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

California Hatchery Review Project Appendix VIII Mokelumne River 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...4 1.2.1 Facilities...4 1.2.2 Broodstock...4 1.2.3 Spawning...6 1.2.4 Incubation...7 1.2.5 Rearing...8 1.2.6 Release...9 2 Populations Affected by the Hatchery Program...9 2.1 Current Conditions of Affected Natural Populations...12 2.1.1 Mokelumne River Steelhead...12 2.1.2 Other Steelhead Populations in the Central Valley...13 2.2 Long term Goals for Natural Populations...16 3 Fisheries Affected by the Hatchery Program...16 3.1 Current Status of Fisheries...16 3.2 Long-term Goals for Affected Fisheries...17 4 Programmatic and Operational Strategies to Address Issues Affecting Achievement of Goals...17 4.1 Issues Affecting Achievement of Goals...17 4.1.1 Natural Production Issues...17 4.1.2 Ecological Interaction Issues...18 4.2 Operational Issues...18 4.3 Programmatic Strategies...18 4.3.1 Broodstock...19 4.3.2 Program Size and Release Strategies...22 4.3.3 Incubation, Rearing and Fish Health...23 4.3.4 Monitoring and Evaluation...30 4.3.5 Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial Organisms....34 5 Literature Cited...35 List of Figures Figure 1. Estimated yearling smolt-to-adult return rates for Mokelumne River steelhead for brood years 1999 to 2008....3 Mokelumne River Hatchery Steelhead Program / June 2012 i

List of Tables Table 1. Number of unmarked natural-origin (NOR) and marked hatchery-origin (HOR) steelhead/rainbow returning to the Mokelumne River Hatchery from 2002 to 2010...3 Table 2. Number of steelhead eggs and fingerling fish transferred to Mokelumne River Fish Hatchery and release dates and locations-1990 through 2007....5 Table 3. Number of female steelhead trapped and spawned from 1999 to 2009....7 Table 4. Number of steelhead eggs taken, fry ponded, and juveniles released from MRFH, Table 5. brood years 2000 through 2010....8 The number and percentage of adipose fin-marked steelhead trapped at the Mokelumne River Fish Hatchery (2002-2010)...13 Table 6. The number of steelhead redds observed in the Mokelumne River (2001-2010)....13 Table 7. Steelhead status, abundance and habitat availability in the Central Valley....14 Table 8. Broodstock Source....19 Table 9. Broodstock Collection....19 Table 10. Broodstock Composition....20 Table 11. Mating Protocols....21 Table 12. Steelhead Spawner Disposition...21 Table 13. Program Size....22 Table 14. Release Strategy....23 Table 15. Fish Health Policy....23 Table 16. Hatchery Monitoring by Fish Health Specialists....24 Table 17. Facility Requirements....26 Table 18. Fish Health Management Plans....27 Table 19. Water Quality....28 Table 20. Best Management Practices....28 Table 21. Hatchery and Genetic Management Plans....30 Table 22. Hatchery Evaluation Programs....30 Table 23. Hatchery Coordination Teams....30 Table 24. In-Hatchery Monitoring and Record Keeping....31 Table 25. Marking and Tagging Programs....32 Table 26. Post-Release Emigration Monitoring....32 Table 27. Adult Monitoring Programs....33 Table 28. Evaluation Programs....33 Table 29. Direct Effects of Hatchery Operations....34 Appendices Appendix A-1 Hatchery Program Review Questions Appendix A-2 Mokelumne Steelhead Program Data Tables Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements Appendix B Central Valley Steelhead Watershed Reports Page ii Mokelumne River Hatchery Steelhead Program / June 2012

Bear River # I - 5 Putah Creek XW Putah Diversion Dam Vallejo Sacramento River Wickland Oil Storage Site I - 80 Sacramento River Sacramento New Hope Landing Antioch iver # Coon Creek Dry Creek Auburn Ravine XW # # ") XW American River Lodi Stockton Cosumnes River ") XW Nimbus Fish Hatchery (CDFG) Nimbus Dam Woodbridge Dam Camanche Dam Calaveras River Mokelumne River US Hwy 50 Mokelumne River Fish Hatchery (CDFG) Stanislaus River San Joaquin River # Modesto # Tuolumne River Turlock Merced River ") XW # San Jose # Merced State Hwy 99 I - 5 Mokelumne Hatchery Steelhead Program Lakes and Other Waterbodies Salinas Rivers Roads # Cities ") Hatcheries Juvenile Release Sites Adult Collection Sites XW Dams t 1 in = 18 miles Miles 0 4 8 16 24 32 San Joaquin River C:\04GISData\ProjectData\CaliHSRG\MapProjects\CentralValley1\ProgramByProgram\MokeSteelhead.mxd Published Date : 12/8/2011

