Upper Yuba River Anadromous Salmonid Reintroduction Plan
Prepared by: R2 Resource Consultants, Inc. Redmond, Washington and: Stillwater Sciences, Inc. Berkeley, California
In collaboration with: National Marine Fisheries Service Santa Rosa, California
February 2014
Upper Yuba River Anadromous Salmonid Reintroduction Plan
Prepared by: Noble Hendrix(1), Phil J. Hilgert, Timothy J. Sullivan R2 Resource Consultants, Inc. 15250 N.E. 95th Street Redmond, Washington 98052
and AJ Keith, Jody Lando, and Abel Brumo Stillwater Sciences, Inc. 2855 Telegraph Ave, Suite 400 Berkeley, California 94705
In collaboration with: Richard Wantuck NOAA/National Marine Fisheries Service 777 Sonoma Avenue, Suite 325 Santa Rosa, CA 95404
February 2014
(1) Noble Hendrix can be contacted at QEDA Consulting, LLC, 4007 Densmore Ave N, Seattle, WA 98103
Cover photographs from Yuba County Water Agency (http://www.ycwa.com) and U.S. Army Corp of Engineers (USACE 2012). Photographs show, from top to bottom: Daguerre Point Dam, Englebright Dam, New Bullards Bar Dam, Our House Diversion Dam, and Log Cabin Diversion Dam. NMFS Upper Yuba River Anadromous Salmonid Reintroduction Plan
CONTENTS
PREFACE ...... XIV EXECUTIVE SUMMARY ...... XVI 1. INTRODUCTION ...... 1
1.1 BACKGROUND AND OBJECTIVE ...... 1
1.2 ACTION AREA ...... 6
1.3 LAND USE ...... 8
1.4 HYDROLOGY ...... 9
1.5 REGULATORY AND MANAGEMENT ISSUES ...... 12
1.5.1 Federal ESA and California ESA: Listing Status ...... 12 1.5.2 Hydropower: Federal Power Act and FERC Licensing ...... 16 1.6 STRUCTURAL FEATURES AND FACILITIES ...... 21
1.6.1 Daguerre Point Dam ...... 22 1.6.2 Englebright Dam and Reservoir ...... 24 1.6.3 New Bullards Bar Dam and Reservoir ...... 26 1.6.4 Our House Diversion Dam ...... 29 1.6.5 Log Cabin Diversion Dam ...... 30 2. BIOLOGICAL INFORMATION ...... 32
2.1 CV SPRING-RUN CHINOOK SALMON ...... 32
2.2 CV STEELHEAD ...... 33
2.3 GREEN STURGEON ...... 34
2.4 OTHER SPECIES ...... 36
3. DISTRIBUTION OF EXISTING HABITAT ...... 38 4. HABITAT CONNECTIVITY ...... 40
4.1 UPSTREAM CONNECTIVITY...... 42
4.2 DOWNSTREAM CONNECTIVITY ...... 45
4.2.1 Reservoirs ...... 45 4.2.2 Tributary Collector ...... 47
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4.2.3 Forebay Passage ...... 48 4.2.4 Turbines ...... 50 4.2.5 Spillways ...... 51 4.3 TEMPERATURE CONCERNS ...... 52
4.4 PHASED PASSAGE FACILITIES ...... 53
5. STOCK SELECTION AND GENETIC MANAGEMENT ...... 61
5.1 INTRODUCTION ...... 61
5.2 UPPER YUBA RIVER WATERSHED CHARACTERISTICS ...... 61
5.2.1 Flow ...... 61 5.2.2 Barriers to Anadromy ...... 62 5.2.3 Water Temperature ...... 63 5.3 CENTRAL VALLEY SPRING-RUN CHINOOK SALMON AND STEELHEAD LIFE HISTORIES ...... 63
5.3.1 Central Valley Spring-run Chinook Salmon ESU ...... 63 5.3.2 California Central Valley Steelhead DPS ...... 70 5.4 REINTRODUCTION STRATEGY ...... 71 5.4.1 Recovery Priorities for Central Valley Spring-run Chinook Salmon and Steelhead ...... 71 5.4.2 Viable Salmonid Populations ...... 72 5.5 POTENTIAL SOURCES OF DONOR STOCK FOR REINTRODUCTION TO THE UPPER YUBA WATERSHED ...... 73
5.5.1 Spring-run Chinook Salmon ...... 76 5.5.2 Steelhead ...... 77 5.5.3 Hatchery Stocks ...... 77 5.6 STOCK SELECTION CONSIDERATIONS ...... 78
5.6.1 Criteria Used by Other Reintroduction Efforts ...... 78 5.6.2 Genetics ...... 79 5.6.3 Recommendations and Additional Considerations ...... 81 6. PRODUCTION POTENTIAL OF YUBA RIVER ...... 83
6.1 MODELING APPROACH AND MANAGEMENT SCENARIOS ...... 83
6.1.1 Dry Conditions Scenario ...... 85
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6.1.2 Alternative Management Scenarios ...... 85 6.2 POPULATION DYNAMICS (POP)...... 86
6.2.1 POP Module Structure ...... 86 6.2.2 POP Module Parameterization ...... 92 6.3 SPRING-RUN CHINOOK SALMON RESULTS...... 92
6.3.1 Predicted Distribution of Suitable Habitat ...... 92 6.3.2 Carrying Capacity Estimates ...... 94 6.3.3 Smolt Production Estimates ...... 96 6.3.4 Summary ...... 98 6.4 STEELHEAD RESULTS ...... 98
6.4.1 Predicted Distribution of Suitable Habitat ...... 98 6.4.2 Carrying Capacity Estimates ...... 100 6.4.3 Smolt Production Estimates ...... 101 6.4.4 Summary ...... 102 7. LIFE-CYCLE AND PASSAGE MODEL ...... 103
7.1 INTRODUCTION ...... 103
7.2 METHODS ...... 106
7.2.1 The Life-cycle Model ...... 106 7.2.3 Evaluating Passage Alternatives and Hydrologic Scenarios ...... 111 7.2.4 Model Assumptions ...... 114 7.3 RESULTS AND CONCLUSIONS ...... 114
7.3.1 North Yuba Passage ...... 114 7.3.2 Englebright Dam Passage ...... 117 7.3.3 Conclusions ...... 125 8. PHASED PLANNING APPROACH ...... 127
8.1 CONNECTIVITY ...... 127
8.2 DEVELOP OPERATIONAL REINTRODUCTION PLANS ...... 131
8.3 PHASE I: PILOT REINTRODUCTION EXPERIMENTS ...... 134
8.3.1 Goals and Objectives ...... 135
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8.3.2 Critical Elements ...... 135 8.3.3 Studies ...... 136 8.3.4 Utility of Information ...... 139 8.4 PHASE II: SHORT TERM REINTRODUCTION PLAN IMPLEMENTATION WITH ADAPTIVE MANAGEMENT ...... 140
8.4.1 Goals and Objectives ...... 140 8.4.2 Critical Elements ...... 141 8.4.3 Studies ...... 143 8.4.4 Utility of Information ...... 145 8.5 PHASE III: LONG TERM REINTRODUCTION PLAN IMPLEMENTATION WITH ADAPTIVE MANAGEMENT ...... 150
8.5.1 Goals and Objectives ...... 150 8.5.2 Critical Elements ...... 150 8.5.3 Studies ...... 151 8.5.4 Utility of Information ...... 151 8.6 HOW TO INCORPORATE ADAPTIVE MANAGEMENT INTO THE PHASES OF THE REINTRODUCTION ...... 152
9. REFERENCES ...... 154
APPENDIX A Life-Cycle Model Parameters APPENDIX B Technical Memorandum: Review of MWH 2010 Yuba River Fish Passage, Conceptual Engineering Project Options
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FIGURES
Figure 1-1. Map of the Upper Yuba River Basin and associated sub-basins...... 7 Figure 1-2. Average monthly Yuba River flow at the Smartville gage (USGS 11418000) 0.5 of a mile downstream of Englebright Dam from WY 1970 through WY 2008 (Source: YCWA 2010)...... 10 Figure 1-3. Flow exceedance of historical mean daily streamflow for the Yuba River at the Smartville gage (USGS 11418000) 0.5 of a mile downstream of Englebright Dam from WY 1970 through WY 2008 (Source: YCWA 2010)...... 10 Figure 1-4. Hydrographs for the South, Middle, and North Yuba rivers for the overlapping period of record (1969–1987). Source: Stillwater Sciences (2013a) from USGS gage data...... 11 Figure 1-5. Daguerre Point Dam at RM 11.5 on the Yuba River. Source: USACE (2012)...... 24 Figure 1-6. Englebright Dam located at RM 23.9 on the Yuba River. Source: YCWA (2010) ...... 26 Figure 1-7. New Bullards Bar Dam at RM 2.3 on the North Yuba River. Source: YCWA (2010) ...... 28 Figure 1-8. Monthly temperature profiles of New Bullards Bar Reservoir (2008). Elevation range of upper power intake, which is not used, is shown as horizontal black lines, and lower power intake elevation range is shown as horizontal red lines. Source: YCWA 2010...... 28 Figure 1-9. Our House Diversion Dam at RM 12.1 on the Middle Yuba River. Source: YCWA (2010)...... 30 Figure 1-10. Log Cabin Diversion Dam at RM 4.1 on Oregon Creek, a tributary to the Middle Yuba River. Source: YCWA (2010)...... 31 Figure 4-1. Relationship of head to mortality for Francis turbines (Eicher et al. 1987)...... 51 Figure 5-2. Weekly migration of spring-run Chinook Salmon into Mill, Deer, and Butte creeks (source: Lindley et al. 2004)...... 66 Figure 5-3. Run size and composition of spring-run Chinook Salmon from 1970 to 2008 (source: NMFS 2009, based on CDFG GrandTab spawning data 2009)...... 67 Figure 5-4. Mean monthly catches of juvenile spring-run Chinook Salmon in rotary screw traps in Mill, Deer, and Butte creeks (source: Lindley et al. 2004)...... 69
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Figure 6-1. Schematic diagram showing the relationships between each life stage in the POP module and the point at which each carrying capacity (K) is applied to the population. BY = brood year...... 87 Figure 7-1. Schematic for life-cycle model of spring-run Chinook Salmon in the Yuba River. Production potential in the North Fork Yuba (NY), Middle Fork (MY), South Fork (SY), and New Bullard Bar (NBB) are moved out of the Yuba River through reservoirs and dams (solid lines) to the ocean where juveniles mature and return as spawners to the Yuba River and return (dashed lines) through passage structures at dams and reservoirs...... 105 Figure 7-2. Example of triangular probability distribution. The triangular distribution is defined by the lower bound, upper bound, and mode or peak: therefore, the distribution can be either symmetric or asymmetric...... 111 Figure 7-3. Example of life-cycle model trajectories for CV spring-run Chinook Salmon in the Yuba River. Twenty model trajectories are plotted (each in a different color) showing the initial reintroduction period in years 1 through 10 when the population is established. In years 51 through 53, the smolt to adult return ratio (SAR) is halved and the population declines, after which the SAR returns to its base level and the population recovers...... 115 Figure 7-4. Estimates of mean CV spring-run Chinook Salmon spawner abundance in the North Yuba under three hydrologic scenarios. Scenario D (solid line) has the lowest mean abundance relative to either scenario S3 (dashed line) or scenario S4 (dotted line)...... 116 Figure 7-5. Distribution of the modeled spawner abundance in year 100 in the North Yuba. Hydrologic scenarios D (red), S3 (black), and S4 (blue) are plotted...... 116 Figure 7-6. Cohort replacement rate (CRR) for two periods on the North Yuba. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1...... 117 Figure 7-7. Estimates of mean CV spring-run Chinook Salmon spawner abundance in the Middle Yuba (top), South Yuba (middle), and Englebright Dam sub- basins (bottom) under three hydrologic scenarios. Scenario D (red solid line) has the lowest mean abundance relative to either scenario S3 (black dashed line) or scenario S4 (blue dotted line)...... 118 Figure 7-8. Distribution of the modeled spawner abundance in year 100 in the Middle Yuba. Hydrologic scenario D (red), S3 (black), and S4 (blue) are plotted...... 119
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Figure 7-9. Cohort replacement rate (CRR) for two periods on the Middle Yuba. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1...... 120 Figure 7-10. Distribution of the modeled spawner abundance in year 100 in the South Yuba. Hydrologic scenario S3 (black) and S4 (blue) are plotted...... 121 Figure 7-11. Cohort replacement rate (CRR) for two periods on the South Yuba. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1...... 122 Figure 7-12. Distribution of the modeled spawner abundance in year 100 in the Englebright Dam sub-basin (NBB). Hydrologic scenario D (red), S3 (black), and S4 (blue) are plotted...... 123 Figure 7-13. Cohort replacement rate (CRR) for two periods on the Englebright Dam sub-basin. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1...... 124 Figure 8-1. Potential connectivity to spring-run Chinook Salmon habitats in the Upper Yuba basin under Current Conditions (i.e., Dry Conditions scenario [Stillwater 2013a]) assuming upstream and downstream fish passage facilities are implemented at Englebright and Our House dams...... 130 Figure 8-2. Potential connectivity to spring-run Chinook Salmon habitats in the North Yuba Sub-basin under Current Conditions assuming upstream fish passage facilities are implemented at Englebright Dam and downstream passage facilities are implemented above New Bullards Bar Dam. Adult spring-run Chinook Salmon collected below Englebright Dam will be released into suitable habitat above New Bullards Bar Dam, and juvenile outmigrants collected above New Bullards Bar Dam will be released below Englebright Dam...... 131 Figure 8-3. Graphical display of passage alternative related to reservoir survival...... 147
