California Hatchery Review Project. Appendix VIII. Feather River Hatchery Steelhead Program Report

Transcription

1 California Hatchery Review Project Appendix VIII Feather River Hatchery Steelhead Program Report June 2012

2 Introductory Statement from the California HSRG This program report was developed by contractor staff tasked with providing background information to the California HSRG on hatchery programs, natural population status and fisheries goals in California. The resulting report is one of many sources of information used by the California HSRG in their review process. Information provided in this program report was developed through interviews with hatchery staff, regional, state and tribal biologists working in the basins and a review and summarization of the pertinent scientific literature. The draft program report was then provided to interview participants for review and comment on multiple occasions. Comments received were incorporated into the report and the report finalized. Because of the review process, it is believed the report represents an accurate snapshot in time of hatchery operations, natural salmon population status and fisheries goals in California as of This program report may or may not be consistent with the consensus positions of the California HSRG expressed in the main report, as their primary involvement was in the preparation of Section 4.3, Programmatic Strategies, which compares existing program practices to the statewide Standards and Guidelines developed by the California HSRG.

3 Table of Contents 1 Description of Current Hatchery Program Programmatic Components Operational Components Facilities Broodstock Collection Broodstock Age Structure Spawning Incubation Rearing Release Fish Health Populations Affected by the Hatchery Program Current Conditions of Affected Natural Populations Feather River Population Other Central Valley Steelhead Populations Long term Goals for Natural Populations Fisheries Affected by the Hatchery Program Current Status of Fisheries Long-term Goals for Affected Fisheries Programmatic and Operational Strategies to Address Issues Affecting Achievement of Goals Issues Affecting Achievement of Goals Natural Production Issues Ecological Interaction Issues Operational Issues Programmatic Strategies Broodstock Program Size and Release Strategies Incubation, Rearing and Fish Health Monitoring and Evaluation Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial Organisms Literature Cited...35 Feather River Hatchery Steelhead Program / June 2012 i

4 List of Tables Table 1. Age distribution of adult steelhead captured from the Sacramento River in Table 2. Age distribution of adult steelhead collected at Coleman National Fish Hatchery, Battle Creek, from Table 3. Feather River Hatchery adult steelhead returns, 2000 to Table 4. Steelhead status, abundance and habitat availability in the Central Valley (NMFS 2009) Table 5. Broodstock Source Table 6. Broodstock Collection Table 7. Broodstock Composition Table 8. Mating Protocols Table 9. Steelhead Spawner Disposition Table 10. Program Size Table 11. Release Strategy Table 12. Fish Health Policy Table 13. Hatchery Monitoring by Fish Health Specialists Table 14. Facility Requirements Table 15. Fish Health Management Plans Table 16. Water Quality Table 17. Best Management Practices Table 18. Hatchery and Genetic Management Plans Table 19. Hatchery Evaluation Programs Table 20. Hatchery Coordination Teams Table 21. In-Hatchery Monitoring and Record Keeping Table 22. Marking and Tagging Programs Table 23. Post-Release Emigration Monitoring Table 24. Adult Monitoring Programs Table 25. Evaluation Programs Table 26. Direct Effects of Hatchery Operations Appendices Appendix A-1 Hatchery Program Review Questions Appendix A-2 Feather Steelhead Program Data Tables Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements Appendix B Central Valley Steelhead Watershed Reports Page ii Feather River Hatchery Steelhead Program / June 2012

5 Red Bluff Diversion Dam Black Butte Dam Thomes Creek XW Stony Creek Sacramento River Mi State Hwy 99 Thermalito Annex Rearing Facility (CDFG) Deer Creek # Chico Butte Creek Big Chico Creek State Hwy 99 ") ") XW XW Bedrock Park Honcut Creek Feather River Fish Hatchery (CDFG) Oroville Dam Feather River Hatchery Dam uba River I - 80 Feather River Boyds Pump Bear River Putah Diversion Dam Vallejo # I - 5 Putah Creek XW I - 80 Sacramento River Sacramento River Sacramento # Coon Creek Dry Creek Auburn Ravine XW # # ") XW American River Lodi Stockton Cosumnes River ") XW Nimbus Fish Hatchery (CDFG) Nimbus Dam Mokelumne River Fish Hatchery (CDFG) Woodbridge Dam Calaveras River Mokelumne River Camanche Dam US Hwy 50 Stanislaus River Feather River Hatchery Steelhead Program # Cities Lakes and Other Waterbodies Rivers Roads ") Hatcheries Juvenile Release Sites Adult Collection Sites XW Dams San Joaquin River # Modesto t 1 in = 20 miles Miles Tuolumne River Turlock Merced River Croc Merce C:\04GISData\ProjectData\CaliHSRG\MapProjects\CentralValley2\ProgramByProgram\FeatherSteelhead.mxd Published Date : 12/8/2011

