Attachment_14-Biological_Assessment_of_Artificial_Propagation.pdf

Colema progr

Bio n Nationa ram descr ological A al Fish Hat ription and

U.

Red

U.

Coleman

Assessment tchery and d incident

Pre

.S. Fish an Bluff Fish

Red Blu

.S. Fish an n National

Anders

Ju t of Artific d Livingst al take of epared by nd Wildlife h and Wild uff, CA 96

And nd Wildlife l Fish Hatc son, CA 96 uly 2011 cial Propa ton Stone N Chinook s y fe Service dlife Offic fe Service chery Com agation at National F salmon an ce mplex

Fish Hatch nd steelhea hery:

ad

Biological Assessment of Artificial Propagation at Coleman National Fish Hatchery and Livingston Stone National Fish Hatchery:

program description and incidental take of Chinook salmon and steelhead trout

Document Overview

Purpose of the Document: This Biological Assessment (BA) is submitted to fulfill the U.S. fish and Wildlife Services (Service) obligations for consultation under section 7(2)(a) of the federal Endangered Species Act of 1973 (ESA) with the National Marine Fisheries Service (NMFS).

This document is intended to provide a single, comprehensive source of information to describe and assess incidental impacts of current or proposed operations of the Coleman and Livingston Stone National Fish Hatcheries (NFH) on ESA-listed Central Valley populations of anadromous salmonids, the southern distinct population segment of North American Green Sturgeon and Southern Resident Killer Whales. The ESA Section 7(2)(a) consultation process is specifically designed to determine if proposed activities are or are not likely to jeopardize the continued existence of listed species or result in the destruction or result in adverse modification of their critical habitats. The assessment presented in this BA focuses on potential impacts of hatchery facilities and operations within the Battle Creek watershed, where the hatchery is located. The Service recognizes the importance of integrating hatchery operations with natural salmonid production in Battle Creek, especially in light of pending restoration activities within the watershed.

Within this assessment, the Service acknowledges that incidental take1 of ESA-listed species of anadromous salmonids may occur during the course of conducting fish propagation programs at the Coleman and Livingston Stone NFH. In some cases, estimates of incidental take are directly quantified. Quantified estimates of take are produced largely for activities occurring at the hatchery facilities, and are based largely on observations from recent years. In other situations estimates of take can be reasonably assessed only on a qualitative basis. For example, take resulting from interactions of hatchery and natural fishes in the wild occur over a wide range of space and time, and, therefore, cannot be directly observed or measured. Based on our assessment, the Service believes that operations of Coleman and Livingston Stone NFHs are not likely to jeopardize the continued existence of listed (or candidate) species or adverse modification to critical habitat.

Format of Biological Assessment: The format of this BA follows the highly-detailed format of the Hatchery and Genetic Management Plan (HGMP) developed by NMFS. The HGMP template is intended to provide a single source of hatchery information for comprehensive planning purposes, and to satisfy permitting requirements under the ESA. The document is divided into 14 Sections. A brief description of each section is presented below.

Section 1: General Program Description Section 1 provides a broad overview of Coleman and Livingston Stone NFH programs and operations including: 1) facility locations, 2) types and sizes of artificial propagation programs

1 “Take” means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct.

conducted at each facility, 3) purpose and justification for the propagation programs, 4) performance standards and indicators developed to assess program benefits and risks, and 5) some measures of current program performance including estimated smolt-to-adult survival rates, fishery (i.e., harvest) contribution rates, and hatchery return rates.

Section 1 is not intended to stand alone; rather, it provides an introduction and overview of several aspects of the hatchery propagation programs that are more thoroughly discussed in other sections of the document. Likewise, the bulleted statements accompanying descriptions of Performance Standards and Performance Indicators (Sections 1.9 and 1.10) are also not meant to stand alone. In the format they are presented they do not defend a hatchery benefit, nor do they refute or concur with a potential risk of hatchery activities. As with the majority of the information presented in Section 1, they are intended to provide the basis for discussions which follow in subsequent sections of the document. It is recommended that the reader review the table of contents, including the list of appendices (Section 13), for other sections that provide detailed descriptions of specific topic areas.

Section 2: Program Effects on Salmonid Populations Section 2 provides description, status, and listing history of Central Valley anadromous salmonid populations potentially impacted (directly or indirectly) by activities associated with the artificial production programs conducted at Coleman and Livingston Stone NFHs. This section also briefly describes the original legislation authorizing the Central Valley Project (CVP) and the mitigation or “Salvage Plan” for the CVP which included the construction of the Coleman NFH.

The history of ESA permits held by the Service to conduct artificial propagation activities at Coleman and Livingston Stone NFHs is also discussed in this section. Lastly, Section 2 provides a summary of potential impacts on ESA-listed populations of salmonids resulting from hatchery facilities and proposed activities. Whenever possible, quantified estimates of take have been generated, however, for many activities only a qualitative assessment of impact was possible (Section 2.11). Because Section 2.11 is intended to only summarize estimates of take, subsequent sections of this document and appendices should be referenced for the actual derivation of take estimates or the information supporting the qualitative impact assessments.

Section 3: Relationship to Other Management Objectives In Section 3 we describe the relationship between artificial propagation programs at Coleman and Livingston Stone NFHs and other fishery and habitat management objectives and conservation programs in the Central Valley of California. Current and proposed hatchery operations are discussed in relation to major conservation programs designed to restore and recover anadromous salmonids and their habitats in the Central Valley. In this section we also describe the Coleman NFH Re-evaluation Process with its objectives to assess and refine hatchery facilities and operations, and the relationship between Coleman NFH and the Battle Creek Restoration process. We discuss the roles of the U.S. Bureau of Reclamation (primary funding source) and the U.S. Fish and Wildlife Service (operational responsibilities) relative to responsibilities to mitigate for habitat losses due to the Construction of Shasta Dam. Lastly, in Section 3 we describe harvest objectives for Coleman NFH, and identify contribution rates of the Chinook salmon propagation programs to the ocean (commercial and sport) and the in-river sport fisheries. Furthermore, because harvest of fish from Coleman NFH and adult escapement to Battle Creek are closely linked, a discussion is presented on historical and recent adult escapement as a result of hatchery operations, and the potential impact of escapement or over-escapement of hatchery-origin adults back to the Battle Creek watershed.

