C05__Attachment_2_-_ESA_Section_7(a)(2)_Biological_Opinion__06-11-20.pdf

Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response

4d Limit for the Trinity River Coho Salmon Hatchery and Genetic Management Plan

NMFS Consultation Number: WCRO-2019-03414

Action Agency: NOAA’s National Marine Fisheries Service

Table 1. Affected Species and NMFS' Determinations:

ESA-Listed Species Status

Is Action Likely to Adversely

Affect Species?

Is Action Likely To

Jeopardize the Species?

Is Action Likely to Adversely

Affect Critical Habitat?

Is Action Likely To Destroy or

Adversely Modify Critical

Habitat?

Southern Oregon Northern California Coast coho salmon ESU

Threatened May 6, 1997

(62 FR

24588)

Yes No Yes No

Southern Resident Killer Whale DPS

Endangered November 18, 2005 (70

FR 69903)

No No No No

Southern DPS of Eulachon

Threatened March 18, 2010 (75 FR

13012)

No No No No

Southern DPS of Green Sturgeon

Threatened April 6, 2006 (71 FR

17757)

No No No No

Table 2. Essential Fish Habitat and NMFS' Determinations:

Fishery Management Plan That

Identifies EFH in the Project Area Does Action Have an Adverse

Effect on EFH?

Are EFH Conservation

Recommendations Provided?

Pacific Coast Salmon Yes Yes

Consultation Conducted By: National Marine Fisheries Service, West Coast Region

Issued By:

Alecia Van Atta Assistant Regional Administrator California Coastal Office

Date: June 11, 2020

1.

2.

1.1 1.2 1.3

2.1

2.2

2.3 2.4 2.5

2.6

2.7

TABLE OF CONTENTS

INTRODUCTION

Background Consultation History Proposed Federal Action

1.3.1 Program Phases

1.3.2 Broodstock Collection

1.3.3 Mating Practices

1.3.4 Incubation

1.3.5 Smolt Release

1.3.6 Monitoring and Evaluation of Performance Indicators

ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE

STATEMENT

Analytical Approach

2.1.1 Background and Modeling Methods

2.1.2 Factors that are Considered When Analyzing Hatchery Effects

Rangewide Status of the Species and Critical Habitat

2.2.1 Species Description and General Life History

2.2.2 Status of SONCC coho salmon

2.2.3 Status of SONCC coho salmon Critical Habitat

Factors Responsible for the Decline of Species and Degradation of Critical Habitats.. 39 Action Area Environmental Baseline

2.5.1 SONCC Coho Salmon Population Units in the Action Area

2.5.2 Status of SONCC coho salmon Population Units in the Action Area

2.5.3 AHA Results – Historic Hatchery Operations

2.5.4 Status of SONCC coho salmon Critical Habitat in the Action Area

2.5.5 Factors Affecting SONCC coho salmon Population Units and Critical Habitat in the Action Area

2.5.6 Iron Gate and Trinity River Hatchery Chinook Salmon and Steelhead Production . 55

2.5.7 Climate Change in the Action Area

Effects of the Action

2.6.1 AHA Results – HGMP

2.6.2 Factor 1

2.6.3 Factor 2

2.6.4 Factor 3

2.6.5 Factor 4

2.6.6 Factor 5

2.6.7 Factor 6

2.6.8 Factor 7

2.6.9 Effects of the Action on Critical Habitat

Cumulative Effects

2.7.1 Control of wildland fires on non-federal lands

2.7.2 Residential development and existing residential infrastructure

2.7.3 Cannabis Regulation

ii

3.

4.

5.

2.8 2.9 2.10

2.11 2.12 2.13

3.1 3.2 3.3 3.4 3.5

2.7.4 Recreation

Integration and Synthesis Conclusion Incidental Take Statement

2.10.1 Amount or Extent of Take

2.10.2 Effect of the Take

2.10.3 Reasonable and Prudent Measures

2.10.4 Terms and Conditions

Conservation Recommendations Reinitiation of Consultation “Not Likely to Adversely Affect” Determinations

2.13.1 Effects on Southern Resident Killer Whales DPS

2.13.2 Effects on the Southern DPS of North American Green Sturgeon

2.13.3 Effects on Southern DPS of Eulachon

MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT RESPONSE

Essential Fish Habitat Affected by the Project Adverse Effects on Essential Fish Habitat Essential Fish Habitat Conservation Recommendations Statutory Response Requirement Supplemental Consultation

DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW. 91

4.1 Utility

4.2 Integrity

4.3 Objectivity

REFERENCES

iii

LIST OF TABLES

Table 1. Affected Species and NMFS' Determinations:.................................................................. i Table 2. Essential Fish Habitat and NMFS' Determinations:.......................................................... i Table 3. High, moderate and low extinction risk adult abundance levels for Trinity River coho populations (NMFS 2014) Table 4. Adult natural origin (NOR) spawner abundance range by program phase for the Upper Trinity River coho population Table 5. Expected performance metric outcomes at NOR run size forecasts of 100 to 5,801 Upper Trinity River population adult coho Table 6. The number of NOR male and female coho salmon broodstock required to meet annual release of 300,000 coho salmon smolts at a pNOB of 100 percent and achievement of in-hatchery culture survival metrics Table 7. TRH coho salmon hatchery operations indicators, metrics, and M&E methods Table 8. An overview of the range of effects on natural population viability parameters from the two categories of hatchery programs Table 9. Diversity strata of the SONCC coho salmon ESU, including the number of population types (F: functionally independent, P: potentially independent, D: dependent, and E: ephemeral) (Williams et al. 2008) Table 10. Population unit boundaries for SONCC coho salmon populations in the action area (Williams et al. 2008) Table 11. Spawner 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) Table 12. 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 13. AHA modeling results for historic hatchery operations (pre-2015; 500,000 HOR coho salmon smolts) Table 14. Estimated harvest numbers and rates of NOR Trinity River coho salmon in ocean and freshwater fisheries. Run size estimates provided by CDFW, Trinity River project. Ocean incidental mortality rate provided by the Pacific Fisheries Management Council, and is calculated on presumed ocean abundance prior to river return Table 15. Estimated harvest numbers and rates of HOR Trinity River coho salmon in ocean and freshwater fisheries. Run size estimates provided by CDFW, Trinity River project. Ocean incidental mortality rate provided by the Pacific Fisheries Management Council. Ocean incidental mortality calculated on presumed ocean abundance prior to river return Table 16. Factors affecting coho salmon in the action area iv

Table 17. Iron Gate and Trinity River hatcheries Production Goals Table 18. Adult coho salmon AHA modeling results for HGMP hatchery operations (2015-2020;

300,000 HOR coho salmon smolts) Table 19. Unmarked coho salmon run size estimates at the Willow Creek weir from 1997 to 2018 and the numbers and percentage of unmarked adult coho salmon that would be used for broodstock at TRH given the proposed action Table 20. 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 21. The effect of the proposed action on coho salmon resulting from the removal of coho salmon from the natural population Table 22. The effect of the proposed action on coho salmon resulting from the removal of coho salmon from the natural population Table 23. PCDRISK-1 modeling results for coho salmon Table 24. The effect of the proposed action on coho salmon resulting from competition and predation at the 500,000 smolt release level Table 25. The effect of the proposed action on coho salmon resulting from competition in the migration corridor and nearshore areas at the 500,000 smolt release level Table 26. The effect of the proposed action on NOR and HOR coho salmon resulting from monitoring and evaluation in the proposed action Table 27. Standardsfor all Trinity River Hatchery effluent discharges (NCRWQCB 2015) Table 28. Run size estimates for Willow Creek Weir provided by CDFW for marked (HOR) and unmarked (NOR) coho salmon, and harvest estimates in the Yurok Tribe and Hoopa Tribe fisheries Table 29. The effect of the proposed action on NOR and HOR coho salmon resulting from dependent Tribal coho salmon fisheries Table 30. Annual expected take of coho salmon resulting from the proposed action

LIST OF FIGURES

Figure 1. 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 2. Diversity strata for populations of coho salmon in the SONCC ESU. From Williams et

al. (2008) Figure 3. Map of the proposed Action Area (Trinity River basin) and associated anadromous fish hatcheries in the region Figure 4. Coho salmon run size estimates for the Trinity River upstream of the Willow Creek Weir 1997 to 2016 (Kier et al. 2017) v

Figure 5. Panel figure showing predicted top) maximum temperature, middle) minimum temperatures, and bottom) precipitation through 2050 for the region near Lewiston, California.

Data are from cal-adapt.org vi

1.

1.1

INTRODUCTION

This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below.

Background

NOAA’s National Marine Fisheries Service (NMFS) prepared the biological opinion (opinion) and incidental take statement (ITS) portions of this document in accordance with section 7(b) of the Endangered Species Act of 1973 (ESA) (16 USC 1531 et seq.), and implementing regulations at 50 CFR 402, as amended.

We also completed an essential fish habitat (EFH) consultation on the proposed action, in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1801 et seq. ) and implementing regulations at 50 CFR 600.

We completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act (DQA) (section 515 of the Treasury and General Government Appropriations Act for Fiscal Year 2001, Public Law 106-554). The document will be available within two weeks at the NOAA Library Institutional Repository [https://repository.library.noaa.gov/welcome]. A complete record of this consultation is on file at the Arcata, California NMFS office.

The U.S. Bureau of Reclamation (Reclamation) and California Department of Fish and Wildlife (CDFW) provided NMFS with a Hatchery and Genetics Monitoring Plan (HGMP) for the Trinity River coho salmon hatchery program and associated monitoring and evaluation actions.