6

7 1 Description of Current Hatchery Program In 1960, California voters authorized the Department of Water Resources (DWR) to construct and operate the State Water Project. Oroville Dam and reservoir on the Feather River were essential project components, providing water storage, hydroelectric power, flood control, and recreational benefits. The dam is located 5 miles east of the City of Oroville. Feather River Hatchery (FRH) is a component of the Oroville Project that was constructed in the mid-1960s downstream of Oroville Dam and about 66 miles upstream from the confluence of the Feather and Sacramento rivers. An additional facility, the FRH Annex, is located downstream adjacent to the Thermalito Afterbay near Interstate Highway 99. The California Department of Fish and Game (CDFG) operates and maintains FRH under contract with the DWR. Although there are no other agencies, tribes, or cooperators directly involved in operating FRH, one advisory group provides guidance. The Feather River Technical Team advises FRH personnel to help integrate the hatchery operations into management of the salmonid fisheries below Oroville Dam. Steelhead in the Central Valley were identified as a District Population Segment (DPS) and listed as a threatened species under the Endangered Species Act (1973) in In 2006, NMFS reaffirmed the threatened status of the Central Valley steelhead because the resident and anadromous life histories of steelhead remain markedly separated as a consequence of physical, ecological and behavioral factors (NMFS 2009). The DPS includes all naturally spawned anadromous O. mykiss (steelhead) populations below natural and manmade impassable barriers in the Sacramento and San Joaquin rivers and their tributaries, as well as hatchery produced steelhead at the Coleman National Fish Hatchery and the Feather River Fish Hatchery. Steelhead spawned and reared at Nimbus Fish Hatchery and Mokelumne Fish Hatchery are excluded from the listing (NMFS 2009). 1.1 Programmatic Components The FRH Central Valley steelhead Oncorhynchus mykiss program is an integrated harvest program that traps and artificially spawns both marked hatchery-origin and unmarked naturalorigin steelhead. Only a few unmarked fish are trapped annually. The FRH steelhead are intended to migrate to the ocean and return to provide recreational fishing opportunities and hatchery broodstock as mitigation for lost habitat and juvenile fish production capacity resulting from construction of Oroville Dam. The production goal for the program is to release 450,000 yearling steelhead annually at 3 fish per pound (fpp). During the initial 5 to 10 years of hatchery operation, experimentation occurred with stocks from Coleman, Mokelumne, Nimbus, Washougal (WA), Sacramento, and Feather hatcheries (using juvenile fish, eggs and some broodstock). For the last 20 years, only fish returning to the Feather River basin have been used for broodstock. The historical number of steelhead that migrated into the Feather River is unknown, but since operations began at FRH, over 40,000 adult and half-pounder steelhead have been trapped. The number of adult steelhead trapped annually has averaged 972 fish, ranging from 78 to 2,865 fish. These numbers include 1,515 fish trapped since 1997 that were classified as half-pounder steelhead, measuring either less than 16 inches or less than 22 inches. As part of the original FERC license, CDFG evaluated the impact of the Oroville Project on fish populations. In the 8 years following construction, angler creel data, interim fish facility counts, and FRH counts were used to assess the success of steelhead mitigation. Based on this Feather River Hatchery Steelhead Program / June 2012 Page 1

8 assessment, CDFG reported that FRH operations were maintaining pre-project steelhead abundance levels. An average of 565 steelhead were trapped annually at FRH during its first 8 years of operation. This number was comparable to interim fish facility counts (from1963 to 1966) that averaged 582 adult steelhead per year, due in part to cold water releases from Oroville Reservoir that provide suitable holding, spawning and rearing habitat below the dam. These releases, along with the requirement to artificially produce steelhead, were stipulations of the original Oroville Dam mitigation plan. 1.2 Operational Components Facilities The main Feather River Hatchery consists of an office and maintenance building, fish ladder, gathering tank, spawning building, main hatchery building, four holding and twelve juvenile rearing ponds (ten raceways and two channels), ultraviolet water treatment building, and hatchery buildings. Water from eight of the ten rearing raceways, the rearing channel, and the hatchery buildings is collected in a main sump and pumped directly into two settling basins. All upstream migrating fish are stopped at the Fish Barrier Dam at Feather River Mile (RM) 66, about 0.5 miles below the Thermalito Diversion Dam (RM 66.5) and immediately upstream of FRH. The 91-foot-high concrete Fish Barrier Dam releases water to maintain fish habitat in the reach downstream to the Thermalito Afterbay Outlet. The Fish Barrier Dam diverts fish into a 1/3-mile-long gated fish ladder that leads to the FRH. The ladder gates are generally open from about September 15 through the following June to ensure that spring- and fall-run Chinook salmon and steelhead have an opportunity to enter the hatchery. The fish ladder consists of a series of steps and pools. Pool length ranges from 8 to 1,000 feet, with a minimum width of 6 feet and a minimum water depth of 2 feet. Flow velocities range from 2 to 5 feet per second (fps); the maximum drop between pools is 1 foot. An enlarged section of the fish ladder at its upstream terminus functions as a gathering tank, entrapping fish ascending the ladder. A mechanical sweep (crowder) gathers the fish and deposits them into the abutting spawning building. Four concrete circular tanks hold the fish until they are ready to spawn. A secondary hatchery facility, the FRH Annex, is located at RM 55 and includes an office, maintenance building, and four rearing raceways. An on-site well supplies about 12 cubic feet per second (cfs) to this facility. Water is supplied to FRH from Lake Oroville and is diverted by gravity flow into an aeration tower downstream at the Thermalito Diversion Dam. From the aeration tower, water is distributed to the hatchery buildings and fish rearing areas. Up to 110 cfs can be diverted to the hatchery, although only 74 cfs is used at full operation. Currently, more water is diverted to the aeration tower than is used at the hatchery in order to maintain sufficient water pressure. When the minimum discharge through the hatchery is less than 74 cfs, the surplus water is released directly into the Feather River through an overflow pipe at the aeration tower. Between 40 and 74 cfs of flow-through wastewater discharges to two settling basins (approximately 300 feet long, 30 feet wide, and 15 feet deep) located near an embankment on the Feather River. The two settling basins are constructed with overflow pipes that are capable of discharging directly to the Feather River; however, no direct discharges have occurred from these ponds since their completion in Page 2 Feather River Hatchery Steelhead Program / June 2012

