C05__Attachment_4_-_Trinity_Hatchery_and_Genetics_Management_Plan_for_Trinity_River_Hatchery_Coho_Salmon.pdf

Hatchery and Genetics Management Plan for Trinity River Hatchery Coho Salmon

Prepared for:

National Oceanic and Atmospheric Administration National Marine Fisheries Service Arcata, California

Prepared in coordination with:

U.S. Department of the Interior California Department of Fish and Wildlife Bureau of Reclamation Northern Region, Redding, California Northern California Area Office Shasta Lake, California

December 2017

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HGMP for Trinity River Hatchery Coho Salmon Program iii

TABLE OF CONTENTS

LIST OF TABLES .......................................................................................................................................... iv

LIST OF FIGURES ........................................................................................................................................ vi

LIST OF ACRONYMS ................................................................................................................................. vii

EXECUTIVE SUMMARY ........................................................................................................................... ix

1 GENERAL PROGRAM DESCRIPTION

2 PROGRAM EFFECTS ON NMFS ESA-LISTED SALMONID POPULATIONS AND NON-

SALMONID POPULATIONS

3 RELATIONSHIP OF PROGRAM TO OTHER MANAGEMENT OBJECTIVES

4 WATER SOURCE

5 FACILITIES

6 BROODSTOCK ORIGIN AND IDENTITY

7 BROODSTOCK COLLECTION

8 MATING 69

9 INCUBATION AND REARING

10 RELEASE

11 MONITORING AND EVALUATION OF PERFORMANCE INDICATORS

12 RESEARCH

13 ATTACHMENTS AND CITATIONS

14 CERTIFICATION LANGUAGE AND SIGNATURE OF RESPONSIBLE PARTY

List of Appendices

Appendix A- Coho Take Table Appendix B – CDFW Pathology Report

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LIST OF TABLES

Table 1. Estimated abundance of unmarked (naturally produced) Coho adult returns versus various abundance thresholds for the Coho population in the Klamath Basin

Table 2. High, moderate and low extinction risk adult abundance levels for Trinity River Coho populations (NMFS 2014)

Table 3. Adult natural origin (NOR) Coho spawner abundance range by program phase for the Upper Trinity River Coho population

Table 4. Expected performance metric outcomes at NOR run size forecasts of 100 to 5,801 Upper Trinity River population adult Coho. Cells highlighted in blue indicate NOR run size when NOR broodstock, pNOB, pHOS and PNI performance metrics are achieved

Table 5. Recruit -Spawner data used to calculate Beverton-Holt productivity and capacity parameters, unmarked adult spawners (S), unmarked ocean recruits (R), and recruits per spawner (R/S).

Adult numbers are based on adult NOR and HOR counts at the Willow Creek Weir, adult returns to the TRH, spawning surveys, and harvest estimates

Table 6. ADJUSTED Spawner and recruit data used to calculate Beverton-Holt productivity and capacity parameters, unmarked adult spawners (S), unmarked ocean recruits (R) and recruits per spawner (R/S). Adult numbers are based on NOR and HOR counts at the Willow Creek Weir, adult returns to the TRH, spawning surveys, and harvest estimates. Numbers have been adjusted to account for hatchery fish Relative Reproductive Success (RRS of 0.8)

Table 7. AHA modeling results for historic hatchery operations (pre-2015; 500,000 yearling HOR Coho).

Table 8. AHA modeling results for HGMP hatchery operations (2015-2020; 300,000 yearling HOR Coho).

Table 9. AHA modeling results for hatchery operations as described in this HGMP for various levels of percent removal of hatchery fish from the system. Data are average values based on a model run over 100 generations. Green and red values define conditions where the HGMP outperforms or underperforms Historic Hatchery Operations, respectively

Table 10. TRH Coho program performance standards

Table 11. Benefits and risks associated with each performance indicator

Table 12. Number of Coho salmon returns to Trinity River Hatchery by sex, age, and females spawned for BY 2000 through BY 2015 (source: TRH records)

Table 13. The maximum number of NOR male and female Coho required for broodstock for a juvenile release of 300,000 yearling Coho

Table 14. Trinity River Hatchery Coho production goals

Table 15. Number of juveniles released, estimated ocean abundance of adults for the respective release year, and corresponding smolt-to-adult survival ratio (SAR) for TRH Coho (release year 1996- 2012)

Table 16. Estimated number of Coho redds in the mainstem Trinity River and mainstem Trinity River

HGMP for Trinity River Hatchery Coho Salmon Program v upstream of the North Fork Trinity River

Table 17. Estimated harvest numbers and rates of Trinity River Coho in ocean and freshwater fisheries.

Table 18. Estimated days TRH Coho spend in the Trinity River based on capture data at the Willow Creek Screw Trap (2010-2013)

Table 19. PCDRISK-1 modeling results for Coho. Data represent the percentage of the natural Coho fry and yearling populations that may be lost due to the release of 300,000 and 500,000 hatchery yearling Coho based on mean size at release and time in the river

Table 20. Number of Coho salmon returns to Trinity River Hatchery by sex, age, number of females spawned and eggs harvested for BY 2000 through BY 2012

Table 21. NOR adult Coho counted at TRH and spawned (2001-2015)

Table 22. NOR jack Coho counted at TRH and spawned (2001-2015)

Table 23. The number of NORs and HORs to be used for broodstock at varying NOR run-size and resulting pNOB

Table 24. The number of NOR male and female Coho broodstock required to meet annual juvenile release of 300,000 yearling Coho at a pNOB of 100 percent and achievement of in-hatchery culture survival metrics

Table 25. Number of eggs taken and survival rates to eyed stage (2004-2015)

Table 26. Number and survival rate of Coho eggs taken, fry ponded, and fish released from Trinity River hatchery (2004-2015)