The HGMP provides the framework through which Reclamation and CDFW can manage hatchery operations, monitoring, and evaluation activities, while meeting requirements specified under the ESA. The Trinity River Hatchery (TRH) HGMP outlined the Southern Oregon/Northern California Coast (SONCC) coho salmon breeding and associated monitoring and evaluation actions that would occur in the Trinity River watershed. NMFS will determine if the HGMP meets the criteria of Limit 5 of the 4(d) Rule.

The Trinity River is the largest tributary to the Klamath River with a drainage area of approximately 2,900 square miles. The river flows for 172 miles beginning in the Klamath and Coast Ranges, continuing through Trinity and Humboldt Counties, and joining the Klamath River at Weitchpec, CA (43 miles upstream of the Pacific Ocean). The Trinity River supports three distinct coho salmon populations designated by location within the river basin: the Lower Trinity River population, the Upper Trinity River population, and the South Fork Trinity River population (NMFS 2014). Designated as a Wild and Scenic River by the U.S. Department of Interior in 1981, the Trinity River is also valued for its Chinook salmon, steelhead, and trout fisheries, in addition to recreational activities like rafting, kayaking, and canoeing (46 FR 7484).

Upstream anadromous migration ends at Lewiston Dam, which was completed in 1963.

Additionally, Trinity Dam was constructed about seven miles upstream to form Trinity Lake in 1962. Trinity Dam, Lewiston Dam, and Clear Creek Tunnel are components of the Trinity River Division (TRD) of Reclamation’s Central Valley Project. The Central Valley Project provides

1.2 impounded water from the Trinity River to California’s Central Valley via the Clear Creek Tunnel. The TRH is located at the base of Lewiston Dam in Trinity County. Artificial propagation on the Trinity River began in 1958, and has continued at the permanent TRH facility since 1963 to mitigate for 109 miles of habitat lost above Lewiston Dam.

Congress’s original intent was not to diminish Trinity River fisheries and estimated that about 700,000 acre feet could be diverted for agricultural purposes without any negative effect (H.R.

Rep. No. 602, 84th Cong., 1st Sess. 4-5 (1955); S. Rep. No. 1154, 84 Cong., 1st Sess. 5 (1955)).

Furthermore, Department of the Interior reports suggested that the Trinity River Division would actually improve conditions for fisheries below the proposed dams. Based on these conclusions, Congress authorized the TRD as part of the Central Valley Project. Section 2 of the 1955 Act (PL 84-386) also directed the Secretary of the Interior to ensure the propagation and preservation of fish and wildlife in the Trinity Basin. The TRD was completed in 1964 and began diverting 75 to 90 percent of Trinity River flow for several decades. By the 1970s, a precipitous decline in habitat and salmon and steelhead populations were evident. As part of efforts to address this decline, the USFWS, Hoopa Valley Tribe, and other agencies began studies that culminated in the Trinity River Flow Evaluation. Completed in June 1999, this study is the foundation of the Trinity River Restoration Program, which is designed to restore naturally-spawning populations of salmon and steelhead to near pre-dam levels. The Trinity River Basin Fish and Wildlife Restoration Act of 1984 (Public Law 98-541) expressly acknowledges the tribal interest in the basin’s fishery resources by declaring that the measure of successful restoration of the Trinity River fishery includes the “ability of dependent tribal…fisheries” to participate fully through enhanced in-river “harvest opportunities, in the benefits of restoration.” (TRRP 2017).

Consultation History

On December 11, 2017, NMFS received the final HGMP for coho salmon raised at the Trinity River Hatchery (TRH) near Lewiston, California, submitted by the Reclamation and CDFW.

Coho salmon from the TRH are considered part of the Southern Oregon Northern California ESU, which is listed as “threatened” under the ESA. Reclamation and CDFW, pursuant to the ESA, requested that NMFS approve of the coho salmon HGMP under Limit 5 of the 4(d) rule (50 C.F.R. § 223.203(b)(5). Limit 5 of the 4(d) Rule for threatened steelhead and salmon provides that the take prohibition does not apply to activities associated with artificial propagation programs that follow a HGMP that meets certain criteria and has been approved by NMFS (50 C.F.R. 223.203(b)(5)). If NMFS approves the HGMP, then any take of listed SONCC coho salmon caused by TRH operations would not be subject to the ESA’s take prohibition. The HGMP and a draft environmental assessment (EA), pursuant to the National Environmental Policy Act (NEPA), were submitted to the Federal Register for public comment on November 7, 2018. On July 15, 2019, Reclamation clarified the lower and upper boundaries of potential coho salmon production levels that may be considered after 2021. Reclamation further clarified on March 24, 2020, that the upper limit of coho salmon production would remain at 300,000 (plus or minus 10%), until certain conditions outlined in the HGMP are met, at which time production may be adjusted up to 500,000 or down to 150,000. Southern Oregon/Northern California Coast Evolutionarily Significant Unit (SONCC ESU) of coho salmon is listed as threatened under the ESA. Critical habitat includes streambeds and riparian areas throughout the ESU’s entire range.

