Hatchery Scientific Review Group Review and Recommendations Lower Snake River Fall Chinook Population and Related Hatchery Programs January 31, 2009 Lower Snake River Fall Chinook Population Report Page 1
1 Lower Snake River Fall Chinook The Lower Snake River Fall Chinook population is part of the Snake River Fall Chinook ESU that is classified as threatened under the Endangered Species Act. This ESU includes fish spawning in the lower mainstem of the Snake River (downstream of Hells Canyon Dam), and the lower reaches of the Clearwater, Imnaha, Grande Ronde, Salmon, and Tucannon rivers. The Lyons Ferry Hatchery stock, originally derived from returns to the lower Snake River, was included in the ESU by the Interior Columbia Technical Recovery Team (ICTRT) (ICTRT 2003). Unlike the other listed Chinook ESUs in the interior Columbia River Basin, Snake River fall Chinook generally exhibit a subyearling, ocean-type life history. Some Snake River fall Chinook exhibit an alternative life history that includes reservoir rearing and migration as yearlings. 2 Current Conditions Fall Chinook in this population historically spawned in the mainstem Snake River from Hells Canyon Dam to the confluence of the Columbia River and in major tributaries. With construction of the Idaho Power dams in Hells Canyon as well as the federal Columbia River hydropower system, most fall Chinook mainstem spawning habitat has been blocked or inundated by reservoirs. Fall Chinook salmon were extirpated from the Clearwater River subbasin following the construction of Lewiston Dam in 1927. While fish passage facility improvements were made to the dam in subsequent years, historical attempts to propagate fall Chinook in the Clearwater River subbasin were largely unsuccessful. More recently, an integrated hatchery program operating at the Nez Perce Tribal Hatchery has been releasing juvenile fall Chinook into the subbasin with the express purpose of increasing the numbers of fish spawning, incubating and rearing in the natural environment. A majority (70%) of the lower Snake River fall Chinook population spawns in the mainstem Snake River between the top of Lower Granite Reservoir and Hells Canyon Dam, with the remaining among lower sections of the major tributaries. Spawners in the mainstem Snake are apparently distributed in aggregates from the Asotin Creek confluence to River Km 353, although small numbers have been reported to spawn in the tailraces of the Lower Snake River dams. ICTRT recovery targets for adult abundance and productivity are 3,500 and 1.25 respectively. Of the 3,500 adult spawners, the ICTRT recommends that at least 2,500 of these fish spawn in the mainstem Snake River. Spawning escapement consist of both natural-origin and hatchery-origin adults. Hatchery adults come from eggs or juvenile fish produced at Lyons Ferry Hatchery and reared and released at multiple locations in the Snake River, or from four artificial propagation programs in the Clearwater River (all based on Lyons Ferry Hatchery stock): the Lyons Ferry Hatchery, Fall Chinook Acclimation Ponds Program, Nez Perce Tribal Hatchery, and Oxbow Hatchery fall-run Chinook hatchery programs. 2.1 Current Population Status and Goals This section describes the current population, status, and goals for the Snake River Fall Chinook. ESA Status: Threatened Lower Snake River Fall Chinook Population Report Page 2
Population Description: For the HSRG review, the population has been classified as Primary. Recovery Goal for Abundance: 3,500 wild spawners Productivity Improvement Expectation: Unknown Habitat Productivity and Capacity: Productivity: A range of values was provided to the HSRG based on managers best professional judgment. Productivity: 2.2-3.7; Capacity: 6,000-8,250. For this analysis, the mid-point of each range was used: Productivity: 2.95; Capacity: 7,125. 2.2 Current Hatchery Programs Affecting this Population Lyons Ferry and Nez Perce Tribal hatcheries spawn fall Chinook for releases into the Snake River Basin. The WDFW releases both yearling and subyearling fall Chinook at Lyons Ferry Hatchery, and it releases subyearlings into the Snake River near Couse Creek (downstream of the Captain John Acclimation site). Lyons Ferry is capacitylimited and unable to separately rear all of the groups of fish, so Umatilla and Irrigon hatcheries are shipped eggs to ensure enough fish are produced to meet the release goals stated in US v Oregon mandates. Currently, 20% of the run (tagged and untagged) to Lower Granite Dam is trapped and sampled. Fish are shipped to Lyons Ferry and Nez Perce Tribal hatcheries for broodstock, and data collected are used to estimate the run to the dam. In addition, fish are trapped downstream of Lower Granite Dam at Lyons Ferry Hatchery to supplement broodstock. Nez Perce Tribal Hatchery also traps fish at their hatchery. In 2003, the program began including unmarked/untagged hatchery females in an effort to include wild fish and untagged in-basin hatchery fish in production. Scale