Table 27. Historical monthly growth information for Coho at Trinity River Hatchery

Table 28. Example of disease/parasite infections, implemented treatments and measured juvenile Coho mortality rate for 2007-2011

Table 29. Release dates, location, number, and average size of Coho salmon releases from the Trinity River Hatchery, 2001 to 2015

Table 30. TRH Coho hatchery operations indicators, metrics and M&E methods

HGMP for Trinity River Hatchery Coho Salmon Program vi

LIST OF FIGURES

Figure 1. Klamath-Trinity River Basin and associated anadromous fish hatcheries (CA HSRG 2012)

Figure 2. Estimated run-size of hatchery and natural origin Coho salmon in the Trinity River based on data collected at the Willow Creek weir. The numbers presented include Coho production from all or part of the three Trinity River Coho populations. The number of Coho from each population is unknown

Figure 3. Estimated increase in adult abundance (green line) and fitness (red line) over 100 generations for a hatchery program operated to attain a PNI of 1.0 (Top), 0.67 (Middle) and 0.5 (Bottom).

The analysis assumes that the initial hatchery program has a fitness value of 0.5

Figure 4. Estimated hatchery and natural origin Coho escapement in the Upper Trinity River from 1997 through 2014 (Source: CDFW staff)

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LIST OF ACRONYMS

AD Adipose fin BW Body Weight CA HSRG California Hatchery Scientific Review Group CDFW California Department of Fish and Wildlife CFS Cubic Feet per Second CWT Coded Wire Tag DPS Distinct Population Segment ESA Federal Endangered Species Act ESU Evolutionarily Significant Unit FDA Federal Food and Drug Administration FPP Fish per Pound GIS Geographic Information System GPD Grams per Day GPM Gallons per Minute HACCP Hazardous Analysis and Critical Control Point HSRG Hatchery Scientific Review Group HCT Hatchery Coordination Team HGMP Hatchery and Genetic Management Plan HOR Hatchery Origin Recruit HOS Hatchery Origin Spawner IGH Iron Gate Hatchery IP Intrinsic Potential KBRA Klamath Basin Restoration Agreement KHSA Klamath Hydroelectric Settlement Agreement KRTF Klamath River Task Force LM Left Maxillary-clip MGD Million Gallons per Day ML Milliliters MM Millimeters mtDNA Mitochondrial DNA NCRWQCB North Coast Regional Water Quality Control Board NMFS National Marine Fisheries Service NOAA National Oceanic Atmospheric Administration NOR Natural Origin Recruit NOS Natural Origin Spawner NPDES National Pollutant Discharge Elimination System PCD Predation, competition and disease PFMC Pacific Fisheries Management Council pHOS Proportion Hatchery Origin Spawners pNOB Proportion Natural Origin Broodstock PNI Proportionate Natural Influence

HGMP for Trinity River Hatchery Coho Salmon Program viii

PPM Parts per Million RM Right maxillary-clip RWQCB Regional Water Quality Control Board SAR Smolt-to-adult survival rate SONCC Southern Oregon/Northern California Coast (ESU) USFWS United States Fish and Wildlife Service TRH Trinity River Hatchery TRT Technical Recovery Team VSP Viable Salmonid Population YOY Young-of-the-year

HGMP for Trinity River Hatchery Coho Salmon Program ix

EXECUTIVE SUMMARY

The US Bureau of Reclamation (BOR) is funding development of a Hatchery and Genetic Management Plan (HGMP) for Coho salmon (Coho) reared at the Trinity River Hatchery (TRH). The California Department of Fish and Wildlife (CDFW) is contracted to operate and maintain the hatchery. The Hoopa Valley Tribe assists with propagation of Coho salmon at TRH. The Hoopa Valley and Yurok tribes assist in evaluating the performance and operations of the TRH. The National Marine Fisheries Service (NMFS) will use the information in this HGMP to evaluate the risks hatchery Coho pose to naturally produced ESA-listed Coho in the Trinity River. The primary goal of an HGMP is to devise biologically based hatchery management strategies that ensure the conservation and recovery of salmon and steelhead populations.

(www.westcoast.fisheries.noaa.gov/hatcheries/salmon_and_steelhead_hatcheries.html)

The TRH produces Endangered Species Act (ESA) listed Coho and Spring Chinook, Fall Chinook and steelhead to mitigate habitat and fish production lost from construction and operation of Lewiston Dam. This HGMP focuses solely on hatchery operations associated with the production of ESA-listed Coho salmon. The effects that the Chinook and steelhead programs may have on ESA listed Coho are analyzed separately in a Biological Assessment (BOR 2017 in press).

The Coho program will be managed consistent with the principles and recommendations of the Pacific Northwest Hatchery Scientific Review Group (HSRG) and the California HSRG (CA HSRG). The direction provided by these two groups represents the best available science for operating hatchery facilities consistent with salmon and steelhead conservation and recovery objectives.

The Coho program will be operated as an integrated type as defined by the HSRGs. The intent of an integrated program is to have the natural environment drive the adaptation and fitness of a composite population of fish that spawn both in the hatchery and in the wild (i.e., naturally). A fundamental purpose of an integrated program is to increase total adult abundance, productivity and fitness while minimizing genetic divergence of hatchery broodstock from the naturally spawning population.

Integration of the two components (hatchery and natural) of the population will be achieved by incorporating naturally produced fish from the Upper Trinity River Coho population into the broodstock and limiting gene flow from hatchery origin to natural origin spawners by controlling the proportion of hatchery origin fish that spawn naturally (pHOS) within this population. The goal of the program is to provide fish for harvest in a manner consistent with the conservation of the Trinity River Coho population while meeting TRH mitigation requirements.