1 Description of Current Hatchery Program The Mokelumne River originates in the Sierra Nevada Mountains and flows through the Central Valley before entering the Delta forks of the Mokelumne just downstream of the Delta Cross Channel. The watershed drains some 627 square miles and contains a number of dams and reservoirs. Pardee Dam and Reservoir (RM 39.6) is owned and operated by East Bay Municipal Utilities District (EBMUD) to provide water for 1.2 million customers in Alameda and Contra Costa counties. Camanche Dam and Reservoir, completed by EBMUD in 1964, provides flood control storage, flows for agriculture, fisheries and recreation. Camanche Dam (RM 29.6) is the upstream limit of anadromous salmonid migration. The Mokelumne River Fish Hatchery (MRFH) is on the lower Mokelumne River just downstream of Camanche Dam. The California Department of Fish and Game (CDFG) operates a fall Chinook and steelhead trout program under contract with the EBMUD. These programs comply with the 1961 requirements of the California State Water Resources Control Board for the loss of spawning and juvenile rearing areas after construction Camanche Dam. The 1961 agreement, and related amendments, directed the construction of a hatchery to provide rearing capacity for 100,000 juvenile salmon and spawning channels with a capacity for up to 15 million Chinook salmon eggs. The hatchery is funded and operated to meet the requirements of EBMUD s Lower Mokelumne River Project Federal Energy Regulatory Commission (FERC) license order (P-2916). In 1998, EBMUD, CDFG and the U.S. Fish and Wildlife Service (USFWS) entered into an agreement to resolve various FERC licensing and state water right issues. EBMUD agreed to fund an expansion and upgrade of the MRFH as an integral part of a strategy to supplement the natural production of and to meet the mitigation requirement for anadromous fish in the lower Mokelumne River. Hatchery reconstruction/expansion was completed in 2002. The Mokelumne River steelhead program goal is to release 250,000 yearling steelhead at 4 fish per pound (fpp). The program has been experimenting with small releases of two-year-old steelhead juveniles (less than 2,000) using a natures rearing strategy (i.e., presence of structure, low rearing density, shallow pond depth, cover and colored raceways). 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 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. Naturally spawned steelhead in the Mokelumne River are included in the DPS; steelhead spawned and reared at Mokelumne River Hatchery are excluded (NMFS 2009). 1.1 Programmatic Components The original hatchery program objective was to mitigate for anadromous (steelhead) production lost due to dam development. Over time, the program shifted to more of a resident rainbow catchable trout program. Local biologists noted that there were a number of complete fish kills in the Mokelumne River (personal communication with various biologists and managers, April 26, 2011) and that the current resident population may be of Eel River origin. Mokelumne River Hatchery Steelhead Program / June 2012 Page 1

