California Hatchery Review Project. Appendix VIII. Coleman National Fish Hatchery Steelhead Program Report

California Hatchery Review Project Appendix VIII Coleman National Fish Hatchery Steelhead Program Report June 2012

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 2012. 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.

Table of Contents 1 Description of Current Hatchery Program...1 1.1 Programmatic Components...1 1.2 Operational Components...1 1.2.1 Facilities...1 1.2.2 Broodstock...2 1.2.3 Spawning...4 1.2.4 Incubation...4 1.2.5 Rearing...5 1.2.6 Release...5 1.2.7 Fish Health...5 2 Populations Affected by the Hatchery Program...5 2.1 Current Conditions of Affected Natural Populations...8 2.1.1 Battle Creek Steelhead Population...8 2.1.2 Other Central Valley Steelhead Populations...10 2.2 Long term Goals for Natural Populations...12 3 Fisheries Affected by the Hatchery Program...12 3.1 Current Status of Fisheries...12 3.2 Long-term Goals for Affected Fisheries...13 4 Programmatic and Operational Strategies to Address Issues Affecting Achievement of Goals...13 4.1 Issues Affecting Achievement of Goals...13 4.1.1 Natural Production Issues...13 4.1.2 Ecological Interaction Issues...13 4.2 Operational Issues...14 4.3 Programmatic Strategies...14 4.3.1 Broodstock...15 4.3.2 Program Size and Release Strategies...18 4.3.3 Incubation, Rearing and Fish Health...20 4.3.4 Monitoring and Evaluation...25 4.3.5 Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial Organisms....30 5 Literature Cited...30 Coleman National Fish Hatchery Steelhead Program / June 2012 i

List of Tables Table 1. Steelhead broodstock collected at Coleman NFH, 1990 2008....3 Table 2. Escapement of adult steelhead upstream of Coleman NFH barrier weir, 1995-2007...9 Table 3. Steelhead status, abundance and habitat availability in the Central Valley (NMFS 2009)....10 Table 4. Broodstock Source....15 Table 5. Broodstock Collection....15 Table 6. Broodstock Composition....16 Table 7. Mating Protocols....17 Table 8. Steelhead Spawner Disposition...17 Table 9. Program Size....18 Table 10. Release Strategy....19 Table 11. Fish Health Policy....20 Table 12. Hatchery Monitoring by Fish Health Specialists....20 Table 13. Facility Requirements....22 Table 14. Fish Health Management Plans....23 Table 15. Water Quality....23 Table 16. Best Management Practices....24 Table 17. Hatchery and Genetic Management Plans....25 Table 18. Hatchery Evaluation Programs....26 Table 19. Hatchery Coordination Teams....26 Table 20. In-Hatchery Monitoring and Record Keeping....26 Table 21. Marking and Tagging Programs....28 Table 22. Post-Release Emigration Monitoring....28 Table 23. Adult Monitoring Programs....28 Table 24. Evaluation Programs....29 Table 25. Direct Effects of Hatchery Operations....30 Appendices Appendix A-1 Hatchery Program Review Questions Appendix A-2 Coleman Steelhead Program Data Tables Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements Appendix B Central Valley Steelhead Watershed Reports Page ii Coleman National Fish Hatchery Steelhead Program / June 2012

Livingston Stone Fish Hatchery (USFWS) Sacramento River I - 5 McCloud River Pit River Keswick Dam Whiskeytown Dam Beegum Creek Clear Creek SF Cottonwood Creek ") XW XW XW # Redding Cottonwood Creek Red Bluff Red Bluff Diversion Dam Black Butte Dam Thomes Creek XW # XW Shasta Dam ") Stony Creek Cow Creek Battle Creek XW Bend Bridge Antelope Creek Sacramento River Mill Creek State Hwy 99 Deer Creek # Chico Thermalito Annex Rearing Facility (CDFG) Coleman Fish Hatchery (USFWS) Butte Creek Coleman Dam Big Chico Creek State Hwy 99 ") Feather River Fish Hatchery (CDFG) ") XW XW Honcut Creek Oroville Dam Feather River Hatchery Dam uba River I - 80 Coleman Hatchery Steelhead Program Lakes and Other Waterbodies Rivers Roads # Cities I - 5 ") Hatcheries Juvenile Release Sites Adult Collection Sites XW Dams Feather River Coon Creek Bear River Auburn Ravine 1 in = 18 miles Miles 0 4 8 16 24 32 t C:\04GISData\ProjectData\CaliHSRG\MapProjects\CentralValley2\ProgramByProgram\ColeSteelhead.mxd Published Date : 12/8/2011