The actual number of hatchery adult Coho harvested annually would depend on juvenile release numbers, their freshwater and marine survival rates, take levels of naturally produced Coho established by NMFS and the ability of fishers to harvest hatchery Coho using various gear types.

Based on modeling, the program is expected to produce on average approximately 10,000 adult Coho.

The program proposes to use a weir to reduce the number of hatchery origin (HOR) Coho spawning naturally and collect natural origin adult recruits (NORs) for broodstock. The weir would be located

HGMP for Trinity River Hatchery Coho Salmon Program x upstream of Canyon Creek in the mainstem Trinity River. Natural origin fish captured at the weir would be returned unharmed to the stream or transported to the hatchery and used as broodstock for the program. Natural origin fish released to the river may be marked for study purposes.

Aside from the proposed weir, this HGMP recognizes that selective harvest by others may be a tool to regulate HORs in natural spawning areas outside of the spatial scope of the integrated population. For example, in 2016, the Hoopa Valley Tribe implemented a selective harvest weir within the Lower Trinity population unit to reduce HOR abundance and the proportion of hatchery origin spawners (pHOS) in natural spawning areas while optimizing harvest opportunity of hatchery marked Coho. In addition, the Yurok and CDFW may implement additional selective fisheries in the basin for hatchery Coho. Because these harvest actions are outside of the control of the hatchery program, any take of Coho associated with these actions are not accounted for in this HGMP.

The TRH program will contribute to Coho recovery by acting as a genetic reserve for the Upper Trinity River Coho population and increasing population fitness and abundance over the long term.

Analyses provided in this HGMP indicate that Trinity River Coho may not be sustainable without continued hatchery support.

Hatchery conservation priorities will vary by recovery phase as defined by the HSRG (2014). The four phases of recovery and their respective conservation priorities are as follows:

1. Preservation

• Prevent extinction

• Retain genetic diversity and identity of the existing population

• Increase abundance (i.e., provide demographic benefit)

• Restore habitat

2. Re-colonization

• Re-populate restored and/or depleted habitat

• Increase abundance and temporal and spatial diversity (spawning and rearing) of the population

• Increase population fitness

• Retain population genetic identity and diversity

3. Local Adaptation

• Meet and exceed minimum viable spawner abundance for natural origin spawners

• Increase fitness, reproductive success and life history diversity through local adaptation

(e.g., by reducing hatchery influence by maximizing the proportionate natural influence

(PNI))

4. Full Restoration

• Maintain a viable population, based on all viable salmonid population (VSP) attributes using long-term adaptive management

HGMP for Trinity River Hatchery Coho Salmon Program xi

The program will move between phases based on the achievement of quantitative biological triggers that include natural origin adult Coho abundance, genetic contribution of hatchery origin fish to the naturally spawning population (approximated by census pHOS) 1, harvest impacts to naturally produced Coho and proportionate natural influence (PNI). The program will be managed to achieve, whenever adult NOR run size allows, four criteria: pHOS <30 percent (Upper Trinity River Coho population), minimum PNI of 0.5, average PNI > 0.67 and proportion natural origin broodstock (pNOB) of 100 percent. Achievement of the four criteria ensures that the natural rather than the hatchery environment drives local adaptation of the population. Attainment of the criteria will also be used to determine future hatchery production levels.

The program will also strive to maintain pHOS levels in the South Fork Trinity River and Lower Trinity River Coho population geographic areas at < 5 percent as recommended by the HSRGs.

Achieving this objective may require that HOR adults be removed using weirs or other methods in the Lower Trinity River or tributaries; however, these actions are not incorporated into this HGMP at this time. Spawning surveys (or other methods) will be conducted over the next few years throughout the Trinity River Basin to determine pHOS levels and need for the removal of HORs from other Coho populations.

The natural fish abundance triggers are linked to the high, medium and low extinction risk adult abundance criteria developed by NMFS for the Upper Trinity River Coho population (NMFS 2014).

These triggers will be used to adaptively manage the program on an annual basis to reduce hatchery effects on NOR Coho and increase the fitness of the composite population (i.e., NOR + HOR).

The number of juvenile Coho to be released yearly from 2015-2020 is set at 300,000 (yearlings). At the end of this period, a technical team (such as the previously functioning Hatchery Coordination Team) will review the program to determine if fish production levels require adjustment. The recommendation by this group to alter production level will be based on the program’s ability to achieve performance metrics described in the HGMP while achieving legal obligations for mitigation and harvest purposes. The decision to alter hatchery production will be made in coordination with a decision-making body (such as the former Governance Board).

Fish mating will occur based on a 1:1 (male to female) spawning protocol as defined by the CA HSRG (2012). Genetic samples will be taken from all broodstock to determine the proportion of sibling crosses (i.e., inbreeding) in the hatchery population. If this proportion is too high (as determined by CDFW and NMFS geneticists), hatchery managers will implement a genetically-based spawning matrix for selecting pairings. The ability to implement such a system is dependent on achieving high adult holding survival rates (>95 percent). Whenever possible, hatchery staff will use only natural origin fish for broodstock. Using only NOR adult Coho for broodstock ensures that PNI will not be less than 0.5, regardless of pHOS level.

1 Census pHOS, the proportion of the naturally spawning population consisting of hatchery origin fish, is a conservative estimate of gene flow. HSRG standards for hatchery influence are defined in terms of gene flow or “effective pHOS” , which is calculated by discounting the number of hatchery origin spawners (HOS), typically by a factor of 0.8 for Coho and Chinook (HSRG 2014, 2015). This accounts for lower assumed reproductive success of HOS.

HGMP for Trinity River Hatchery Coho Salmon Program xii

Coho jacks will be incorporated into the broodstock at a rate between 5-15 percent of the total males spawned each spawning event, unless altered by CDFW and NMFS geneticists.