Since the 1990s, program operations (broodstock source 1, release locations, etc.) have been in flux. Starting in 2008, the use of only Mokelumne River-origin fish as broodstock and consistent release locations, fish size and time of release has stabilized the program. How this stabilization of hatchery operations will affect program performance is unknown. The hatchery production goal is to release 250,000 yearling steelhead annually. The program does not have goals for adult production, the proportion of hatchery-origin fish allowed to spawn naturally, the proportion of natural-origin fish used as broodstock, or the composition of resident versus anadromous-origin adults used as broodstock. Steelhead returns to the hatchery since the 2002-2003 collection season have ranged from 60 to 412 fish, with an average of 192 (Table 1). Fish less than 16 inches are not spawned as they are not classified as steelhead (i.e., only fish 16 inches or longer are considered steelhead). The majority of the adult migration past Woodbridge Dam (RM 39.6) occurs from December through February, peaking in January. Hatchery personnel have estimated that approximately 6% of the broodstock is of natural origin (Table 1). Based on discrepancy in fish counts at Woodbridge Dam and the hatchery, a large portion of the natural-origin adults used as broodstock are likely resident fish 2. This finding is consistent with steelhead life-history modeling which indicated the Mokelumne River would produce a mixture of anadromous and resident life-histories, dominated by the resident form. Using the best available information, the estimated return rate to the hatchery of age two (halfpounder) and age three adult steelhead from 1999 to 2008 averaged 0.08% (range 0% to 0.26%) (Figure 1). Because of low smolt-to-adult survival rates for the program, the hatchery imported steelhead eggs from Feather River in most years from 1990 to 2007 (see Section 1.2.2). From 2008 to the present, enough steelhead have returned to the hatchery to meet broodstock goals. The low smolt-to-adult survival rates for hatchery-origin (HOR) fish likely result from poor habitat conditions (flow, temperature and amount of rearing habitat) in the Mokelumne River and low juvenile emigration survival to the ocean. Mokelumne River juvenile migrants are susceptible to entrainment into the large irrigation pumping station at Clifton Court. They survive at rates less than a third of juvenile steelhead released from Nimbus Fish Hatchery in the American River. 1 Genetic samples of rainbow trout are being collected in stream reaches above Pardee Dam to determine if these fish would be a better candidate for program broodstock. These samples will be compared with samples collected on NOR and HOR steelhead in the lower river. 2 At the April 26, 2011 biological data collection meeting, attendees provided data showing that while only 80 steelhead were counted (video) at Woodbridge Dam in 2010-2011, over 350 steelhead were collected at the hatchery. Because biologists believe that the majority of fish cannot migrate past the dam without being counted, the larger number of fish entering the hatchery compared to the dam count indicates that resident fish rearing upstream of the dam are being used as broodstock. There is a possibility that some fish may not be counted (by video) after February when the counting facility may not be operational. Page 2 Mokelumne River Hatchery Steelhead Program / June 2012

Table 1. Number of unmarked natural-origin (NOR) and marked hatchery-origin (HOR) steelhead/rainbow returning to the Mokelumne River Hatchery from 2002 to 2010. Return season Unmarked (NOR) Adults Marked (HOR) Adults Total Adults Unmarked (NOR) fish < 16 inches Marked (HOR) fish <16 inches (HOR) Total <16 inches Total Fish Trapped 2002-2003 27 25 52 25 4 29 81 2003-2004 22 36 58 15 4 4 62 2004-2005 14 33 47 n/a 1/ 13 13 60 2005-2006 26 114 140 n/a 49 49 189 2006-2007 47 198 245 n/a 167 167 412 2007-2008 24 210 234 0 110 110 344 2008-2009 15 186 201 0 108 108 309 2009-2010 4 47 51 0 13 13 64 Average 22 106 129 8 59 62 192 0.30% 0.25% 0.26% 0.24% 0.20% 0.15% 0.13% 0.10% 0.05% 0.04% 0.03% 0.03% 0.08% 0.06% 0.05% 0.08% 0.00% 0.00% 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 Average Figure 1. Estimated yearling smolt-to-adult return rates for Mokelumne River steelhead for brood years 1999 to 2008. Notes: Data in the figure assumes that 5% of the natural spawning population consists of hatchery-origin adults and that hatcheryorigin adults are harvested at a 10% rate. Data includes fish returns to hatchery, spawning grounds and fish caught in fisheries. Mokelumne River Hatchery Steelhead Program / June 2012 Page 3