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Figure 8-4. Graphical display of passage alternative related to reservoir survival after conducting an experiment with 100 fish...... 148 Figure 8-5. Graphical display of passage alternative related to reservoir survival after conducting an initial experiment with 100 fish and a second experiment with 1000 fish...... 149 Figure 8-6. Graphical display of passage alternative related to reservoir survival after conducting an initial experiment with 100 fish, and a second and third experiment with 1000 fish each...... 150
TABLES
Table 2-1. Migration periodicity for CV Chinook Salmon and CV steelhead in the Lower Yuba River. Source: MWH (2010)...... 34 Table 5-1. Life history timing of spring-run Chinook Salmon in the Sacramento River basin...... 64 Table 5-2. Characteristics of potential donor stocks for reintroduction to the upper Yuba River watershed...... 74 Table 6-1. Life stages represented in the spring-run Chinook Salmon POP module...... 88 Table 6-2. Biological parameters input into the POP module for each Chinook salmon model run...... 89 Table 6-3. Spring-run Chinook Salmon habitat predicted under each modeling scenario in sub-basins of the upper Yuba River watershed...... 93 Table 6-4. Predicted habitat carrying capacities (K) of spring-run Chinook Salmon holding, spawning (redds), and summer rearing life stages for each modeled sub-basin and scenario in the upper Yuba River watershed...... 94 Table 6-5. Predicted equilibrium population sizes for select spring-run Chinook Salmon life stages for each modeled sub-basin and scenario in the upper Yuba River watershed...... 97 Table 6-6. Steelhead habitat predicted under each modeling scenario in sub-basins of the upper Yuba River watershed...... 99 Table 6-7. RIPPLE-predicted habitat carrying capacities for steelhead life stages for each modeled sub-basin and scenario in the upper Yuba River watershed...... 100
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Table 6-8. Steelhead smolt production estimates based on RIPPLE-predicted summer carrying capacities for age 1+ steelhead for each modeled sub-basin and scenario in the upper Yuba River watershed...... 102 Table 7-1. Model abbreviations and their descriptions...... 107 Table 7-2. Hydrologic scenarios evaluated with the passage model for the Upper Yuba...... 112 Table 8-1. Probability of a self-sustaining population under hypothetical states of nature and passage alternatives...... 147
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LIST OF ACRONYMS AND SCIENTIFIC LABELS Abbreviation Definition ac acres AF Acre-Feet BLM U.S. Department of Interior, Bureau of Land Management BY Brood Year C Celsius CDFG California Department of Fish and Game CDFW California Department of Fish and Wildlife CESA California Endangered Species Act cfs cubic feet per second CI Confidence Interval CRR Cohort Replacement Rate CV Central Valley CWT Coded Wire Tagging D Dry Conditions Scenario DPS Distinct Population Segment DWR California Department of Water Resources ESA Endangered Species Act ESU Evolutionarily Significant Unit F Fahrenheit FERC Federal Energy Regulatory Commission FGE Fish Guidance Efficiency FRFH Feather River Fish Hatchery FSC Floating Surface Collector ft feet GIS Geographic Information System in inches K carrying capacity m meter mm millimeters msl mean sea level MW Megawatt MWAT Maximum weekly average temperature MY Middle Yuba NBB New Bullards Bar
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Abbreviation Definition NBBD New Bullards Bar Dam NFL National Forest Lands NMFS National Marine Fisheries Service NY North Yuba PAD Pre-Application Document PG&E Pacific Gas and Electric Company PIT Passive Integrated Transponder POP Population Dynamics PSE Puget Sound Energy RM River Mile RMT Yuba River Management Team S3 First Alternative Water Management Scenario S4 Second Alternative Water Management Scenario SAR Smolt to Adult Return ratio sDPS southern Distinct Population Segment SJRRP San Joaquin River Restoration Program sq. mi square miles SY South Yuba USACE U.S. Army Corp of Engineers USFWS U.S. Fish and Wildlife Service USGS U.S. Geological Survey VSP Viable Salmon Population WY Water Year YBDS Yuba Bear and Drum Spaulding YCWA Yuba County Water Agency YRDP Yuba River Development Project YSF Yuba Salmon Forum
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PREFACE
by Richard L. Wantuck Project Leader National Marine Fisheries Service
The idea to begin a comprehensive plan for the reintroduction of anadromous fish into the Upper Yuba River watershed started in 2008. At that time, the National Marine Fisheries Service (NMFS) was involved with a variety of participants in numerous regulatory activities and stakeholder-driven management actions in watersheds across California’s Central Valley. The Agency convened a Biological Review Team to study the threatened and endangered status of anadromous fish species in the Central Valley and to help plan for actions that could be implemented to recover these species. In 2009, NMFS first released “Public Draft Recovery Plan for Central Valley Winter-Run and Spring-run Chinook Salmon and Steelhead,” dated October 7, 2009 (NMFS 2009), pursuant to the federal Endangered Species Act. The Yuba River is identified in the draft Recovery Plan as one of the Central Valley watersheds where reintroduction for spring-run Chinook Salmon and steelhead would significantly contribute to recovery of the species.
This document puts forth a Plan that offers a strategic framework, along with short term and long term action steps, to help guide the path for successful reintroduction of anadromous fish to the upper Yuba River. The Plan is meant to be a living, working document that can be built upon through the cooperative efforts of interested stakeholders. While a great deal of time, resources, and effort has gone into the compilation of this work over the past four years, it is not seen by the authors or NMFS as a final and prescriptive work. Rather, it represents a starting place for effective future action. It also serves as an initial foundation for near term implementation of phased actions that can be modified over time, and built upon accordingly. To the extent that contributors and collaborators have been willing and forthright to participate in a joint planning effort, their ideas and inputs have been solicited, considered and incorporated to the maximum practical extent. However, a realistic approach to reintroduction planning and implementation requires the dedicated efforts of multiple parties - especially those who are benefitting from use of the watershed’s considerable natural resources, and are in a position to provide ongoing leadership and stewardship into the future.
We developed the following Reintroduction Plan to address many of the fundamental science and management needs. We provide a general background on the Upper Yuba watershed and its
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current conditions (Chapter 1). We then furnish important biological information on the target fish species: Central Valley spring-run Chinook Salmon and Central Valley steelhead (Chapter 2), to understand their life-history requirements relative to the distribution of habitat (Chapter 3). We discuss the role of habitat connectivity given the existence of natural and man-made barriers to upstream and downstream migration (Chapter 4). We then begin to discuss the components of a reintroduction strategy by starting with stock selection (Chapter 5). RIPPLE, a habitat-based model developed by Stillwater Sciences for estimating juvenile salmonid production potential, was applied to the Upper Yuba Watershed (Chapter 6). The production potential was then evaluated in a full life-cycle model to simulate passage and survival through the San Francisco estuary, ocean, and back to the Upper Yuba- enabling the calculation of estimates of spawner abundances and cohort replacement rates (Chapter 7). Finally, we end with a recommended set of goals, objectives, and studies to be performed over three time periods for implementing the reintroduction of spring-run Chinook Salmon and steelhead to the Upper Yuba watershed (Chapter 8).
More work needs to be done to further develop the reintroduction plan, including a more in- depth treatment of the following issues:
The history of watershed development, including dams and diversions;
The updated status of anadromous species in the Yuba River from the standpoint of regulatory and management issues necessary to allow for an effective reintroduction program;
The philosophy, practicality, and approach to reintroduction planning and implementation efforts;
The architecture and organization of reintroduction program management structures, via public-private partnership, cooperative management actions, and active engagement of interested stakeholder parties;
Identification of funding sources, required permitting and regulatory processes, and more detailed scheduling of specific implementation steps once a project design and implementation plan is agreed upon by stakeholders.
Now that this initial Upper Yuba River Reintroduction Plan is available, we hope that all stakeholders will continue to engage in collaborative efforts, and take the next steps toward planning, design, and implementation of a successful program to assist in the recovery of Central Valley spring-run Chinook Salmon and steelhead.
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EXECUTIVE SUMMARY
This document represents a first generation Plan for the reintroduction of spring-run Chinook Salmon and steelhead to historic habitats in the upper Yuba River watersheds. The aim is to develop strategies and implementable actions to promote recovery of these fish species. The details and information contained in this Plan are the culmination of several years of interactions in resource management forums, scientific study, engineering analysis, and synthesis of relevant information from a variety of sources.
California’s Central Valley (CV) spring-run Chinook Salmon and steelhead were listed by the National Marine Fisheries Service (NMFS) as threatened species under the federal Endangered Species Act (ESA) in 1999. Both designations were affirmed and continued in a recent (2011) status review. ESA Section 4(f) mandates the development and implementation of recovery plans for listed species - a process that is underway. NMFS publicly released a draft Central Valley Recovery Plan document that provides strategies and guidance for recovery of listed anadromous fishes in Central Valley watersheds. As part of the recovery planning process, the Yuba River is identified as a high priority watershed for recovery actions, specifically including actions associated with reintroduction of spring-run Chinook Salmon and steelhead upstream of Englebright Dam. In addition, the riverine habitats upstream of Englebright Dam are designated as essential fish habitat for Chinook salmon under the essential fish habitats amendments to the Magnuson-Stevens Fisheries Conservation and Management Act, lending further support to reintroduction planning.