Technical staff will conduct a fish release timing study to determine if juvenile migration time from hatchery release to collection at the Willow Creek Screw Trap on the mainstem Trinity River can be reduced to 21 days or less. A reduction in juvenile migration time is theorized to decrease possible competition and predation risks hatchery fish pose to naturally produced Coho and other salmonids.

The hatchery monitoring and evaluation program is focused on ensuring that Program performance indicators are met and determining when biological triggers are achieved. Hatchery practices will be improved to increase adult holding, egg incubation and egg-to-yearling survival rates. Hatchery staff will track survival by life stage and the number and quality of the fish released.

HGMP for Trinity River Hatchery Coho Salmon

1 GENERAL PROGRAM DESCRIPTION

1.1 NAME OF HATCHERY PROGRAM

Trinity River Hatchery (TRH) Coho Salmon Program

1.2 SPECIES AND POPULATION UNDER PROPAGATION AND ESA STATUS

Coho salmon (Oncorhynchus kisutch) propagated at TRH are part of the Southern Oregon/Northern California Coast (SONCC) Evolutionary Significant Unit (ESU), which includes all Coho salmon populations from Cape Blanco, Oregon to Punta Gorda, California. On May 6, 1997, the National Marine Fisheries Service (NMFS) published the final rule establishing a threatened status for Coho salmon in the SONCC ESU (62 FR 24588). On June 28, 2005, the Federal Register (70 FR 79202) promulgated final listing determinations and 4(d) protective regulations that included TRH Coho Salmon as a part of the SONCC, as well as amended 4(d) protective regulations to provide for management of artificial propagation programs and consistency with the conservation needs of the ESA-listed SONCC

ESU.

The California Fish and Game Commission also listed Coho salmon as a threatened species pursuant to the California Endangered Species Act within the California portion of the SONCC on March 30, 2005.

According to NMFS (2010), nine Coho salmon population units are present in the Klamath-Trinity Basin. Of these, three population units occur in the Trinity River Basin:

1) South Fork Trinity River Population, which uses the mainstem South Fork Trinity River and its tributaries;

2) Lower Trinity River population, which uses the mainstem Trinity River and its tributaries between the confluence of the North Fork Trinity River to the mouth of the Trinity River; and

3) Upper Trinity River population, which uses the mainstem Trinity River and its tributaries between the North Fork Trinity River (inclusive) and Lewiston Dam, the upstream barrier to anadromous fish migration.

2 HGMP for Trinity River Hatchery Coho Salmon

1.3 RESPONSIBLE ORGANIZATION AND INDIVIDUALS

Hatchery and Provider of Operation and Maintenance Funding:

Name and Title: Paul Zedonis, Chief, Environmental and Natural Resources Division Agency or Tribe: U.S. Bureau of Reclamation Address: Northern California Area Office 16349 Shasta Dam Blvd.

Shasta Lake, CA 96019 Telephone: (530) 276-2047 Fax: (530) 275-2005 Email: pzedonis@usbr.gov

Statewide Fisheries Program Branch

Name and Title: Kevin Schaffer, Branch Chief, Fisheries Branch Agency or Tribe: California Department of Fish and Wildlife (CDFW) Address: 830 S Street

Sacramento, CA 95811 Telephone: (916) 445-3181 Fax: (916) 327-8854 Email: Kevin.Schaffer@willdife.ca.gov

Northern Region Fisheries Project Leader

Name and Title: Curtis Milliron, Fisheries Program Manager Agency or Tribe: CDFW Address: 601 Locust Street

Redding, CA 96001 Telephone: (530) 225-2280 Fax: (530) 225-2381 Email: Curtis.Milliron@willdife.ca.gov

Northern Region Hatchery Program Supervisor

Name and Title: Linda Radford, Senior Hatchery Supervisor Agency or Tribe: CDFW Address: 601 Locust Street

Redding, CA 96001 Telephone: (530) 225-2369 Fax: (530) 225-2381 Email: Linda.radford@wildlife.ca.gov

Trinity River Hatchery Management

Name (and title): Craig Layman, Hatchery Manager I I Agency or Tribe: CDFW Address: Trinity River Hatchery

P.O. Box 162 Lewiston, CA 96502

Telephone: (530) 778-3931 Fax: (530) 778-3982 Email: craig.layman@wildlife.ca.gov

Trinity River Hatchery Coho Program Assistance

Name (and title): George Kautsky, Senior Fisheries Biologist Agency or Tribe: Hoopa Valley Tribe Address: Hoopa Valley Tribal Fisheries Department

P.O. Box 415 Hoopa, CA 95546

Telephone: (530) 625-4267 Fax: (530) 625-4995 Email: hupafish@hoopa-nsn.gov

Preparers of the HGMP

Name (and title): Paul Zedonis, Chief, Environmental and Natural Resources Division Agency or Tribe: U.S. Bureau of Reclamation Address: Northern California Area Office 16349 Shasta Dam Blvd.

Shasta Lake, CA 96019 Telephone: (530) 276-2047 Fax: (530) 275-2005 Email: pzedonis@usbr.gov

Other agencies, Tribes, cooperators or organizations involved, including contractors, and the extent of their involvement in the Coho program are as follows:

• This HGMP was prepared in coordination with, and with extensive assistance from the California Department of Fish and Wildlife, Hoopa Valley Tribe, and Yurok Tribe.

• The Hoopa Valley and Yurok tribes assist in evaluating the performance and operations of the

TRH.

• The Hoopa Valley Tribe assists with propagation of the Coho salmon at TRH.

• The Trinity River Restoration Program (TRRP) Office oversees implementation of the Trinity River Restoration Program.

4 HGMP for Trinity River Hatchery Coho Salmon

1.4 FUNDING SOURCE, STAFFING LEVEL, AND ANNUAL HATCHERY

PROGRAM OPERATIONAL COSTS

The Bureau of Reclamation (BOR), Northern California Area Office, provides funding for operations and maintenance of the TRH.

