to other Chinook salmon populations along the Pacific coast. No work 2

3 to specifically test for differences among Rogue Basin populations has been completed, with one exception. A DNA assessment of Chinook salmon that passed Gold Ray Dam in 24 indicated that CHF that were trapped in late September, and early October, were out of compliance with Hardy- Weinberg equilibrium. In non-technical terms, this finding suggests that the sampled fish exhibited a very narrow (restricted) ancestral lineage. Such a finding is rare among healthy populations of salmonids and leads one to conclude that CHF that spawn upstream of Gold Ray Dam likely differ from those that spawn in areas farther downstream. Brief Description of databases available for CHF in the Rogue River Basin Summary of available data for each provisional population of NP CHF follows, along with a brief planner interpretation of the suitability of the data for inclusion in the conservation planning process. Illinois population: Some sporadic aerial redd count data and spawning survey data from some small tributary streams. CHF spawning primarily occurs in the larger streams. Data judged insufficient for the purposes of the conservation plan. Applegate population: Systematic spawning survey data (carcass counts) gathered during Systematic sampling of juvenile migrants during Data collection terminated for both juveniles and adults, and is unlikely to be re-instituted. Data was judged to be insufficient for most purposes of the conservation plan. Middle Rogue population: Systematic spawning survey data (carcass counts) gathered during Systematic sampling of juvenile migrants (beach seine) during Data collection terminated for both juveniles and adults, and is unlikely to be re-instituted. Data was judged to be insufficient for the most purposes of the conservation plan. Lower Rogue population: Systematic spawning survey data gathered during Spawning escapement estimates were previously distributed to the advisory committee. Upper Rogue population: Systematic passage estimates made at the fish counting station at Gold Ray Dam during Estimates are useful for inclusion in the conservation planning process. All populations: Systematic sampling with a large net (beach seine) at Huntley Park (river mile 8) during the period when almost all CHF pass to upstream spawning areas. Site was sampled during Data can be used to estimate freshwater escapement and so is useful for inclusion in the conservation planning process. Agenda Item 4a - Development of a new method to estimate abundance of adult CHF Population size should be estimated in order to evaluate population status and be able to evaluate the impacts of consumptive fisheries. Currently, ODFW monitors CHF returns to the Rogue River with an abundance index. This section describes planner efforts to develop methods that could be used to instead estimate population size. Background: Currently, ODFW indexes CHF returns to the Rogue River by sampling with a 3 beach seine at Huntley Park (river mile 8) three days weekly during July 15 through October 28. Sampling begins early in the morning and continues until the seine has been set 15 times. Captured CHF are examined for fin clips, measured, and then released. This sampling has been conducted annually since

4 During 1983 and 1984, it was readily apparent that high flows in the Rogue River were affecting the efficacy of sampling with the beach seine. During high flows, the net could not be fished deeply and the current moved the net faster through the sampling site. During these years, sampling was being conducted as part of a United States Army Corps of Engineers project designed to assess the effects of Lost Creek Dam on salmon and steelhead in the Rogue River. To meet the objectives of the project, some method had to be devised to account for the effects of high flows on the sampling efficiency of the beach seine. The resultant method was based on estimates of seining efficiency on coho salmon of hatchery origin that were destined to mostly return to Cole Rivers Hatchery. Data that was available indicated that few coho salmon died during upstream migration, few strayed to spawn naturally, and, at the time, there was no directed freshwater fishery for coho salmon. Seining efficiency on coho salmon of hatchery origin was estimated, compared to flow at time of seine capture, and a catch efficiency model was developed. Basically, results from this analysis were used to estimate coho run size, and were also subsequently used to generate passage estimates for halfpounders, late-run adult summer steelhead and CHF. A subsequent review of estimation procedures in 199 indicated that the model remained effective in relation to estimating the number of late-run adult summer steelhead that passed Huntley Park. Sometime during the 199s, a second method was employed to estimate coho salmon passage at Huntley Park. The method employed, which is commonly used to estimate population size of various animals, is called the Peterson mark-recapture method. ODFW now uses the Peterson mark-recapture method to estimate the number of coho salmon the pass Huntley Park. The following graph shows the relationship between the two estimation methods for coho salmon: Estimate 2 (Flow Expansion Method) Line = 1 to 1 relationship Estimate 1 (Mark - Recapture Method) Estimates of Hatchery Coho in Rogue, There is a very good relationship (actually amazingly good) between the two estimation methods. The relevance of this matter is that the flow based estimator method is currently used by ODFW to index CHF passage at Huntley Park. ODFW has tried twice (197s and 2-22) to estimate CHF numbers with a Peterson mark-recapture effort. Both efforts were deemed unsuccessful because the survival rates of tagged CHF was lower than the survival rates of non-tagged CHF during years of marginal water quality. 4