The upper and lower Yuba River habitats are highly fragmented and hydrologically altered by the presence and operations of dams. Therefore, the distribution of existing (or potential) habitat for anadromous salmonids in the Upper Yuba River basin is a function of both connectivity between upstream and downstream sub-basins and the quality of available habitat. Englebright Dam blocks upstream fish migration at River Mile (RM) 23.9 on the Yuba River. Assuming fish passage was provided at downstream barriers, New Bullards Bar Dam prevents upstream migrating fish from accessing the majority of the North Yuba River basin; Our House Diversion Dam prevents the upstream passage of fish at RM 12.0 on the Middle Yuba River; and Log Cabin Diversion Dam prevents the upstream passage of fish at RM 4.1 on Oregon Creek. While the success of anadromous fish reintroduction(s) to any or all of these areas would generally depend on the development of effective fish passage facilities, it is certain that providing connectivity to (and from) selected upstream habitats is critical to expanding available habitat for spring-run Chinook Salmon and steelhead.
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We developed this Reintroduction Plan (Plan) for the Yuba River with several goals in mind. First, the overall goal for implementation of a reintroduction strategy in the Yuba River basin is to improve the overall viability status for the Central Valley spring-run Chinook Salmon Evolutionarily Significant Unit (ESU) and California Central Valley steelhead Distinct Population Segment (DPS) so that they may be removed from federal protection under ESA, and so they will sustain long-term persistence and evolutionary potential. Second, the short-term goal is to increase the geographic distribution and abundance of ESA listed species by using habitat located upstream of Englebright Dam. Third, the long-term goal is to increase abundance, productivity, and spatial distribution, and to improve the life history and genetic diversity of the CV spring-run Chinook Salmon ESU and steelhead DPS. These goals are consistent with fundamental tenets of Viable Salmonid Population Theory as put forward by the National Marine Fisheries Service (McElhany et al. 2000) to guide reintroduction and recovery actions.
The Plan was constructed with several objectives in mind: (1) identify the reintroduction potential in stream sub-basins above Englebright Dam where existing information and professional judgment indicate a reasonable expectation of salmonid survival; (2) evaluate the number of reintroduced spring-run Chinook Salmon predicted to return to the Yuba river using models of production and survival throughout the entire salmonid life-cycle; (3) describe a pilot program that can commence in the near term (2-3 years) to identify critical issues to reintroducing anadromous fish to targeted areas of the watershed above Englebright Dam; (4) describe a short-term reintroduction strategy, focused on the most feasible reintroduction options under current conditions, as well as alternate scenarios that include supplemental instream flows or construction of fish passage facilities; (5) describe a long-term management and operations framework that will enable the program to continue into the future; and (6) describe how to utilize adaptive management to ensure that specific objectives of the reintroduction program can be informed through experiments and monitoring at each phase of the reintroduction.
Successful reintroduction of Central Valley spring-run Chinook Salmon and steelhead to historic habitats upstream of high head dams is contingent on re-establishing habitat connectivity in both upstream and downstream directions. As a means to this end, removal of certain dams can be considered as one form of fish passage, but because of the need to balance fisheries recovery actions with other beneficial uses of watershed resources, other forms of fish passage must be considered as well. Englebright Dam and its associated hydroelectric complex, for instance, is an impassable barrier to upstream migration for anadromous salmonids and other migratory fish. There are a variety of strategies that can be applied to passing fish upstream of Englebright Dam; and each of the strategies is tied to assessments of the targeted areas in the upper watershed
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where fish passage methods and habitat productivity have been evaluated. For purposes of this Plan, the Upper Yuba River basin is comprised of four sub-basins upstream of Englebright Dam – the North Yuba (NY), Middle Yuba (MY), and South Yuba (SY) rivers, as well as a “mainstem” section (NBB) between New Bullards Bar Dam (NBDD) and Englebright Dam (ED).
The quality of connected habitat will be a determining factor in the ultimate success of any fish reintroduction. Under existing conditions, juvenile salmonids passing downstream from the Upper Yuba to below Englebright Dam are exposed to mortality factors much different than would be encountered in a free-flowing system. Depending on their migratory pathway, juvenile fish could encounter reservoirs, dams, turbines, spillways, and bypass facilities. In addition, instream flows in parts of the upper Yuba watershed are substantially altered by hydropower operations. Therefore, reduced flows and higher summer water temperatures are important concerns, especially during critically dry years in certain sub-basins. Under current water management conditions, the distribution of suitable habitats is limited by flow and water temperature. Water diversion and flow regulation constrains habitat quantity by reducing the amount of wetted area and increasing water temperature. These are the existing conditions in the South Yuba, Middle Yuba, and New Bullards Bar stream reaches. Flows discharged from the upper watershed’s hydropower dams are generally characterized by low and consistent (regulated) summer flows from mid-July through October, with distinct winter storm peaks and spring snowmelt runoff events that vary in timing, frequency, magnitude, and duration according to regional climate cycles.
Potential stock sources for reintroduction into the Yuba River basin may be comprised of eggs, juvenile, and adult Chinook salmon and steelhead from one or more source populations, and may either be of natural or hatchery origin. There are three stocks of spring-run Chinook Salmon in the Central Valley that we consider to be the most appropriate donor sources for reintroduction in the upper Yuba River watershed: the Butte Creek stock, the Mill Creek/Deer Creek stock, and the Feather River stock. This conclusion is consistent with the recommendation of the San Joaquin River Restoration Program (SJRRP) Stock Selection Strategy (SJRRP 2010). Because spring-run Chinook Salmon from different populations vary with respect to important traits such as run timing, spawn timing, and natal fidelity, a reintroduced population with a wide variety of these and other traits would maximize adaptation potential. There is likely significant potential for evolution of traits to occur as a result of the strong, novel selective pressures that would be experienced by fish reintroduced to the upper Yuba River watershed. For these reasons, the SJRRP Stock Selection Strategy (SJRRP 2010) recommends that a simultaneous multiple stock reintroduction experiment be pursued as part of an adaptive management program. The multi-
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stock approach would include the Deer/Mill Creek, Butte Creek, and Feather River spring-run Chinook Salmon stocks. While genetic management plans are being constructed for CV spring- run Chinook Salmon for reintroduction, less information is available for developing such management plans for CV steelhead. Central Valley steelhead may have had substantial genetic diversity in historical populations within the DPS, but much of this is believed to have been lost because of the existence of dams (Lindley et al. 2006). Remaining steelhead in Central Valley DPS streams are critically depressed, with the anadromous form of O. mykiss being rare in some systems (CDFG 2008 as cited in NMFS 2009).
The biological production potential of the Upper Yuba River was evaluated with a habitat and juvenile production based model called RIPPLE (Stillwater Sciences 2013a). At the moderate smolt-to-adult survival parameter values used, predicted adult escapement was sufficient to fully seed available habitat for most model runs; therefore, RIPPLE production estimates represented juveniles at capacity. The RIPPLE model output also provided an estimate of the proportion of each juvenile life stage (efry- estuary-bound fry, smolt0 – sub-yearling migrant, and smolt1 – yearling migrant). The upper Yuba River watershed, upstream of Englebright Dam, was modeled in the four separate sub-basins described earlier: NY, MY, SY, and NBB. Three alternatives were evaluated: a “dry conditions scenario” (scenario D) and two “alternative water management scenarios” (scenarios S3 and S4) that represent potential future conditions by increasing flow and performing habitat enhancement measures to different degrees. Under alternative management scenarios 3 and 4 (S3 and S4), juvenile production from each sub-basin was predicted to increase substantially compared with the Dry Conditions scenario. RIPPLE model results indicated that substantial numbers of spring-run Chinook Salmon juveniles and smolts could be produced in the NY sub-basin under all scenarios; and likewise in the SY, MY, and New Bullards Bar (NBB) sub-basins under scenarios 3 and 4. The population production portion of the RIPPLE model was not run for steelhead due to data limitations. However, estimates of steelhead habitat capacity indicated the NY sub-basin has the potential to produce more steelhead than the SY and MY sub-basins; and the modeled production of steelhead on the SY and MY indicated substantial increases under the augmented flow scenarios. Importantly, the RIPPLE model did not explore the possibility that spring-run Chinook Salmon and steelhead may use the existing reservoirs as summer holding and rearing habitat. This is a potential behavior that should be investigated during the pilot experimentation phase, because it could substantially improve the productivity and survival outlook for both species in all sub-basins, particularly during drought years.
Because anadromous salmonids do not currently inhabit the Upper Yuba River basin, there is no contemporary biological information specific to this particular area. Therefore, information on
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Chinook salmon and steelhead for model development was based on: (1) populations in the Lower Yuba River or elsewhere in the Sacramento River Basin, (2) information gleaned from historical accounts, (3) information compiled from habitat studies of the upper watershed, and (4) any relevant information from native Sacramento River or hatchery stocks.
Juveniles that are produced in the Upper Yuba watershed sub-basins will need to emigrate downstream past existing dams and reservoirs, thence through the San Francisco estuary to the ocean where they will live and mature for two to four years. After maturation, adult survivors will need to complete their migration back to the Yuba River to habitat that is suitable for spawning in order to perpetuate the life-cycle. In addition to the intrinsic production potential and survival prospects for early life stages in the upper Yuba River, survival rates during the outmigration and estuarine/ocean phases of the life-cycle will also determine whether the population of spring-run Chinook Salmon on the Yuba River can be self-sustaining (i.e., every spawner produces enough offspring such that they are replaced by at least one other spawner). Because of the desire to examine reintroduction potential from the larger perspective of the entire salmonid life-cycle, a Life-cycle model was constructed to evaluate the likelihood of a self- sustaining population of spring-run Chinook Salmon on the Yuba River.
The Life-cycle model evaluated two passage alternatives: 1) a collection and transport program to the North Yuba; 2) construction of a fish ladder and juvenile downstream passage facilities at Englebright Dam and upstream and downstream passage facilities at Our House on the MY. Furthermore, each passage alternative incorporated several hydrologic scenarios as modeled in RIPPLE. It is important to note that these alternatives are not mutually exclusive, nor are they the only means to provide safe, timely, and effective passage for anadromous fish. Variations and combinations of these options are possible, including alternatives for fish passage modifications to certain barriers over time. The Life-cycle model generated initial hypotheses regarding passage and mortality rates that can be targeted through the pilot, short, and long-term phases of the Reintroduction Plan. The Life-cycle model utilized the juvenile production estimates from RIPPLE and used methods to account for uncertainty in survival and fish passage. These freshwater components were combined with estimates of delta and ocean survival to generate the full life-cycle dynamics, and thus predict the relative outcomes associated with various reintroduction scenarios.
Life-cycle model results indicated that providing successful fish passage (via collection and transport methods) to the upper NY could support self-sustaining populations of spring-run Chinook Salmon under dry, wet, and average flow conditions. In the MY, SY, and NBB sub- basins, passage at Englebright Dam would support self-sustaining populations under hydrologic
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flows and habitat enhancements as defined in alternative management scenarios S3 and S4. Of those three sub-basins under S3 and S4, the NBB and MY sub-basins are the most likely to support self-sustaining populations of spring-Chinook with productivity and abundances higher in the NBB reach relative to the MY. Regarding steelhead, it is assumed that steelhead (O. mykiss) would be more tolerant (than Chinook) of water temperatures and habitat conditions in the upper Yuba River watershed. This notion is supported by the RIPPLE model results, in-stream presence/absence surveys, and conventional biological knowledge. However, identifying and implementing successful fish passage facilities including effective collection and transport protocols is a significant challenge for reintroduction programs involving steelhead.