The CDFW operates and maintains the TRH under contract with the BOR. The Hoopa Valley Tribe has been participating in hatchery operations at TRH since 2014 in coordination with CDFW and BOR. The Hoopa Valley and Yurok tribes also assist in evaluating the performance and operations of the TRH. The TRH staff consists of six fish and wildlife technicians, two managers, three fish and wildlife seasonal aides, and one half-time secretary.

The annual TRH operations and maintenance (O&M) cost was approximately $1,006,000 in FY 2012 and the cost for fish feed in 2012 through 2017 is projected to be $1,489,000, ($297,800 annually). With implementation of the HGMP, costs are expected to increase.

1.5 LOCATION(S) OF HATCHERY AND ASSOCIATED FACILITIES

The TRH is located on the Trinity River at the base of the Lewiston Dam (River Mile [RM] 110), near the town of Lewiston in Trinity County, California (Figure 1). Lewiston Dam is the upstream limit of anadromous fish migration on the Trinity River. Water from Lewiston Reservoir, located approximately 100 feet upstream of the hatchery, serves as the water supply to the TRH. The hatchery water supply is withdrawn from a 12-foot strata between 9 and 20 feet below the surface of the lake. The volume withdrawn ranges from 20 cubic feet per second (cfs) to 125 cfs depending on hatchery needs at any given time. Diverted water enters the hatchery by way of an intake structure and an aeration facility capable of processing 130 cfs.

The hatchery building consists of 60 incubator stacks, 148 standard California troughs, and 26 deep tanks. TRH uses all of the incubator stacks during spawning season from October through December. In addition, the hatchery has 30-60 Hatch jars that are used primarily for Chinook production.

The TRH has 40 concrete raceways that are each 10 feet wide by 3.5 feet deep and 200 feet long. Each raceway is operated as a one-pass system with an inflow of up to 2 cfs. If all raceways are in use, the instantaneous water demand totals 100 cfs.

1.6 PROGRAM TYPE

During the term of this HGMP, the TRH Coho program will be operated as an integrated program as defined by the California Hatchery Scientific Review Group (CA HSRG 2012) and the Pacific Northwest Hatchery Scientific Review Group (HSRG 2004). The intent of an integrated program is for the natural environment to drive the adaptation and fitness of a composite population of fish that spawn both in the hatchery and in the wild (i.e., naturally in the stream). Integration of the two components of the population will be achieved by incorporating naturally produced fish from the Upper Trinity River Coho population into the broodstock and controlling the number of hatchery origin fish that spawn naturally with this population.

The geographic integration area is defined as extending from a weir to be located upstream of Canyon Creek to Lewiston Dam. Thus, adults from the entire geographic area of the Upper Trinity River Coho population unit, as defined by NMFS, may not be included in broodstock.

1.7 PROGRAM PURPOSE

The purpose of the hatchery program is to provide adult Coho salmon for harvest by meeting mitigation requirements for the Trinity River Division (TRD) of the Central Valley Project and to reduce ecological and genetic impacts to ESA-listed Coho. The TRD of the Central Valley Project initiated the hatchery program in 1963 to mitigate for lost spawning and rearing habitat resulting from construction of the Lewiston and Trinity dams on the Trinity River. The total annual adult Coho production (catch plus escapement) goal for the hatchery was defined as 7,500 by Frederickson et al. (1980).

This HGMP seeks to harmonize this primary purpose of the hatchery in a manner consistent with the conservation and recovery of the ESA listed Coho salmon.

1.8 PROGRAM JUSTIFICATION

This integrated hatchery program is designed to meet harvest and conservation requirements for Trinity River Coho and the ongoing legal requirement to mitigate for the loss of Coho production and habitat due to the construction and operation of the TRD.

According to NMFS (2014), all nine Coho salmon population units in the Klamath-Trinity Basin have declined dramatically in abundance relative to historical levels, including the three populations within the Trinity River Basin. In general, the collective population of Coho returning to the Trinity River is dominated by a large hatchery component (Figure 2). In consideration of this trend, NMFS (2014) concluded that these population units are at risk of extinction because population trends for naturally produced Coho exhibit decreasing productivity and decreasing density (Table 1). This trend is important in the conservation of the Coho populations because any further decline in natural Coho abundance reduces the population’s average productivity, resulting in a steep slide toward extinction (McElhany et

al. 2000).

6 HGMP for Trinity River Hatchery Coho Salmon

Figure 1. Klamath-Trinity River Basin and associated anadromous fish hatcheries (CA HSRG 2012).

Figure 2. Estimated run-size of hatchery and natural origin Coho salmon in the Trinity River based on data collected at the Willow Creek weir. The numbers presented include Coho production from all or part of the three Trinity River Coho populations. The number of Coho from each population is unknown.

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

45,000

1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

N um be r o f a du lt Co ho

Above Willow Creek Trinity River Coho Estimated Run-size

TRH Natural

8 HGMP for Trinity River Hatchery Coho Salmon

Table 1. Estimated abundance of unmarked (naturally produced) Coho adult returns versus various abundance thresholds for the Coho population in the Klamath Basin.

Population Unit Estimated Unmarked

Coho Run Size High Risk Annual Abundance Level1

Low Risk Annual Abundance Level2

Upper Trinity 1,879 (Upper Trinity only)3

500-9,0004 (all Trinity populations combined)

36511 5,800 Lower Trinity 11211 3,60013 South Fork Trinity 24211 970

Lower Klamath 0-1,5005 20511 5,900 Middle Klamath 0-1,5006 11312 450 Upper Klamath 100-4,0007 42512 8,500 Scott River 60-1,6008 44112 6,500 Shasta River 0-4009 53112 4,700 Salmon River 5010 11412 450

1 High risk annual abundance level corresponds to a population threshold below which there exists a high risk of depensation (i.e., decreasing productivity with decreasing density). Depensatory processes at low population abundance result in high extinction risks for very small populations because any decline in abundance further reduces the population’s average productivity, resulting in a steep slide toward extinction (McElhany et al. 2000). Values in this column are from Williams et al.