Section 4: Hatchery Water Source Section 4 provides a description of current hatchery water rights and water usage patterns, and hatchery intake structures and water delivery systems for Coleman and Livingston Stone NFHs.

Estimates of entrainment of ESA-listed are presented. Also discussed in Section 4 are: 1) potential impacts of water discharges from the hatchery facilities; 2) potential impacts to instream flow associated with hatchery water diversions, including emergency hatchery water-supply situations; and, 3) the potential for instream flow impacts during times of extremely low water or drought years.

Section 5: Facilities Section 5 provides a description of physical facilities at Coleman and Livingston Stone NFHs, including schematics of the property and a description of all physical structures at each facility.

An assessment of the potential impacts of facility maintenance and on-site construction on critical habitat is provided in this section.

Section 6: Broodstock Origin and Identity Section 6 presents information regarding the source of broodstock used at Coleman and Livingston Stone NFHs, the history of their use, and the numbers of broodstock proposed to be used annually. Phenotypic and genetic differences between hatchery broodstock and natural adults are discussed. Also discussed in Section 6 are past and proposed future levels of incorporating naturally-produced adults as hatchery broodstock. Lastly, a discussion is presented of risk aversion measures that are being used to minimize the likelihood of negative impacts on naturally produced salmonids.

Section 7: Broodstock Collection In Section 7 we discuss aspects of broodstock congregation and collection, including descriptions of collection locations, collection timing, and, stocks and numbers targeted. Also discussed are methods to identify runs (phenotypic and genetic criteria) and methods to differentiate hatchery and natural stocks (i.e., mark identification). Because of the importance of the Coleman barrier weir in regards to collecting hatchery broodstock and managing and monitoring passage of salmonids into upper Battle Creek, a large portion of Section 7 is dedicated to the hatchery barrier weir.

Section 8: Mating In Section 8 we discuss broodstock selection methodologies, spawn timing and spawning schedules, and mating protocols.

Section 9: Incubation and Rearing Section 9 provides information on current and anticipated incubation and rearing practices at Coleman and Livingston NFHs. Specific data provided include: 1) survival rates over various life stages for all species propagated, 2) initial and final density indices and fork lengths at time of release; and, 3) feed types and expected conversion rates.

Section 10: Juvenile Releases Section 10 provides a description of juvenile release practices, including marking and tagging rates, release location and timing, and size at release for all species propagated at Coleman and Livingston Stone NFHs. The section also provides comprehensive assessment of impacts resulting from hatchery releases (i.e., predation, competition, displacement, disease transmission) to all stocks of naturally-produced anadromous salmonids.

Section 11: Monitoring and evaluation We provide in Section 11 a general description of the Hatchery Evaluation Program coordinated out of the Red Bluff Fish and Wildlife Office. Also presented is a discussion of monitoring activities associated with evaluating hatchery performance, and assessing impacts to natural salmonid populations. Data collected during monitoring efforts are used to adaptively manage hatchery programs in order to maximize hatchery benefits and minimize hatchery risks.

Section 12: Research Section 12 provides information on current research activities conducted in direct association with the hatchery propagation programs.

Section 13: Citations, Appendices, and Attachments Section 13 provides the list of literature referenced in this document. Also contained in Section 13 are several appendices that include information and analyses that are critical to understanding the impact assessments found within this document, including:

• Derivation of estimates of take at hatchery water Intake 2

• Summary of hatchery spawning

• Genetics and Hatchery Programs

• Collection locations and spawn timing

• Compilation of previous Releases from CNFH

Section 14: Certification language and signatures Section 14 contains signatures of appropriate officials to certify the primary purpose of the Biological Assessment is to obtain limits from take prohibitions under the Endangered Species Act of 1973.

i

Table of Contents

1 GENERAL PROGRAM DESCRIPTION

1.1 Name of hatchery

1.2 Species and populations under propagation, and ESA/CESA status of associated salmonids

1.3 Responsible organization and individuals

1.4 Funding source, staffing level, and annual hatchery program operational costs

1.5 Locations of hatcheries and associated facilities

1.6 Type of programs

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

Delta Smelt

1.7 Purpose of programs

Fall and Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

Delta Smelt

1.8 Justification for the program

Coleman National Fish Hatchery

Livingston Stone National Fish Hatchery

History of the Winter Chinook Propagation Program

1.9 List of program performance standards

Performance Standards to Evaluate Benefits

Performance Standards to Evaluate Risks

1.10 List of program performance indicators, designated by benefits and risks

Performance Indicators Addressing Benefits

Performance Indicators Addressing Risks

1.11 Expected size of programs

Proposed Annual Number of Broodstock Spawned

1.12 Proposed annual fish release levels by life stage and location ii

1.13 Current program performance including estimated smolt-to-adult survival rates, adult production levels, and escapement levels