analysis is used to differentiate wild from hatchery-origin fish, but as of 2007, it was unable to determine in-basin from out-of-basin hatchery fish. DNA was used in 2007 to determine origins of untagged hatchery fish, but it was only able to assign origins to approximately 30% of the fish with 85% confidence. WDFW is seeking to identify ways to tag production for a more accurate determination of origin of returning adults. At the end of the season, any fall Chinook not needed for production are hauled back to the Snake River to supplement the natural population. Adult holding, spawning, egg incubation and juvenile rearing occur at Lyons Ferry and Nez Perce Tribal hatcheries. Incubation and rearing may also occur at Oxbow, Irrigon, and Umatilla hatcheries. Fall Chinook salmon production in the Clearwater River occurs through two programs the Lower Snake River Compensation Plan/Fall Chinook Acclimation Project and the Nez Perce Tribal Hatchery. The Fall Chinook Acclimation Project uses three facilities: (1) Pittsburg Landing, located on the Idaho side of the Snake River at River Mile (RM) 215, approximately 31 miles downstream of Hells Canyon Dam, (2) Captain John Rapids, located on the Washington side of the Snake River at River Mile (RM) 164, and (3) Big Canyon Creek, located on the lower Clearwater River near Peck, Idaho at (RM) 35. The project began operation to release yearlings at Pittsburg Landing in 1996, Big Canyon Creek in 1997, and Captain John Rapids in 1998. In addition, subyearling fall Chinook salmon, the predominant emigration life history characteristic, have been available for release in most years from the Fall Chinook Acclimation Project facilities since 1997. The acclimation facilities at Pittsburg Landing and Big Canyon consist of 16 circular tanks (6 m diameter). Captain Lower Snake River Fall Chinook Population Report Page 3
John Rapids consists of a single in-ground 150 x 50 acclimation pond lined with natural river rock. Water is supplied to the facilities pumped directly from the river. The acclimation goal for the FCAP facilities is 450,000 yearlings (150,000 at each facility) released at 10 fish/lb around mid-april, and 1,400,000 subyearlings (500,000 at each Captain John Rapids and Big Canyon Creek and 400,000 at Pittsburg Landing) released at 50 fish/lb around the end of May. Nez Perce Tribal Hatchery was constructed in 2001 and is authorized to produce 1.4 million subyearling fall Chinook juveniles. Targeted releases are 500,000 smolts on station at Site 1705; 500,000 smolts acclimated and released from the North Lapwai Valley facility; 200,000 smolts acclimated and released from Lukes Gulch facility (South Fork Clearwater); and 200,000 smolts acclimated and released from Cedar Flats facility (Selway River). The Nez Perce Tribal Hatchery on-station release of 500,000 sub-yearlings is scheduled to occur June 15 th. Of these, 100,000 smolts will be adipose fin-clipped and receive coded wire-tags. An additional 200,000 smolts will receive wire only. Approximately 3,000 smolts will receive PIT-tags. Approximately 200,000 sub-yearlings are slated for release from the North Lapwai Valley Acclimation facility. The transfer of the fish occurs in mid- to late-april. Prior to release, 3,000 fish will be adipose fin-clipped and coded wire-tagged. One release component will receive wire only and approximately 3,000 fish will be PIT-tagged. Fish are scheduled to be released May 5 th. The Cedar Flats and Lukes Gulch release groups (release plan = 200,000 smolts at each site) are transferred to acclimation sites in late April through early May. The scheduled release dates for both groups is June 15 th. Approximately 100,000 fish from each release group receive coded wire-tags. An additional 8,178 fish from each release group receive PITtags. Estimated number of hatchery strays affecting this population: Hatchery strays from in-basin integrated programs: 7,100 fall Chinook of Snake River hatchery-origin Hatchery strays from in-basin segregated and out-of-basin hatchery programs: Approximately 300 fish were assumed in the AHA modeling. Observed out-of-basin hatchery strays to Lower Granite Dam have ranged from 280-2,170 fish each year since 2003. Based on coded wire-tags and Blank wire-tags, the main contributors to strays are yearling fall Chinook reared at Bonneville National Fish Hatchery and released into the Umatilla River. These fish originate from Umatilla broodstock. WDFW occasionally recovers fish from Priest Rapids and Klickitat hatcheries. 3 HSRG Review The HSRG has developed guidelines for minimal conditions that must be met for each type of program as a function of the biological significance of the natural populations they affect. For populations of the highest biological significance, referred to as Primary, the proportion of effective hatchery origin spawners (phos) should be less than 5% of the naturally spawning population, unless the hatchery population is integrated with the natural population. For integrated populations the proportion of natural origin adults in the broodstock should exceed phos by at least a factor of two, corresponding to a PNI (proportionate natural influence) value of 0.67 or greater. For Contributing populations, the corresponding guidelines are: phos less than 10% or PNI greater than 0.5. It is important to note that these represent minimal conditions not targets. For example, the Lower Snake River Fall Chinook Population Report Page 4