1.3 Proposed Federal Action

“Action” means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402.02). The proposed action is the NMFS’ decision to approve the implementation of the Trinity River Hatchery (TRH) coho salmon program, as described in the HGMP submitted by Reclamation and CDFW, pursuant to Limit 5 of the 4(d) rule. In this section we describe: the proposed hatchery operations that are part of the “proposed action” using information provided in the HGMP. For EFH, a federal action means any action authorized, funded, or undertaken, or proposed to be authorized, funded, or undertaken by a Federal Agency (50 CFR 600.910).

NMFS describes a hatchery program as a group of fish that have a separate purpose and that may have independent spawning, rearing, marking and release strategies (NMFS 2008). The operation and management of every hatchery program is unique in time, and specific to an identifiable stock and its native habitat (Flagg et al. 2004). In this case, the Proposed Action is NMFS’ proposed approval of Reclamation and CDFW’s Trinity River coho salmon HGMP (Reclamation and CDFW 2017) that proposes to collect and spawn adult coho salmon and release coho salmon smolts (yearlings) into the Trinity River near Lewiston, California. This opinion analyses the effects from the implementation of the Proposed Action on ESA-listed species and their critical habitats.

This opinion does not predetermine the outcome of the 4(d) decision and only provides NMFS’ opinion on the anticipated effects of the proposed action and whether it is likely to jeopardize listed species and/or adversely modify critical habitat. In the event that the ultimate 4(d) decision differs from the proposed action analyzed here, NMFS may reinitiate consultation. Reclamation provides funding for Trinity River Hatchery and CDFW operates the facility and neither this opinion nor approval of the HGMP would authorize those programs. The 4(d) rule exempts the take of salmon and steelhead listed as threatened species under the Endangered Species Act (ESA) if the entity follows a Hatchery and Genetics Management Plan (HGMP) that meets the 4(d) rule criteria and is approved by NMFS (July 10, 2000; 65 FR 42422, amended June 28, 2005, 70 FR 37160)—that approval step is informed by but separate from the analysis and conclusion of this biological opinion.

The coho salmon program would be operated as an integrated program as defined by the Hatchery Scientific Review Group (HSRG 2014). 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. 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. Additionally, spawning of TRH coho salmon will be limited to no more than five percent downstream of the Upper Trinity River such that coho salmon populations in the Lower Trinity River and South Fork Trinity River will effectively be segregated from the TRH coho salmon. In the Upper Trinity River, the goal for TRH coho salmon spawning in the natural environment is less than 30% of the total adult spawners. Managers will operate the program consistent with the concepts of hatchery reform as expressed by the CA HSRG (2012) and

HSRG (2014, 2015).

A consequence is caused by the proposed action if it would not occur but for the proposed action and it is reasonably certain to occur. We considered whether or not the proposed action would cause any other activities that would have consequences on SONCC coho salmon or its critical habitat and determined that it would cause the following activity:

• may contribute to a prolonged tribal fisheries in the Klamath and Trinity rivers.

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 salmon in the Trinity River and specifically in the Upper Trinity River coho salmon population. The TRH Coho program will continue as long as the Trinity River Division of the Central Valley Project operates.

1.3.1 Program Phases

Implementation of the TRH coho salmon 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 natural origin (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 salmon recovery plan (NMFS 2014) (Table 3). The ranges of adult abundance values corresponding to each program phase are shown in Table 4.

Table 3. High, moderate and low extinction risk adult abundance levels for Trinity River coho populations (NMFS 2014).

Extinction Risk

Population Population Type

High (Depensation Threshold) Moderate

Low (Required for

ESU Viability) Upper Trinity River Core 365 1,460 5,800

Table 4. Adult natural origin (NOR) 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+

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

1. Proportion of hatchery origin spawners (pHOS) < 30 percent (3-year running average).

2. Proportion of natural origin broodstock (pNOB) = 100%.

3. Take no more than 400 NOR coho for broodstock in any year.

4. Minimum annual proportionate natural influence (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 Canyon Creek Weir (e.g., North Fork Trinity River). The blue highlighted cells in Table 5 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 salmon 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 5).1 At NOR coho run sizes less than 800 adults, a sliding scale is used to determine the number of NORs taken for broodstock (Table 5). The sliding scale is used to ensure that some NORs are available to spawn naturally.

1.3.1.1 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 4). This trigger value represents the depensation threshold defined by NMFS for the Upper Trinity River population (Table 3).

NMFS considers an independent population with a spawner abundance at the depensation level to have a high extinction risk (NMFS 2014).

1 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.

Preservation Phase management priorities are:

• 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, Reclamation and CDFW may truck adults downstream from the hatchery, approximately 0.5 mile, to the turnout near the Trinity Dam Blvd and Trinity River overpass, to minimize fish from simply re-entering the hatchery as they do now when released nearby.