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

1.14 Date programs started

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

1.15 Expected duration of program

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

1.16 Watersheds targeted by program

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

1.17 Alternative actions considered for attaining program goals, and reasons why those actions are not being proposed

2 PROGRAM EFFECTS ON LISTED POPULATIONS

2.1 History of listing determinations

Sacramento River Winter Chinook Salmon

Central Valley Spring Chinook Salmon

Central Valley Fall and Late-fall Chinook Salmon

Central Valley Steelhead

Southern Distinct Population Segment of North American Green Sturgeon

Southern Resident Killer Whales

2.2 List all ESA permits or authorizations in hand for the hatchery program

Coleman and Livingston Stone National Fish Hatcheries iii

2.3 ESA Permits

Section 7 Permitting History:

Section 10 Permitting History:

2.4 Description of ESA-listed anadromous and marine fish populations affected by the program

Sacramento River Winter Chinook Salmon

Central Valley Spring Chinook Salmon

Central Valley Steelhead

Southern DPS of North American Green Sturgeon

Southern Resident Killer Whales

2.5 Description of non-listed salmonid populations affected by the program

Central Valley Fall Chinook Salmon

Central Valley Late-fall Chinook Salmon

2.6 ESA-listed and non-listed populations that will be directly affected by the program

Sacramento River Winter Chinook Salmon (Endangered)

Central Valley Steelhead (Threatened)

Central Valley Fall and Late-Fall Chinook Salmon (Candidate Species)

2.7 ESA-listed populations that may be incidentally affected by the program

2.8 Status of ESA-listed populations affected by the program

Sacramento River Winter Chinook Salmon

Central Valley Spring Chinook Salmon

Central Valley Steelhead

Southern DPS of North American Green Sturgeon

Southern Resident Killer Whales

2.9 Status of unlisted salmonid populations affected by the program

Central Valley Fall Chinook Salmon

Central Valley Late-fall Chinook Salmon

2.10 Status of salmonid populations in Battle Creek

Central Valley Fall Chinook Salmon

Central Valley Late-fall Chinook Salmon

Sacramento River Winter Chinook Salmon

Central Valley Spring Chinook Salmon iv

Central Valley Steelhead

2.11 Description of hatchery activities that may lead to the take of listed populations, the likelihood of occurrence, and an assessment of the effects of the take

Risk Assessment Framework

Impact Assessment: Effects on Salmonid Populations

Impact Assessment: Effects on Southern DPS North American Green Sturgeon

Impact Assessment: Effects on Southern Resident Killer Whale

3 RELATIONSHIP OF PROGRAM TO OTHER MANAGEMENT OBJECTIVES

3.1 Existing cooperative agreements, memoranda of understanding, memoranda of agreement, or other management plans or court orders under which the program operates

3.2 History of the current Interagency Agreement

3.3 Integration of artificial propagation programs at Coleman NFH with conservation initiatives developed to conserve and restore anadromous fish resources and their habitats

The Central Valley Project Improvement Act

The Anadromous Fish Restoration Program

The CALFED Bay-Delta Program

The Battle Creek Restoration Project

Alignment between the Battle Creek Restoration Program and Coleman NFH

3.4 Direct effects of artificial propagation programs at Coleman and Livingston Stone NFHs on the restoration and recovery of listed species

Sacramento River Winter Chinook Salmon

3.5 Relationship of program to harvest objectives

Ocean harvest

Ocean Contribution by Brood Year

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Freshwater harvest

Fall and Late-fall Chinook Salmon

Steelhead v

3.6 Escapement to Battle Creek

3.7 Impacts of hatchery-origin salmonid (over) escapement on Battle Creek Restoration

Fall Chinook Salmon

Late-fall Chinook Salmon

Steelhead

3.8 Relationship of harvest and escapement

Impacts of Mixed-stock Fisheries

4 HATCHERY WATER SOURCE

4.1 Coleman National Fish Hatchery

Water Rights

Water Diversion and use of water diversion Intakes

Water Treatment Facility

Water Discharge

4.2 Livingston Stone National Fish Hatchery

Water Intake

Water Discharge

4.3 Fish salvage efforts associated with Coleman NFH water diversions

Fish salvage efforts

4.4 Take of ESA-listed and non-listed salmonids resulting from hatchery water withdrawal and discharge

Coleman NFH-water diversion

Coleman NFH—Water Discharge

Livingston Stone NFH—Water Diversion

Livingston Stone NFH – Water Discharge

4.5 Effects of water diversions for Coleman NFH on Battle Creek salmonid habitats after proposed restoration

Emergency Situations

Drought

5 FACILITIES

5.1 Coleman National Fish Hatchery

Property

Physical Structures

Broodstock Collection Facilities vi

Adult Holding and Spawning Facilities

Incubation and Indoor Rearing Facilities

Outdoor Rearing Facilities

Fish Transportation Equipment

Water Treatment Facilities

Operational Difficulties or Disasters That Led to Significant Fish Mortality

Back-up Systems and Risk Aversion Measures to Minimize the Likelihood for the Take of Fish Resulting from Equipment Failure, Water Loss, Flooding, Disease Transmission, or Other Events That Could Lead to Injury or Mortality

Impacts of Facility Maintenance and On-site Construction on Listed Stocks or Critical Habitat

5.2 Livingston Stone National Fish Hatchery

Property

Broodstock Collection Facilities

Fish Transportation Equipment

Broodstock Holding Facilities

Spawning, Incubation, and Rearing Facilities

Facilities for propagation of delta smelt

Back-up Systems and Risk Aversion Measures That Will Be Applied to Minimize the Likelihood for the Take of Listed Natural Fish That May Result from Equipment Failure, Water Loss, Flooding, Disease Transmission, or Other Events That Could Lead to Injury or Mortality .114

Impacts of Facility Maintenance and On-site Construction on Listed Stocks or Critical Habitat