potential for fitness loss when effective phos is 5% is significantly greater than it would be at 3%. For Stabilizing populations we assume the current phos or PNI would be maintained. The HSRG analyzed the current condition and a range of hatchery management options for this population, including the effect of removing all hatchery influence, and arrived at one or more proposed solutions intended to address the manager s goals consistent with the HSRG guidelines for Primary, Contributing, and Stabilizing populations. The solution included in the cumulative analysis is the last option described in the Observations and Recommendation box below. In order to highlight the importance of the environmental context, two habitat scenarios were considered: current conditions and a hypothetical 10% habitat quality improvement. See HSRG Observations and Recommendations in the box below for more information. 3.1 Effect on Population of Removing Hatchery The No Hatchery scenario is intended to look at the potential of the natural population absent all hatchery effects with projected improved fish passage survival in the Snake and Columbia mainstem (FCRPS Biological Opinion May 5, 2008). Our analysis estimated Adjusted Productivity (with harvest and fitness factor effects from AHA) would increase from 0.8 to 1.6. Average abundance of natural origin spawners (NOS) would decrease from approximately 1,737 fish to approximately 1,661 fish. Harvest contribution of the natural and hatchery populations would go from 18,767 fish to approximately 1,924 fish. 3.2 HSRG Observations/Recommendations In the Observation and Recommendation box below we describe elements of the current situation (Observations) that were important to evaluate the natural population and where applicable the hatchery program(s) affecting that population. We also describe a solution (Recommendations) that appeared to be consistent with manager s goals. However, this is not the only solution. In some cases more than one solution is described. Summary results of this analysis are presented in Table 1. The adjusted productivity values reported for each alternative incorporates all factors affecting productivity (i.e., habitat quality, hatchery fitness effects, and harvest rates). Observations Congress authorized the Lower Snake River Compensation Plan (LSRCP) in 1976. As a result of that plan, Lyons Ferry Hatchery (LFH) was constructed and has been in operation since 1984. One objective of the hatchery was to compensate for an estimated annual loss of 18,300 adult, Snake River stock, fall Chinook salmon (U.S. Army Corps of Engineers 1975). This mitigation program was modified in the early 1990s by agreement of the United States v. Oregon parties to supplement natural fall Chinook production above Lower Granite Dam. This action was consistent with the U.S. Endangered Species Act and Washington s Wild Salmonid Policy. The WDFW has two general goals in its fall Chinook evaluation program: (1) monitor hatchery practices at LFH to ensure quality smolt releases, high downstream migrant survival, and sufficient adult fish contribution to fisheries and escapement to meet the LSRCP compensation goals; and (2) gather Lower Snake River Fall Chinook Population Report Page 5
genetic information to help maintain the integrity of the Snake River Basin fall Chinook salmon stock (WDF 1994). (Lyons Ferry Hatchery Evaluation Fall Chinook Salmon Annual Report: 2005, April 2007). The current hatchery program releases 5.8 million smolts into the Snake River at various locations. Managers have not assigned a population designation for Snake River Fall Chinook although conservation and harvest objectives have been identified. Snake and Clearwater River fall Chinook salmon are managed as one population for recovery purposes. Currently, this program is not meeting the standards for a Contributing or Primary population (currently pnob = 5%, phos = 77%). The hatchery program is providing some conservation benefit to the natural population. The HSRG was unable to develop a solution that achieved the standards of either a Primary or Contributing population under the existing conditions. Lyons Ferry and Nez Perce Tribal hatcheries spawn fall Chinook for release into the Snake River Basin. The Lyons Ferry Hatchery produces approximately 900,000 yearling and 3.5 million subyearling juveniles annually. Yearlings are released on-station at the hatchery (450,000), in the Snake River (300,000) and the Clearwater River (150,000). Most of the Snake and Clearwater River smolt