1 Description of Current Hatchery Program Coleman National Fish Hatchery (NFH) was developed by the US Bureau of Reclamation (USBR) to partially mitigate for habitat and fish losses caused by construction of two Central Valley Project features, Shasta and Keswick dams. The hatchery is funded by the USBR and operated by the US Fish and Wildlife Service (USFWS). Coleman NFH occupies 75 acres adjacent to Battle Creek, a tributary to the Sacramento River, about 20 miles southeast of Redding. The steelhead program at Coleman was initiated in 1947 to mitigate for the losses resulting from the Central Valley Project. Steelhead in the Central Valley were identified as a Distinct Population Segment (DPS) and listed in 1998 as a threatened species under the Endangered Species Act (1973). In 2006, NMFS reaffirmed the threatened status of 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 steelhead program at Coleman is operated as a segregated harvest program intended to contribute to the sport fishery in the Sacramento River. Another program goal is to provide escapement back to the hatchery for broodstock. These goals are balanced with a third goal of minimizing risks to the natural population. Coleman NFH releases 600,000 steelhead at 4 fish per pound (fpp) every January. Hatchery steelhead have been 100% marked since 1998 so that adults can be accurately identified as to origin. All steelhead are released in the mainstem Sacramento River at Bend Bridge to reduce predation on newly emerging Chinook in the Sacramento River and Battle Creek. The adult production goal for the program is 3,000 adults. Of these, 2,000 fish are expected to return to Coleman NFH and 1,000 to be caught in freshwater fisheries. The adult return goal to the hatchery has been met in seven of the last eleven years. Creel survey data indicate that approximately 500 steelhead were harvested in the upper Sacramento River from July 2009 through June 2010; the majority of these fish were likely Coleman steelhead, as only hatchery fish can be retained in the fishery. Prior to 2008, this was an integrated harvest and recovery program that incorporated naturalorigin broodstock from the Sacramento River (1947-1986) and from Battle Creek (1952-2009). After 2008, the USFWS temporarily halted use of Battle Creek natural-origin steelhead until the population level increases sufficiently to withstand removal of fish for broodstock. 1.2 Operational Components 1.2.1 Facilities Facilities at Coleman include the main hatchery building containing incubation stacks, trays and early rearing tanks; administration building, feed storage building, warehouse and storage buildings, spawning building, ozone treatment plant and three residences. Exterior features Coleman National Fish Hatchery Steelhead Program / June 2012 Page 1

include twenty-eight 150-foot-long concrete raceways, thirty 80-foot-long raceways, adult holding ponds, fish ladder, pollution abatement pond and facilities for congregating, collecting, holding and spawning broodstock. Within the hatchery building are 178 vertical incubators and 67 fiberglass tanks. Outdoor rearing facilities include twenty-eight 15-foot by 150-foot by 4-footdeep raceways and thirty eight-foot by 80-foot by 2-foot-deep raceways, all of which have predator protection. Battle Creek is the source of water for all fish culture activities at the Coleman NFH. Three water intake structures and associated conveyance facilities are used to deliver water to the hatchery. The water delivery system at Coleman NFH is highly complex and has numerous piping interconnections between facilities. Water from all three intakes can be shunted to the ozone water treatment facility or sent directly to various fish rearing areas. From the hatchery s inception and until about the past ten years, disease and sediment problems associated with the water supply had confounded fish culture at Coleman NFH. High sediment loads, generally associated with high flow events in Battle Creek, periodically caused mortality of juvenile and adult salmonids at the hatchery. Likewise, recurrent disease outbreaks, possibly associated with the hatchery water supply, resulted in increased mortality of juveniles (Foott and Williamson 1997). More than ten significant pathogens have been detected in salmonids at Coleman NFH (Foott 1996). To reduce sediment in the hatchery water supply and to alleviate recurrent disease problems, a water treatment facility capable of filtering 45,000 gpm and ozonating 30,000 gpm was constructed beginning in 1993. Although ozone production capability reached full capacity in 2000, construction and final build-out was not completed until 2002. Operation of the ozone water treatment facility has substantially reduced the occurrence of disease in hatchery production and the potential for disease transmission to naturally-produced stocks. Since brood year 1999, juvenile salmonids propagated at the Coleman NFH have been reared and released with no incidence of IHNV. A barrier weir spans Battle Creek approximately six miles upstream from its confluence with the Sacramento River. The weir is designed to be effective at flows up to 800 cfs and can be operated to allow selective passage at up to 3,000 cfs, at which point the creek overflows its banks. All upstream migrants are directed into the Coleman ladder which bifurcates and either guides fish into the hatchery or allows them to continue migrating up Battle Creek. Adults entering the hatchery are routed into a holding pond. Two additional ponds located in the spawning building allow extended holding of fish after they are initially sorted. During sorting, fish can be routed to the spawning station, holding ponds, or released to Battle Creek upstream of the weir. 1.2.2 Broodstock Steelhead broodstock are selected from adults collected at Coleman Hatchery. Currently only hatchery-origin adults are used; however, the USFWS is exploring options to collect naturalorigin broodstock. The goal is to annually incorporate 10-20% natural-origin spawners into the program broodstock in order to reduce effects of domestication and reduce genetic divergence between hatchery- and natural-origin stocks. A 100% marking program was initiated with brood year 1998, and since 2002, all returning adult hatchery-origin steelhead in Battle Creek have been identifiable by an adipose fin-clip. The number of broodstock collected and spawned from 1990 through 2008 is presented in Table 1, with origin identified in the years after marking began. Page 2 Coleman National Fish Hatchery Steelhead Program / June 2012