6 BROODSTOCK ORIGIN AND IDENTITY

6.1 Source

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

6.2 History

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon vii

Steelhead

6.3 Transfers from other hatcheries

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

6.4 Annual size

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

6.5 Past and proposed level of natural fish in broodstock

Fall Chinook Salmon

Past Levels of Natural Fall Chinook Broodstock

Future Levels of Natural Fall Chinook as Broodstock

Late-fall Chinook Salmon

Past Levels of Natural Late-fall Chinook as Broodstock

Future Levels of Natural Late-fall Chinook as Broodstock

Winter Chinook Salmon

Steelhead

Past Levels of Natural Steelhead as Broodstock

Future Levels of Natural Steelhead as Broodstock

6.6 Genetic or ecological differences

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

6.7 Reasons for choosing broodstock

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead viii

6.8 Risk aversion measures to minimize the likelihood of negative impacts on naturally-produced salmonids

Natural Fall Chinook Salmon

Natural Late-fall Chinook Salmon

Natural Winter Chinook Salmon

Natural Spring Chinook Salmon

Steelhead

7 BROODSTOCK COLLECTION

7.1 Life-history stage to be collected

7.2 Congregation and collection of broodstock

Fall and Late-fall Chinook Salmon and Steelhead in Battle Creek

Escapement Upstream of the Barrier Weir

Timing of Broodstock Collection at the Barrier Weir

Additional Functions of the Barrier Weir

Function of the Upstream Fish Ladder

Winter and Late-fall Chinook Salmon from the Sacramento River

Timing of Broodstock Collection

7.3 Broodstock transportation and holding methods

Fall Chinook Salmon

Transportation

Holding and Sorting

Late-fall Chinook Salmon

Transportation

Holding and Sorting

Winter Chinook Salmon

Transportation

Holding and Sorting

Steelhead

Transportation

Holding and Sorting

7.4 Identifying target populations and hatchery vs. natural-origin fish

Target Population: Fall Chinook Salmon collected from Battle Creek ..140

Hatchery-origin Late-fall Chinook Salmon ix

Natural-origin Late-fall Chinook Salmon

Spring Chinook Salmon

Hatchery- and natural-origin Steelhead

Target Population: Hatchery–origin Late-fall Chinook Salmon collected from Battle Creek

Hatchery-origin Fall Chinook Salmon

Natural-origin Fall, Late-Fall, and Winter Chinook salmon

Steelhead

Target Population: Natural-origin Late-fall Chinook Salmon collected from Keswick Dam Fish Trap

Fall Chinook Salmon

Hatchery-origin Fall and Late-fall Chinook Salmon

Hatchery-origin Winter Chinook Salmon

Natural-origin Winter Chinook Salmon

Steelhead

Target Population: Natural-origin Winter Chinook Salmon

Fall, Late-fall, and Spring Chinook Salmon

Target Population: Hatchery-Origin Steelhead

7.5 Proposed number to be collected

Collection and Spawning Targets

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

7.6 Disposition of surplus and unripe adults

Fall Chinook Salmon

Disposition of Surplus Adults

Disposition of Unripe Adults

Late-fall Chinook Salmon

Disposition of Surplus Adults

Disposition of Unripe Adults

Winter Chinook Salmon x

Disposition of Surplus Adults

Steelhead

Disposition of Surplus and Unripe Adults

7.7 Health maintenance and sanitation procedures applied

Fall and Late-fall Chinook Salmon and Steelhead

Winter Chinook Salmon

7.8 Disposition of carcasses

Fall and Late-fall Chinook Salmon and Steelhead

Winter Chinook Salmon

7.9 Risk aversion measures to reduce the likelihood for adverse genetic or ecological effects on naturally-produced salmonids

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Spring Chinook Salmon

Steelhead

7.10 Annual take levels for ESA-listed fish resulting from broodstock congregation and collection at Coleman and Livingston Stone NFH

Battle Creek

Winter Chinook Salmon

Spring Chinook Salmon

Steelhead

Sacramento River

Keswick Dam Fish Trap

8 MATING

8.1 Selection method

Fall and Late-fall Chinook Salmon

Winter Chinook Spawning

Steelhead

8.2 Spawn timing

Spawning Schedules

8.3 Back-up, precocious, and repeat spawners

Fall and Late-fall Chinook Salmon xi

Winter Chinook

Steelhead

8.4 Fertilization

Fall and Late-fall Chinook Salmon

Winter Chinook

Steelhead

8.5 Cryopreserved gametes

9 INCUBATION AND REARING

9.1 Incubation

Egg Collection

Fall and Late-fall Chinook Salmon and Steelhead

Winter Chinook Salmon

Surplus Egg Takes

Fall and Late-fall Chinook Salmon and Steelhead

Winter Chinook Salmon

Loading Densities

Fall and Late-fall Chinook Salmon and Steelhead

Winter Chinook Salmon

Fish Health Maintenance and Monitoring

9.2 Rearing

Survival Rates

Density and Loading Criteria

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook

Steelhead

Feeding and Food Conversion

Fish Health Maintenance and Monitoring

Smolt Development Indices

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook xii

Steelhead

10 JUVENILE RELEASES

10.1 Juvenile release levels and release strategies

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

10.2 Acclimation procedures

10.3 Marks applied, and proportions of the total hatchery population marked

Fall Chinook Salmon

Late-fall Chinook Salmon

Winter Chinook Salmon

Steelhead

10.4 Disposition of fish identified at the time of release as surplus to approved levels

10.5 Disease management

Infectious Hematopoeitic Necrosis Virus

Renibacterium salmoninarum or Bacterial Kidney Disease

Assessment of Impacts Resulting from Releases of Juvenile Salmonids from the Coleman and Livingston Stone NFH