releases are associated with the Fall Chinook Acclimation Project, but not those direct stream releases at Couse Creek, Lyons Ferry Hatchery, or Hells Canyon Dam. Subyearlings are released on-station at the hatchery (200,000), various locations in the Snake River (2.4 million), in the Grande Ronde River (400,000), and in the Clearwater River (500,000). The Fall Chinook Acclimation Project accounts for 1.4 million of the total subyearling release of 3.5 million. The Nez Perce Tribal Hatchery also targets the release of 1.4 million subyearlings to the Clearwater River and tributaries annually although this target has not been consistently met. Adults are collected at Lower Granite Dam, the Lyons Ferry Hatchery and the Nez Perce Tribal Hatchery. Adult holding, spawning, incubation, and juvenile rearing occur at Lyons Ferry and Nez Perce hatcheries. Incubation and rearing may also occur at Oxbow, Irrigon, and Umatilla hatcheries. The increase in Snake River fall Chinook returns over the last several years is the result of a number of habitat, fish passage, marine survival and hatchery actions together with harvest management. As currently operated, there is little opportunity for local adaptation and spatial structure in the ESU. Recommendations The HSRG looked at various hatchery scenarios that could improve productivity while meeting the standards for a Primary or Contributing population, but could not significantly increase natural-origin spawning under current habitat conditions. To promote spatial structure, local adaptation and to improve productivity, the HSRG recommends that managers pursue development of broodstock collection capabilities for releases into the Clearwater River. Due to the lack of adult capture facilities, the HSRG recommends that managers develop, test and deploy live capture selective fishing gears to collect local Clearwater brood to accomplish this end, provide additional harvest opportunity, and manage phos. Managers should avoid removing Clearwater-origin fish at Lower Granite Dam. Managers should also develop similar broodstock collection Lower Snake River Fall Chinook Population Report Page 6
capabilities within the Snake River upstream of the confluence of the Clearwater River (e.g., Captain John s, Pittsburg Landing, and Hells Canyon Dam). The HSRG recommends that managers implement a BKD control strategy for their spring and summer/fall Chinook hatchery programs where BKD has proved a recurring problem. Ideally, the strategy should include culling (destroying) eggs/progeny from hatchery- and natural-origin brood that are found to be infected with the BKD agent. However, because brood fish with high levels of the BKD agent are more likely to transmit the agent to their progeny than brood with lesser levels of the agent, the culling of eggs/progeny from infected brood fish, should, at the very least, be applied to those with high levels of the BKD agent (e.g., ELISA OD value of 0.4 and above when broodstock are not in short supply and ELISA OD value of 0.6 and above when broodstock are in short supply). In addition, in programs using ESA-listed natural-origin brood fish, the culling of their eggs/progeny may, at the managers discretion, be dispensed with. However, the ESA-listed broodstock should be injected, pre-spawning, with an appropriate antibiotic (preferably, azithromycin at 40 mg/kg fish), and the resulting eggs should be surface-disinfected with an iodophor. All pre-spawning brood injections may be limited to females, ESA-listed or otherwise. Finally, eggs and hatchlings derived from broodstock found to be heavily infected with the BKD agent should be incubated/reared in isolation from those obtained from broodstock with no or lesser levels of the BKD agent. In addition, the hatchlings should be reared at the lowest possible densities (below current standards), and, at the first signs of infection with the BKD agent, they should be treated with orally administered erythromycin (100 mg/kg fish) for 28 days. The treatment should be repeated if there is evidence that the BKD agent has persisted in the hatchlings. Lower Snake River Fall Chinook Population Report Page 7
Table 1. Results of HSRG analysis of current condition and HSRG Solution for Lower Snake River Fall Chinook. The light green row indicates the natural population and yellow indicates the segregated hatchery population, if applicable. A 10% habitat improvement is applied to the HSRG Solution to evaluate the additional effect of improved habitat towards conservation objectives. Alternative Type and Purpose Prog Size (/1000) HOR Recapture Additional Weir Efficiency Effective phos PNI NOS Esc Adj Prod Harvest Hatchery Surplus Current No Hatchery HSRG Solution HSRG Solution w/ Improve Hab Int Both 5,802.7 50% 0% 77% 0.06 1,737 0.8 18,767 2,269 None None - 0% 0% 0% 1.00 1,661 1.6 1,924 - Int Both 5,802.7 50% 0% 75% 0.06 1,729 0.8 22,925 1,538 Int Both 5,802.7 50% 0% 73% 0.06 1,952 0.9 23,198 1,538 Lower Snake River Fall Chinook Population Report Page 8