(2008) unless noted below.

2 Low risk annual abundance level represents the minimum number of spawners required for a population to be considered at low risk for the spatial structure and diversity thresholds. Values are from Table 4-2 in NMFS (2014) and represent the minimum number of spawners needed in each population to meet the biological recovery criteria.

3 Average run-size from 1997 to 2014 (CDFW, pers. comm. 2015).

4 Average run-size from 2001 to 2004 for all 3 Trinity populations combined (Ackerman et al. 2006).

5 Numbers reported in NMFS (2014), p. 18-8, based on Ackerman et al. (2006). Includes all adults.

6 Numbers reported in NMFS (2014), p. 33-5, based on Ackerman et al. (2006). Includes all adults.

7 Numbers reported in NMFS (2014), p. 34-7, based on Ackerman et al. (2006). Includes all adults.

8 Numbers reported in NMFS (2014), p. 36-9, based on Knechtle and Chesney (2013). Includes all adults.

9 Numbers reported in NMFS (2014), p. 37-7, based on Knechtle and Chesney (2013). Includes all adults.

10 Number reported in NMFS (2014), p. 35-5, based on SRRC (2008). Includes all adults.

11 Number reported in NMFS (2016), p. 22.

12 Number reported in Williams et al. (2008). Not updated in NMFS (2014).

13 Number reported in NMFS (2014), Table 4-2. Low risk level reported as 3,900 on p. 38-6 in NMFS (2014).

Primary factors leading to the decline of the Trinity River Coho populations include:

The construction of Trinity and Lewiston dams, which blocked access to 109 miles of salmon and trout spawning and rearing habitat;

Degradation of mainstem Trinity River habitat below the dams;

Degradation of tributary habitat; and

The role that hatchery fish play in population structure and resiliency.

In the recovery plan for SONCC Coho, the NMFS concluded that TRH operations pose a very high Stress and Threat risk to the diversity of all three Coho populations in the Trinity River (NMFS 2014).

The very high-risk rating was based on the large proportion of the natural spawning population composed of hatchery fish (i.e., high pHOS). NMFS (2014, Table 2-4) provided data showing that pHOS ranged from 36 to 100 percent in all three population units. In addition, NMFS was concerned that the large number of hatchery fish released by the program posed substantial competition, predation and disease risks to naturally produced Trinity River Coho. The NMFS recovery plan therefore recommended a reduction in ecological and genetic impacts to ESA-listed Coho due to hatchery operations. This HGMP describes how the ecological and genetic risks associated with the hatchery program will be reduced to achieve NMFS objectives.

1.8.1 Management Approach

The Coho program will be operated consistent with the principles and recommendations of the California HSRG (CA HSRG 2012) and Pacific Northwest HSRG (HSRG 2004, 2014, 2015). The direction provided by these two scientific groups represents the best available science for operating hatchery facilities consistent with salmon conservation and recovery objectives.

1.8.1.1 Scientific Framework

The Coho program will be operated as an integrated program as defined by the HSRG. The intent of an integrated program is to have the natural environment drive the adaptation and fitness of a composite population of fish that spawn both in the hatchery and in the wild (i.e., naturally). A fundamental purpose of an integrated program is to increase adult abundance, productivity and fitness while minimizing genetic divergence of hatchery broodstock from the naturally spawning population.

Managers achieve integration of the two components (hatchery and natural) of the population by incorporating naturally produced fish from the Upper Trinity River population into the broodstock and controlling the number of hatchery origin fish that spawn naturally with this population and the Lower Trinity River and South Fork Trinity River populations.

For a properly integrated program, the HSRGs require that the proportion of natural origin (NOR) Coho incorporated into the hatchery broodstock (pNOB) exceed the proportion of the natural spawning population composed of hatchery fish (pHOS). Maintaining this ratio above 0.5 results in the natural environment having a greater influence on the adaptation of the composite NOR and HOR population than the hatchery environment. Referred to as the proportionate natural influence (PNI), this parameter is calculated as follows:

PNI = pNOB/(pNOB + pHOS)

High PNI values are expected to result in increased fitness, reproductive success, life history diversity and productivity of the population over time. Increasing the fitness of natural populations also increases the benefits that current and future habitat improvements produce with respect to fish production (HSRG 2014). The change in fitness over time from achievement of various levels of PNI is shown in Figure 3.

As defined by the HSRG (2014, 2015), effective pHOS, which is a measure of gene flow, differs from census pHOS by a factor of less than one, i.e., effective pHOS is less than census pHOS (pHOScen).

10 HGMP for Trinity River Hatchery Coho Salmon

PNI = 1.0

PNI = 0.67

PNI = 0.5

Figure 3. Estimated increase in adult abundance (green line) and fitness (red line) over 100 generations for a hatchery program operated to attain a PNI of 1.0 (Top), 0.67 (Middle) and 0.5 (Bottom). The analysis assumes that the initial hatchery program has a fitness value of 0.5.

Effective pHOS discounts the contribution of hatchery origin spawners (HOS) by assuming that HOS have lower reproductive success than natural origin spawners (NOS). In this HGMP, pHOScen is used as a conservative approximation of gene flow. Census pHOS does not apply a discount factor to the reproductive success of HOS, and is calculated as follows (HSRG 2014):

pHOScen = HOS/(HOS + NOS) where:

HOS = number of hatchery origin spawners in nature

NOS = number of natural origin spawners in nature

The HSRG selected pHOScen as the preferred gene flow indicator because it can be readily measured based on carcass surveys and weir counts. The use of pHOScen is conservative in that it assumes that the reproductive success of hatchery fish is similar to naturally produced fish. That is, it does not discount the reproductive success of hatchery fish.