10.6 Risk assessment framework

Predation

Relative Abundance - Temporal and Spatial Overlap

Predator/prey Size Relationships and the Onset of Piscivory

Training Time

Environmental Conditions

Recent Research involving Predation

Competition/Displacement

Disease Transmission

10.7 Strategies designed to minimize potential negative impacts from juvenile releases

Reduce Temporal and Spatial Overlap

Disease Transmission xiii

10.8 Analysis of risks resulting from releases of hatchery-origin fall Chinook salmon

Predation

Competition /Displacement

Carrying Capacity of Lower Battle Creek

Disease Transmission

10.9 Analysis of risks resulting from releases of hatchery-origin late-fall Chinook Salmon

Predation

Competition/Displacement

Disease Transmission

10.10 Analysis of risks resulting from releases of hatchery-origin winter Chinook salmon

Predation

Competition/Displacement

Disease Transmission

10.11 Analysis of risks resulting from releases of hatchery-origin juvenile steelhead .205

Predation

Residualization

Competition/Displacement

Disease Transmission

10.12 Other potential risks to natural salmonid populations from hatchery releases

Potential Risks from Interactions in Estuarine and Ocean Environments

Potential Risks of Altered Migratory Behavior (i.e., Pied Piper Effect) .209

Potential Risks from Straying of Hatchery-origin Salmonids

11 MONITORING AND EVALUATION OF PERFORMANCE INDICATORS

11.1 Monitoring and evaluation of performance indicators

11.2 Performance indicators addressing hatchery benefits

11.3 Performance Indicators addressing hatchery risks

12 RESEARCH

12.1 Studies associated with monitoring the winter Chinook propagation program ...217

12.2 Studies associated with monitoring the Battle Creek Restoration Process

12.3 Investigation of steelhead/rainbow trout life history using otolith microchemistry xiv

12.4 Reproductive success of naturally spawning winter Chinook salmon

12.5 Acoustic monitoring of emigrating hatchery-origin late-fall Chinook

13 CITATIONS, APPENDICES, AND ATTACHMENTS

13.1 LITERATURE CITED

13.2 APPENDICES

Appendix 4A Derivation of take estimates for ESA-listed salmonids at the Coleman National Fish Hatchery associated with use of Intake #2. All flow measurements are in units of cubic feet per second (cfs)

Appendix 6A Summary of Chinook spawning at Coleman and Livingston Stone National Fish Hatcheries including brood year, run (race); collection location; capture and spawning dates; number of females, males, and jacks collected and spawned; number of eggs collected; and lot number. Information in this table may be cross-tabulated with distribution data (Appendix 10A) using “lot number.”

Appendix 6B Summary of steelhead and rainbow trout spawning at Coleman National Fish Hatchery including: brood year, stock, stock source, capture and spawning dates, total number of fish handled, numbers of females and males spawned, number of eggs collected, and lot number.

Historic data presented were reconstructed from hatchery records that are incomplete and may not be accurate. This table may be cross-tabulated with distribution data (Appendix 10B) using "lot number" as an index field

Appendix 6C Genetic selection of winter Chinook salmon broodstock

Appendix 6D Genetic Risks of Hatchery Propagation

Appendix 8A Collection locations and approximate spawn timing of fall and late-fall Chinook salmon for Battle Creek Egg Taking Station, 1909-1941, and Coleman National Fish Hatchery, 1942-2008

Appendix 8B Collection location and spawn timing of winter Chinook salmon for Coleman National Fish Hatchery, brood years 1955-1997 and Livingston Stone National Fish Hatchery, brood years 1998-2008 xv

Appendix 8C Collection locations and spawn timing of steelhead trout at Coleman National Fish Hatchery, brood years 1948-2008

Appendix 10A Distribution of Chinook salmon from Coleman National Fish Hatchery (NFH) from 1941 through July 2008.

Data include release date(s), species, race (run), brood year (BY), production lot number, number released, coded-wire tag (CWT) status, CWT code, size at release (fork length [inches] and number per pound, and release location. Information in this table may be cross-tabulated with Coleman NFH spawning data (Appendix 6A) using “CWT code” as an index field

Appendix 10B Broodstock source and distribution summary of steelhead and non-anadromous rainbow trout at Coleman National Fish Hatchery. STT, RBT, and KAM denote steelhead trout, non-anadromous rainbow trout, and Kamloops (Gerrard strain rainbow trout), respectively

13.3 ATTACHMENTS

Attachment 3-1: Interagency Agreement between U.S. Fish and Wildlife Service and U.S. Bureau of Reclamation concerning the funding and operation of the Coleman National Fish Hatchery, Anderson, California

Attachment 3-2: Amendment to the Interagency Agreement between U.S. Fish and Wildlife Service and U.S. Bureau of Reclamation to include the funding and operation of the Livingston Stone National Fish Hatchery, Shasta Lake City, California

Attachment 3-3 Revised Position Paper on the Battle Creek Watershed, Shasta and Tehama Counties, California

Attachment 4-1: Adopted waste discharge requirements for Coleman National Fish Hatchery (Order No. R5-2004-0123 as adopted by the California Regional Water Quality Control Board)

Attachment 4-2: Waste discharge requirements for Livingston Stone National Fish Hatchery (Winter Run Rearing facility), Shasta County (NPDES No. CAG135001) xvi

14 CERTIFICATION AND SIGNATURE OF RESPONSIBLE PARTY

xvii

List of Tables

Table 1-1 Federal Endangered Species Act (ESA) and California Endangered Species Act (CESA) status of fish stocks propagated at the Coleman and Livingston Stone National Fish Hatcheries, including natural and hatchery Chinook salmon, steelhead, and delta smelt. The Evolutionarily Significant Unit (ESU) or Distinct Population Segment (DPS) status of the hatchery stock is also indicated