9 Water from eight of the ten rearing raceways, the rearing channel, and the hatchery buildings is collected in a main sump and pumped directly into two settling basins. Wastewater from the two newer raceways is discharged directly to one of the settling basins. If the main sump pumps are overwhelmed or fail, this wastewater can be discharged to the Feather River via the sump overflow pipe. Wastewater from the holding tanks adjacent to the main hatchery building also discharges directly to the sump overflow pipe. The FRH also has several raw water discharge points - the aerator overflow pipe, the fish ladder and gathering tank, the four holding tanks adjacent to the main hatchery building, and a fish return pipe in the spawning room of the main hatchery building. When the fish ladder is in use during broodstock and spawning periods, water from the fish ladder, a gathering tank, and four holding tanks is discharged directly to the Feather River. These direct discharges contain minimal quantities of fecal material, but no chemicals or unconsumed fish food are present, since fish are not fed or treated in these locations Broodstock Collection An informal goal to collect 1.5 million steelhead eggs has been established by hatchery personnel to achieve the 400,000 yearling-sized steelhead mitigation goal for FRH. An additional 50,000 yearling steelhead are reared and released as part of the 1986 Delta Fish Agreement between the DWR and the CDFG to mitigate for adverse fishery impacts caused by water diversion at the Harvey O. Banks Delta Pumping Plant, a key part of the SWP at the head of the California Aqueduct. The program has not met egg-take goals since Egg-take numbers have consistently dropped since 2005 and reached a low of 77,000 eggs for the last year reported (2009). The cause of this drop may be the result of poor smolt survival rates, straying due to transportation or other unknown effects. Adult Central Valley steelhead that ascend the fish ladder and are trapped are used as broodstock. Hatchery personnel attempt to distinguish steelhead from resident rainbow trout through physical characteristics such as size, coloration, and body conformation. All steelhead less than 16 inches are identified as half-pounder steelhead. Half-pounder steelhead are a distinct life history and can be produced by both adult winter and summer steelhead. After their freshwater growth period, half-pounder steelhead migrate to the ocean but return to freshwater within a few months. They do not overwinter in the ocean and do not sexually mature during their first season returning to freshwater. In river systems with halfpounder steelhead, not all returning adult steelhead will have demonstrated a half-pounder life history. Half-pounder steelhead are reported from the Klamath and Rogue rivers and in a few other systems in North America and Russia. It is doubtful that half pounder steelhead commonly occur in the Sacramento River system and adipose fin-marked fish less than 16 inches trapped at FRH may be juvenile hatchery-origin steelhead that did not migrate to the ocean. Historically, adult steelhead entered the FRH fish ladder and trap in September. Currently, steelhead that are trapped during the early part of the run are not retained for hatchery broodstock because of difficulties holding sexually immature fish. These sexually immature fish are returned to the river via a metal discharge tube that enters the river approximately 0.5 miles downstream from the ladder entrance. Only sexually mature steelhead are retained for spawning, with timing ranging from late October to the first week of January. If it appears that the run is small and difficulties may be encountered collecting enough eggs to meet mitigation goals, sexually Feather River Hatchery Steelhead Program / June 2012 Page 3

10 immature adult steelhead may be held in one of four round tanks and sorted weekly for eventual spawning. All steelhead that enter the trap and gathering tank are sorted a minimum of once each week during the run, examined for marks, and the degree of sexual maturity determined. Fish smaller than 16 inches are returned to the river. All post-spawn adults (kelts) are returned to the river without reconditioning. Based on the average number of eggs taken from a female steelhead spawned at FRH (a 10-year average of 3,618) and an egg to juvenile survival rate averaging 33%, a minimum of about 400 female fish are needed each season to meet the release goal of 450,000 yearling steelhead Broodstock Age Structure Hallock et al. (1961) examined the scales from 100 Sacramento River steelhead trapped above the Feather River in 1954 and reported that 29 of the 100 fish had spent one year in fresh water before entering the ocean, 70 had spent 2 years, and one had spent 3 years. The age distribution of returning adults is shown in Table 1. Table 1. Age distribution of adult steelhead captured from the Sacramento River in ear Total Number of Steelhead Sampled Age 2 Age 3 Age 4 Age Percentage 17% 41% 33% 6% 3% Source: Hallock et al Age 6 and older More recent analysis of steelhead collected at the Coleman National Fish Hatchery demonstrated that the majority of adult steelhead in Battle Creek are comprised of age 2 and age 3 fish and only a small portion were age 4 and older fish (Table 2). It is likely that steelhead returning to the FRH demonstrate similar changes in the age composition. Page 4 Feather River Hatchery Steelhead Program / June 2012