In 2002, the annual broodstock objective was to incorporate 10% natural-origin adults into the broodstock (n = 40; 400 broodstock are required to meet egg take goals; 800 fish are targeted for collection). This objective could not be achieved because most returning steelhead were not sexually mature at the time of capture. A revised strategy was adopted in 2004 to retain unripe broodstock. While this increased the number of natural-origin fish that were spawned, targets still were not achieved. In 2008, use of natural-origin steelhead was suspended. Table 1. Steelhead broodstock collected at Coleman NFH, 1990 2008. Return Collected Spawned Origin ear Females Males Total Females Males Total 1990 Unknown 1905 2267 4172 629 463 1092 1991 Unknown 661 482 1143 394 436 830 1992 Unknown 2185 2244 4429 323 205 528 1993 Unknown 652 510 2862 343 332 675 1994 Unknown 1805 1582 3387 363 322 685 1995 Unknown 1088 949 2185 311 279 590 1996 Unknown 1323 1324 3106 231 215 446 1997 Unknown 1342 1187 2529 181 186 367 1998 Unknown 738 671 1409 193 187 380 1999 Unknown 908 847 1755 164 165 329 2000 Unknown 976 1000 1976 183 187 370 2001 Unknown 1160 1134 2294 179 190 369 2002 Unknown 1895 1591 3486 298 315 613 2003 Hatchery 1062 825 2261 326 276 602 Natural 265 162 427 3 9 12 2004 Hatchery 718 660 1378 439 378 817 Natural 127 98 225 19 19 38 2005 Hatchery 629 714 1343 450 485 935 Natural 186 126 312 22 15 37 2006 Hatchery 527 467 994 362 287 649 Natural 158 124 282 10 15 25 2007 Hatchery 703 677 1380 536 475 1011 Natural 91 73 164 11 7 28 2008 Hatchery 1342 1626 2968 454 450 904 Natural 83 101 184 11 12 23 1 Prior to 2002, origin could not be determined because hatchery steelhead were not consistently marked. Adult holding ponds operate from October through February. The branch of the ladder to the hatchery is opened intermittently during this period, depending on broodstock needs and salmon abundance below the weir. Fall Chinook are collected from early October through mid- to late- November, after which the branch of the ladder to the hatchery is generally closed until late December when it reopens to collect late-fall Chinook. This practice promotes separation of spawn timing and reduces hybridization between the fall and late-fall Chinook. Hatchery-origin Chinook that enter the branch of the ladder to the hatchery when it is periodically opened between late November and late December are culled. Hatchery-origin steelhead are collected concurrently with fall and late-fall Chinook, from October through February. All natural-origin steelhead are returned to Battle Creek. Since 2002, closures of the branch of the ladder to upper Battle Creek have been extended to August 1 through February to preclude fall Chinook from accessing spring Chinook critical habitat in upper Battle Creek. Coleman National Fish Hatchery Steelhead Program / June 2012 Page 3

Hatchery-origin steelhead arriving from early October through mid-december are held and spawned during the first half of egg takes. Those arriving after mid-december are held and spawned separately. This ensures that broodstock covers the spectrum of run timing. Additional early returning fish are held to ensure that adequate numbers are available to meet total egg-take goals. The average pre-spawning mortality for hatchery-origin steelhead being held was 12.4% from 2003 through 2008. 1.2.3 Spawning The spawning target for Coleman Hatchery steelhead is 800 adults with a male to female ratio of 1:1. The number actually spawned varies considerably, depending on the availability of adults. A production target of 600,000 smolts has been adopted to balance competing needs for hatchery rearing space and water with the late-fall Chinook program. This requires a green egg take of 790,000. Collected steelhead that are not needed to meet spawning goals are stripped of eggs and milt and placed in the pre-release pond, reconditioned, and released into Battle Creek after 1 to 3 months of holding. This retention period allows fish to recover, eliminates the potential that they will recycle through the hatchery, and reduces predation and competition with naturally reproducing salmonids in lower Battle Creek. All kelts are marked with either a floy tag, a CWT, or a visible implant elastomer to identify fish that return in subsequent spawning years. Data collected from 2005-2008 show that 23-39 repeat spawners returned annually (2% of the total adult returns). Repeat spawners are randomly incorporated into the broodstock. Because Coleman Hatchery steelhead are part of the Distinct Population Segment of ESA listed Central Valley steelhead, all excess fish are released (except those with CWTs, which are sacrificed for tag recovery). Any excess eggs are culled prior to hatch. Spawning begins in late December and continues through early March. Steelhead to be livespawned are first anesthetized, then eggs are extracted from the females and milt is expressed from the males. One-to-one pairing is used. Males may be spawned with more than one female if alternate males are unavailable. Fish over 406 mm (16 inches) and less than 553 mm (21.8 inches) are considered Age 2 (shorts), while fish over 553 mm are considered Age 3 (longs). Steelhead 406 mm are spawned at the rate of their collection before the middle of December. Fish under 406 mm are not spawned. Studies have shown that most of these smaller fish are not anadromous (USFWS 2011). A standard disinfection protocol is followed using iodophor solution (100 ppm for 10 to 15 minutes) prior to placing eggs in trays. 1.2.4 Incubation Eggs are kept separate based on whether they are from shorts or longs (by female). Typically the eggs of two females are placed in an incubator tray that holds 9 to 20,000 long steelhead eggs or 12 to 15,000 short steelhead eggs. After the eyed egg stage, densities are reduced to about 11,100 eggs for longs and 13,700 eggs for shorts until ponding. A standard disinfection protocol is followed using iodophor solution and periodic formalin washes. Non-viable eggs are removed after eye-up. Culling of eggs, when necessary, is conducted to avoid losses of phenotypic diversity. Substrate is not used during incubation. Page 4 Coleman National Fish Hatchery Steelhead Program / June 2012