A three-phase reintroduction program framework is contained herein: (1) Pilot Experimentation Phase, (2) Short-Term Reintroduction Phase, and (3) Long-Term Reintroduction Phase. The results of simulation models suggest that successful spring-run Chinook Salmon and steelhead reintroductions are possible in some sub-basins depending on hydrologic conditions. As a result, it is important to conduct field experiments to evaluate the key assumptions that were made in support of the RIPPLE model and the Life-cycle model. Accordingly, an initial pilot experimentation phase (first 2-3 years) is recommended to conduct focused studies that will attempt to validate assumptions and identify any critical factors that would severely limit the likelihood of a successful reintroduction. This phase can commence without delay, and it is the next logical step in development of a phased reintroduction program. Next, the short-term reintroduction phase will feature science and engineering evaluations over a period of approximately 9-12 years (3 to 4 generations) by focusing on evaluating population vital rates (survival, reproduction, migration) and fish passage performance. During the early part of the short-term experimentation period, interim fish passage facilities will be designed, constructed, and operated with the intent to allow for later facility development and added capabilities. Finally, the long-term reintroduction phase covers the subsequent 12-20 + years and focuses on improving performance of the fish passage system, understanding evolutionary and genetic factors, and evaluating long term viability of the reintroduced population.
Successful reintroduction of anadromous salmon will be the product of iterative experimentation and refinement of program components. The intent of using a discretely “phased reintroduction process” is to ensure that actions taken in early stages can be used to inform decisions required by later stages of the program. Through passive and active adaptive management, the ability to learn about the reintroduction potential of the Upper Yuba watershed can be evaluated in light of the costs to obtain such information. The use of the adaptive management framework can therefore help guide the allocation of resources to those experiments, studies, and facility designs that provide the best gains in terms of overall cost and performance.
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1. INTRODUCTION
1.1 BACKGROUND AND OBJECTIVE The purpose of this document is to synthesize existing and recently developed scientific and engineering information into a Plan that can guide reintroduction of spring-run Chinook Salmon and steelhead to their historic habitats in the upper Yuba River.
Operation and maintenance of dams can hinder or preclude fish access to stream sub-basins, which historically provided holding, spawning, incubation and rearing habitats. In addition to the effects of harvest, hatcheries, and habitat degradation, the effects of hydropower dams and other water and sediment control facilities have contributed to the significant decline of Central Valley salmon since the mid-1800s. In the Yuba River, which is the focus of this Plan, Englebright Dam and its associated Narrows 1 & 2 hydroelectric complex presents an impassable barrier to upstream migration for anadromous salmonids and marks the upstream extent of currently accessible Chinook salmon habitat. Downstream from the Englebright- Narrows facilities, Daguerre Point Dam is a partial barrier to upstream migration of anadromous salmonids, and a complete barrier to anadromous Green Sturgeon. Other dams, located further upstream from the Englebright-Narrows facilities, also constrain fish movements or exert control over instream flows. These facilities and their operations have important implications for the fish reintroduction planning process. All of these facilities are addressed in this Plan, along with a menu of considered fish passage solutions and reintroduction strategies that may be advanced in the future.
Spring-run Chinook Salmon and steelhead are listed as threatened species under the federal Endangered Species Act. Recovery of the Evolutionarily Significant Unit (ESU) of Central Valley (CV) spring-run Chinook Salmon (Oncorhynchus tshawytscha) and the Distinct Population Segment (DPS) of CV steelhead (Oncorhynchus mykiss) requires a strategic approach to address multiple environmental and biological stressors. Rather than attempt to address every stressor for each species across the entire Central Valley ESU, the National Marine Fisheries Service (NMFS) identified specific actions that have the highest likelihood of alleviating those stressors with the most significant effects on the species. Anadromous fish passage and successful reintroduction to the upper Yuba River watershed is one of those identified actions that would contribute significantly to the recovery of these listed species (NMFS 2009).
There are several constraints that affect the successful reintroduction of anadromous fish and establishment of naturally-reproducing, self-sustaining fish populations. The number, size, and spatial arrangement of barriers will largely determine reintroduction pathways and may require
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prioritization among alternative options. Habitat quality within newly accessible habitats will ultimately govern the reproductive success of introduced fish and egg-to-smolt survival. Survival during migration through multiple migratory pathways will have a large influence on successful reintroductions. In addition, the selection of a source population, management during colonization, and the time frame needed to achieve recovery are all factors that affect reintroduction success (McClure et al. 2011). Therefore, a Fish Passage Evaluation and Assessment needs to be developed to look more closely at the details of spring-run Chinook Salmon and steelhead passage upstream of Daguerre Point, Englebright, New Bullards Bar, Log Cabin, and Our House dams. The assessment will combine the efforts of experienced fish passage engineers and biologists to develop information necessary for consideration and development of specific fish passage options for the Northern Sierra Diversity Group of Central Valley steelhead and spring-run Chinook Salmon in order to determine the best location for reintroducing these fish.
Programs to conduct large-scale reintroduction of anadromous fish require an articulation of goals. The goals presented here are consistent with the principles of Viable Salmonid Population (VSP) theory as presented by McElhany et al. (2000). As an approach to determining the conservation status of salmonids, NMFS developed the VSP analytical framework for identifying attributes of a viable salmonid population. One of the intents of this framework is to provide resource managers with the ability to assess the effects of management and conservation actions and ensure their actions effectively promote the listed species’ survival and recovery. The VSP conceptual model measures population performance and viability in terms of four key parameters: abundance, population growth rate, spatial structure, and diversity.
By applying ESA recovery mandates and VSP conservation principles to the Yuba River Reintroduction Plan, we offer the following goals as a logical starting point:
The broad, overarching goal for implementation of a reintroduction strategy in the Yuba River basin is to improve the overall viability for populations of the Central Valley Spring-run Chinook Salmon ESU and California Central Valley Steelhead DPS so that they will sustain long-term persistence and evolutionary potential, and be removed from federal protection under the Endangered Species Act.
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This overall goal statement may be further articulated as a set of short-term and long-term goals that are more specific to the Yuba River:
The short-term goal is to increase the geographic distribution, and abundance of listed species, with particular focus on areas of the upper Yuba River targeted for reintroduction actions.
The long-term goal is to increase abundance, productivity, and spatial distribution, and to improve the life history and genetic diversity of the target species in the Yuba River watershed.
The goals are presented here are general in nature. To complement these goals, quantitative and qualitative objectives are discussed in subsequent sections of this document.
The following paragraphs provide a brief chronology of some significant actions that are central to this reintroduction plan: In 2009, NMFS released a draft recovery plan for Central Valley salmon and steelhead that specifically addresses recovery goals and needs for CV spring-run Chinook Salmon and CV steelhead (NMFS 2009). The draft plan states that reintroducing spring-run Chinook Salmon and steelhead populations into the upper Yuba River basin above Englebright Dam would contribute to the recovery of both species by increasing their abundance, improving their spatial structure and diversity, and reducing their overall extinction risk.
In 2010, NMFS organized a multi-stakeholder group known as the Yuba Salmon Forum (YSF). The YSF is comprised of representatives of more than 15 different stakeholder groups including water users, environmental groups, tribal interests, and state and federal resource agencies. Between 2010 and 2013, the YSF’s Technical Working Group conducted extensive field studies, hydrologic analysis, and preliminary engineering work to add to the base of knowledge needed to evaluate the production potential, as well as the costs and benefits of various anadromous fish reintroduction alternatives in the upper Yuba River. The Yuba Salmon Forum provides an organizational framework that is suitable to evolve into a management forum should reintroduction programs be instituted. Such an organizational structure would need to be integrated with other management activities in the Yuba River, such as the lower Yuba River Management Team (RMT) sponsored by Yuba County Water Agency (YCWA).
To investigate possible fish passage engineering alternatives, NMFS sponsored a pilot reintroduction study by Montgomery-Watson-Harza, Inc. titled: Yuba River Fish Passage: Conceptual Engineering Options (MWH 2010). The purpose of the study was to begin the
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process of looking at viable modes of anadromous fish passage in the Yuba River, and to describe potential facilities and preliminary cost estimates for systems that could feasibly be implemented according to a number of future management scenarios.
In 2012, another NMFS-sponsored reintroduction study was published by Stillwater Sciences, Inc. titled: Modeling Habitat Capacity and Population Productivity for Spring-run Chinook Salmon and Steelhead in the Upper Yuba River Watershed (aka: RIPPLE habitat assessment model) (Stillwater Sciences 2012). The study included areas upstream of existing dams (e.g., Englebright, New Bullards Bar, Our House, and Log Cabin dams) and included reaches upstream of minor fish passage obstacles that could reasonably be remediated for fish passage. This study was subsequently revised in 2013 based on stakeholder feedback. The Revised Technical Report featured updated information, a detailed sensitivity analysis, and more refined modeling scenarios (Stillwater Sciences 2013a).
In 2012, NMFS initiated two additional studies to help inform decision-making about fish passage options and reintroduction plan alternatives. The first study is titled: Yuba River Fish Passage Improvement Investigation, Gathard Engineering Consulting (2014). The second study is titled: Modeling Sediment Transport Dynamics and Evaluating Flood Risks in the Yuba and Feather Rivers, California, Following Modifications to Englebright and Daguerre Point Dams, Stillwater Sciences (2013b). These studies are complementary in nature. The first study focuses on engineering aspects of dam removal or dam modification as a means to provide improved anadromous fish passage. The second study uses sediment transport modeling techniques to evaluate the flood risks of dam modification scenarios. Both studies are intended to increase the knowledge base and broaden the scope of potential options available for providing safe, timely, and effective passage for anadromous fish to the upper Yuba River.
Other important activities and studies associated with reintroduction efforts on the Yuba River included: Evaluation of Habitat and Opportunities for Reintroduction on the Yuba River (UYRSPST 2007). Also, as part of the YCWA Yuba River Project relicensing submittal to the Federal Energy Regulatory Commission (FERC), there was an evaluation of natural potential barriers to migration above Englebright Dam on the Yuba River, North Yuba, Middle Yuba, and Oregon Creek (HDR 2012). In addition, several other habitat and fish passage studies have been performed by consultants involved in FERC relicensing, and to the support work of Yuba Salmon Forum Technical Work Group. These studies were reviewed and considered in formulating the findings in this Plan.
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Finally, NMFS sponsored a contract to develop a phased anadromous salmonid reintroduction plan for the Upper Yuba River, which this document represents. It is intended to be a living document in the sense that other stakeholders are encouraged to evaluate the concepts and information presented herein, and engage in collaborative efforts to further develop and refine the Plan to a point where it can serve as a comprehensive guidance document for a successful anadromous fish reintroduction program.
We originally set out to develop this phased reintroduction planning effort with several specific objectives in mind: 1) identify the reintroduction potential in stream sub-basins above Englebright Dam where existing information and professional judgment indicate a reasonable expectation of salmonid survival; 2) describe a pilot reintroduction program that can commence in the near term (2-3 years) to reintroduce anadromous fish to targeted areas of the watershed above Englebright Dam with detail on approaches, methods, and materials; 3) describe a short- term reintroduction strategy focused on the most feasible reintroduction options under current conditions, as well as alternatives that may include supplemental instream flows or construction of fish passage facilities; 4) evaluate the relative number of reintroduced spring-run Chinook Salmon forecasted to return to the Yuba river to spawn under different hydrologic and habitat restoration scenarios by coupling the juvenile production potential with a full life-cycle model for spring-run Chinook Salmon; 5) describe a long-term management and operations framework that will enable the program to continue into the future; and 6) describe how to utilize adaptive management to ensure that specific objectives of the reintroduction can be informed through experiments and monitoring at each phase of the reintroduction.