Data on adult stray rates to other river systems for Mokelumne River hatchery steelhead are anecdotal. It is assumed that because of egg transfers, poor flow conditions and use of out-ofbasin release sites in some years that straying does occur. 1.2 Operational Components The MRFH occupies approximately 80 acres owned by EBMUD below Camanche Dam. Major facilities are described below. 1.2.1 Facilities Water Supply: Up to 71 cubic feet per second (cfs) is supplied to the MRFH from Camanche Reservoir through two outlets located at the 202.5- and 102.6-foot levels. Operational needs vary from month to month, with spawning and incubation operations using up to 6 cfs and the rearing facilities up to 65 cfs. Water quality is typically suitable for salmonid production and temperatures seasonally range from 8.8 to 16.6 C (48-62 F). Flow to the raceways and holding ponds is aerated while flow to the hatchery building is filtered through sand media filters and can be chilled (1.0 to 3.5º C cooler than ambient water temperatures). All water is used on a single pass basis. The water supply into the hatchery is equipped with an alarm system; however, there are no alarms in the hatchery itself (i.e., adult holding, incubation and rearing structures do not have flow alarms). Ladder and Trap: The primary fish ladder is a 490-foot-long weir-pool step-type ladder, with two 4-foot-wide gated entrances in the lower Mokelumne River. The ladder terminates in a fish trap adjacent to the spawning/incubation building. A secondary 180-foot-long ladder with a gated entrance from the Mokelumne River is located adjacent to the hatchery holding ponds near Camanche Dam. Most, if not all, fish enter the hatchery from the primary fish ladder. The fish trap is equipped with a mechanical crowder that moves fish into a hydraulic lift basket where they are anesthetized by electric shock, then lifted and slid across a fish-sorting table. Hatchery personnel sort the fish by species, sex, size, ripeness, and identifying marks. Ripe males and females pass to the spawning table. Unripe fish are placed in the holding ponds or are returned to the river adjacent to the primary fish ladder. Broodstock Holding and Spawning Facilities: There are four 45-foot-long, 10-foot-wide, 4- foot-deep concrete holding tanks adjacent to the fish trap. Incubation Facilities: The spawning/incubation building contains 34 incubator stacks with 16 trays in each stack. Water from an overhead 3-inch pipe supplies the top tray of each stack, which is empty to buffer the force of the cascading water. The hatchery building also has 48 fiberglass troughs and 96 upwelling jars in the fiberglass tanks. Rearing Facilities: There are ten pairs of concrete raceways with an effective rearing space in each that is 300 feet long and 10 feet wide, with an average water depth of 3.5 feet. Each raceway can be screened at approximately 50-foot intervals to isolate groups of fish. Outflow from the raceways is collected in a common tailrace for each series pair that allows fish to be volitionally released from the hatchery into the river. 1.2.2 Broodstock The fish ladders are generally opened on October 1 and remain open through the end of the steelhead run, typically in late March. The ladders are accessible to any upstream migrating fish. From 1964 through 2010, 2,645 steelhead were trapped, including 2,137 adults (>16 inches) and Page 4 Mokelumne River Hatchery Steelhead Program / June 2012

Table 2. Source of Fish 508 fish listed as <16 inches 3. The number of adults trapped annually has averaged 63 fish (range 0 to 245). From the 1975-76 through 1985-1986 seasons, no adult steelhead were reported trapped. Most if not all Central Valley anadromous streams and drainages were stocked with hatcheryorigin steelhead or resident rainbow trout prior to operation of MRFH and progeny of these fish may have contributed to the MRFH steelhead broodstock. Most likely, these non-indigenous steelhead stock transfers to MRFH have made a contribution to the present MRFH broodstock (Table 2). It is noted that McEwan (2001) reviewed the ecology and population biology of Central Valley steelhead but did not include specifics regarding steelhead runs in the Mokelumne River. Number of steelhead eggs and fingerling fish transferred to Mokelumne River Fish Hatchery and release dates and locations-1990 through 2007. Location Brood ear Eggs Imported Release Date(s) Release Location Number Released Release Size 1 CNFH Battle Creek 1990 463,573 earlings NFH American River 1990 221,058 July 1990 - June 1991 Mokelumne River/Sacramento River 506,180 2 Various FRH Feather River 1991 100,000 July 1991 - June 1992 Mokelumne River 51,977 earlings FRH Feather River 1992 247,600 July 1992 - June 1993 Mokelumne River 51,977 earlings NFH American River 1992 443,250 July 1992 - June 1993 Sacramento River 392,785 earlings NFH American River 1995 341,000 July 1995 - Feb 1996 Mokelumne River 229,560 Various NFH American River 1996 202,306 Jan 1997 Mokelumne River 85,650 earlings NFH American River 1997 217,280 Dec 1997 Mokelumne River 118,610 earlings NFH American River 1998 101,837 Dec 1998 Mokelumne River 102,440 2 earlings NFH American River 1999 125,746 Dec 1999 Mokelumne River 124,117 earlings NFH American River 2000 137,939 Jan 2001 Mokelumne River 111,680 earlings NFH American River 2001 124,939 0 earlings FRH Feather River 2002 186,577 Nov - Dec 2002 Mokelumne River 138,744 earlings FRH Feather River 2003 300,178 Feb 2004 Mokelumne River 196,528 earlings FRH Feather River 2004 431,190 Feb - Apr 2005 Mokelumne River 347,455 earlings FRH Feather 2005 266,816 Feb and Jun Mokelumne River 199,827 earlings 3 Annual hatchery reports indicate that more fish <16 inches were trapped but not enumerated. Mokelumne River Hatchery Steelhead Program / June 2012 Page 5