1.2.5 Rearing After hatching, steelhead fry are transferred to early rearing tanks in the hatchery building until they reach about 500 per pound. Then they are moved into the smaller outdoor raceways where they are fed semi-moist and dry pellets based on percent body weight per day. Feeding levels are adjusted twice monthly until fish are moved outside, after which adjustments are made once monthly. Rearing loadings at release are: flow index (FL) 1.5 with a density index (DI) of 0.3 (maximum values). Feed conversion rates depend upon the age of the fish; for Coleman steelhead, the conversion efficiency is from 1.02 for semi-moist pellets to 1.31 for dry food. Growth rate is managed through summer and fall prior to release in January. Strict control of growth rate is required to avoid exceeding the target of four fish per pound. Fish are not graded. Pond covers are used to provide shade over the outdoor raceways. 1.2.6 Release Coleman NFH produces an average of about 620,000 steelhead per year that are released in the mainstem Sacramento River at Bend Bridge (RM 258) in January at a size of 4 fish per pound (195-205 mm fork length). All fish are marked with an adipose fin-clip. Infrequently, CWTs may be applied to a portion of the releases in association with specific studies. Fish are trucked to the release site, located about 13 miles downstream of the confluence of Battle Creek. Transportation of steelhead to Bend Bridge is conducted to reduce predation on newly emerging fall Chinook in the Sacramento River and Battle Creek. 1.2.7 Fish Health Pathogen outbreaks have been detected at the Coleman NFH in returning feral hatchery broodstock. Infectious hematopoietic necrosis virus (IHNV) is commonly detected in 46-100% of the adult fall and late-fall Chinook returning to Coleman NFH. Steelhead are resistant to this disease strain. With the inception of ozone treatment in 2000, this pathogen has not been detected in juveniles reared at Coleman. Chinook are separated from steelhead during the initial broodstock sorting process. 2 Populations Affected by the Hatchery Program The California Central Valley steelhead DPS is listed as threatened under the Endangered Species Act and includes all naturally spawned populations of steelhead and their progeny in the Sacramento and San Joaquin rivers and their tributaries, excluding steelhead from San Francisco and San Pablo bays and their tributaries. Existing naturally produced stocks are mostly confined to the upper Sacramento River and its tributaries. Recent monitoring in the San Joaquin River subbasin has identified steelhead in the Stanislaus, Mokelumne, and Calaveras rivers at low levels. 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 (Interagency Ecological Program [IEP] Steelhead Project Work Team 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 in Moyle et al. 2008). Emigration Coleman National Fish Hatchery Steelhead Program / June 2012 Page 5

out of the freshwater generally occurs from late December through the beginning of May, with a peak in mid March (Moyle et al. 2008). The Central Valley steelhead DPS also includes artificially propagated stocks from Coleman NFH and the Feather River Hatchery. The Nimbus Hatchery (American River) and Mokelumne River Hatchery steelhead stocks were excluded from the DPS because they represent highly introgressed mixtures of various stocks (McEwan and Jackson 1996). Over the period 1957 to 1993, nearly three million eggs and juveniles were transferred to Nimbus Fish Hatchery from sources in California, Oregon, Washington (Lee and Chilton 2007, U.S. Bureau of Reclamation 2008). Coleman, Feather, Nimbus and Mokelumne River hatcheries produce about 1.5 million yearling steelhead annually based on current production goals. All four hatcheries were originally constructed to mitigate for habitat lost to dam construction. All of these hatcheries release yearling smolts (approximately 4 fish per pound) at downstream locations in January and February during the natural outmigration period. 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 to be 20,540 adult steelhead through the 1960s in reaches 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 not more than 10,000 adults (McEwan and Jackson 1996, McEwan 2001). All of the abundance numbers above include hatchery-origin adult escapement. 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). 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). Steelhead runs in the American and Feather rivers are largely sustained by Nimbus and Feather River hatcheries. Overall, hatchery-origin fish appear to comprise the majority of the DPS (Lindley et al. 2007). Nobriga and Cadrett (2003) used Delta fish monitoring data to estimate that the overall Central Valley spawning origin currently is comprised of 63 to 77% hatchery origin fish. There is evidence that the proportion of hatchery origin steelhead in the spawning escapement of the four rivers with hatchery programs is comparable (Battle Creek, Feather River, American River, and Mokelumne River). There may, however, be a number of smaller populations with only minor hatchery influence. For example, no adipose clipped steelhead were observed during 2003 to 2007 kayak and snorkel surveys in Clear Creek, for which mean escapement during those five years was estimated to be 290 (USFWS 2007). Of 12 steelhead observed in a counting weir on the Stanislaus River in the 2006 07 counting season, only one was observed to be adipose clipped (Anderson et al. 2007). CDFG and NMFS (2001) concluded that the genetic integrity and population viability of natural stocks of Central Valley steelhead have been diminished by increases in the proportion of Page 6 Coleman National Fish Hatchery Steelhead Program / June 2012