11 Table 2. Age distribution of adult steelhead collected at Coleman National Fish Hatchery, Battle Creek, from Total Number of ear Steelhead Sampled Age 2 Age 3 Age 4 Age , , ,102 1,021 1, , ,865 1,391 1, , ,072 1,006 1, , Totals 14,968 7,267 7, Percentage 48.6% 50.0% 1.4% 0.04% Spawning During the past 10 years, the FRH has trapped an annual average of 1,310 adult steelhead (754 males and 556 females). Steelhead are trapped and spawned through the season to ensure that sufficient eggs are taken to meet the production goal and to ensure that the eggs taken represent the entire run. Spawning has occurred as early as the end of October and as late as the beginning of January. Only steelhead 16 inches or larger that are sexually mature and demonstrate free flowing eggs/milt are selected for spawning. The objective is to take 1.5 million steelhead eggs to meet mitigation and enhancement goals. During the past decade, all mating and pairing of adult fish has been conducted with no attempt to select fish for any morphological characteristic. Fish selected for spawning are anesthetized using CO 2 gas. Air spawning as described by Leitritz and Lewis (1976) is used to collect steelhead eggs. Eggs and sperm from only one male and one female are introduced into a single pan. Prior to introducing eggs and sperm, a saline solution is added to the pan to improve fertilization. After the eggs are fertilized they are washed in fresh water and drained in a colander, then placed in a bucket with fresh water for transfer to vertical stacked incubators. No steelhead eggs or sperm are preserved at FRH. Once the eggs have been fertilized, they are immersed in a PVP-Iodine solution to help eliminate pathogens. PVP-Iodine is effective against a broad spectrum of disease-causing microorganisms, and is used to kill on contact a wide variety of bacteria, viruses, fungi, protozoa, and yeasts. All steelhead mortalities and eggs collected in excess of those needed to meet production goals are disposed of by a processing/rendering company Incubation After spawning, steelhead eggs are transferred to vertical stacked incubators. All eggs taken and fertilized on a single day are identified as an egg lot and assigned a lot number. Individual families are not kept separate during incubation. The incubation period or average hatching time of the eggs is not fixed for a given temperature and the incubation period may vary as much as 6 days between egg lots taken from different parent fish. Leitritz and Lewis (1976) reported that Feather River Hatchery Steelhead Program / June 2012 Page 5

12 steelhead eggs take 30 days at 51 Fahrenheit (F) to hatch. Water temperatures at FRH during the period of steelhead egg incubation vary annually but typically range from 46 and 49 o F, suggesting that eggs incubated at FRH will hatch in slightly more than 30 days. Eggs are typically held in the trays until 90% of the alevins have absorbed their yolk sacs (buttoned-up). During incubation, fresh water that has been passed through an ultraviolet disinfection system is circulated through the incubators. Water temperature during steelhead egg incubation can range from 46 to 55 F. The eggs receive daily flushes of an iodophor disinfectant to help eliminate vertically transmitted pathogens. Hatchery personnel maintain records of the number of eggs taken annually and fish released from those eggs. Efforts are made to take eggs that are representative of the entire run and enough eggs to meet mitigation and enhancement goals. Usually eggs are not culled, but when necessary, culling is performed in a manner that ensures representative lots of eggs are not removed Rearing Since 1991, all juvenile steelhead have been reared and released as yearling-sized fish. Fish remain in the rearing channel until released the following spring. The average percentage of eggs taken, reared, and released as juveniles in the past 10 years has been approximately 30%, varying from 17.5 to 82%. Juveniles are placed in the outdoor rearing channel, which holds approximately 360,000 gallons of water. Up to 1.5 million fry may be transferred to the channel at a density of approximately 4 fish per gallon of water. This channel is 0.5-miles long, 20 feet wide, and 4 feet deep, and is partitioned into four sections. A constant flow of 10 to 12 cfs passes through the channel before being discharged to the Feather River. The channel is routinely cleaned and the fish are fed several times daily. As needed or recommended by CDFG fish pathologists, up to 2,000 pounds of salt may be added to the rearing channel intake as a treatment to help remove and eliminate external pathogens. Final rearing loadings have a flow index (FI) of 3.37 and a density index (DI) of 0.06 (450,000 fish at 3 fpp and 10 cfs). Rearing water is also irradiated to reduce effects to fish from pathogen exposure. Weekly growth expressed as mean weight of individual juvenile steelhead is collected routinely by hatchery personnel. Information on average lengths or condition factors is not routinely collected. Fry are fed a diet of semi-moist or dry fish food. For the remaining period until released, they are fed a dry, floating pellet food. Fry are fed up to 12 times per day. The amount of food fed through the rearing period depends on body weight and appetite, although the ideal amount of food per fish is 3% of their total body weight (Leitritz and Lewis 1976). Feed conversions are not calculated. No formal methods are used to indicate smolt development. Instead, visual indications such as silvery appearance to the juvenile fish body and loosening of the scales signal smolting. No natural rearing methods are employed at FRH Release The number of juvenile steelhead to be released annually is determined by mitigation agreements established by DWR and CDFG. Current levels are 400,000 juveniles at 4 fpp or larger (generally released at 3 fpp). An additional 50,000 juvenile steelhead of a similar size are reared Page 6 Feather River Hatchery Steelhead Program / June 2012