1.3.1.2 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 4). 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, Reclamation and CDFW will target a minimum PNI of 0.5, pHOS < 0.6, pNOB >

0.6 and adult natural escapement target of > 500 (NOR+HOR).

Table 5. Expected performance metric outcomes at NOR run size forecasts of 100 to 5,801 Upper Trinity River population adult coho.

Phase NOR Run Size

Forecast # NOR Taken

For Broodstock

% of NOR Run Taken For

Broodstock pNOB

HOR

Broodstock NOS Target

HOS

Total Escapement pHOS PNI

Preservation

100 50 50% 13% 350 50 365 415 0.88 0.12 200 100 50% 25% 300 100 365 465 0.78 0.24 300 150 50% 38% 250 150 350 500 0.70 0.35 365 183 50% 46% 217 182 318 500 0.64 0.42

Re-Colonization

366 183 50% 46% 217 183 317 500 0.63 0.42 500 250 50% 63% 150 250 280 530 0.53 0.54 600 300 50% 75% 100 300 240 540 0.44 0.63 700 350 50% 88% 50 350 290 640 0.45 0.66 800 400 50% 100% 0 400 290 690 0.42 0.70 900 400 44% 100% 0 500 290 790 0.37 0.73

1,000 400 40% 100% 0 600 290 890 0.33 0.75 1,100 400 36% 100% 0 700 300 1,000 0.30 0.77 1,200 400 33% 100% 0 800 310 1,110 0.28 0.78 1,460 400 27% 100% 0 1,060 400 1,460 0.27 0.78

Local Adaptation

1,461 400 27% 100% 0 1,061 400 1,461 0.27 0.79 1,500 400 27% 100% 0 1,100 400 1,500 0.27 0.79 1,600 400 25% 100% 0 1,200 400 1,600 0.25 0.80 1,700 400 24% 100% 0 1,300 400 1,700 0.24 0.81 1,800 400 22% 100% 0 1,400 400 1,800 0.22 0.82 1,900 400 21% 100% 0 1,500 400 1,900 0.21 0.83 2,000 400 20% 100% 0 1,600 400 2,000 0.20 0.83 5,800 400 7% 100% 0 5,400 1400 6,800 0.21 0.83

Full Restoration 5,801 400 7% 100% 0 5,401 400 5,801 0.07 0.94

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

1.3.1.3 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 4). 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 > 0.80, which exceeds the HSRG recommended standard (0.67) for populations with high biological significance (HSRG 2014).2

The Upper Trinity River Coho population is considered biologically significant because NMFS (2014) classified it as a Core population.

1.3.1.4 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 4). This value exceeds the low extinction risk viability criteria for effective population size, population size per generation, and population size per year as described in the SONCC recovery plan (NMFS 2014).

Full Restoration Phase management priorities (HSRG 2014) are:

• maintain a viable population, based on all viable salmonid population criteria attributes using long-term adaptive management.

1.3.2 Broodstock Collection

Adult NOR and HOR females, males and jacks will be collected for broodstock. The goal of the broodstock collection protocol is to meet egg take goals and at the same time maintain genetic diversity and genetic continuity with the naturally spawning coho salmon population in the Trinity River. The intent is also to establish conditions under which the natural environment drives the adaptation of both the natural and hatchery components of the Upper Trinity River coho salmon population unit.

2 The 0.67 value is measured as effective PNI. For ease of measurement, the program will use census PNI.

Broodstock will be collected at the TRH fish ladder and at a weir located upstream of Canyon Creek. Coho salmon adult run timing, abundance and composition will be collected at the Canyon Creek weir from August 27 to January 15 each year, dependent on river discharge. The weir will be operated nightly, up to 7 days per week, and open during the day. The amount of time the weir is operated depends on the effort required to remove HOR adults and jacks from the system and collect NOR adults for broodstock. Additionally, if a buildup of salmonids occurs downstream of the weir, which will be monitored visually and with snorkel observations, the weir will be opened to allow passage of delayed salmonids. The handling of non-target species will be minimized by operating the weirs during peak coho salmon migration timing. In addition, handling will be conducted by experienced and trained personnel. If large numbers of non-target species congregate at the weir, fish will be allowed to ascend upstream of the weir unhandled and unharmed and the weir location and/or timing may be changed to reduce interactions with non-target species.

The weir is a traditional Alaskan style picket fence weir. Both NOR and HOR adults and jacks will be collected without conscious selection for specific traits and proportionate to arrival time (i.e., run-timing) and abundance at the collection locations. Preference will be given to collecting broodstock at the weir located upstream of Canyon Creek as this facility is located nearest the downstream extent of the Upper Trinity River population geographic boundary. Fish encountered at this weir are more likely to include the full range of population genetic diversity.