5 Development of Revised Method to Estimate CHF Passage at Huntley Park: The planner considered the feasibility of estimating CHF passage at Huntley Park so that better population assessments could be completed as part of the conservation planning process. As detailed in the previous section, there is good evidence that the flow based estimator method effectively estimated coho salmon passage at Huntley Park. The planner thus decided to investigate the possibility of modifying the flow based estimator (also used to calculate Huntley Park CHF index) with a goal of estimating the number of CHF that passed Huntley Park. There were a few (five) CHF tagged in the lower Rogue during that eventually passed the fish counting station at Gold Ray Dam (river mile 126). All of these fish were captured at Huntley Park between the middle of July and early August. As 1% of the passing fish are counted at Gold Ray Dam, and if one assumes that all of the early-run CHF are headed to spawning areas upstream of Gold Ray Dam, then an appropriate expansion factor can be applied to the Huntley Park CHF index. The data from the five tagged fish indicated that early-run CHF headed upstream of Gold Ray Dam passed Huntley Park during July 15 through August 4. Comparisons of the Huntley Index for early-run CHF and the number of CHF passing Gold Ray Dam indicated that, during , the Huntley Index accounted for an average of 4% of the early-run CHF that actually passed Huntley Park. Data from years prior to 1992 were not included because concern that the population of CHF in the upper Rogue was still increasing relative to CHF in the remainder of the basin. Because of variations in CHF migration timing, this approach would not be appropriate if there was data from only a few years. However, with 17 years ( ) of data, variations in CHF migration timing would be mostly cancelled; provided that annual variations in CHF run timing were random. Bottom line: The current ODFW index can be simply divided by.4 to estimate annual CHF passage at Huntley Park. Evaluation of Revised Method: Two approaches were employed to evaluate the propriety of the possible method to estimate CHF passage at Huntley Park. Application of radio-tags to CHF caught at Huntley Park in 28 afforded the opportunity to test the assumption that early-run CHF migrate upstream to spawning areas above Gold Ray Dam. There were three early-run CHF tagged at Huntley Park that passed Gold Ray Dam. One passed on August 11 and was classified as a CHS by ODFW. The other two passed later and were classified by ODFW as CHF. ODFW uses August 15 as a demarcation date by which to classify CHS versus CHF at Gold Ray Dam. In addition, there were another three CHF that were radiotagged at Huntley Park after August 4 and were subsequently detected on spawning grounds downstream of Gold Ray Dam. Bottom line: Radio-tagging results in 28 suggested that it is appropriate to assume that CHF caught at Huntley Park during July 15- August 4 are destined for spawning areas upstream of Gold Ray Dam. The second evaluation approach is based on accounting for all CHF known to be present in the Rogue River Basin. There were three sources of data that could be used for the accounting: 1. Passage estimates of CHF at Gold Ray Dam (Upper Rogue population) 2. CHF harvest estimates from salmon-steelhead tags (punchcards) 3. CHF carcasses recovered within five survey areas (two in Middle Rogue and three in the Applegate River). These survey areas covered only a small portion of the total CHF spawning area, and only a portion of the spawners are recovered as carcasses. 5