13 and released as part of the 1986 Delta Fish Agreement. In the past, juvenile steelhead reared at FRH have been released (trucked) at several locations in the Feather and Sacramento rivers, but current releases occur at one of three locations in order of priority: Boyd s Pump Launch Ramp, Feather River (RM 22) Live Oak Boat Ramp, Feather River (RM 38) Verona Marina, confluence of Feather and Sacramento rivers (RM 0) Since FRH operations began, approximately 28 million juvenile steelhead have been released. Beginning in 1991 all of the releases have been yearling-sized fish, except in 2001, 2002, and 2003, when small groups of advanced fingerling size fish were released. During the past ten seasons, FRH has released an average of 402,902 yearling juvenile steelhead annually. The advanced fingerling size fish have averaged 64 fpp, while the yearling size fish averaged 5 fpp. These fish are substantially smaller than the 3-4 fpp release size target. Juvenile steelhead are released from late January through February (the target is February 1), with specific release dates dependent on fish size, equipment, and personnel availability. Regardless of size, juvenile steelhead are not held past March 15 th, due to increased water temperatures and greater likelihood of predation. Juvenile steelhead are moved from the rearing ponds to the fish transportation tank and transported to the release site. No specific acclimation procedures are conducted prior to fish release. Efforts are made to maintain the transportation tank water temperatures at the same temperature of the hatchery and river during transportation. Since broodyear 1998, 100% of the juvenile hatchery-origin steelhead released from California fish hatcheries into anadromous waters have been adipose fin-marked. Additionally, some juvenile steelhead released from FRH from broodyears 1999 through 2001 were marked with coded-wire tags (CWTs). Returns of CWTs reported by the Regional Mark Processing Center (RMIS) revealed only three observed/estimated recoveries from across brood years for 1,194,981 coded-wire tagged fish released. The hatchery has no specific plans for the release of fish surplus to the existing mitigation or enhancement goals. However, the CDFG Operation Manual provides that if approved by the Chief of the Fisheries Branch, surplus fish may be stocked in waters where they do not and will not conflict with existing management goals or policies. During four of the past ten seasons, FRH has released juvenile steelhead in excess of the number identified for mitigation. These fish have been released at the same time and location as fish identified for mitigation and enhancement. Recently up to 10,000 larger-sized juvenile steelhead were reared and released in the Thermalito Afterbay to replace domestic catchable rainbow trout that were stocked for recreational fishing opportunities. These fish are adipose- and pectoral-fin marked prior to release for identification Fish Health Fish health is monitored by the CDFG Fish Health Laboratory personnel during times of increased fish mortality. Diagnostic procedures for pathogen detection follow American Fisheries Society professional standards as described in Thoesen (1994). Appropriate treatments are recommended or prescribed by a CDFG fish pathologist/veterinarian as appropriate, and follow-up examinations are performed as needed. Feather River Hatchery Steelhead Program / June 2012 Page 7

14 Ceratomyxa shasta is present in the system, but Feather River steelhead are relatively resistant. Rearing water is irradiated to reduce incidences of disease, but power outages can cause the system to malfunction. 2 Populations Affected by the Hatchery Program The potential effects of the Central Valley steelhead hatchery programs, including the FRH program, on natural populations of salmon and steelhead in the Central Valley are reviewed below. The following summarizes the major programmatic issues, with emphasis on the FRH steelhead program. Existing wild steelhead stocks in the Central Valley are mostly confined to the upper Sacramento River and its tributaries, including Antelope, Deer, and Mill creeks. Naturally spawning populations occur in the Feather, uba, American, and Mokelumne rivers, but these populations have had substantial hatchery influence and their ancestry is unclear (Busby et al. 1996). Natural production of steelhead occurs in other tributaries of the Sacramento and San Joaquin rivers, but at relatively low levels (Good et al. 2005). Steelhead can be divided into two life history types, summer run and winter run, based on their state of sexual maturity at the time of river entry and the duration of their spawning migration. Only winter steelhead are currently found in Central Valley rivers and streams (McEwan and Jackson 1996), although there are indications that summer steelhead were present in the Sacramento River system prior to large-scale dam construction in the 1940s (IEP 1999). Central Valley steelhead exhibit flexible reproductive strategies that allow for persistence in spite of variable flow conditions (McEwan 2001). Peak adult migration into the river historically occurred from late September to late October (Hallock 1989 as cited in Moyle et al. 2008). Emergent fry occupy shallow water areas and as they increase in size, move into higher velocity, deeper, mid channel areas by late summer and fall (Everest and Chapman 1972, Fontaine 1988, and Hartman 1965, cited in Moyle et al. 2008). Age data from a sample of 100 fish taken in 1954 indicated that steelhead spent 1 (29%), 2 (70%), or 3 (1%) years in freshwater before migrating to the ocean (Hallock et al. 1961). This migration generally occurs from late December through the beginning of May, with a peak in mid March (Moyle et al. 2008). Central Valley steelhead habitat requirements during the freshwater residence time include cool, clear, and well-oxygenated water (Moyle 2002). Juveniles (ages 1+ and 2+) occupy deeper water than fry and show a stronger preference for pool habitats with ample cover, as well as for rapids and cascade habitats (Dambacher 1991). Preferred habitat for juveniles generally includes large structures that provide feeding opportunities, segregation of territories, refuge from high water velocities, and cover from fish and bird predators (Moyle et al. 2008). The Central Valley steelhead DPS includes artificially propagated steelhead stocks from Coleman NFH on Battle Creek and from the FRH. The Nimbus Hatchery (American River) and Mokelumne River Hatchery steelhead stocks were excluded from the DPS. These stocks represent highly introgressed mixtures of various stocks (McEwan and Jackson 1996). From 1957 to 1993, nearly 3 million eggs and juveniles were transferred to Nimbus Fish Hatchery from other California hatcheries, including the Snow Mountain Egg Collection Station and Cedar Creek Hatchery, Eel River; the Coleman NFH, Battle Creek; Warm Springs Hatchery, Dry Creek, Russian River; and Mad River Hatchery, Mad River; as well as summer run fish from the Washougal River (Skamania stock) in Washington and the Siletz River in Oregon (Lee and Chilton 2007; U.S. Bureau of Reclamation 2008). Page 8 Feather River Hatchery Steelhead Program / June 2012