The number and origin (NOR or HOR) of the broodstock collected each year will vary based on run size of each component (Table 4) and in-hatchery culture survival rates. Because weirs have not previously been used to collect broodstock, it will take hatchery staff a few years to refine collection methods. This may lead to more NOR adults collected than are needed for broodstock.

Hatchery staff will release surplus NOR adults back to the river. Surplus HOR adults will be: (1) sent to Tribes and food banks, (2) released alive/dead back to the river if directed by fisheries managers, or (3) disposed of in an upland landfill if in extremely poor condition.

1.3.2.1 Identity of Fish Collected for Broodstock

Unmarked and TRH-marked coho captured at weirs and returning to the TRH will be candidates for use as broodstock. Left maxillary (LM) marked fish captured at these locations will not be used for broodstock as they are strays from Iron Gate Hatchery. Disposition of Iron Gate Hatchery coho collected at the Trinity River Hatchery will be made through consultations with

NMFS.

1.3.2.2 Proposed Number to be Collected for Broodstock

All adult collections occur at the fish ladder and gathering tank (trap) located directly below Lewiston Dam. Capture efficiency is 100 percent of fish that exit the ladder into the gathering tank. Because 100 percent of TRH-origin fish receive a right maxillary clip, identification between hatchery and natural- origin fish at the trap is highly accurate.

The TRH coho salmon program will collect enough NOR adults (400) to achieve a pNOB of 100 percent when run size allows (Table 6). An additional 200 coho HOR adults will also be collected and used for broodstock until such time as in-hatchery culture survival metrics are achieved. The number of NOR adults required for program broodstock is calculated using the following formula: Broodstock = Release No./Pre-spawn/Egg:Smolt/Fecundity*2.

Where:

Broodstock = Number of female and males to be collected Release No = Number of smolts released Pre-spawn = Pre-spawn survival rate Egg:Smolt = Green egg to smolt survival rate Fecundity = Number of eggs per female Bacterial Kidney Disease (BKD) Culling rate = ~15 percent

Assumptions regarding survival and other factors can be found in Reclamation and CDFW (2017). Based on this formula, the program will need to collect 400 NOR adults for broodstock to meet the target release size of 300,000 at a pNOB of 100 percent.

Table 6. The number of NOR male and female coho salmon broodstock required to meet annual release of 300,000 coho salmon smolts at a pNOB of 100 percent and achievement of in-hatchery culture survival metrics.

Release Number Males (includes Jacks) Females Total 300,000 200 200 400

The pre-spawn and green egg to smolt survival rate metrics used in the broodstock calculation above is substantially higher than what the program has historically achieved. Because it will take time to implement and test proposed improvements, and the effectiveness of these improvements may still not achieve the survival metrics, the program will collect an additional 200 HOR for use as broodstock to ensure a release of 300,000 coho salmon smolts. Thus, the total number of coho salmon collected for broodstock each year will be a maximum of 600 at the 300,000 coho salmon release level. This value is approximately 50 percent of the historical number of coho salmon spawned at TRH.

1.3.2.3 Disposition of Surplus Broodstock

Surplus HOR adults will be: (1) sent to Tribes and food banks, (2) released alive back to the river if directed by fisheries managers, or (3) disposed in an upland landfill if in extremely poor condition.

1.3.2.4 Fish Transportation and Holding

Adult coho salmon collected at the weir located above Canyon Creek will be loaded into tanker trucks and transported to Trinity River Hatchery. A transportation procedures plan and Hazardous Analysis and Critical Control Point (HACCP) Plan will be in place and followed when fish are collected at the weir, transported and off-loaded at Trinity River Hatchery. Each tanker truck will be insulated and equipped with oxygenation and a water recirculation system, and will have a salmon discharge gate. Unripe spawners of both natural and hatchery origin will be held in round tanks, in tubes, adjacent to the spawning building and reassessed every 5 to 7 days for sexual maturity. Only NOR fish that are in excess to those needed to meet hatchery program objectives will be released back to the river.

To improve pre-spawn survival rate, hatchery staff will test holding adults individually in tubes.

Initial trials will commence by holding HOR adult coho salmon in tubes and upon documented success NOB coho salmon will be used. Different flow, water temperature and oxygen regimes may be tested over time as a means to increase survival.

1.3.2.5 Fish Health Maintenance and Sanitation

TRH workers use a commercial Iodophor solution to disinfect materials and equipment throughout the hatchery, especially invasive equipment such as spawning needles and knives.

Hatchery workers sanitize equipment between and among all incubation and rearing units, especially during disease outbreaks or parasitic infestations. Hatchery workers will take additional precautions, as necessary, to avoid the spread of disease by using equipment in given incubation stack or rearing pond that is specific to that unit.

1.3.2.6 Risk Aversion Measures to Minimize Adverse Genetic or Ecological Effects from Broodstock Operations

• Trinity River Hatchery coho salmon will be maxillary clipped until further direction from NMFS is given. At that time 100 percent externally and internally marked (ad-clipped/coded wire tagged) may be instituted to aid with evaluations including high seas distribution. These marks will enable managers to determine the number and ratio of hatchery and natural fish spawning within and outside of the Trinity River Basin.