Source of Fish FRH Brood Eggs Release Location ear Imported Date(s) River 2006 Release Location Number Release Released Size 1 Dec 2006, Jan - Feb 2007 Mokelumne River 268,934 earlings Feather River 2006 307,275 Feather River 2007 311,325 earlings FRH 1/ Fingerlings = < 16 fish per pound, earlings = approximately one year of age, catchable = > 4 fish per pound. 2/ Release numbers reported in annual reports exceeds number of eggs or fish transferred and is presumed to include both Mokelumne River and American River-origin juvenile steelhead. 3/ Steelhead fingerlings There are no goals for the number of adult steelhead trapped or spawned annually at MRFH; however, release goals are identified each year which result in a target broodstock need. Recently, the goal has been to release 250,000 yearling steelhead that average 4 fish per pound. An estimated 500,000 eggs are needed to ensure this goal is achieved (personal communication, B. Anderson, Fish Hatchery Manager II, CDFG). Based on average egg take from females spawned at MRFH during the past, an estimated minimum of 185 female steelhead and a commensurate number of males are needed. Additional steelhead may be spawned throughout the season to ensure that sufficient eggs are taken to represent the entire run period. Prior to the 2006-2007 season, less than 50 female steelhead were typically trapped and spawned. Transfers of fish and eggs were made to provide enough fish to meet release goals. All adult steelhead that enter the gathering tank are sorted at least once a week during the run and examined for marks and tags. Fish 16 inches are identified with a hole punch in the caudal fin and immediately returned to the river. Unripe adults are retained in the holding ponds and sorted weekly. All adult steelhead trapped prior to January 1 st receive a distinct fin mark; those arriving after this date receive a different mark. Spawned adult steelhead (kelts) are held in ponds prior to release and then transported downstream to New Hope Landing and released into the Mokelumne River. Based on visual observations, survival of transported fish to release is generally in excess of 90%. 1.2.3 Spawning Sexually mature steelhead are spawned at MRFH throughout the period fish are trapped. To achieve the egg take goal, approximately 500,000 green eggs are taken to be representative of the spawning period of Mokelumne River Central Valley steelhead. Only adult steelhead (> 16 inches) with free-flowing sperm/eggs are selected for spawning. All mating and pairing of adult fish is done randomly and no attempt is made to select fish for any morphological characteristic. Both natural-origin (indicated by the presence of an adipose fin) and hatchery-origin (no adipose fin present) steelhead are used in the spawning process. Current mating protocols include hatchery x hatchery, hatchery x natural, and natural x natural pairings. Natural x natural pairings are the least common since only about 6% of the adult steelhead trapped are unmarked. After eggs are fertilized, they are washed in fresh water, drained in a colander, then placed in a bucket with a fresh water/ Iodaphore bath before being transferred to hatching jars or incubators. All eggs taken and fertilized on a single day are identified as an egg lot and assigned a lot Page 6 Mokelumne River Hatchery Steelhead Program / June 2012