15 Coleman NFH, FRH, Nimbus Hatchery, and Mokelumne River Hatchery produce about 1.5 million yearling steelhead annually, based on current production goals (CDFG 2008). All four hatcheries were originally constructed to mitigate for habitat lost to dam construction. In 1998, Coleman NFH modified its operations to emphasize conservation (USFWS 2001). All of these hatcheries release yearling smolts (approximately 4 fpp) at downstream locations in January and February during the natural outmigration period. All California hatchery steelhead programs began fin-clipping all hatchery juveniles in 1998 to differentiate between hatchery and natural steelhead. In the NMFS (2005) status update for the Central Valley Steelhead DPS, the biological review team considered the DPS in danger of extinction or likely to become endangered. Abundance, productivity, and spatial structure were of greatest concern, although genetic and life history diversity was also considered a risk factor (Good et al. 2005). Although abundance data for steelhead are scarce, Central Valley steelhead have shown a negative growth rate pattern since the late 1960s, and limited evidence suggests that this pattern has continued (Lindley et al. 2007). Hallock et al. (1961) estimated the average population in the 1960s to be 20,540 adult steelhead in the Sacramento River upstream of the Feather River. Steelhead counts at the Red Bluff Diversion Dam (RBDD) declined from an average of about 8,000 in 1967 to 1977, to an average of about 2,000 in the early 1990s. The estimated total annual run size for the entire Sacramento- San Joaquin system, based on RBDD counts, was no more than 10,000 adults (McEwan and Jackson 1996; McEwan 2001). All of the abundance numbers above include hatchery-origin adult escapement. The most recent estimate of wild steelhead production in the Central Valley (Good et al. 2005) is a female population between 363 and 3,628 and, assuming an equal sex ratio, a total wild population between 726 and 7,256. This estimate is based on the relative abundance of juvenile hatchery (ad clipped) and natural-origin (unclipped) steelhead in the Chipps Island trawl between 1998 and 2000, known release numbers of hatchery steelhead, an assumed wild fecundity of 5,000 eggs per female, and an egg to smolt survival rate ranging from 1% to 10%. A major cause of decline in steelhead abundance and their present status has been the loss of access to much of their historical spawning and rearing habitat above impassable dams, which have blocked access to more than 80% of historic spawning and rearing habitat (Lindley et al. 2007). Anadromous O. mykiss populations may have been extirpated from their entire historical range in the San Joaquin Valley and from most of the larger basins of the Sacramento River. Much of the current production of O. mykiss (anadromous and resident) occurs in the tailraces of impassable dams below major storage reservoirs that release cool, hypolimnetic water. Other factors in species decline include degradation of remaining habitat and threats to the genetic integrity of wild populations from hatchery steelhead production (Moyle et al. 2008). The genetic integrity of Central Valley steelhead is affected by past and present hatchery practices, habitat fragmentation, and population declines that have resulted in small, isolated populations that are subject to inbreeding, loss of rare alleles, and genetic drift (NMFS 2009). NMFS and CDFG (2001) concluded that the genetic integrity and population viability of natural stocks of Central Valley steelhead has been diminished by increases in the proportion of hatchery fish relative to natural-origin fish, the use of out-of-basin stocks for hatchery production, and straying of hatchery-origin fish. However, an accurate assessment of the viability of the DPS is not possible because of the lack of effective monitoring programs and the unknown effect of resident fish on the viability and persistence of steelhead populations (Lindley et al. 2007). Since 1998 and the inception of 100% marking of hatchery steelhead, the proportion of hatchery-origin smolts sampled in the Chipps Island trawl survey has ranged between 60 and 80% (U.S. Bureau of Reclamation 2008). There is some evidence that this proportion may also approximate the Feather River Hatchery Steelhead Program / June 2012 Page 9