6 A summary of the above sources of CHF numbers follows and the total accounting of CHF is also expressed as a percentage of the newly developed estimates of CHF passage at Huntley Park. Gold Ray Total % of new Year Dam Punchcards Carcasses a known return estimate ,181 3,771 3,745 12, % ,878 2,43 1,193 18,51 9.9% ,93 1,679 8,467 13, % 198 2, ,632 6, % ,767 2,386 6,399 13, % ,595 2,453 3,52 1, % ,839 2,467 3,8 9, % ,184 1,489 3,663 8, % ,455 3,841 7,986 2, % ,239 5,121 2,4 39, % ,699 12,55 28,45 51, % ,497 16,616 32,965 61, % ,93 9,995 7,889 24, % 199 3,65 3,98 1,914 9, % ,25 4,588 2,956 1, % ,797 3,776 2,83 13, % ,711 1,1 5,74 22, % ,53 11,315 7,895 3, % ,366 1,83 4,131 28, % ,385 6,329 2,569 2, % ,857 3,488 1,711 1, % ,332 3,462 3,641 12, % ,54 3,31 2,65 9,5 16.% 2 9,892 8,14 3,592 21, % 21 13,66 8,337 7,152 29, % 22 19,823 9,927 12,741 42, % 23 24,857 17,3 15,63 57, % 24 15,7 8,57 8,868 32, % a Surveys covered 24 miles of the possibly the best spawning habitat in the Rogue River Basin. Total CHF spawning habitat in the basin estimated to be about 54 miles, of which about 3 miles is considered by the planner to be highly productive spawning habitat. Note that relatively more CHF could be accounted for after the mid 198s. Increased CHF production in the Upper Rogue and Applegate populations were responsible for the change. More context related to this matter will be conveyed at the April 13 meeting. Bottom line: A summation of known numbers of CHF, to be present in the Rogue River Basin, averaged about 32% of the newly developed estimates of the total (not index) number of CHF that passed Huntley Park during Given that only a small portion of the spawners were recovered as carcasses, the newly developed CHF return estimates seem reasonable, in the opinion of the planner. Agenda Item 4b - Estimates of CHF passage at Huntley Park The planner used the newly developed method to estimate the number of CHF that passed Huntley Park during The next step was to estimate the origin (hatchery or wild) and 6

7 age of the return. These estimation steps were straight forward for the returns because scale samples were collected and the analysts were able to age the samples and differentiate wild and hatchery fish based on differences in circuli (similar to tree rings) patterns. In freshwater, hatchery fish grow faster than wild fish. Scale samples were not interpreted for CHF seined during the return years, so different methods had to be employed. All CHF seined at Huntley Park were examined for fin clips and were also measured. Age-length relationships from data collected in were used to assign ages to the measured CHF. This step resulted in age estimates for all of the CHF with and without fin clips. As not all hatchery fish were marked with fin clips, the mark rates within hatchery release groups were used to account for unmarked hatchery fish. Application of mark rates were specific to each brood year. Only data from hatchery fish releases in the Rogue River Basin was used for this purpose. Results: CHF passage estimates at Huntley Park averaged about 97, fish during and ranged between 19, fish in 1991 and 246, fish in The 13-fold difference in annual returns is very similar to the 15-fold differences in annual survival rates estimated for CWT marked CHS smolts released from Cole Rivers Hatchery. 3 CHF Returns (1,s) Estimated passage of CHF at Huntley Park Hatchery fish accounted for an average or 4% of the returning adults, with annual returns ranging between and 15% hatchery fish. Estimates of annual returns can be found in the spreadsheet that was also distributed with this note. Agenda Item 5 - Estimates of spawning escapement and recruitment Spawning escapement: CHF spawning escapement in the Rogue River Basin was estimated as: Passage estimates at Huntley Park - (prespawning mortality + angler harvest) 7