Managers will operate the program consistent with the concepts of hatchery reform as expressed by the CA HSRG (2012) and HSRG (2014, 2015). The program will:

• Manage hatchery broodstock to achieve proper genetic integration with the natural population (Upper Trinity River Coho population)

• Promote local adaptation

• Minimize adverse ecological interactions between NOR and HOR Coho

• Minimize the effects of hatchery and monitoring facilities on the ecosystem in which they operate

• Establish program goals based on adult abundance

• Define the geographic area of the integrated population

• Externally mark all hatchery fish

• Manage the program in a scientifically defensible manner

With respect to the last bullet, the HSRG (2014) defines a scientifically defensible program as follows:

“A scientifically defensible program is one that explains, in terms of benefits and risks, how the hatchery program expects to achieve its purpose. The benefits of the program must outweigh the risks, and the chosen strategy must be consistent with current scientific knowledge. Where there is uncertainty, hypotheses and assumptions should be documented so that those assumptions can be evaluated and modified as new information becomes available.”

The following recommendations of the CA HSRG (2012) for the TRH have been considered in the development of this HGMP:

12 HGMP for Trinity River Hatchery Coho Salmon

• Natural-origin fish should be incorporated into broodstock at a minimum rate of 10 percent to prevent divergence of the hatchery and natural components of the integrated population. This may require auxiliary adult collection facilities or alternative collection methods (e.g., seining or trapping).

• Adult holding facilities in the hatchery should be upgraded/expanded to provide adequate space, water flows and temperature regimes to hold the number of adults required for broodstock at high rates of survival (more than 90 percent). Facilities need to be adequate to hold the expected number of unripe adults for extended periods with minimal hatchery-caused mortality.

• The adult spawning facility is inadequate to meet current needs for fish sorting, spawning and monitoring and should be upgraded.

• Managers should investigate the feasibility of collecting natural-origin adult fish at alternate locations. The existing trapping location is very limited in its ability to capture fish representing the entire spectrum of life history diversity. Only fish that migrate to the furthest upstream reaches are susceptible to capture.

• Performance standards for each phase of the fish culture process should be established and tracked annually. Summaries of data collected with comparisons to established targets must be included in annual hatchery reports.

• A Monitoring and Evaluation Program should be developed and implemented and a Hatchery Coordination Team formed for the program. Implementation of these processes will inform hatchery decisions and document compliance with best management practices defined in this report.

• Develop and promulgate a formal, written fish health policy for the operation of the hatchery.

Hatchery compliance with this policy should be documented annually as part of a Fish Health Management Plan. The current fish health policy is inadequate to protect native stocks.

• Develop an updated Hatchery Procedure Manual that includes performance criteria and culture techniques presented in IHOT (2005) Fish Hatchery Management (Wedemeyer 2001) or comparable publications. The fish culture manual (Leitritz and Lewis 1976) is outdated and does not reflect current research and advancements in fish culture.

• Identify the purposes and goals of this program and determine the appropriate program size given existing hatchery escapement goals for hatchery Coho salmon, the ESA-listed status of the population, and the Tribal trust issues raised by construction of Lewiston and Trinity dams.

Adult returns to the hatchery have averaged over 7,000 adults, more than three times the hatchery escapement goal of 2,100 fish.

• Jacks should be incorporated into the broodstock at a rate that does not exceed 50 percent of the total number of jacks encountered during spawning operations and in no case exceeds 10 percent of the total males spawned.

1.8.1.1.1 Working Hypothesis

The program’s working hypothesis assumes that implementing hatchery recommendations of the

HSRGs will result in a reduction in the negative effects hatchery fish have on ESA-listed Trinity River Coho populations. A reduction in hatchery effects is expected to increase the productivity, capacity, diversity, fitness and abundance of naturally produced Coho in the Trinity River and specifically in the Upper Trinity River Coho population.

1.8.1.2 Program Phases

Implementation of the TRH Coho program will occur in four phases as defined by the HSRG (2014, 2015). The hatchery program priorities will vary by recovery phase and are described in detail below.

The four recovery phases are:

• Preservation

• Re-colonization

• Local Adaptation

• Full Restoration

The program will move between phases based on NOR abundance. The abundance targets for each phase are set based on low, moderate and high extinction risk /viability thresholds established in the SONCC Coho recovery plan (NMFS 2014) (Table 2). The ranges of adult abundance values corresponding to each program phase are shown in Table 3.

Table 2. High, moderate and low extinction risk adult abundance levels for Trinity River Coho populations (NMFS 2014).

Population Population

Type

EXTINCTION RISK

High

(Depensation Threshold)* Moderate**

Low (Required for ESU

Viability) Upper Trinity River

Core 365 1,460 5,800

*The number of Intrinsic Potential (IP) kilometers times one adult per IP kilometer ** The number of IP kilometers times four adults per IP kilometer

Table 3. Adult natural origin (NOR) Coho spawner abundance range by program phase for the Upper Trinity River Coho population.