16 proportion of hatchery origin steelhead adults in the spawning escapement, at least in the streams with long running hatchery programs (Battle Creek and the Feather, American and Mokelumne rivers). Nobriga and Cadrett (2003) used Delta fish monitoring data to estimate that the overall Central Valley spawning escapement currently is comprised of 63% to 77% hatchery origin fish. There are no baseline genetic data to evaluate the extent to which steelhead populations (natural and hatchery components) may have diverged genetically from the stocks that existed before major hatchery operations, dam building, and other environmental changes occurred in the Central Valley in recent decades. There is still evidence of local genetic structure, but recent analyses of the genetic structure of O. mykiss populations in the Central Valley indicate that steelhead hatchery propagation has had a significant effect on natural stocks (Garza and Pearse 2008). Clustering of below-barrier populations with northern California coastal stocks suggest that out-of-basin transfers of Eel River steelhead to Nimbus Hatchery, and subsequent transfers and straying in the Central Valley, has resulted in widespread introgression of this stock. Clustering of above-barrier populations with one another, and their position relative to other California stocks, indicate that these populations may most closely represent the ancestral population genetic structure of Central Valley steelhead (Garza and Pearse 2008). The principal mechanisms by which the hatchery stocks may affect the genetic integrity of wild fish include the harvest of native fish that might otherwise spawn in the wild, hatchery rearing and associated selection of traits beneficial in the hatchery environment (which can reduce the ability of fish to survive in the wild), and the interbreeding of fish exhibiting hatchery selected genetic traits with wild fish. These mechanisms may result in two types of genetic hazards to wild salmon and steelhead populations: loss of genetic diversity within and among populations, and reduced fitness of a population, affecting productivity and abundance. Araki et al. (2008) summarized a number of studies and reported a loss of reproductive success (fitness) of hatchery fish in nature (40% loss per generation of hatchery culture). Some populations may be more affected than others, due to a variety of factors such as the length of exposure to the hatchery environment, the use of non local stocks in the hatchery broodstock, the degree of habitat fragmentation, the degree of interbreeding, and the reproductive success of hatchery fish in the wild population. The potential for predation and competition between hatchery reared and naturally produced salmonids depends on the degree of spatial and temporal overlap, differences in size and feeding habitats, migration rate and duration of freshwater residence, and the distribution, habitat use, and densities of hatchery and natural juveniles (Mobrand et al. 2005). Recently, concern has been expressed about the potential for hatchery reared salmon and steelhead to prey on or compete with natural-origin juvenile salmonids and the impact this may have on threatened or endangered salmonid populations (Williams 2006). Hatchery steelhead present a greater risk to natural populations because they are relatively large at release and a relatively high portion can residualize, providing more opportunities for them to compete for resources and prey on naturally produced salmon and steelhead throughout the year (Kostow 2009). All Central Valley hatcheries release yearling smolts (approximately 4 fpp) at downstream locations in January and February during the natural outmigration period. The potential for these hatchery fish to prey on juvenile fall and spring Chinook salmon exists because this period coincides with peak emergence and downstream dispersal of salmon fry (January-March) from upstream spawning areas. The potential for competitive interactions between hatchery steelhead produced by Feather River, Nimbus, and Mokelumne River hatcheries and natural-origin steelhead is considered low because all hatchery releases are made below the primary steelhead rearing areas in these tributaries. Page 10 Feather River Hatchery Steelhead Program / June 2012

17 2.1 Current Conditions of Affected Natural Populations The FRH steelhead program has the greatest potential to affect natural reproduction of steelhead in the Feather River. Steelhead occurrence in the Feather River is described below, followed by a summary of other potentially affected natural populations in the Central Valley Feather River Population The tributaries of the Upper Feather River flow from the northern Sierra Nevada, eventually into Lake Oroville, a major reservoir of the California State Water Project. 1 The lower Feather River watershed (downstream of Lake Oroville) encompasses about 803 square miles. Steelhead distribution is limited to accessible reaches below the Oroville Project Fish Barrier Dam at RM 67. Flows are regulated for water supply and flood control at Oroville Dam. Under normal operations, the majority of water released is directed into the Thermalito Complex. Except for local water diversions, the rest is returned to the Feather River through the Thermalito Afterbay Outlet. The river then flows southward through the valley to the confluence with the Sacramento River at Verona. The remainder of releases from Lake Oroville, typically 600 cfs, runs through the historic river channel locally known as the low flow channel. The river is almost entirely contained within a series of levees as it flows through the fertile agricultural lands of the Sacramento Valley. There are approximately 190 miles of major creeks and rivers, 695 miles of minor streams, and 1,266 miles of agricultural water delivery canals in the lower Feather River watershed. Significant management issues include concerns over growth (farmland conversion to urbanization), demands on water supply, preservation of water quality and aquatic habitat, and potential risks from fire and floods. 2 Historically, steelhead spawned above the present Oroville Dam, with numbers in the order of a few hundred fish (Brown et al 2004). Conditions in the watershed had been degraded by mining, dam construction, logging, etc. to the extent that the historic run numbers had been diminished considerably. Completion of Oroville Dam in 1967 (and its associated barriers) blocked steelhead passage above the town of Oroville and it was assumed that prior to the construction of Oroville Dam most steelhead spawned in the upstream reaches. Little information was available on pre-dam populations of Feather River steelhead. Hallock et al. (1961) provided background information on Sacramento River steelhead, but the report provides only limited information on Feather River steelhead. As part of the original FERC license for Oroville Dam, a study was performed (Painter et al. 1977) to evaluate the impact of the Oroville project on fish populations. Angler creel data, interim fish facility counts, and subsequent Feather River Hatchery counts were used to assess the success of steelhead in the first eight years after construction. Their research determined that Feather River Hatchery operations were maintaining pre-project abundance levels of steelhead (interim fish facility counts from 1963 to 1966 averaged 582 adult steelhead per year, while Feather River Hatchery counts averaged 565 the first eight years after project construction). 1 The Oroville Reservoir is the principal water storage facility of the State Water Project, which conserves and delivers water to over two-thirds of California s population. 2 Feather River Hatchery Steelhead Program / June 2012 Page 11