hatchery fish, the use of out-of-basin stocks for hatchery production, and straying of hatcheryproduced fish. However, an accurate assessment of the viability of the DPS is not possible with available data and is confounded by the unknown effect of resident fish on the viability and persistence of steelhead populations (Lindley et al. 2007). 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 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 natural-origin 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. (2007) 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 natural environment. The steelhead program at Coleman NFH is currently operated as a segregated harvest program intended to contribute to the sport fishery in the Sacramento River. Hatchery-origin steelhead are not intended to spawn naturally, nor are natural-origin steelhead currently being incorporated into the hatchery broodstock. For many years (1947-1987), natural-origin steelhead collected from the upper Sacramento River were regularly incorporated as hatchery broodstock. In addition, natural- and hatchery-origin steelhead from Battle Creek were used as hatchery broodstock from 1952 to 2008. Recently (2009), due to concerns about low abundance of steelhead in Battle Creek, the USFWS temporarily discontinued the incorporation of natural steelhead into the hatchery broodstock. The USFWS intends to investigate methods to resume incorporation of natural-origin steelhead in the near future (USFWS 2011). The hatchery programs at Coleman NFH have been under review by NMFS through ESA consultations since 1993. In 2011, the USFWS prepared an updated Biological Assessment (BA) following the NMFS format of a Hatchery and Genetic Management Plan. This BA includes consideration of current and future practices to integrate the facility and programs into the Battle Creek Salmon and Steelhead Restoration Project. This proposed restoration project includes reestablishing over 40 miles of salmon and steelhead habitat in Battle Creek primarily through modification of Battle Creek Hydroelectric Project facilities and operations, including instream flow releases (Jones & Stokes 2005). As part of the restoration project, an adaptive management plan will be developed for Coleman NFH, along with pilot studies to further assess and reduce the impacts of facility operations on natural origin salmonids in the Battle Creek watershed and Sacramento River system. Coleman National Fish Hatchery Steelhead Program / June 2012 Page 7

A Technical Review Panel, convened by the CALFED Bay-Delta Program, addressed a number of questions and presented a number of findings, conclusions, and recommendations regarding the compatibility and potential role of Coleman NFH in the recovery of anadromous salmonids in the Battle Creek watershed (Technical Review Panel 2004). The risk to restoration of Battle Creek populations attributable to hatchery domestication effects varied from intermediate in late fall Chinook salmon to high in fall Chinook salmon and steelhead (note that fall Chinook are not presently a recovery objective in Battle Creek). With regard to potential genetic effects on local adaptations and genetic diversity, Coleman Hatchery operations were judged to have low to intermediate risks to restoration of Battle Creek populations. To address questions regarding the fitness of hatchery-origin steelhead relative to natural-origin fish, the USFWS has been applying modern genotyping technologies to construct pedigrees of hatchery- and natural-origin steelhead (http://www.fws.gov/aftc/congen_repro_sucess.html). The goal of the study is to assess the natural reproductive success and genetic contribution of both hatchery- and natural-origin adult steelhead to returning natural-origin adults in Battle Creek. The results of this study will be used to address questions regarding the hatchery s role in the recovery of Battle Creek steelhead. The potential for predation and competition between hatchery- and natural-origin 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). Central Valley hatcheries release yearling smolts (approximately 4 fish per pound) at downstream locations in January and February during the natural outmigration period. There is potential for hatchery fish to prey on natural-origin juvenile fall and spring Chinook because this period coincides with peak emergence and downstream dispersal of salmon fry (January March). The potential for competitive interactions between hatchery and natural-origin steelhead is considered low because all hatchery releases are made below the primary steelhead rearing areas in these tributaries. The Technical Review Panel (2004) concluded that the risk to successful restoration of Battle Creek salmon and steelhead populations associated with competition between hatchery origin and natural-origin fish was generally low or intermediate (but was potentially high for fall Chinook salmon), although the Panel acknowledged that there were considerable gaps in the knowledge required for a thorough evaluation. Substantial uncertainties also precluded a full evaluation of the potential for hatchery origin juveniles to prey on natural-origin juveniles, but release schedules and relative sizes of individuals were deemed very important. Risks were assessed to be low for natural populations of Battle Creek steelhead and spring and winter Chinook salmon because released hatchery fish would be of similar size to natural fish. Risks to natural fall and late-fall Chinook fry may be intermediate or high because of hatchery releases of late-fall and fall juveniles, respectively; spring and fall run Chinook salmon also may be at high risk from adult hatchery steelhead. 2.1 Current Conditions of Affected Natural Populations The Coleman NFH steelhead program has the greatest potential to affect natural-origin steelhead in the Battle Creek watershed. Steelhead occurrence in this watershed is described below, followed by a summary of other potentially affected natural populations in the Central Valley. 2.1.1 Battle Creek Steelhead Population The Battle Creek watershed is about 360 square miles and includes North Fork Battle Creek (29.5 miles long), South Fork Battle Creek (28 miles long), the mainstem valley reach (15.2 miles Page 8 Coleman National Fish Hatchery Steelhead Program / June 2012