Population Preservation

Phase Re-Colonization

Phase

Local Adaptation

Phase Full Restoration

Phase Upper Trinity River

0-365 366-1,460 1,461-5,799 5,800+

14 HGMP for Trinity River Hatchery Coho Salmon

The key performance metrics for the program that apply to the Upper Trinity River Coho population are:

1. pHOS < 30 percent (3-year running average)

2. pNOB = 100%

3. Take no more than 372 NOR and 200 HOR Coho for broodstock in any year.

4. Minimum annual PNI of 0.5 and 3-year average PNI > 0.67

5. 1,460+ natural origin (NOR) spawners (3-year running average)

6. Total escapement of > 1,460 (HOR +NOR) (3-year running average)

In addition, the program will strive to achieve a census pHOS of <5 percent for Coho populations in the South Fork Trinity River, Lower Trinity River, and portions of the upper Trinity River downstream of the broodstock collection weir (e.g., North Fork Trinity River).

Adult run forecasts determine program management priorities (Table 4). The blue highlighted cells in Table 4 indicate the NOR adult run sizes at which each performance metric are expected to be achieved or exceeded. All performance metrics will be met when NOR run size is 1,100 fish or greater. The minimum PNI criterion (>0.5) and 3-year average PNI (>0.67) will be achieved when NOR Coho run size is 500 and ~800 fish, respectively.

Managers’ ability to attain the key performance metrics will depend on the accuracy of run size forecasts and efficiency of weirs and other methods to collect broodstock and remove hatchery fish from the spawning grounds. Because it is unknown how effective these actions may be, the program targets a pNOB value of 100 percent to ensure that PNI is never less than 0.5 (regardless of pHOS) when NOR run size permits (~800 NORs, Table 4)2. At NOR Coho run sizes less than 800 adults, a sliding scale is used to determine the number of NORs taken for broodstock. The sliding scale is used to ensure that some NORs always spawn naturally.

Additionally, based on the results of the spawner recruit (S/R) analysis presented below (see Section 1.8.2.1), the productivity of the natural Upper Trinity River Coho population will need to increase substantially to achieve NOR abundance targets identified for the Local Adaptation and Full Restoration phases.

1.8.1.2.1 Preservation Phase

The program is classified as being in the Preservation Phase when NOR adult Coho abundance for the Upper Trinity River population is 365 or less (Table 3). This trigger value represents the depensation threshold defined by NMFS for the Upper Trinity River population (Table 2). NMFS considers an independent population with a spawner abundance at the depensation level to have a high extinction risk

(NMFS 2014).

2 Note however that the data in Table 4 shows that a PNI of > 0.5 can be achieved at lower NOR abundance so long as the pHOS value is not greater than ~0.55.

Table 4. Expected performance metric outcomes at NOR run size forecasts of 100 to 5,801 Upper Trinity River population adult Coho. Cells highlighted in blue indicate NOR run size when NOR broodstock, pNOB, pHOS and PNI performance metrics are achieved.

NOS – Natural origin spawners, HOS – Hatchery origin natural spawners

Preservation Phase management priorities are to:

• Prevent demographic extinction

• Retain genetic diversity and identity of the population

• Maintain or increase population fitness

• Increase adult abundance

In this phase, the priority for returning NOR adults is for use as hatchery broodstock. However, the number of NORs to use as broodstock at low run-size (<365 NORs) will be made annually in consultation with fisheries managers. Hatchery Coho entering the hatchery and not needed for broodstock may be released back to the river to spawn naturally to ensure that the depensation target of 365 naturally (NOR +HOR) spawning adults is achieved. To accomplish this, it may be necessary to truck the adults downstream from the hatchery, approximately ½ mile, to the turnout near the Trinity Dam Blvd and Trinity River overpass, to prevent fish from simply re-entering the hatchery as they do now when released nearby.

1.8.1.2.2 Re-colonization Phase

The program is classified as being in the Re-colonization Phase when NOR adult Coho abundance for the Upper Trinity River population ranges between 366 and 1,460 NORs (Table 3). This range was selected as the trigger criterion because it represents an adult abundance level with a moderate risk of extinction based on the criteria of effective population size (50 < N effective < 500) and population size per generation (250 <N generation < 2,500) (NMFS 2014). The upper value of the range (1,460) is based on achieving the moderate extinction risk threshold of 4 adults per IP-km of currently accessible Coho habitat for the Upper Trinity population (4 adults/IP-km*365 IP-km = 1,460) (NMFS 2014).

Re-colonization Phase management priorities are to:

• Re-populate restored and/or depleted habitat

• Increase abundance and temporal and spatial diversity (spawning and rearing) of the population

• Retain population genetic identity and diversity

• Increase population fitness

In this phase, managers will target a minimum PNI 0.5, pHOS < 0.6, pNOB > 0.6 and adult natural escapement target of > 500 (NOR+HOR).

1.8.1.2.3 Local Adaptation Phase

The Local Adaptation Phase begins when NOR adult Coho abundance for the Upper Trinity River population abundance ranges between 1,460 and 5,800 NORs (Table 3). The lower end of the range (1,460) corresponds to the moderate extinction risk threshold of 4 adults per IP-km for the currently accessible Coho habitat below Lewiston Dam for this population (365 IP-km) (NMFS 2014). The upper end of the range (5,800) is the break point above which the Upper Trinity River population achieves the spawner abundance required for ESU viability (NMFS 2014).

Local Adaptation Phase management priorities are to:

• Meet and exceed minimum viable spawner abundance for natural origin spawners

• Increase fitness, reproductive success and life history diversity through local adaptation

The program will be operated to the extent possible to achieve a minimum natural escapement objective of 1,460 (NOR+HOR) adult Coho and a pHOS < 0.30 for the Upper Trinity River population. Broodstock will be managed to achieve a PNI of > 0.78, which exceeds the HSRG recommended standard (0.67) for populations with high biological significance (HSRG 2014)3. The Upper Trinity River Coho population is considered biologically significant because NMFS (2014) classified it as a Core population.

1.8.1.2.4 Full Restoration Phase

The Full Restoration Phase begins when NOR adult abundance for the Upper Trinity River Coho population exceeds 5,800 NORs (3-year average) (Table 3).