number. An attempt is made to retain egg lots so that the natural spawning period (including its temporal distribution) of Mokelumne River steelhead is represented. Estimates of the number of eggs collected are reported annually; however, the number of eggs collected from a female may not be an accurate estimate of fecundity due to variations in spawning and egg taking methods. During a recent 11-year period, 390 females produced 751,865 eggs for an average of ~3,000 eggs per female (Table 3). From 1964 to 2006, the percent of male steelhead trapped varied annually from 44 to 100% (mean of all years 61%) of all adults trapped. Since 1985, there has been a decrease in the percent of males trapped, but the trend is approaching a more normal 1:1 ratio. Table 3. Number of female steelhead trapped and spawned from 1999 to 2009. Return Season Number of Females Spawned Number of Eggs Taken Number of Eggs per Female 1999-2000 2 4,800 2,400 2000-2001 0 1 2001-2002 18 62,919 3,496 2002-2003 29 87,215 3,007 2003-2004 29 59,915 2,066 2004-2005 21 60,920 2,901 2005-2006 45 149,319 3,318 2006-2007 87 326,776 3,756 2007-2008 59 159,642 2,706 2008-2009 79 221,052 2,798 2009-2010 20 61,596 3,080 Total 390 1,194,154 Average 43 119,415 3,014 1 No adult steelhead were trapped. Steelhead eggs surplus to the needs of the MRFH are not intentionally collected. Because of efforts to mimic the natural run and spawning period, some eggs may become surplus to the mitigation objectives of MRFH and are disposed. 1.2.4 Incubation All steelhead eggs are placed in either upwelling jars or vertical tray incubators with a maximum loading density of about 10 ounces of eggs per jar and not more than two layers of eggs per tray (10,000 eggs). All eggs incubated in the vertical trays and hatching jars remain until 90% of the alevins have absorbed their yolk sacks (buttoned-up). The fry, along with any remaining eggs are then transferred into the deep tanks. During incubation, fresh hatchery water is circulated through the jars or vertical tray incubators at a rate of approximately 0.5 gpm per jar and 2 to 5 gpm. Water temperature during steelhead egg incubation can range from 46 to 52 F. Incubation water is sand filtered, chilled (when river temperatures are above 56 F), and treated with an ultra-violet system. The chilling system has enough capacity to handle the entire egg-take. Based on available information, egg-to-fry ponding and egg-to-smolt release survival averaged 83% and 72%, respectively (Table 4). Mokelumne River Hatchery Steelhead Program / June 2012 Page 7

Table 4. Brood ear Number of steelhead eggs taken, fry ponded, and juveniles released from MRFH, brood years 2000 through 2010. Number of eggs 1 Number of Fry Hatched Egg to Fry Survival Number of Juvenile Fish Released Egg to Smolt Release Survival 2000 129,739 n/a 111,680 86% 2001 62,919 2002 249,496 n/a 168,671 68% 2003 387,393 240,491 62% 240,127 62% 2004 491,105 378,330 77% 375,111 76% 2005 327,736 225,132 69% 222,761 68% 2006 439,394 363,935 83% 359,609 81% 2007 638,101 426,417 67% 418,556 2 66% 2008 159,642 100,725 63% 99,580 2 62% 2009 221,052 171,617 78% 172,053 2 74% 2010 61,596 41,620 68% 40,943 66% Mean 259,713 341,312 83% 239,063 72% 1 Includes eggs taken at MRFH and transferred from other hatcheries. 2 Fish released as yearlings and two-year olds. 1.2.5 Rearing The steelhead juveniles remain in the deep tanks for about six months until they reach a size of 50 to 100 fish per pound. At maximum depth, the deep tanks can hold approximately 15,000 to 20,000 steelhead fry at a density of about 50 fish per gallon. Once they become free swimming and are actively feeding, the water depth in the deep tanks is increased to prevent overcrowding. After about six months, they are moved to the concrete raceways. Each raceway can hold approximately 85,000 steelhead young-of-the-year and 40,000 yearlingsized juveniles. Fish density in the ponds varies based on water temperature and size of the fish, but due to the number of ponds and number of juvenile steelhead, this is not a limiting factor at MRFH. Final rearing loadings are estimated to be 0.82 pounds/gpm/inch at 4 fpp and 3.0 cfs. Two of the new raceways were constructed with a colored concrete substrate to mimic the lower Mokelumne River. In addition, log structures are placed in one raceway and natural shade covering provided to replicate natural cut bank-type habitat. These raceways are used to rear the two-year-old natures fish. The amount of food fed through the rearing period depends on fish body weight and appetite, although the ideal amount of food per fish is 3% of their total body weight (Leitritz and Lewis 1976). Juvenile steelhead are initially fed 16 times per day, which is reduced to 6 times per day when they are 300 fish/lb, and 3 times per day after they reach a size of 100 fish/lb. Hatchery staff indicate that their goal for growth is a 20% increase in weight per week until fish are about 50 fpp. Growth rate is then slowed by feeding modulation. In the last three weeks prior to release, the feeding rate is increased to improve condition. Fish are graded by size during early rearing in the hatchery and prior to moving them outside. Juveniles for the yearling steelhead program are inventoried to determine number and weight at least weekly, and then monthly as fish increase in size. The feeding schedule is adjusted each time the sample weights are taken to Page 8 Mokelumne River Hatchery Steelhead Program / June 2012