This reintroduction plan is targeted at establishing a population of the Central Valley spring-run Chinook Salmon ESU and the Central Valley steelhead DPS in the upper Yuba River watershed. The scientific rationale behind a planned reintroduction is to reduce the risk of extinction, and promote recovery of the ESU of CV spring-run Chinook Salmon and the DPS of CV steelhead. The reintroduction thus spreads the risk of extinction among two or more populations, increasing the viability of the entire ESU/DPS. The degree to which the reintroduced population can spread the risk of extinction is dependent upon how the reintroduced population responds to anthropogenic and environmental driving variables; populations that act independently provide the greatest degree of risk reduction, whereas populations that act identically only reduce risk through spatial expansion. The most straightforward manner in which a reintroduction can reduce the risk of ESU/DPS extinctions is by adding self-sustaining populations to the ESUs of spring-run Chinook Salmon and DPS of steelhead. The Yuba River is located within the Northern Sierra Nevada Diversity Group, and NMFS Draft Recovery Plan indicates that at least
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2 viable populations should be established within each of the diversity groups to achieve recovery (NMFS 2009).
A quantitative framework for evaluating the viability of ESUs/DPSs was developed for CV steelhead and CV Chinook Salmon stocks in the Central Valley by Lindley et al. (2007). The goal of the effort was to provide specific, quantitative criteria by which CV Chinook Salmon and CV steelhead could be evaluated for listing and delisting under the ESA. As Lindley et al. (2007) note, “The ESA, as amended in 1988, requires that recovery plans have quantitative, objective criteria that define when a species can be removed from the list, but does not offer detailed guidance on how to define recovery criteria.” Lindley et al. (2007) provide several key quantitative metrics by which the viability can be evaluated:
1. Extinction risk from population viability analysis 2. Population size 3. Population decline 4. Catastrophe rate and effect 5. Hatchery influence
CV spring-run Chinook Salmon in the Central Valley are currently not viable; CV spring-run Chinook Salmon are vulnerable to catastrophic disturbances due to the relatively few existing populations and their spatial proximity to each other (Lindley et al. 2007). In particular, Lindley et al. (2007) found that volcanic activity from Mt. Lassen, exposure to regional drought, and wildfires could provide a catastrophic event that would affect all the CV spring-run Chinook Salmon populations simultaneously. The DPS of CV steelhead were not evaluated for viability in Lindley et al. (2007) due to data limitations on the 80 or so DPS thought to inhabit the Central Valley. However, the listing status (threatened species) by definition means that the DPS of CV steelhead is likely to become endangered, with extinction in the foreseeable future, unless definitive management actions are instituted to reverse the population decline and promote recovery.
1.2 ACTION AREA For the purposes of this reintroduction plan, the Upper Yuba River basin is comprised of four sub-basins upstream of Englebright Dam, the North Yuba (NY), Middle Yuba (MY), and South Yuba (SY) rivers, as well as a “mainstem” section (NBB) between Englebright Dam and New Bullards Bar Dam (NBBD) (Figure 1-1). Sub-basin boundaries were defined by hydrologic breaks and complete upstream passage barriers believed to limit passage irrespective of flow conditions, as described by Vogel (2006) and Yoshiyama et al. (2001). These sub-basins are
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Figure 1-1. Map of the Upper Yuba River Basin and associated sub-basins.
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consistent with the boundaries used for the RIPPLE salmonid population dynamics modeling effort (Stillwater Sciences 2013a). Based on these boundaries, the action area sub-basins are:
New Bullards Bar Dam sub-basin (NBB): Upstream of the reservoir created by Englebright Dam beyond the NY and MY confluence (Yuba River RM 39.6) to New Bullards Bar Dam (North Yuba River RM 2.2).
South Yuba sub-basin (SY): From the confluence with Yuba River Mainstem at Englebright Reservoir (South Yuba River RM 0.0) upstream to first complete barrier at South Yuba River RM 35.7.
Middle Yuba sub-basin (MY): From confluence with North Yuba River (Middle Yuba River RM 0.0) upstream to first complete barrier at Middle Yuba River RM 35.1. The MY sub-basin is further divided into sub-basins between the mouth of the MY and Our House Dam (MYL) and between Our House Dam and the first complete barrier at RM 35.1 (MYU). North Yuba sub-basin (NY): From New Bullards Bar Dam (North Yuba River RM 2.2) upstream to first complete barrier at Loves Falls (North Yuba River RM 51).
Englebright Reservoir and associated tributaries downstream of Rice’s Crossing (Yuba River RM 32) were not included in the RIPPLE Model (Stillwater Sciences 2013a) and are not included here in the NBB sub-basin. Additional sub-basins that were excluded from the RIPPLE Model are upper portions of the SY, MY, and NY that are upstream of the first complete natural barriers in each sub-basin. These areas upstream of complete natural barriers are not directly relevant to the Plan in terms of primary spawning and holding habitats for anadromous fish, and so they are also excluded here.
1.3 LAND USE Lands in the Upper Yuba River basin are comprised of a patchwork of ownership (YCWA 2010). Much of the higher elevation areas upstream of Englebright Dam are public lands managed by the U.S. Department of Agriculture, U.S. Forest Service (Forest Service) as parts of the Plumas National Forest and Tahoe National Forest. We refer to the higher elevation lands under management by the U.S. Forest Service surrounding the Upper Yuba as National Forest Lands (NFL). At elevations above 3,000 feet, other land managers and owners include private corporations such as timber companies. At elevations below 3,000 feet, land is mostly privately owned. However, small portions are owned and managed by the Forest Service as part of National Forest Lands (NFL), or administered by the U.S. Department of the Interior, Bureau of Land Management (BLM) as part of the Sierra Resource Management Area. Lands managed by federal agencies are administered according to their respective resource management plans that include the Land and Resource Management Plans for each respective National Forest and the
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Sierra Resource Management Plan for BLM. Within the NFL, land is primarily managed for timber, grazing, and recreation. For private land within the Upper Yuba River basin, land use policies are primarily established by the counties. The majority of Yuba, Sierra and Nevada county lands upstream of Englebright Reservoir are primarily designated for agricultural, timber, grazing, and open space uses. Intensive hydraulic mining, logging, water impoundment and diversion, and other anthropogenic disturbances have occurred in the Upper Yuba River basin since the beginning of the Gold Rush era (Stillwater Sciences 2013a). Hydraulic mining resulted in large increases in sediment loads and extensive downstream channel aggradation.
1.4 HYDROLOGY In the Upper Yuba River Basin, flows are generally characterized by low and consistent summer flow (generally mid-July through October), winter storm peaks, and spring snowmelt runoff (Stillwater Sciences 2013a) (Figure 1-2, Figure 1-3). Flows in the Upper Yuba River Basin are affected by diversions out of basin or diversion to storage within basin, particularly in the South Yuba and Middle Yuba rivers where there are numerous dams and associated water conveyance systems. The upper reaches of the North Yuba River and tributaries are largely unregulated until flows are captured downstream by the New Bullards Bar Dam and reservoir, which is located at North Yuba River RM 2.2. There is also diversion of approximately 100,000 AF from Slate Creek (a tributary entering just upstream of New Bullards Bar Reservoir) to the Feather River watershed, by the South Feather Power Hydroelectric Project, P-2088. The North Yuba River has larger flow peaks and a more pronounced spring runoff than the South Yuba and Middle Yuba rivers. However, hydrographs for the North Yuba, Middle Yuba, and South Yuba rivers show similar timing, duration, and frequency of runoff (Figure 1-4). The three sub-basins also have similar peak flow magnitudes on a per unit drainage area basis for return intervals of 2–10 years (Stillwater Sciences 2013a).
In the North Yuba River downstream of New Bullards Bar Dam and in much of the South Yuba and Middle Yuba rivers, seasonal flows are frequently controlled by water releases from upstream dams. These upstream dams and reservoirs have limited capacity to store water, however, so fill and spill events occur periodically, even in relatively dry water years. Such facilities in the South Yuba basin include Spaulding Dam which impounds Lake Spaulding and Bowman Dam on Canyon Creek. Lake Spaulding receives water from Bowman Lake through the Bowman-Spaulding Canal. Flows in the South Yuba River are largely regulated by releases from Spaulding and Bowman dams. On the Middle Yuba River, Jackson Meadows Dam and Milton Dam are the major water storage and diversion facilities. Flows in the Middle Yuba River are largely regulated by these facilities which are located in the headwaters of the Middle
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Figure 1-2. Average monthly Yuba River flow at the Smartville gage (USGS 11418000) 0.5 of a mile downstream of Englebright Dam from WY 1970 through WY 2008 (Source: YCWA 2010).
Figure 1-3. Flow exceedance of historical mean daily streamflow for the Yuba River at the Smartville gage (USGS 11418000) 0.5 of a mile downstream of Englebright Dam from WY 1970 through WY 2008 (Source: YCWA 2010).
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5,000 North Yuba (#11413100) South Yuba (#11417500) Middle Yuba (#11408880)
4,000
3,000
2,000 Average daily discharge (cfs) for WY 1969-1987 (cfs) for discharge WY daily Average 1,000
0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Date Figure 1-4. Hydrographs for the South, Middle, and North Yuba rivers for the overlapping period of record (1969–1987). Source: Stillwater Sciences (2013a) from USGS gage data.
Yuba River. Our House Dam impounds water for diversion from the Middle Yuba River to Oregon Creek through the Lohman Ridge Tunnel and is located on the Middle Yuba River at RM 12.5. Log Cabin Dam is located on Oregon Creek, a tributary to the Middle Yuba River, and is used to divert water to New Bullards Bar Reservoir.
The network of dams and water control structures comprising the Yuba-Bear and Drum- Spaulding hydroelectric power projects in the Middle and South Yuba River can control and divert (away from the lower Yuba River) approximately 410,000 acre feet (annual average) from the upper reaches of the South and Middle Yuba Rivers. This amount of water is approximately 42% of the capacity of nearby Folsom reservoir – one of the largest impoundments in California’s Central Valley Project. Similarly, the North Yuba River is highly regulated by operations of New Bullards Bar Dam and its associated hydroelectric generating facilities, as part of the Yuba River Development Project. The New Bullards Bar reservoir captures all stream flow from the upstream reaches of North Yuba River, as well as diverted flows from Oregon Creek and the Middle Yuba River. The usable capacity of the New Bullards Bar reservoir is
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very large: up to 996,103 acre feet can be impounded and discharged according to a flow schedule which is managed primarily for power production, flood control, water supply, and fish habitat maintenance in the lower river. However, very little water is released directly from New Bullards Bar Dam itself. Instead, the river is diverted at the dam, and virtually all of its flow is bypassed through pipes and penstocks, in order to generate electricity about 10 miles downstream at the New Colgate hydroelectric plant. Currently, all of these large-scale hydroelectric projects are undergoing relicensing pursuant to the Federal Power Act and the Federal Energy Regulatory Commission’s (FERC) Integrated Licensing Process. FERC is responsible for establishing license conditions to ensure that hydroelectric facilities operate in a manner that balances all beneficial uses of the affected waterways, including power and non- power (natural) resources. Thus, with the exception of the upper North Yuba, modification of flows in the Upper Yuba requires coordination among the three projects and their stakeholders.