long), and numerous tributaries. The upper 16 miles of the North Fork and the upper 10 miles of the South Fork are not accessible to anadromous salmonids due to natural barriers. Battle Creek is unique among the tributaries to the upper Sacramento River downstream of Shasta Dam but quite similar to tributaries upstream of Shasta Dam. It has the largest base flow (approximately 225 cfs) of any of the tributaries to the Sacramento River between the Feather River and Keswick Dam. Currently, the Battle Creek watershed has five dams blocking upstream migration of salmonids to much of the suitable and historic habitat; however, there is a major restoration project underway. The Battle Creek Salmon and Steelhead Restoration Project (Restoration Project) began implementation in 2009. Once complete, the Restoration Project will open 21 miles of historical habitat and restore and enhance nearly 50 miles of habitat. The existing population of steelhead returning to Battle Creek is a mixture of hatchery- and natural-origin adults. Artificial propagation at Coleman NFH has had a major influence on steelhead in Battle Creek since the early 1950s. Considerable integration of hatchery and natural steelhead in the hatchery and on the spawning grounds has occurred for many years. Because hatchery- and natural-origin steelhead were not distinguishable based on appearance, both have been used as broodstock at Coleman NFH. Coleman spawning records from 1953 through 1995 indicate frequent releases of adults above the Coleman barrier weir. Between 1995 and 2002, there was a steady increase in the numbers of steelhead passed upstream of the barrier weir to spawn naturally in upper Battle Creek (Table 2); the origin of steelhead released upstream of the barrier weir or used as broodstock in the hatchery was uncertain until 2001 when all or nearly all returning hatchery steelhead were distinguishable from natural fish based on the absence of an adipose fin. In 2002, about 65% of the steelhead passed upstream of the weir were of hatchery origin (USFWS 2011). Table 2. Escapement of adult steelhead upstream of Coleman NFH barrier weir, 1995-2007. ear Hatchery Origin Natural Origin (marked) (unmarked) Total 1995 -- -- 161 a 1996 -- -- 317 a 1997 -- -- 344 a 1998 -- -- 469 a 1999 -- -- 1,263 a 2000 -- -- 1,520 a 2001 1,382 225 1,607 2002 1,442 593 2,035 2003 772 534 1,306 2004 329 304 633 2005 0 344 344 2006 1 438 439 2007 3 346 349 Source: NMFS (2009) a Marking was not used to differentiate hatchery- and natural-origin adult steelhead returns until 2001 (marking started in 1998). Coleman National Fish Hatchery Steelhead Program / June 2012 Page 9

Coleman NFH continues to modify practices and infrastructure to integrate the facility and programs into the Battle Creek Salmon and Steelhead Restoration Project. In 2004, the practice of releasing hatchery-origin steelhead upstream of the Coleman NFH barrier weir was discontinued at the recommendation of the Technical Review Panel (2004). Documented upstream escapement of hatchery steelhead since 2004 has occurred only for fish that did not enter the hatchery facility, but rather were observed migrating through the upstream fish ladder. The facility s barrier weir and fish ladders were modified in 2008 to improve monitoring and management of fish passage into the upper Battle Creek watershed. 2.1.2 Other Central Valley Steelhead Populations There is evidence that Coleman Hatchery steelhead may stray throughout the Central Valley and spawn naturally in other streams where hatcheries are not present. Both juvenile releases and hatchery strays have the potential to affect naturally spawning steelhead in other watersheds. The status (viability), distribution, and abundance of steelhead in the Central Valley were compiled by the NMFS (2009) in the draft Chinook and Steelhead Recovery Plan. In summary, steelhead distribution and abundance data is generally lacking in the Central Valley (Table 3). 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 tributary to the Upper Sacramento River, although steelhead adults and progeny recently have been documented sporadically throughout the Central Valley. Overall watershed habitat conditions and steelhead abundance and distribution are described further in Appendix B by each major watershed where substantial recent steelhead abundance data exists or where data are lacking, but general consensus is that significant natural steelhead production currently occurs. Watershed Upper Sacramento River Clear Creek Cow Creek Cottonwood/ Beegum creeks Battle Creek Table 3. Steelhead status, abundance and habitat availability in the Central Valley (NMFS 2009). Viability Known Steelhead Distribution Steelhead Abundance Potential 1 Low-Moderate High Moderate Moderate High Mainstem Sacramento River and its minor accessible tributaries downstream of Keswick Dam (RM 302) to its confluence with the Feather River. 18.1 miles of accessible habitat downstream of Whiskeytown Dam (RM 18.1) Several accessible tributaries, but distribution unknown Several accessible tributaries, but distribution unknown 50 miles of accessible habitat after planned restoration projects completed Abundance unknown. Steelhead spawning and rearing is known to occur and is influenced by Coleman NFH returns, but abundance data has not been collected since counting at Red Bluff Diversion Dam was discontinued. Recent otolith analysis documented that less than 50% of age 1 and 2 O. mykiss sampled were steelhead progeny z Abundance unknown. Spawner abundance has been inferred from redd counts, which varied from about 100 to 700 between 2003 and 2009. Abundance unknown. Surveys conducted in South Cow Creek in 2002 documented 7 adult steelhead and 2 possible redds Abundance unknown. Small steelhead runs are known to occur, but no abundance data is available. There is widespread distribution of O. mykiss in watershed. Coleman NFH steelhead program present; naturalorigin adult escapement above the hatchery weir averaged 398 adults/year from 2001-2007 (min = 225, max = 593). Page 10 Coleman National Fish Hatchery Steelhead Program / June 2012