minimize food waste and solid accumulation. Fish are routinely not fed prior to handling to minimize stress, expulsion of excess solids, and mortality. The two-year-old natures steelhead are reared in separate raceways. Their feeding rate is similar to the yearlings for the first year. Feed is then withheld for five months and the fish have to rely on naturally-produced food delivered from the reservoir via the water source. After five months, the fish are again fed to increase growth rates. 1.2.6 Release No formal methods are used to indicate smolt development. Visual indications such as a silvery body appearance and loosening of scales are used as general indicators of smoltification. Presently, all juvenile steelhead are released in the Mokelumne River at the New Hope Landing, approximately 10.5 miles upstream from the mouth of the Mokelumne River. In past years, MRFH has also planted juvenile steelhead in the San Joaquin River and in the Mokelumne River at MRFH. earling size juvenile steelhead are released from the end of February through March. Specific release dates depend on fish size, and equipment and personnel availability. Catchable size juvenile steelhead have not been released since 1984 and fingerling size fish have not been released since 1995. Since 1996, all juvenile steelhead have been released as yearlings after approximately one year of growth and at a size of approximately four fish per pound. Regardless of size, juvenile steelhead are typically not held past March 30 th. A pre-release fish health assessment, an annual assessment for disease certification, and broodstock screening and diagnostic tests are conducted by fish health staff. The natures fish are released at approximately 2.5 fpp. Releases occurred in February in 2009 and October in 2010. Based on 2010 PIT tagging information, the size of fish 21 days prior to release (October 29, 2010) ranged from 256 mm to 521 mm, with an average of 392 mm (N= 220). Since brood year 1998, all of MRFH-produced juvenile steelhead have been marked with an adipose-fin clip denoting a hatchery-origin fish. Since 2004, groups of juvenile steelhead have been coded wire-tagged as part of experiments and studies. 2 Populations Affected by the Hatchery Program The potential effects of the Central Valley steelhead hatchery programs, including the Mokelumne Hatchery 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 MRH steelhead program. The California Central Valley steelhead Distinct Population Segment (DPS) is listed as threatened under the federal 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 detected steelhead presence 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. Mokelumne River Hatchery Steelhead Program / June 2012 Page 9

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). Emergent fry migrate into shallow water areas; by late summer and fall, juveniles move into higher velocity, deeper, mid channel areas (Everest and Chapman 1972, Fontaine 1988, and Hartman 1965, all in Moyle et al. 2008). Age data from a sample of 100 fish taken in 1954 indicated that steelhead spent one (29%), two (70%), or three (1%) years in freshwater before migrating to the ocean as smolts (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 also includes artificially propagated steelhead stocks from Coleman National Fish Hatchery on Battle Creek and from the Feather River Hatchery. 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). Over the period 1957 to 1993, nearly three million eggs and juveniles were transferred to Nimbus Fish Hatchery from the Snow Mountain Egg Collection Station and Cedar Creek Hatchery, Eel River, CA; the Coleman National Fish Hatchery, Battle Creek, Sacramento River tributary; Warm Springs Hatchery, Dry Creek, Russian River, CA; and Mad River Hatchery, Mad River, CA, 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). Coleman National Fish Hatchery, Feather River Hatchery, Nimbus Hatchery, and Mokelumne River Hatchery produce about 1.5 million yearling steelhead annually based on current production goals (California Department of Fish and Game 2008). All four hatcheries were originally constructed to mitigate for habitat lost to dam construction. In 1998, Coleman National Fish Hatchery modified its operations to emphasize conservation (U.S. Fish and Wildlife Service 2001). 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 Page 10 Mokelumne River Hatchery Steelhead Program / June 2012