8 CHF in the Rogue River are susceptible to high rates of prespawning mortality during years of low flow and warm water temperatures. Such losses were first documented in the 194s. During the early 198s, ODFW developed methods to estimate the percentage of the CHF that died during upstream migration. Empirical estimates of mortality rates ranged between % and 81% during ; years when ODFW conducted CHF prespawning mortality surveys. An estimate was also available for 21, which was a drought year. Concern about a possible high rate of prespawning mortality lead to surveys being conducted in 21. Rates of prespawning mortality in all years without surveys were assumed to be 2%. Angler harvest of CHF in areas upstream of Huntley Park was estimated based on estimates derived from salmon-steelhead tags (punchcards). Beginning in 1993, the Rogue River was segregated into multiple catch areas for use on angler punchcards. These areas include: (1) bay - Elephant Rock, (2) Elephant Rock - Grave Creek, (3) Grave Creek - Gold Ray Dam, and (4) upstream of Gold Ray Dam. Two steps were required to estimate angler harvest upstream of Huntley Park: 1. Harvest estimates from Elephant Rock upstream were pooled. Thus, CHF caught between Elephant Rock and Huntley Park were included in the upstream harvest. There was no other choice in the matter and the resultant error was judged to be minor. 2. CHF jacks (age 2) are to small to be recorded on angler punchcards. The planner assumed that harvest rates of jacks were equal to the harvest rates of larger adults. In addition, it was assumed that harvest rates of age 3-6 CHF were equal among age classes. For the years before 1993, the Rogue River was segregated into only two catch areas, upstream and downstream of Gold Ray Dam. The planner used the average harvest distribution estimate from 1993 and later years to estimate the distribution of harvest (upstream and downstream of Huntley Park) for years before One issue that arose during estimation of spawner escapement was related to natural spawning by hatchery fish. Passage estimates at Huntley Park indicated that hatchery fish accounted for an average of 4% of the CHF that entered the Rogue. However, very few hatchery fish were observed during spawning surveys. During , ODFW recovered about 78, carcasses during surveys of the middle Rogue and Applegate. Only nine of those fish were marked with adipose fin clips and coded wire tags. Hatchery releases during the 197s and 198s, were mostly made at Cole Rivers Hatchery. Returning adults primarily homed to the hatchery and thus did not spawn naturally. As the primary CHF spawning occurs in the middle Rogue and Applegate, the planner concluded that it was most appropriate to assume that no hatchery fish spawned naturally. There is some natural spawning of CHF that originate from Indian Creek and the planner will be working on those estimates at a later date. Finally, it is known that hatchery CHF of Klamath River Basin origin have been caught in the Huntley Park seine. It is unknown whether a significant portion of these fish eventually spawn in the Rogue River Basin. There have been instances where ODFW tagged CHF in the Rogue River, and those fish were later found in the Klamath River Basin. Recruitment: The number of wild CHF recruits was estimated by methods outlined in the meeting material distributed before the March 2 meeting, with two points of clarification: 1. Angler harvest of CHF in locations downstream from Elephant Rock was added to the Huntley passage estimates in order to estimate freshwater escapement. Estimation methods followed those described in the previous section. 8

9 2. Ocean harvest rates (age specific) were assumed to equal those estimated for CHF of Klamath River origin. As Rogue and Klamath CHF have a similar ocean distribution, and because survival rates of CHS and CHF released from Rogue and Klamath Basin hatcheries covary on an annual basis, this assumption seemed reasonable. In any case, there was no other option available because the highly variable rates of ocean harvest have to be accounted for in order to estimate recruitment. Results: Estimates of CHF spawner escapement averaged about 82, fish during and ranged between 15, fish in 1991 and 226, fish in Excluding age 2 jacks (all are male), the spawning escapement of age 3-6 CHF averaged about 63, fish during and ranged between 13, fish in 1991 and 193, fish in 23. Fishery biologists most often report recruits as the sum of those salmon caught in the ocean and those salmon that return to freshwater. Using this approach, estimates of CHF recruits (wild fish only) of Rogue River Basin origin averaged about 17, fish during and ranged between 39, fish (1989 brood year) and 374, fish (1983 brood year). A less common way of reporting recruits originates from attempts to estimate the number of fish that are alive in the ocean before any exposure to potential ocean harvest. Using this approach, the number of age 2 recruits of Rogue Basin origin (wild fish only) averaged about 425, fish for the brood years and ranged between 89, fish (1989 brood year) and 1,876, fish (1975 brood year). Agenda Item 6 - Stock-recruitment relationship for Rogue CHF As discussed in previous advisory committee meetings, a comparison of the number parents (spawners) and the resultant number of progeny can offer guidance in the attempt to identify a desired status element for CHF abundance. The graphs that follow were crafted with that specific purpose in mind. The planner identified four different ways to look at the stockrecruitment relationship for Rogue CHF, so there are four graphs. 1 8 Recruits (1,s) Spawners (1,s) Rogue stock-recruitment relationship 1: Recruit numbers (ocean harvest + freshwater escapement) compared with the number of spawners (all ages). 9