Viability Watershed Known Steelhead Distribution Steelhead Abundance Potential 1 Dry Creek Antelope Creek Mill Creek Thomes Creek Deer Creek Stony Cr. Big Chico Creek Butte Creek Feather River uba River Bear River Auburn Ravine/ Coon Creek American River Putah Creek Low High High Moderate High Low Low-Moderate Moderate Moderate Moderate Low Low Low Moderate Spawning/rearing is possible in Secret and Miners ravines, but distribution is unknown. 20 miles of suitable spawning habitat 25 miles of suitable spawning habitat Flashy flows and high gradient limit distribution, which is largely unknown. Accessible reaches downstream of Deer Cr. Falls, with 25 miles of suitable spawning habitat. Accessible reaches downstream of Black Butte Dam (RM 24) Lowermost 24 miles of Big Chico Creek are accessible Accessible reaches downstream of Quartz Bowl Falls provide 53 miles of accessible habitat Accessible reaches downstream of Oroville Project Fish Barrier Dam (RM 67) Accessible reaches downstream of Englebright Dam (RM 24) Accessible reaches downstream of South Sutter Irrigation District diversion dam (RM 15) Distribution unknown Accessible reaches downstream of Nimbus/Folsom Dam complex (RM 23) Accessible reaches downstream of Putah Diversion Dam (RM 23) No steelhead conclusively documented, although O. mykiss are present. Abundance unknown. Observations of 47 adults and 52 redds in 2001 in 53% of accessible habitat; 140 adults counted in 2007 at new fish ladder at Edwards Diversion. There is reported to be a high density of O. mykiss throughout watershed. Abundance unknown. Observations of 280 adults 1980, 34 adults in 1993 (Clough Dam counts), 15 adults and 31 redds in 2001 in 3-4% of the accessible habitat. Abundance unknown. Steelhead use has not been documented; however, O. mykiss were reported as abundant in 1982. Abundance unknown. Reportedly high O. mykiss density. Recent otolith analysis documented over 75% O. mykiss sampled were steelhead progeny z Abundance unknown. Spawning has not been documented, although some rearing use of the lower river may occur sporadically. No steelhead conclusively documented, although O. mykiss are present. Abundance unknown. Steelhead reported by CDFG wardens in angler catches. Abundance unknown. A minimum of 108 adults and 75 redds counted in 2003. Hatchery fish are present from the Feather River Hatchery program. Abundance unknown. Recent O. mykiss otolith analysis in lower uba R. show most are residents, but steelhead progeny were detected (~40% of age 2 fish) z Steelhead may spawn in high flow years. They likely originate from the Feather River Hatchery program. No steelhead conclusively documented, although O. mykiss are present. Nimbus Hatchery steelhead program present; 1-6% of adult returns to Nimbus Hatchery were naturalorigin and ~300 spawners/year (2001-2007). Abundance unknown. Steelhead were sporadically reported to occur downstream of Putah Diversion Dam, but these reports are unconfirmed. Coleman National Fish Hatchery Steelhead Program / June 2012 Page 11

Viability Watershed Known Steelhead Distribution Steelhead Abundance Potential 1 Mokelumne River Calaveras River Stanislaus River Tuolumne River Merced River Low Moderate Low-Moderate Low-Moderate Low-Moderate Accessible reaches downstream of Camanche Dam (RM 29.6) Accessible reaches downstream of New Hogan Dam (RM 42) when flows allow Accessible reaches downstream of Goodwin Dam (RM 58) Accessible reaches downstream of La Grange Dam (RM 54) Accessible reaches downstream of Crocker-Huffman Dam (RM 52) Upper San Low Distribution unknown Joaquin Source: NMFS (2009) Draft Recovery Plan, Appendix A Central Valley Watershed Profiles Notes: 1 = Ranking from NMFS (2009) of potential to support self sustaining local population in watershed. Z = Zimmerman et al. (2009) An average of 36 redds/year reported from 2001-2010 (max= 61, min = 3). Hatchery fish present from Mokelumne Hatchery program, but excluded from upper river by hatchery weir. Abundance unknown. A few steelhead carcasses and redds have been documented, but abundance is unknown and may be hatchery strays. O. mykiss are reportedly abundant. Recent otolith analysis documented over 30% O. mykiss sampled were steelhead progeny z. Abundance unknown. 12 steelhead documented at a counting weir in 2007. Recent otolith analysis documented about 10% O. mykiss sampled were steelhead progeny z. Abundance unknown. Generally low abundance of O. mykiss downstream of La Grange Dam. No documentation of steelhead spawning. Recent otolith analysis documented less than 10% O. mykiss sampled were steelhead progeny z. Abundance unknown. O. mykiss present, recent otolith analysis documented about 1 of 23 O. mykiss sampled was steelhead progeny z Abundance unknown. Steelhead use not documented or suspected. 2.2 Long term Goals for Natural Populations NMFS has classified Battle Creek naturally-produced steelhead as a Core 1 population. A Core 1 population must meet the following low risk extinction criteria: Census population size is >2,500 adults, or the effective population size is >500 No productivity decline is apparent No catastrophic events have occurred or are apparent within the past 10 years Additionally, the restoration plan for Battle Creek has a long-term spawner target of 5,700 fish in stream reaches above the hatchery weir. 3 Fisheries Affected by the Hatchery Program 3.1 Current Status of Fisheries Coleman NFH releases steelhead into Battle Creek, a tributary to the upper Sacramento River. Sport catch data indicate that 455 natural-origin and 161 hatchery-origin steelhead were caught from 2003 through 2005 (Jackson 2007). Similar numbers of steelhead are caught in the middle Page 12 Coleman National Fish Hatchery Steelhead Program / June 2012