Table 1-2 Annual propagation targets at Coleman and Livingston Stone National Fish Hatcheries are presented, including number of adults spawned, initial egg take, and number of juveniles released. Also shown are target release timing, life stage and size, and release location

Table 1-3. Estimated ocean harvest, freshwater returns and survival to adulthood for Coleman National Fish Hatchery fall Chinook salmon, brood years 1973-

Table 1-4. Ocean and freshwater contribution numbers and total contribution percent for late-fall Chinook salmon juveniles released from Coleman National Fish Hatchery (brood years 1989-1995)

Table 1-5. Ocean and freshwater contribution numbers and total contribution percent for winter Chinook salmon juveniles released from Coleman National Fish Hatchery (brood years 1989-1995)

Table 2-1. Size ranges, means, and sex ratios of spawning winter Chinook salmon captured at the Coleman NFH barrier weir, Red Bluff Diversion Dam, and Keswick Dam for 1998-20008a,b

Table 2-2. Fall, late-fall, winter, and spring Chinook salmon and steelhead spawner population estimates in the Sacramento River, Battle Creek, and Coleman National Fish Hatchery; 1952-2007. Estimates from the Sacramento River include estimated harvests

Table 2-3. Projected levels and types of incidental take of listed salmonids resulting from artificial propagation programs at Coleman and Livingston Stone National Fish Hatcheries. Take of adults in indicated by “A” and juveniles by “J”. Where a fish may be affected by more than one type of take it is included in the category that would have the greatest impact;

such that the total number of potentially affected individuals of each species can be estimated by the sum of each column xviii

Table 2-4. Qualitative summary of population-level impacts associated with fish production activities conducted at Coleman and Livingston Stone National Fish Hatcheries that may result in direct or indirect take of ESA-listed and non-listed species, or destruction or alteration of critical habitat. Impact assessment is based on discussions, data, and analyses presented in this document and represent the U.S. Fish and Wildlife Service’s evaluation of available information. Complete discussions of these activities and impacts can be found in the specified sections of this document

Table 3-1 Specific actions of the Anadromous Fish Restoration Program associated with hatchery operations or Battle Creek restoration. Items in bold are specific to the Coleman NFH

Table 3-2 Estimated ocean contribution for fall Chinook salmon from Coleman National Fish Hatchery (NFH), by brood year, based on the number of salmon released

Table 3-3 Percentage of Coleman National Fish Hatchery (NFH) fall Chinook salmon caught in the West Coast troll and recreational ocean fisheries.

Harvest and effort data were obtained from the Review of 2006 Ocean Salmon Fisheries report (Pacific Fishery Management Council 2007)

Table 3-4 Estimated ocean contribution for late-fall Chinook salmon from Coleman National Fish Hatchery (NFH), by brood year, based on the number of salmon released

Table 3-5 Estimated ocean harvest of winter Chinook salmon from Coleman NFH Complex, listed by brood year. Harvest rates are based on the number of salmon released

Table 3-6 Allocation of Coleman NFH Chinook Salmon to Sacramento River, California Creel Survey estimates

Table 3-7 Numbers of Coleman NFH Fall and Late-fall Chinook salmon harvested and hours spent angling in the freshwater recreational fishery, 1998 through 2002

Table 4-1. Estimated salmonid take resulting from entrainment from Battle Creek into the Coleman National Fish Hatchery water delivery system.

Numerical take estimates do not include fishes salvaged from the hatchery’s water supply system (i.e., actual lethal take will likely be less as some of these fish will be rescued during salvage operations. Take for rescued fishes will be decreased to handling and delay of emigration) xix

Table 4-2 Flows providing maximum weighted usable area (WUAa) for different species and life stages for the mainstem reach of Battle Creek (from the Coleman barrier weir to approximately 10 miles upstream). Flows are from the Battle Creek Working Group Technical Committee (reported in Ward and Keir {1999}) and are based primarily on four studies of Battle Creek completed by Thomas R. Payne and Associates (Thomas R. Payne and Associates 1998a through 1998d). Blank cells indicate life stage was not present or habitat was not used at this time. May 95% of total WUA flows higher to cover some late possible late spawning of steelhead and October and November 95% of total WUA flows adapted to reflect only steelhead rearing

Table 4-3 Average monthly discharge for Battle Creek (BC), recommended minimum flows after Battle Creek restoration, monthly water requirements for Coleman National Fish, and average flows in excess of minimum flows and Coleman NFH water requirements

Table 6-1. Number of late-fall Chinook salmon collected from Battle Creek and the Sacramento River at the Keswick Dam fish trap, for return years 1988 - 2008. Beginning with return year 2003, eggs collected from natural-origin fish are not culled; therefore, the percentage of natural-origin broodstock is obtained by dividing the number of fish collected at the Keswick Dam fish trap by the number of broodstock required to meet egg collection targets (i.e. 540)

Table 6-2 Number of natural-origin steelhead collected and spawned at Coleman NFH during return years 2003-2008. These fish are categorized as returned (total number into the hatchery), retained (number of fish held for spawning), or spawned (the number of fish actually spawned)

Table 7-1 Total count and pre-spawn mortalities of natural-origin late-fall Chinook salmon observed during late-fall Chinook broodstock collection (late- December through February) at the Keswick Dam fish trap and Coleman National Fish Hatchery, return years 2002-2008

Table 7-2 Total collected and pre-spawn mortalities of winter Chinook salmon collected at the Keswick Dam fish trap during winter Chinook broodstock collection (March 1 through July), return years 2000-2008

Table 7-3 Numbers of fall Chinook salmon broodstock collected at the Coleman National Fish Hatchery, return years 1990-2008. Jacks (i.e., males with a fork length < 650 mm) are included with “Males” for counts of spawned fish only xx