Managers will use this information to alter hatchery practices to reduce genetic and fitness impacts that hatchery fish spawning naturally pose to natural origin coho populations.

• Broodstock collection facilities will be used to remove excess hatchery origin fish from the system. The objective of these collection efforts would be to achieve program performance indicators for pHOS (<30 percent) and PNI (minimum of 0.5 and average target of > 0.67). Operating the program to achieve a minimum PNI of 0.5 and the average target PNI > 0.67 ensures that the natural environment, rather than the hatchery environment, drives local adaptation of the combined natural and hatchery components of the integrated population.

• Monitoring programs tracking adult coho salmon escapement to other coho salmon populations will be looking for and enumerating marked coho salmon from TRH. This information will be used to determine if the program achieves the < 5 percent pHOS criterion for coho salmon populations not integrated with the hatchery program. If the criterion is exceeded, managers will take action to reduce pHOS levels in these streams.

• If broodstock were not collected from the North Fork Trinity River or Canyon Creek, the < 5 percent pHOS value would apply to these streams. Spawning surveys will be conducted in the streams to determine compliance with criterion.

• The TRH broodstock policy described above and the mating protocol are intended to help reduce demographic extinction risks while preserving genetic diversity of the composite NOR and HOR population. The genetically based spawning matrix is designed to minimize inbreeding effects associated with hatchery production.

• Specific measures to reduce risk include managing composition of hatchery and natural fish in both the hatchery and natural spawning populations to allow the natural environment to drive adaptation of the integrated population. The use of jacks will achieve gene flow among brood years.

• Only local broodstock will be spawned, either hatchery fish originating from TRH or unmarked fish captured at weirs or returning to the Trinity River Hatchery.

• The NOR broodstock incorporation target is 100 percent (pNOB of 100 percent).3

• Broodstock will be collected throughout the run with no bias toward physical characteristics (e.g., size) other than those indicating readiness to spawn.

• Jacks to be incorporated into broodstock should not exceed the lesser of: 1) 50 percent of the total number of jacks encountered at the hatchery, and 2) 10 percent of the total males used for spawning.

1.3.3 Mating Practices

1.3.3.1 Selection Method

Initially, males and females will be selected for mating based on readiness to spawn. Genetic tissue samples will be taken from all broodstock used in the program. Genetic analysis (Parental Based Tagging) of genotypes will be used to confirm broodstock origin (HOR and NOR) and number of sibling crosses (inbreeding) over time. These data will allow managers to confirm pNOB levels and document the rate of mismarked hatchery fish. If the results identify high rates of sibling crosses, a genetically based spawning matrix will be implemented (see Section 8.1.1 of the HGMP).

1.3.3.2 Genetic spawning matrix

Spawner selection will be based on the results of genetic analysis of relatedness among broodstock candidates using tissue samples collected from all potential coho salmon broodstock.

The results of this analysis will be used to develop a mating matrix designed by geneticists to minimize inbreeding and to allow for gene flow between brood years. The breeding protocol will specify which male and female crosses will result in the lowest level of inbreeding in their

3 Until the NOR component and the ability to catch them improves with installation of the weir, the program will likely be unable to achieve a pNOB of 100%. Until that time, a substantial portion of broodstock will be HOR.

Priority will be given to incorporating as many NOR fish as possible each year.

offspring. The threshold will be to avoid spawning fish related at the half-sibling level or greater.

The breeding matrix will allow for spawning crosses to occur regardless of fish origin (HOR or NOR) or age.

If the adult pre-spawn survival does not achieve the 90 percent metric, implementation of the genetic spawning matrix may be delayed until it is met. If this occurs, fish will be mated randomly based on readiness to spawn and origin (HOR or NOR). Mating crosses by origin will be performed as described in Section 8.3 of the HGMP.

1.3.3.3 Fertilization

Fish mating will use a true 1M:1F spawning protocol.4 The broodstock sex ratio will initially be 1M:1F (i.e., same number of male and female broodstock). If there is evidence of a low fertilization rate problem, CDFW and NMFS geneticists and pathologists will be consulted to resolve the issue. If conditions are not met for the use of a genetically informed spawning matrix, mating by origin will be prioritized as follows:

NOR x NOR NOR x HOR HOR x HOR

Adult coho salmon entering the spawning house will be anesthetized by applying carbon dioxide to the holding tank for 3 minutes. Eggs will be fertilized using wet spawning by stripping milt of a single male into an egg pan with salt solution (one ounce of salt per gallon of water) prior to adding the eggs of a single female. Eggs will be treated with 100 ppm iodine solution for a minimum of 15 minutes, allowed to water harden, and then transferred to incubation facilities.