18 Today the run is supported almost entirely by the Feather River Hatchery, which produces about 400,000 yearling steelhead annually. The FRH was built by DWR to mitigate for the loss of salmon and steelhead spawning habitat from Oroville Dam. The CDFG operates the hatchery. The contribution of hatchery fish to the naturally spawning population is unknown but the very high proportion (99%) of hatchery steelhead (adipose-clipped) returning to the hatchery indicates that the majority of natural spawners are likely of hatchery-origin. Hatchery returns have averaged 1,019, with a minimum of 78 in 1971 and a maximum of 2,865 in 2003 (Table 3). Table 3. Feather River Hatchery adult steelhead returns, 2000 to Brood ear Females Males ,153 1, , Average Source: Mills et al. (2003) Feather River hatchery steelhead juveniles released below the confluence of the Feather River and uba River have been reported to migrate back upstream and rear in the colder waters of this system. Little is known about the life history and abundance of naturally-spawning steelhead in the Feather River. Most of the natural steelhead spawning occurs in the upper end of the low flow channel between RM 66 and 67 (FERC 2007). Surveys conducted in indicated that spawning activity began in late December, peaked in late January, and was essentially complete by the end of March. A total of 75 steelhead redds and 108 steelhead were observed, and nearly half (48%) of all redds were in the uppermost mile of the Feather River (Mills et al. 2003). An accurate estimate of the number of spawning steelhead was not possible. Weir counts of adult steelhead have occurred since 2007, but reports are not readily available ( Steelhead are also found in Honcut Creek, uba River, and the Bear River. Biologists present at the June 16, 2011 biological data collection meeting noted that there is a relatively large run of chrome bright fish (16-21 inches) present in the Feather River in April and May. These chromers don t appear to be spawning. This same life history appears in the uba River as well, although these fish are generally inches in length and referred to as halfpounders by anglers. The fish have a smaller head and different body shape than Feather River hatchery fish. Scale samples indicated the fish were primarily 2-year-olds, but were inconclusive as to whether or not these fish (uba River) had been to the ocean. Genetic analysis has not been conducted on the chromers; however, there may be enough tissue material to do such an analysis if funding were to be provided. Page 12 Feather River Hatchery Steelhead Program / June 2012

19 The status of the Feather River resident rainbow trout population is not known; however, anglers do not consider the Feather River to be a good resident fishery. As part of the 2006 FERC Settlement Agreement, DWR is proposing to install a fish counting weir to obtain accurate information on the abundance, timing, and composition of steelhead and Chinook salmon in the low flow channel. The counting weir will also be used to improve the ability to mark spring-run Chinook and separate them from fall-run Chinook in the hatchery (DWR 2010). DWR is also proposing to install a fish segregation weir to improve management and conservation of naturally spawning spring-run Chinook salmon, fall-run Chinook salmon, and steelhead in the low flow channel. No estimates of juvenile steelhead abundance or survival in the Feather River are available. Juvenile steelhead are thought to primarily emigrate at age 1 or less, based on studies conducted from 1999 to 2001; age 1 and age 2 steelhead were relatively rare during the surveys (Cavallo et al. 2003). Most juveniles were found in secondary channels to the low flow channel, which accounts for less than 1% of the available habitat (FERC 2007). The limited availability of this habitat and low habitat complexity in this reach may be important limiting factors on natural production (Cavallo et al. 2003). Juvenile fish may grow between 1.0 to 1.5 mm per day from early summer to fall. Fall sampling indicates fish size ranges from inches. Juvenile fish tagged in the fall did not leave the system for the 8 months that the tags were active. No baseline genetic data are available to determine the extent to which Oroville operations (including hatchery operations) may have changed the genetic identity of steelhead that were present in the Feather River before the project was completed in Nor are data available to evaluate the potential effects of the hatchery on the fitness and productivity of Feather River steelhead (Brown et al ). The broodstock used by the FRH was originally derived from native Feather River fish, but Nimbus stock was imported from 1967 to Nevertheless, a recent investigation of the genetic structure of Central Valley rainbow trout and steelhead populations revealed that the Feather River populations align closely with other upper Sacramento River populations, but were most closely linked to the FRH population (Nielsen et al. 2003). An important finding was that the Feather River populations were not closely linked to Nimbus and American river populations. This suggests the possibility that the endemic stock was not extirpated before the hatchery began operations, as perhaps was the case for American River steelhead (McEwan 2001; Gerstung 1971) Other Central Valley Steelhead Populations The status (viability), distribution, and abundance of steelhead in the Central Valley were compiled by NMFS (2009) in the draft Chinook and Steelhead Recovery Plan, which is summarized in Table 4 in geographic order from north to south. In summary, steelhead distribution and abundance data is generally lacking in the Central Valley. Out of the 25 Central Valley watersheds ranked for their current viability potential to support local naturally reproducing populations, only Clear, Battle, Antelope, Mill, and Deer creeks scored High. Each of these streams is a tributary to the Upper Sacramento River, although steelhead adults and progeny recently have been documented sporadically throughout the Central Valley. Habitat conditions and steelhead abundance and distribution are described further in Appendix B for each major watershed where existing data or general opinion indicates that significant natural steelhead production currently occurs. Feather River Hatchery Steelhead Program / June 2012 Page 13