Table 7-4 Numbers of late-fall Chinook salmon broodstock collected at the Coleman National Fish Hatchery and the Keswick Dam Fish Trap, return years 1991-2008. Jacks (i.e., males with a fork length < 650 mm) are included with “Males” for counts of spawned fish only

Table 7-5 Monthly collection goals for adult winter Chinook salmon broodstock based on a run-size estimate of 800 or greater, a trapping level of 15%, and the estimated proportion of the run migrating past the Red Bluff Diversion Dam by month. Passage data provided by the California Department of Fish and Game, Red Bluff, California

Table 7-6 Broodstock collection of winter Chinook salmon from Keswick Dam and Red Bluff Diversion Dam, return years 1990-2008. Salmon were propagated at Coleman National Fish Hatchery (1989-1997) and at Livingston Stone National Fish Hatchery (1998-2008). Jacks (i.e., males with a fork length < 650 mm) are included with counts of “Males”

Table 7-7 Broodstock collection of steelhead at Coleman National Fish Hatchery, return years 1988 through 2008

Table 7-8 Estimated return of fall Chinook salmon to Battle Creek, return to Coleman National Fish Hatchery (NFH), and number excessed at Coleman NFH from 1991 through 2008

Table 7-9 Number and percent of the total run of winter Chinook salmon captured and held for spawning at Coleman (1991-1995) and Livingston Stone (1998-2008) National Fish Hatcheries

Table 7-10 Drugs and treatments applied to maintain health of winter Chinook broodstock at Livingston Stone National Fish Hatchery. The following listing should not be considered all-inclusive as other drugs and treatments may be used as necessary and as recommended

Table 7-11 Estimated take of ESA-listed salmonids resulting from broodstock congregation and collection in Battle Creek. Where a fish may be affected by more than one type of take it is included in the category that would have the greatest impact; such that the total number of potentially affected individuals of each species can be estimated by the sum of each column

Table 7-12 Numbers of steelhead incidentally collected while trapping for late-fall and winter Chinook broodstock at the Keswick Dam fish trap, 2004-2010.

Life history type of collected steelhead is not known xxi

Table 7-13 Estimated incidental take of ESA-listed salmonids resulting from broodstock collection at Keswick Dam fish trap. Where a fish may be affected by more than one type of take it is included in the category that would have the greatest impact; such that the total number of potentially affected individuals of each species can be estimated by the sum of each column

Table 8-1 Numbers of hatchery-origin steelhead and steelhead kelts (repeat spawners) returning to Coleman NFH 2005-2008

Table 9-1 Survival estimates, total egg take targets and release targets for salmonid stocks propagated at Coleman and Livingston Stone National Fish Hatcheries. Estimates are based on historical data (U.S. Fish and Wildlife Service, unpublished data)

Table 9-2 Density indices, final densities, and final fork lengths for three stocks of salmonids propagated at Coleman National Fish Hatchery. Data are five-year averages from 1995 through 1999 (U.S. Fish and Wildlife Service, unpublished data)

Table 9-3 Food type and conversion efficiencies for two rearing ages of Chinook salmon and steelhead. Stocks are propagated at Coleman National Fish Hatchery. Conversion efficiencies are based on five-year averages from 1995 through 1999 (U.S. Fish and Wildlife Service, unpublished data).

Fish and food weights presented are “wet weights”

Table 10-1 Anticipated numbers of juvenile fall Chinook salmon to be released from Coleman National Fish Hatchery (NFH) annually. Fish will be released into Battle Creek at Coleman NFH and the San Pablo Bay. Temporary releases of fall Chinook into the San Pablo Bay have been implemented to increase abundance of fall Chinook salmon to benefit the commercial and recreational ocean salmon fisheries

Table 10-2 Fall Chinook salmon production at Coleman National Fish Hatchery, brood years 1996-2007

Table 10-3 Late-fall Chinook salmon production at Coleman National Fish Hatchery, brood years 1996-2007

Table 10-4 Anticipated numbers of juvenile late-fall Chinook salmon to be released from Coleman National Fish Hatchery (NFH) annually

Table 10-5 Winter Chinook salmon production at Coleman (CNFH) and Livingston Stone (LSNFH) National Fish Hatcheries and Bodega Marine Laboratory (BML), brood years 1996-2007 xxii

Table 10-6 Steelhead production at Coleman National Fish Hatchery, brood years 1996-2007

Table 10-7 Anticipated numbers of juvenile steelhead to be released from Coleman National Fish Hatchery, annually

Table 10-8 Projected release number, anticipated number marked (adipose fin clip), mark rates, and mark type for all runs/species produced at Coleman and Livingston Stone National Fish Hatcheries; brood year 2009. CWT = coded-wire tag

Table 10-9 Summary of impacts to natural-origin salmonid populations resulting from releases of juvenile fall Chinook salmon from Coleman National Fish Hatchery. See text (Section 10.6) for definitions of impact ratings and descriptions of criteria

Table 10-10 Length ranges of natural-origin Chinook salmon and steelhead potentially co-occurring in Battle Creek and the Sacramento River with hatchery-origin fall Chinook salmon (range = 40-109 mm) during April

Table 10-11 Summary of impacts to natural-origin salmonid populations resulting from releases of juvenile late-fall Chinook salmon from Coleman National Fish Hatchery. See text (Section 10.6) for definitions of impact ratings and descriptions of criteria

Table 10-12 Length ranges of natural-origin Chinook salmon and steelhead potentially co-occurring in Battle Creek and the Sacramento River with hatchery-origin late-fall Chinook salmon (range: 65-202 mm) during January

Table 10-13 Summary of impacts to natural-origin salmonid populations resulting from releases of juvenile winter Chinook salmon from Livingston Stone National Fish Hatchery. See text (Section 10.6) for definitions of impact ratings and descriptions of criteria