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. A major cause of historic declines 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 steelhead spawning and rearing habitat (Lindley et al. 2007). Other major threats 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). 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 escapement 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). NMFS and CDFG (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 hatchery fish relative to naturally produced fish, the use of out-of-basin stocks for hatchery production, and straying of hatchery produced 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 capture of native fish that might otherwise spawn in natural waters, the rearing of fish in artificial channels and ponds that cause a preferential selection for traits beneficial in the hatchery environment but that reduce their ability to survive in natural conditions in their streams of origin, and the interbreeding of fish exhibiting hatchery selected genetic traits with the wild fish population. 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 Mokelumne River Hatchery Steelhead Program / June 2012 Page 11

fitness of a population affecting productivity and abundance. Araki et al. (2008) summarized a number of studies that reported a loss of reproductive success (fitness) of hatchery fish in nature. For example, Araki et al. estimated that fitness of steelhead decreases almost 40% 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 wild 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 fish per pound) 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 naturally produced steelhead is considered low because all hatchery releases are made below the primary steelhead rearing areas in these tributaries. 2.1 Current Conditions of Affected Natural Populations The Mokelumne River Hatchery steelhead program has the greatest potential to affect natural reproduction of steelhead in the Mokelumne River watershed. Steelhead occurrence in the watershed is described below, followed by a summary of other potentially affected natural populations in the Central Valley. 2.1.1 Mokelumne River Steelhead The Mokelumne River originates in the Sierra Nevada Mountains and has a watershed that drains 627 square miles and contains a number of dams and reservoirs. No information exists on the size of historic runs of steelhead in the Mokelumne. McEwan and Jackson (1996) and McEwan (2001) report that the river once produced a significant number of natural steelhead, although there is debate about whether there was an indigenous steelhead stock in the Mokelumne River prior to releases of out-of-basin hatchery stocks (Cramer et al. 1995). According to creel census data, steelhead were the most sought after fish in the lower Mokelumne River prior to the completion of Camanche Dam (CDFG 1991). The steelhead run declined significantly following the completion of Camanche Dam in 1963 (CDFG 1991). According to NMFS (2009), Camanche Dam, the Woodbridge diversion, and other structures caused a loss of over 85% of their historical habitat. Currently the O. mykiss population in the Mokelumne River likely consists of both resident and anadromous life histories, with the resident form likely dominating. Natural-origin juveniles tagged with acoustic tags in 2007 and 2008 showed little movement out of the system. In these Page 12 Mokelumne River Hatchery Steelhead Program / June 2012

two years, only 5% (6 of 119) of the natural-origin tagged fish migrated to the ocean (Workman et al. 2008). Since 2002, annual winter steelhead escapement to the Mokelumne River Hatchery has averaged 99 fish. During this same period, approximately 32% of the total return was unmarked O. mykiss that most likely included fish that demonstrate both an anadromous and a resident life history (Table 5). Table 5. The number and percentage of adipose fin-marked steelhead trapped at the Mokelumne River Fish Hatchery (2002-2010). Unmarked Marked Total % Adults Return Season ear Adults Adults Adults Unmarked 2002-2003 2003 27 25 52 52% 2003-2004 2004 22 36 58 38% 2004-2005 2005 14 33 47 30% 2005-2006 2006 26 114 140 19% 2006-2007 2007 47 198 245 19% 2007-2008 2008 - - - - 2008-2009 2009 - - - - 2009-2010 2010 - - 51 - Average 27 81 99 32% The annual number of adult steelhead/rainbow trout redds observed in the lower Mokelumne River since 2001 has ranged from 3 to 61 and averaged 36 (Table 6). Data describing percent natural verses hatchery-origin fish on the spawning grounds are not available. Table 6. The number of steelhead redds observed in the Mokelumne River (2001-2010). Number of ear Steelhead Redds 2001 36 2002 26 2003 50 2004 18 2007 3 2008 41 2009 55 2010 61 Average 36 2.1.2 Other Steelhead Populations in the Central Valley There is evidence that Mokelumne 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 from the MRH 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, which is summarized in Table 7 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 Mokelumne River Hatchery Steelhead Program / June 2012 Page 13

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. Table 7. Watershed Upper Sacramento River Clear Creek Cow Creek Cottonwood/ Beegum creeks Battle Creek Dry Creek Antelope Creek Mill Creek Thomes Creek Steelhead status, abundance and habitat availability in the Central Valley. Viability Known Steelhead Distribution Steelhead Abundance Potential 1 Low-Moderate High Moderate Moderate High Low High High Moderate 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 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. 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). 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. Page 14 Mokelumne River Hatchery Steelhead Program / June 2012