1.5 REGULATORY AND MANAGEMENT ISSUES
1.5.1 Federal ESA and California ESA: Listing Status
Spring-run Chinook Salmon1 On September 16, 1999, NMFS listed the Central Valley ESU of spring‐run Chinook salmon (Oncorhynchus tshawytscha) as a “threatened” species (64 FR 50394). On June 14, 2004, following a five-year species status review, NMFS proposed that the Central Valley spring-run Chinook Salmon remain listed as a threatened species based on the Biological Review Team strong majority opinion that the Central Valley spring-run Chinook ESU is ‘likely to become endangered within the foreseeable future’ due to the greatly reduced distribution of Central Valley spring-run Chinook Salmon and hatchery influences on the natural population. On June 28, 2005, NMFS reaffirmed the threatened status of the Central Valley spring-run Chinook Salmon ESU, and included the Feather River Fish Hatchery (FRFH) spring-run Chinook Salmon population as part of the Central Valley spring-run Chinook Salmon ESU (70 FR 37160).
In August 2011, NMFS completed a 5-year status review of the Central Valley spring‐run Chinook salmon ESU. Based on a review of available information, NMFS recommended that the Central Valley spring-run Chinook Salmon ESU remain classified as a threatened species. NMFS’ review also indicates that the biological status of the ESU has declined
1 Excerpted from U.S. Army Corps of Engineers, Yuba River Biological Assessment, excerpt from Chapter 5 January 2012 Page 5-3
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since the previous status review in 2005, and therefore, NMFS recommended that the ESU’s status be reassessed in 2 to 3 years if it does not respond positively to improvements in environmental conditions and management actions. As part of the 5-year review, NMFS also re-evaluated the status of the FRFH stock and concluded that it still should be considered part of the Central Valley spring-run Chinook Salmon ESU. According to NMFS (2009), critical habitat was designated for spring-run Chinook Salmon on September 2, 2005 (70 FR 52488), and includes stream reaches of the Feather and Yuba Rivers, Big Chico, Butte, Deer, Mill, Battle, Antelope, and Clear creeks, the Sacramento River, as well as portions of the northern Delta. Critical habitat for spring-run Chinook Salmon in the Yuba River extends from the confluence with the Feather River upstream to Englebright Dam.
In addition to federal regulations, the California Endangered Species Act (CESA, Fish and Game Code Sections 2050 to 2089) establishes various requirements and protections regarding species listed as threatened or endangered under state law. California’s Fish and Game Commission is responsible for maintaining lists of threatened and endangered species under CESA. Spring-run Chinook Salmon in the Sacramento River Drainage, including the Yuba River, was listed as a threatened species under CESA on February 2, 1999.
Central Valley Steelhead2 On March 19, 1998 (63 FR 13347) NMFS listed the California Central Valley steelhead ESU as “threatened,” concluding that the risks to Central Valley steelhead had diminished since the completion of the 1996 status review based on a review of existing and recently implemented state conservation efforts and federal management programs (e.g., CVPIA, AFRP, CALFED) that address key factors for the decline of this species. The California Central Valley steelhead ESU included all naturally spawned populations of steelhead in the Sacramento and San Joaquin rivers and their tributaries, but excluded steelhead from the tributaries of San Francisco and San Pablo Bays (NMFS 2004). On June 14, 2004, NMFS proposed listing determinations for 27 ESUs of West Coast salmon and O. mykiss, including the California Central Valley steelhead ESU. In the proposed rule, NMFS concluded that steelhead were not in danger of extinction, but were likely to become endangered within the foreseeable future throughout all or a significant portion of their range and, thus, proposed that steelhead remain listed as threatened under the ESA. Steelhead from the Coleman National Fish Hatchery and the FRFH, as well as resident populations of O. mykiss
2 Excerpted from U.S. Army Corps of Engineers, Yuba River Biological Assessment, excerpt from Chapter 5 January 2012 Page 5-104
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(Rainbow Trout) below impassible barriers that co-occur with anadromous populations, were included in the California Central Valley steelhead ESU and, therefore, also were included in the proposed listing.
During the 2004 comment period on the proposed listings, the U.S. Fish and Wildlife Service (USFWS) provided comments that the USFWS does not use NMFS’ ESU policy in any USFWS ESA listing decisions. As a result of the comments received, NMFS re-opened the comment period to receive comments on a proposed alternative approach to delineating “species” of West Coast O. mykiss (70 FR 67130). NMFS proposed to depart from past practice of applying the ESU Policy to O. mykiss stocks, and instead proposed to apply the Distinct Population Segment (DPS) Policy in determining “species” of O. mykiss for listing consideration. NMFS noted that within a discrete group of O. mykiss populations, the resident and anadromous life forms of O. mykiss remain “markedly separated” as a consequence of physical, physiological, ecological, and behavioral factors, and may therefore warrant delineation as separate DPSs (71 FR 834).
NMFS issued a policy for delineating distinct population segments of Pacific salmon in 1991 (56 FR 58612; November 20, 1991). Under this policy, a group of Pacific salmon populations is considered an “Evolutionarily Significant Unit” if it is substantially reproductively isolated from other conspecific populations, and it represents an important component in the evolutionary legacy of the biological species. Further, an ESU is considered to be a ‘Distinct Population Segment’ (and thus a “species”) under the ESA. In 1996, NMFS and USFWS adopted a joint policy for recognizing DPSs under the ESA (DPS Policy; 61 FR 4722; February 7, 1996). The DPS Policy adopted criteria similar to, but somewhat different from, those in the ESU Policy for determining when a group of vertebrates constitutes a DPS – The group must be discrete from other populations and it must be significant to its taxon. A group of organisms is discrete if it is “markedly separated from other populations of the same taxon as a consequence of physical, physiological, ecological, and behavioral factors.” Significance is measured with respect to the taxon (species or subspecies) as opposed to the full species (71 FR 834).
Although the ESU Policy did not by its terms apply to steelhead, the DPS Policy stated that NMFS will continue to implement the ESU Policy with respect to “Pacific salmonids” (which included O. mykiss). In a previous instance of shared jurisdiction over a species (Atlantic salmon), NMFS and USFWS used the DPS Policy in their determination to list the Gulf of Maine DPS of Atlantic salmon as endangered (65 FR 69459; November 17, 2000). Given NMFS and USFWS shared jurisdiction over O. mykiss, and consistent with joint NMFS and
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USFWS approaches for Atlantic salmon, it was concluded that application of the joint DPS policy was logical, reasonable, and appropriate for identifying DPSs of O. mykiss (71 FR 834). Moreover, NMFS determined that use of the ESU policy — originally intended for Pacific salmon — should not continue to be extended to O. mykiss, a type of salmonid with characteristics not typically exhibited by Pacific salmon (71 FR 834).
On January 5, 2006 NMFS issued a final decision that defined Central Valley steelhead as a DPS rather than an ESU, and retained the status of Central Valley steelhead as threatened (71 FR834). The DPS includes all naturally spawned anadromous O. mykiss (steelhead) populations below natural and manmade impassable barriers in the Sacramento and San Joaquin Rivers and their tributaries, excluding steelhead from San Francisco and San Pablo Bays and their tributaries (63 FR 13347). Steelhead in two artificial propagation programs – the Coleman National Fish Hatchery and FRFH steelhead hatchery programs – are considered to be part of the DPS. NMFS determined that these artificially propagated stocks are no more divergent relative to the local natural population(s) than what would be expected between closely related natural populations within the DPS (71 FR 834).
In August 2011, NMFS completed a 5-year status review of the Central Valley steelhead DPS. Based upon a review of available information, NMFS (2011) recommended that the Central Valley steelhead DPS remain classified as a threatened species. However, NMFS (2011c [sic]) also indicated that the biological status of the DPS has declined since the previous status review in 2005 and, therefore, NMFS recommend that the DPS’s status is reassessed in 2 to 3 years if it does not respond positively to improvements in environmental conditions and management actions. In the interim period, NMFS also recommended that the status of the DPS should be monitored and the most recent genetic information for the DPS, including information for the four steelhead hatchery stocks, should be reviewed to re- assess the DPS membership status of the Nimbus and Mokelumne River hatcheries. New information resulting from the genetics review should be incorporated into any updated status review for the DPS (NMFS 2011c [sic]).
On February 16, 2000 (65 FR 7764), NMFS published a final rule designating critical habitat for Central Valley steelhead. Critical habitat was designated to include all river reaches accessible to listed steelhead in the Sacramento and San Joaquin rivers and their tributaries in California, including the lower Yuba River upstream to Englebright Dam. NMFS proposed new Critical Habitat for spring-run Chinook Salmon and Central Valley steelhead on December 10, 2004 (69 FR 71880) and published a final rule designating critical habitat for these species on September 2, 2005. This critical habitat includes the
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lower Yuba River (70 FR 52488) from the confluence with the lower Feather River upstream to Englebright Dam.
1.5.2 Hydropower: Federal Power Act and FERC Licensing3 Stream flows in the Yuba River watershed have been controlled, altered, and modified since the late nineteenth century, beginning in earnest with the advent of the California gold rush era. Structures were built to facilitate hydraulic mining, and to attempt to address some negative impacts caused hydraulic mining debris flows. Other structures were constructed to provide mechanical and electric power and provide irrigation and drinking water, much of it exported out of the watershed. In accordance with Federal Power Act, many of these historic structures became part of federally-regulated hydroelectric power projects. Project works owned and operated by Nevada Irrigation District became the Yuba-Bear project, and those operated by Pacific Gas and Electric Company (PG&E) became the Drum-Spaulding project. A third large- scale hydropower project in the watershed is the Yuba River Development Project, owned and operated by the Yuba County Water Agency. Its facilities include: New Bullards Bar Dam on the North Yuba River, Our House Dam on the Middle Yuba River, Log Cabin Dam on Oregon Creek, as well as the New Colgate, Fish Release, and Narrows 2 hydroelectric power plants. Recently, Archon Energy of Canada filed a preliminary license application with FERC for a proposed 3MW power project at Daguerre Point Dam.
The Yuba-Bear and Drum-Spaulding Projects
The Yuba-Bear and Drum-Spaulding (YBDS) Integrated Licensing Process involves the combined relicensing of three hydroelectric projects. The Yuba-Bear Project (FERC #2266) is operated by the Nevada Irrigation District (NID). The Drum-Spaulding Project (FERC #2310) and the Rollins Transmission Line Project (FERC #2784) are operated by PG&E. For relicensing purposes, these projects have been combined because of their complex physical interconnectedness. In combination they include 38 on-stream reservoirs, 3 off stream impoundments, 5 diversion dams, many miles of canals, 16 powerhouses, 270 megawatts of electrical power generation, and more than 350,000 acre feet of water storage on the Middle Yuba, South Yuba, Bear, and North Fork American Rivers.
The YBDS relicensing process represents an opportunity to better balance the ecological, economic, and social demands on the Yuba, Bear, and North Fork American Rivers. Current FERC licenses for the YBDS projects were originally issued in 1963, and expired on April 30,
3 Information in this section was adapted with permission from South Yuba Citizens League web page at http://yubariver.org/restoration/dam-licensing/
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2013. FERC is authorizing continued operations under annual license extensions until a new license is issued. The terms of the new licenses will be in place for 30-50 years. FERC is responsible for establishing license conditions to ensure that hydroelectric facilities operate in a manner that balances all beneficial uses of the affected waterways, including power and non- power (natural) resources.
The Nevada Irrigation District, owner-operator of the Yuba-Bear Project, has stated their goal in the Yuba-Bear relicensing is to fulfill its mission to “provide a dependable, quality water supply, strive to be good stewards of the watershed, and conserve the available resources.” PG&E’s stated objective in the Drum-Spaulding relicensing is to obtain a new license that will “provide safe, economical, and reliable electric generation in a responsible and environmentally sensitive manner.”