and lower Sacramento River. The catch data show that on average, approximately 54 hatchery steelhead are caught each year. It is likely that this figure severely underestimates the steelhead sport catch, as the Battle Creek section of the upper Sacramento is heavily targeted by sport fishing guides seeking steelhead. 3.2 Long-term Goals for Affected Fisheries Long-term harvest goals for the fisheries affected by the program have not been established. 4 Programmatic and Operational Strategies to Address Issues Affecting Achievement of Goals This section describes programmatic and operational hatchery strategies that can be used in the Coleman Hatchery to address issues that potentially affect achieving the goals for the fish populations. Issues to be considered in evaluating hatchery strategies are first identified, followed by brief descriptions of how possible strategies relate to those issues. 4.1 Issues Affecting Achievement of Goals A host of issues exist that might affect fishery, fish production, and conservation goals for the Sacramento Basin. Many of these issues are habitat-related and are outside the control of what can be done in the hatcheries. Patterns and magnitude of flow releases from dams or water diversions, for example, are beyond the control of hatchery management. But some issues can be addressed by specific programmatic and operational strategies employed at the hatcheries. A list of issues that can be addressed, at least in part, by the hatchery programs and their operations is given below. Important questions associated with the issues are also identified. 4.1.1 Natural Production Issues Status of viable salmonid population (VSP) parameters for Coleman steelhead populations: What are the expected effects of the Coleman steelhead hatchery program on VSP parameters of natural steelhead populations? Can hatchery strategies be updated to enhance the VSP parameters for the natural populations? Hatchery stock genetic management: What are the effects of current management on genetic diversity of the hatchery stock and possible effects of strays on natural-origin fish? Can hatchery strategies be updated to improve hatchery stock genetic diversity and adaptation to the natural environment (when fish leave the hatchery), both for fish that return to the hatchery and for those that spawn in nature? Natural population genetics: Is the hatchery program affecting the genetic integrity and productivity of the natural populations and, if so, can the program be modified to reduce, or even reverse, effects? Performance of the hatchery stock unrelated to genetic composition: Do hatchery fish released into nature exhibit behavioral traits that adversely affect their performance, unrelated to domestication effects on genetics, prior to returning to the hatchery or if they spawn in nature, and if so, can hatchery strategies be modified to ameliorate effects? 4.1.2 Ecological Interaction Issues Predation effects: What are the predation effects of the hatchery fish released as part of this program on sensitive natural populations? What are the predation effects of other hatchery Coleman National Fish Hatchery Steelhead Program / June 2012 Page 13

programs on fish released as part of this program? Can the hatchery strategies for this program be updated to ameliorate these effects? Competition: What are the competition effects of the hatchery fish released as part of this program on sensitive natural populations? What are the competition effects of other hatchery programs on fish released as part of this program? Can the hatchery strategies for this program be updated to ameliorate these effects? Disease: Does this program exacerbate effects of disease in the basin on other species or programs (including this program), and, if so, how can the hatchery strategies be updated to ameliorate effects? 4.2 Operational Issues Operational issues at the hatchery were identified from answers to a set of questions dealing with all phases of hatchery operations. This questionnaire were initially developed as part the Northwest Power and Conservation Council s Artificial Production Review and Evaluation (APRE) project for Columbia River hatcheries, and the scientific review process of Northwest salmon hatcheries. The California HSRG reviewed and updated the questions for the purpose of this review, and introduced a number of additional questions (see Appendix A-1). The questions were answered by the hatchery manager, M&E biologists and the regional manager(s) in workshops held in June 2011. Responses provided in the workshops (plus clarifying notes) can be found in Appendix A-1. Most of the questions required simple yes, no or NA replies. They are generally framed such that a yes answer implies consistency with Best Management Practices (BMP) and no answer implies a potential risk. The CA HSRG requested five-year disease histories from resource managers as part of this questionnaire, but summaries were not provided for all years. This limited their ability to assess current disease status of the program, or to quantitatively assess the effectiveness of fish health management efforts. Data tables that were provided as follow up to the set of question answers are presented in Appendix A-2, and a benefit-risk analysis of the Appendix A-1 information is provided in Appendix A-3. 4.3 Programmatic Strategies The California HSRG identified a suite of issues that are applicable to hatchery programs statewide. These issues were organized under five topics (1) broodstock management; (2) program size and release strategies; (3) incubation, rearing and fish health management; (4) monitoring and evaluation; and (5) direct effects of hatchery operation on local habitat and aquatic or terrestrial organisms. For each topic, hatchery standards to be achieved were defined and in many cases, suggested implementation guidelines to meet the standard were developed. All standards and guidelines are listed in Chapter 4 of the California Hatchery Review Report. Standards that the California HSRG determined apply to this program are presented below. Where their evaluation determined that this program complies with a standard, this is noted. Where their evaluation determined that this program does not comply with a standard, standard not met is noted, and recommended guidelines to resolve the issue are identified. In many cases, the California HSRG provided program-specific comments as well. Page 14 Coleman National Fish Hatchery Steelhead Program / June 2012