Male reuse will be strongly restricted. Details of spawning/mating protocols will be documented in annual reports. Deviations from this protocol to solve specific problems will be made only on recommendations from CDFW and NMFS geneticists in coordination with the Hatchery Coordination Team (HCT) and CDFW pathologist. No cryopreserved gametes will be held.

1.3.4 Incubation

Egg take from NOR and HOR coho will be set at a maximum of 750,000, with no more than 500,000 taken from NOR adults. This level of egg take is expected to provide ample “cushion” in the event of unforeseen losses at the hatchery due to BKD, poor fertility, etc. to ensure the smolt production goal can still be met.

1.3.5 Smolt Release

1.3.5.1 Proposed Release Levels

The program will release up to 300,000 coho salmon smolts each year. At the end of 2020, the managers will review program performance and status of natural coho salmon production to determine if fish release numbers and or release location should be altered. Changes to the coho salmon smolt release range from 150,000 to 500,000, depending on whether performance metrics are met. The recommended coho salmon production level, and rationale, will be forwarded to

4 A true 1:1 spawning protocol means that the milt of one, and only one, male is placed in a container with the eggs of one, and only one, female. This is not the same as pooling gametes or sequential milt addition.

NMFS for review and approval. No offsite releases or transportation of smolts is proposed. Coho salmon will be released at 10 to 12 fish per pound (fpp).

1.3.5.2 Release Date

Aside from the coho salmon smolts used for the timing of release study, smolts will be volitionally released within 7 days of the March new moon (March 1-15). Fish that do no leave the raceways within 7 days will be removed and destroyed. This action is designed to reduce residualization rate and competition with naturally produced coho salmon. Release timing may be altered dependent on the results of the timing of release study.

Under the proposed HGMP, a fish timing of release study will be undertaken for at least three brood years for a subset of the smolts released. Fish will be released in March, April and May.

Study protocols will be developed by the HCT. At the end of the time at release study, the three groups will be evaluated by the HCT based on:

• Travel-time from release site to the Willow Creek Screw Trap (quicker is better),

• Smolt-to-adult survival rate (higher is better),

• Mini-jack and jack rates (lower is better),

• Theoretical predation and competition impacts to naturally produced coho salmon (lower is better),

• Adult stray rate to other coho populations (Lower Trinity and South Fork) (lower is better),

• Cost of rearing fish (lower is better).

Study results and proposed program changes, as identified by the HCT and managers, will be forwarded to NMFS for review, possible modification and approval

1.3.5.3 Acclimation Procedures

Fish are currently acclimated on-station in the rearing facilities as the water source is the Trinity River via Lewiston Reservoir. This practice will continue under this HGMP. If the managers decide to pursue acclimation, they will make a recommendation to NMFS and permitting of this facility will be undertaken through a separate approval process, such as the ESA 10(a)1(A) process.

1.3.5.4 Marking Procedures

Historically, all hatchery coho salmon smolts have been marked with a right maxillary clip.

Trinity River Hatchery coho salmon will be maxillary clipped until further direction from NMFS is given. At that time 100 percent externally and internally marked (ad-clipped/coded wire tagged) may be instituted to aid with evaluations including high seas distribution.

1.3.5.5 Disposition of Surplus Smolts

Production levels are not expected to exceed 10 percent of target in any release year. NMFS will be notified if the production level is exceeded by more than 10 percent. NMFS’ recommendations for disposition of surplus smolts will be followed.

1.3.5.6 Fish Health Certification Procedures

CDFW pathologists conduct annual pre-release fish health analyses. Fish will not be released until certified disease-free by the CDFW pathologist. The pathologist’s report will be included in the annual report for the program.

1.3.5.7 Emergency Release Procedures

Flooding and water system failure are minimum risks to the facility because of the protection afforded by the Trinity and Lewiston dam systems. Wildfire risk can also occur though rare. If, based on an assessment of the best available data, the facility manager determines that the facility is in imminent danger of flooding, fire, or water system failure, fish may be forced from the hatchery to the mainstem Trinity River based on the judgement of the facility manager.

1.3.6 Monitoring and Evaluation of Performance Indicators

1.3.6.1 Plans and methods to collect data to respond to each “Performance Indicator”

A number of plans and policies within the hatchery program are already in place to minimize and avoid risks to ESA-listed species and other anadromous fish species. Most of the monitoring and evaluation activities of the TRH Coho salmon program are incorporated into, or facilitated by, routine operations within the hatchery and TRRP activities. In addition, an HCT was established to guide program operations and review program performance.

CDFW will collect and record data concerning all aspects of the fish propagation program, including water quality, hatchery returns, spawners, egg take, rearing number and survival, and number released. These efforts will continue under this HGMP. A summary of the in-hatchery monitoring and evaluation (M&E) activities is included in Table 7. The primary focus of the M&E program will be quantification of program performance indicators of pHOS, PNI, adult natural escapement and pNOB.