The Yuba River Development Project
The Yuba River Development Project (FERC No. 2246) is owned and operated by the Yuba County Water Agency (YCWA). The project is located on the Yuba River, North Yuba River, Middle Yuba River, and Oregon Creek in Yuba County, California, and consists of 1 major reservoir (New Bullards Bar on the North Yuba River), 2 diversion dams (Our House Diversion Dam on the Middle Yuba River and Log Cabin Diversion Dam on Oregon Creek), 3 powerhouses (New Colgate, Fish Release and Narrows No. 2) and various recreation facilities. The Project generates up to 361.9 megawatts. The initial FERC license for the Project expires April 30, 2016. The Yuba River Development Project (YRDP) is also using FERC’s Integrated Licensing Process.
YCWA’s stated goal in the YRDP relicensing is to obtain, “…a new license with minimal adverse impact to Project economics, while helping to foster YCWA’s relationship with the community, resource agencies, and other interested parties. YCWA desires to obtain a new license of maximum term for the Project at a minimum cost (both initially and ongoing) that allows the Project to maximize profits from the production of electrical power while also meeting environmental, recreational, irrigation and other non-power requirements and needs.”
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NMFS Public Draft Central Valley Recovery Plan The NMFS produced a Draft Central Valley Recovery Plan4 for ESA-listed anadromous fishes which are under its jurisdiction in California, pursuant to section 4(f) of the Endangered Species Act.5 The Plan identifies currently unoccupied habitats that have been prioritized for potential anadromous fish reintroductions, and characterizes them as either primary areas, candidate areas, or areas that have been removed from consideration- based on the intrinsic or assessed potential of the habitats to support successful reintroduction actions. The Yuba River is cited as one of the primary areas for reintroduction of spring-run Chinook Salmon and steelhead within the Northern Sierra Nevada Diversity Group.
Englebright Dam, owned and operated by the U.S. Army Corps of Engineers, currently blocks access of anadromous fishes to habitat historically used by spring-run Chinook Salmon and steelhead. The Draft CV Recovery Plan includes the following Priority 1 Recovery Action:
“Develop and implement a program to reintroduce spring-run Chinook Salmon and steelhead to historic habitats upstream of Englebright Dam. The program should include feasibility studies, habitat evaluations, fish passage design studies, and a pilot reintroduction phase prior to implementation of the long-term reintroduction program.”
The Draft Recovery Plan also identifies some of the (non-flow-related) factors that influence the status of naturally-spawning spring-run Chinook Salmon and steelhead in the Yuba River:
1) blockage of historic spawning habitat resulting from the construction of the Corps’ Englebright Dam in 1941, which has implications for the spatial structure of the populations; 2) impaired adult upstream passage at Daguerre Point Dam; 3) high hatchery influence; 4) unsuitable spawning substrate in the uppermost area (i.e., Englebright Dam to the Narrows) of the lower Yuba River; 5) limited riparian habitats, riverine aquatic habitats for salmonid rearing, and natural river function and morphology; and 6) impaired juvenile downstream passage at Daguerre Point Dam.
4 Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-run Chinook Salmon and Central Valley Spring-run Chinook Salmon and the Distinct Population Segment of California Central Valley Steelhead, Public Draft, October 2009, National Marine Fisheries Service, Southwest Region, Sacramento, California. 5 ESA, 7 U.S.C. § 136, 16 U.S.C. § 1531 et seq
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These factors support the need to conduct habitat restoration and reintroduction programs for anadromous fish on the Yuba River as effective recovery actions.
The NMFS Public Draft Recovery Plan goes on to state:
“NMFS has prioritized the upper Yuba River (upstream of Englebright Dam) as a primary area to re-establish viable populations of spring-run Chinook Salmon and steelhead for several reasons. First, spring-run Chinook Salmon and steelhead historically occurred there (Lindley et al. 2004, Yoshiyama et al. 1996) and studies suggest that multiple areas in the upper river would currently still support those species (DWR 2007; Stillwater Sciences 2013a). Second, evidence suggests that significant amounts of summer holding habitat in the upper Yuba River are expected to remain thermally suitable for spring-run Chinook Salmon throughout the 21st century even if the climate warms by as much as 5°C (Lindley et al. 2007). That expectation of thermally suitable habitat in the upper Yuba River watershed in the face of climate change is based on a simple analysis of air temperatures and did not account for the presence of New Bullard’s Bar Reservoir, a deep, steep-sloped reservoir with ample coldwater pool reserves that could be used to provide suitable flows and water temperatures in the upper watershed downstream of the reservoir in perpetuity. The coldwater pool in New Bullards Bar Reservoir has never been depleted, even during the most extreme critically dry year on record (1977) (YCWA 2010). Third, there is considerable distance between the Yuba River watershed and the cluster of watersheds in the diversity group that currently support wild spring-run Chinook Salmon. This spatial isolation is important because if one or more spring-run Chinook Salmon populations were established in the upper Yuba River watershed, those populations would not be at risk if there was a volcanic eruption at Mt. Lassen, a volcano that the USGS views as highly dangerous. In contrast, all three extant independent populations (Mill, Deer, and Butte creeks) of spring- run Chinook Salmon are in basins whose headwaters occur within the debris and pyroclastic flow radii of Mt. Lassen. Even wildfires, which are of much smaller scale than large volcanic eruptions, pose a significant threat to the spring-run Chinook Salmon ESU in its current configuration. A fire large enough to burn the headwaters of Mill, Deer and Butte creeks simultaneously, has roughly a 10% chance of occurring somewhere in the Central Valley each year (Lindley et al. 2007). Fourth, the Yuba River watershed has an ample supply of water to support spring-run Chinook Salmon and steelhead with one of the highest annual discharges (~2,300,000 acre-feet/year) in the Central Valley (Lindley et al. 2004). Lastly, there is potential to modify or remove Englebright Dam in order to provide volitional fish passage to and from the upper watershed. Allowing for volitional fish passage to the
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upper watershed is the only way to establish a self-sustaining population, but the challenges with doing so may cause non-volitional fish passage options to be selected.”
Yuba Salmon Forum The Yuba Salmon Forum was established as a stakeholder forum to seek consensus regarding the complex natural resource management issues associated with the Yuba River watershed. The first meeting took place in February 2010, featuring representatives of 15 different stakeholder groups – including water and hydropower interests, environmental groups, tribal representatives, and federal and state resource agencies. Professional facilitation was provided by Kearns & West, Inc., who produced a “Convening Report” in September 2010. In reaction to the initial participant interview process, the facilitators included the following observations in their Report:
“Numerous (participants) see the forum as an opportunity to look at the Yuba watershed in a comprehensive manner. They suggest that the forum should seek creative ways of using water that is available and look for restoration opportunities throughout the watershed. Some noted that making water available for fish does not have to mean that other parties lose access to it for their own purposes. Others expressed a deep interest in the forum keeping in mind the impacts and opportunities that involve parties out of the basin, including the HEA from the Oroville relicensing and the Western Placer creeks.”6 and:
“Recovery of anadromous fish and water resource management in the Yuba River watershed presents a complex set of topics that deserves serious, dedicated attention and requires a complex set of process recommendations. People care deeply about these issues and are dedicated to identifying and implementing long-term solutions that improve and protect resources for future generations.”7
The Yuba Salmon Forum members produced a joint document on September 29, 2010 called: “Proposed Process and Organizational Outline” (or, draft Charter) which has become a working guidance document for the group’s regular activities and discussions. The draft Charter describes the Yuba Salmon Forum process and protocols for participating in it. It is “…intended to provide a framework for participation, cooperation, communication, and decision-making among Forum participants” (section 1.0).
6 Kearns & West/Yuba River Multi-Party Forum Final Convening Report/September 2010, p. 18 7 Ibid., p. 23
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The draft YSF Charter states that:
“The purpose of the Forum will be to identify, evaluate, recommend, and seek to achieve implementation of effective near-term and long-term actions to achieve viable salmonid populations in the Yuba River watershed to contribute to recovery goals, while also considering other beneficial uses of water resources and habitat values in neighboring watersheds, as part of Central Valley salmonid recovery actions”
Following the initial organizational activities of 2010, the YSF concentrated on filling key scientific information gaps and developing a common set of understandings among participating groups. The scientific and technical sub-group conducted extensive field studies and analysis between 2011-2012. Data was collected, interpreted, and presented in Forum meetings throughout 2012 and 2013; and the Forum members continue to discuss the meaning and implications of the results, along with new information that is coming available. It is hoped that this “first generation reintroduction plan” will be thoughtfully appraised by the Yuba Salmon Forum, and the Forum may choose to use it as a guidance document, and perhaps seek to refine it for ultimate implementation as a comprehensive reintroduction plan.
The Yuba Salmon Forum continues to convene on a regular basis, with long-standing participants representing the key interest groups still engaged. As such, the YSF continues to represent a nucleus for collaborative discussions, jointly-conducted scientific studies, and information-sharing. The YSF has the potential to evolve into a settlement forum with respect to outstanding resource management issues in the Yuba basin, as well as a long-term science and management collaborative that can effectively implement an agreed upon reintroduction plan.
1.6 STRUCTURAL FEATURES AND FACILITIES Within the action area considered for reintroduction, dams that represent fish passage barriers are, from downstream to upstream: Daguerre Point Dam (Yuba River RM 11.5) and Englebright Dam (Yuba River RM 23.9), owned by USACE; and New Bullards Bar Dam (North Yuba River RM 2.3), Our House Diversion Dam (Middle Yuba River RM 12.0), and Log Cabin Diversion Dam (Oregon Creek RM 4.1, a tributary to the Middle Yuba River), owned by YCWA as part of FERC P-2246. Brief descriptions of each feature, as related to anadromous salmonid reintroduction and fish passage issues, are provided in the following sections. Structural and physical features of dams and reservoirs that influence the feasibility and appropriate designs of fish passage facilities include the following:
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Dam type and height
Type, depth, and hydraulic characteristics of discharge outlets and spillways
Reservoir physical characteristics: depths/lengths/widths
Reservoir complexity (number of arms)
Reservoir seasonal pool levels and daily fluctuations
Timing, frequency, magnitude of spill events and ramping rates
Reservoir volumes, inflow, residence time, and hydraulic patterns
Controlled releases: timing, frequency, magnitude, and facility temperature control capabilities
Reservoir water quality, including surface temperatures and thermoclines
Total storage/active storage
Winter/spring refill rate and summer/fall discharges and diversions
Bathymetry
1.6.1 Daguerre Point Dam Daguerre Point Dam (Figure 1-5) is 24 feet high and situated in the lower Yuba River approximately 11 miles downstream of Englebright Dam at Yuba River RM 11.5. It is equipped with fish ladders; but they do not meet modern fish passage design standards, and they are not effective in passing all species of concern over a full range of flows.8
Daguerre Point Dam features include the following (USACE 2012):
Overflow concrete ogee (“s-shaped”) spillway with concrete apron and abutments
Ogee spillway section is 575 feet wide and 24 feet tall
Originally designed to retain hydraulic mining debris
Currently used to facilitate water diversion for irrigation purposes
Not operated for flood control
No storage capacity – reservoir filled with hydraulic mining debris and sediments
Juvenile fish passing downstream over the dam may become disoriented and especially vulnerable to predation in the deep, low-velocity water of the pool (Entrix and Monroe 2003).
8 Personal communication, Richard Wantuck, Fisheries Bioengineering Program Supervisor, National Marine Fisheries Service, August 2013.