10 1 8 Recruits (1,s) Spawners (1,s) Rogue stock-recruitment relationship 2: Recruit numbers (ocean harvest + freshwater escapement) compared with the number of spawners (no age 2 jacks - they are all males). From the perspective of the planner, plots of recruits and spawners shown in the above two graphs do not provide much insight in relation to trying to select desired status in relation to CHF spawning escapement in the Rogue River Basin. There is another way to look at the parent-progeny relationship. Survival rate estimates (smolt - age 2) for hatchery fish can be applied to the number of wild fish estimated alive at age 2 in order to estimate the number of wild smolts that migrated from the Rogue River. The planner used survival rate estimates for CWT marked CHS released from Cole Rivers Hatchery (estimates were available for the broods) for this purpose, and the results are shown in the following two graphs: 25 2 Smolts (millions) Spawners (1,s) 1

11 25 2 Smolts (millions) Spawners (1,s) Rogue stock-recruitment relationship 3: Progeny numbers (estimated number of wild CHF smolts) compared with the number of spawners (all ages). Rogue stock-recruitment relationship 4: Progeny numbers (estimated as the number of wild CHF smolts) compared with the number of spawners (no age 2 jacks - they are all males). From the perspective of the planner, plots of estimated smolt numbers and spawners provide a little better insight in relation to trying to select desired status in relation to CHF spawning escapement in the Rogue River Basin. Planner conclusion: From the perspective of the planner, the plots of recruits and spawners do not appear to provide much insight in relation to trying to select desired status in relation to CHF spawning escapement in the Rogue River Basin. Of the guidance choices available to the advisory committee, the planner believes that stock-recruitment relationship 4 (immediately above), represents the best guidance choice available to the advisory committee. One choice of a predictive equation that best fits (a poor statistical fit) the data is shown in the following graph. 11

12 25 2 Smolts (millions) Spawners (1,s) Agenda Item 7 - Desired status element - Rogue CHF abundance As previously discussed, the Native Fish Conservation Policy calls for inclusion of an element of fish abundance in a statement of desired status. At the April 13 meeting, the advisory committee should be prepared to discuss the following matters: 1. Given the information which is currently available, is the committee ready to initiate discussion related to development of a desired status element related to the abundance of CHF in the Rogue River Basin? If the answer is yes, then discussion should proceed. If the answer is no, then committee work on the matter will tabled for an unknown period of time. 12

13 2. If the committee wishes to proceed, then the committee should decide whether the desired status element for CHF abundance in the Rogue River Basin should be in units of CHF spawning escapement and/or in units of CHF freshwater escapement. There are benefits and drawbacks associated with either choice. In general, freshwater escapement will basically reflect spawning escapement as shown in the following graph. 25 Spawners (1,s) Huntley Park Passage (1,s) 3. One possible format for a desired status element could read as: At least XX,XXX naturally produced fall Chinook salmon should pass Huntley Park (or spawn). Under this format, the committee should decide: A. whether to include jacks B. whether some type of running average is appropriate C. what period of years would be appropriate (i.e. every year, every other year, etc.) Other options are possible. 13