Table 10-14 Summary of impacts to natural-origin salmonid populations resulting from releases of juvenile steelhead from Coleman National Fish Hatchery. See text (Section 10.6) for definitions of impact ratings and descriptions of criteria

Table 10-15 Length ranges of natural-origin Chinook salmon and steelhead potentially co-occurring in the Sacramento River with hatchery-origin steelhead following their release (range: approx. 82-302 mm) in January xxiii

List of Figures

Figure 1-1 Locations of Coleman and Livingston Stone National Fish Hatcheries and other major features in the upper Sacramento River, California

Figure 2-1. Estimated numbers of adult fall Chinook salmon returning to Coleman National Fish Hatchery and lower Battle Creek, and estimates of fall Chinook salmon returning to the mainstem Sacramento River for 1952- 2008. Also shown is the proportion of the total run of fall Chinook salmon returning to Battle Creek

Figure 2-2. Numbers of returning steelhead adults intentionally passed upstream of the Coleman National Fish Hatchery barrier weir from 1995 through 2008

Figure 3-1 Escapement of fall Chinook salmon to Battle Creek from 1952-2008 (source California Department of Fish and Game GrandTab). Escapement includes both adults taken into Coleman National Fish Hatchery and adults spawning naturally in Battle Creek. Heavy black lines denotes broodstock collection requirement (approximately 8,000) for fall Chinook salmon at Coleman National Fish Hatchery

Figure 4-1. Existing water diversion and delivery system at Coleman National Fish Hatchery, Battle Creek, California

Figure 4-2 Annual hydrograph for Battle Creek and expected diversions at Coleman National Fish Hatchery intakes. Total diversions at Coleman National Fish Hatchery intakes includes approximately 13 cfs delivered to downstream water users. Monthly flow averages are based on data for Battle Creek from 1961 through 2008

Figure 5-1 Physical layout of hatchery facilities at Coleman National Fish Hatchery

Figure 5-2 Physical layout of hatchery facilities at Livingston Stone National Fish Hatchery

Figure 6.1 Unrooted Neighbor-Joining tree (Service, unpublished data). Branches with bootstrap probabilities are provided

Figure 6-2 Increase of breeding per generation (Delta F) as a function of the number of effective parents (Ne; from Ryman and Ståhl 1980)

Figure 7-1 Operational purpose of the fish ladder at Coleman National Fish Hatchery.

The upstream ladder is opened for salmonid passage from March 1 through July 31 xxiv

Figure 7-2 Timing of barrier weir fish ladder operations at the Coleman NFH since

Figure 7-3 Broodstock collection timing for late-fall and winter Chinook salmon at the Keswick Dam fish trap on the Sacramento River

Figure 7-4 Transition from fall to late-fall migrations of adult Chinook salmon at Coleman National Fish Hatchery, Battle Creek, California. Data are from coded-wire tag recoveries from November 2003 through January 2004 and represent typical proportions by return

Figure 7-5 Approximate timing for salmonid migration in Battle Creek and operation of the Coleman National Fish Hatchery barrier weir. Peaks correspond to peaks in migration, and spread indicates range of migration timing. Area does not indicate the proportion of the run passing. Adapted from Vogel and Marine (1991) and U.S. Fish and Wildlife Service (unpublished data)

Figure 7-6 Number of Chinook salmon passing the Coleman NFH barrier weir from March 7 to September 1, 2000. Also shown are probable run compositions of three discrete migration periods

Figure 10-1 Catch per unit volume (CPUV) of hatchery- and natural-origin juvenile fall Chinook salmon, brood year 1998. Data are from rotary screw traps operated on the Sacramento River, Red Bluff Diversion Dam (river mile 243). Displayed CPUV for natural-origin fall Chinook salmon has been smoothed by calculating 3-day rolling averages. Daily CPUV is shown for hatchery-origin fall Chinook salmon. Hatchery-origin juveniles were released at Coleman National Fish Hatchery, Battle Creek. Hatchery release dates were March 31 and April 20, 21, 27 and 28, 1999

Figure 10-2 Box plots for fork lengths of fall Chinook salmon released from the Coleman National Fish Hatchery, brood years 2004-2008

Figure 10-3 Box plots for fork lengths of late-fall Chinook smolts released from the Coleman NFH, brood years 2004-2008

Figure 10-4 Hydrograph of average daily discharge in cubic feet per second (cfs) for the Sacramento River at Bend Bridge (river mile 258), 1999. Data are from the California Data Exchange Center (CDEC), March 5, 2000

Figure 10-5 Average daily turbidity in nephelometric turbidity units (NTU) for the Sacramento River at Bend Bridge (river mile 258), 1999. Data are from the California Data Exchange Center (CDEC), March 5, 2000

Figure 10-6 Box plots for fork lengths of winter Chinook smolts released from the Livingston Stone NFH, brood years 2004-2008 xxv

Figure 10-7 Box plots for fork lengths of steelhead smolts released from the Coleman NFH, brood years 2004-2008 xxvi

List of Abbreviations

Anadromous Fish Restoration Program ...................................................................................AFRP Anderson-Cottonwood Irrigation District ................................................................................ ACID Bodega Marine Laboratory ....................................................................................................... BML California Bay Delta Authority .......................................................................................... CALFED California Department of Fish and Game ............................................................................... CDFG California Endangered Species Act ........................................................................................ CESA California-Nevada Fish Health Center ......................................................................... CA-NV FHC carbon dioxide ............................................................................................................................. CO2 Central Valley Project ................................................................................................................ CVP Central Valley Project Improvement Act ..............................................................................CVPIA coded-wire tag ........................................................................................................................... CWT cubic feet per second ................................................................................................