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Options for modifying or removing Daguerre Point Dam are presented in the report by Gathard Engineering Consultants in the 2013 report titled: Yuba River Fish Passage Improvement Investigation, GEC 2014. The report provides conceptual engineering alternatives to enhance fish passage using nature-like fish passage design concepts, as well as a conceptual option that involves moving the point of diversion further upstream to maintain gravity-diversion capability at current levels. This option should be investigated for engineering feasibility because it would: 1) eliminate the fish passage impediment and predation issues associated with the current dam configuration, and 2) provide continuity of water diversion to existing users.
A Preliminary Permit for a proposed 3 mega-watt hydroelectric project on the south side of Daguerre Point Dam is also undergoing a preliminary FERC proceeding (P-14432). As proposed, a significant structure would be built to divert 80-90 % of the water around Daguerre Point Dam, which could significantly affect fish passage. However, due to its preliminary nature, this study does not discuss this proposed project. A future, separate, assessment regarding any new modifications to Daguerre Point Dam could be completed at a later stage to supplement this plan if the proposed project moves forward.
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Figure 1-5. Daguerre Point Dam at RM 11.5 on the Yuba River. Source: USACE (2012).
1.6.2 Englebright Dam and Reservoir Englebright Dam (Figure 1-6) is located at RM 23.9 on the Yuba River and represents the delineation between the upper and lower Yuba River (USACE 2012). Englebright Dam and its associated hydropower facilities are impassable in the upstream direction and therefore represent the upstream limit of anadromous fish migration in the Yuba River. The dam was constructed in 1941, primarily to trap sediment derived from hydraulic mining operations in the Yuba River watershed. Englebright Reservoir is currently used for recreation and hydroelectric power generation. The penstocks to two hydroelectric plants, and a bypass valve, are the only outlets from Englebright Dam, and are the only means of discharging water downstream, except for occasional spills over the top of the dam during high flood flow events. The Narrows 2 plant, owned by Yuba County Water Agency (YCWA) and part of FERC P-2246, is located approximately 400 feet downstream of the dam on river right, and the Narrows 1 plant, owned by Pacific Gas and Electric Company (PG&E) as FERC P-1403, is located on the opposite bank
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approximately 1000 feet downstream. The Narrows 2 flow bypass is a valve and penstock branch off the main Narrows 2 penstock added in 2008. It provides the capability to bypass flows of up to 3,000 cfs around the Narrows 2 Powerhouse during times of full or partial Powerhouse shutdowns. The bypass discharge enters the Yuba River just upstream of the Narrows 2 Powerhouse. Water releases are administered in a coordinated fashion by YCWA and PG&E for hydroelectric power generation, irrigation, and maintenance of the downstream riverine ecosystem.
Site details are as follows:
Concrete constant angle arch dam
Dam height 260 feet (from mean sea level or msl)
Overflow section elevation 527 feet msl
Dam base width 80 feet
Dam crest width of 1,142 feet msl
Reservoir 9 miles long
Reservoir storage capacity approximately 70,000 acre-feet (AF)
Reservoir is used as an afterbay for releases from New Bullards Bar Reservoir through the New Colgate Powerhouse and is used as a regulating reservoir to meet recreation and power generation needs and to capture uncontrolled flows from the Middle and South Yuba rivers to manage downstream releases to the lower Yuba River.
Water surface elevation fluctuates between 517 feet to 525 feet msl on a daily and weekly basis
Normal high reservoir water surface elevation is 527 feet msl
Normal low reservoir water surface elevation is 517 feet msl
Storage capacity of 70,000 AF, of which 45,000 AF is usable
Narrows 2 Powerhouse has a single Francis turbine rated for a flow of 3,400 cubic- feet/second (cfs)
Narrows 1 Powerhouse has a rated flow of 730 cfs
Narrows 2 bypass has capacity to discharge variable flows up to 3,000 cfs around the Narrows 2 Powerhouse during full or partial shutdowns.
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Figure 1-6. Englebright Dam located at RM 23.9 on the Yuba River. Source: YCWA (2010)
1.6.3 New Bullards Bar Dam and Reservoir The New Bullards Bar Dam (Figure 1-7) is located on the North Yuba River roughly 2.3 miles upstream of its confluence with the Middle Yuba River. The dam was completed in 1969 by the Yuba County Water Agency as part of FERC P-2246 to provide water for power generation, irrigation and domestic needs, flood control, and recreation (YCWA 2010). The dam includes one low-level outlet (a 72-inch hollow jet valve) at an invert elevation 1,395 feet with a maximum design capacity of about 3,500 cfs at full reservoir pool, and an actual capacity of 1,250 cfs. A second outlet is through the Minimum Flow (“Fish Release”) Powerhouse at the base of the dam. A third outlet to New Bullards Bar Reservoir is via the New Colgate Powerhouses (P-2246) that releases to the Yuba River at RM 33.9, about 1.7 miles upstream of Englebright Reservoir and has a rated flow of 3,500 cfs. Temperature profiles of New Bullards Bar Reservoir are shown in Figure 1-8.
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Project details are as follows (YCWA 2010):
1,110-foot radius, double curvature, concrete arch dam
Dam height is 645 feet msl
Overflow-type spillway with a width of 106 feet
Spillway crest elevation of 1,902 feet msl
Three 30-foot wide Tainter Gates on spillway
Maximum spillway design capacity of 160,000 cfs
Reservoir 8.5 miles long (maximum 16 miles)
Reservoir Storage capacity of 966,103 AF
Maximum reservoir surface area of 4,790 acres (ac)
Reservoir shoreline of 71.9 miles
Upstream drainage area of 488.6 square miles (sq. mi)
Reservoir maximum depth 645 feet
Normal maximum water surface elevation of 1,956 feet msl
Minimum pool elevation of 1,735 feet msl
Normal water level fluctuations of 150 feet msl
Minimum Flow Powerhouse with one Pelton Turbine rated for flow of 5 cfs
New Colgate Powerhouse with two Pelton Turbines rated for total flow of 3,430 cfs.
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Figure 1-7. New Bullards Bar Dam at RM 2.3 on the North Yuba River. Source: YCWA (2010)
Figure 1-8. Monthly temperature profiles of New Bullards Bar Reservoir (2008). Elevation range of upper power intake, which is not used, is shown as horizontal black lines, and lower power intake elevation range is shown as horizontal red lines. Source: YCWA 2010.
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Peaking operations on hourly, daily, and weekly schedules (YCWA 2010, p. 6-44) dominate power generation operations at New Colgate Powerhouse. Except under high flow conditions, some or all of the available capacity is used for base load generation (YCWA 2010). Depending upon energy demand, the Powerhouse generation can be fluctuated in less than 10 minutes from a minimum of 1 MW, with only one unit operating, to maximum load of 340 MW with both units operating. As a result, flows in the Yuba River downstream of New Colgate Powerhouse typically have large hourly and daily fluctuations in flow. New Colgate Powerhouse release flows can fluctuate daily from near 0 to about 3,400 cfs.
1.6.4 Our House Diversion Dam Our House Diversion Dam (Figure 1-9) is a located on the Middle Yuba River 12.0 miles upstream of its confluence with the North Yuba River. In addition to the uncontrolled spillway, the diversion dam has two outlets to the Middle Yuba River (YCWA 2010). One outlet is a 5-foot diameter steel pipe that acts as a low-level outlet and has a maximum capacity of 800 cfs. The outlet centerline is at elevation 1,990 feet msl. The other outlet is a 24-inch diameter release pipe with a maximum capacity of 60 cfs located just above the low-level outlet. The dam and its associated Lohman Ridge Diversion Tunnel can divert about 810 cfs of water from the Middle Yuba River to Oregon Creek as part of YCWA’s FERC P-2246. The dam has little storage capacity and the pool only fluctuates passively from a minimum pool size, when natural inflow is below the downstream minimum flow requirement and no diversion is occurring, to a maximum pool size of approximately 280 AF when inflows are greater than diversion capacity and the facility is spilling. The dam has no fish passage facilities and is an upstream barrier to fish passage. Under existing conditions, resident trout moving downstream in the vicinity of the dam are susceptible to entrainment at the dam, into the unscreened water diversion which passes water through the Lohman Ridge Tunnel to the pool at Log Cabin Dam on Oregon Creek. From the Log Cabin pool, diverted water is further directed to Bullards Bar Reservoir via the Camptonville Diversion Tunnel (see Log Cabin Diversion Dam below, also part of P-2246).
Project details are as follows (YCWA 2010):
130-foot radius, double curvature, concrete arch dam
Dam height of 70 feet msl
Dam crest length 368 feet msl
Dam crest elevation 2,049 feet msl
Upstream drainage area of 144.8 sq. mi, 39.8 sq. mi of which is upstream of Milton Diversion Dam
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Storage capacity of 280 AF
Storage and water levels do not fluctuate under project operations
Spillway capacity of 60,000 cfs
Figure 1-9. Our House Diversion Dam at RM 12.1 on the Middle Yuba River. Source: YCWA (2010).
1.6.5 Log Cabin Diversion Dam The Log Cabin Diversion Dam (Figure 1-10) is located at RM 4.1 on Oregon Creek, a tributary to the Middle Yuba River. In addition to the uncontrolled spillway, the diversion dam has two outlets to Oregon Creek. One outlet is a 5-foot diameter steel pipe that acts as a low-level outlet with a maximum capacity of 800 cfs and an outlet centerline at elevation 1,938 feet msl (YCWA 2010). The second outlet is an 18-inch diameter release pipe with a maximum capacity of 13 cfs located just above the low-level outlet. The dam and its associated Camptonville Diversion Tunnel can divert about 1,100 cfs of water from Oregon Creek to New Bullards Bar Reservoir as part of P-2246. The dam has little storage capacity and the pool fluctuates passively from a minimum pool size, when natural inflows are at or below the downstream minimum flow requirement and no diversion is occurring, to a maximum pool size of approximately 90 AF when inflows are greater than diversion capacity and the facility is spilling.
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Project details are as follows (YCWA 2010):
105-foot radius, concrete arch dam
Dam height of 53 feet msl
Crest length of 300 feet
Crest elevation of 1,979 feet msl
Spillway capacity of 12,000 cfs
Upstream drainage area of 29.1 sq. mi
Figure 1-10. Log Cabin Diversion Dam at RM 4.1 on Oregon Creek, a tributary to the Middle Yuba River. Source: YCWA (2010).
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2. BIOLOGICAL INFORMATION
Specific biological information related to CV spring-run Chinook Salmon and CV steelhead in the Upper Yuba River is needed to develop aspects of the Reintroduction Plan. In particular, the periodicity, or timing, of adult upstream migration and juvenile downstream migration is critical in determining the feasibility of and appropriate approach for passage and reintroduction efforts. Other important biological information relates to suitable temperatures and other physical habitat characteristics that are needed for the successful passage and persistence of a reintroduced population. Because anadromous salmonids do not currently inhabit the Upper Yuba River basin, there is no contemporary biological information specific to this particular area. Information on CV spring-run Chinook Salmon and CV steelhead must be considered based on: (1) populations in the Lower Yuba River or elsewhere in the Sacramento River Basin, (2) information gleaned from historical accounts, (3) information compiled from habitat studies of the upper watershed, and (4) any relevant information from evaluation other Sacramento River stocks native to other watersheds or produced in hatcheries. Unless otherwise noted, the following information was summarized from other sources (Stillwater Sciences 2006; USACE 2012). While other species of anadromous and resident fish may occur in the Yuba River, NMFS recommends the expansion of CV spring-run Chinook Salmon and CV steelhead habitat as the focus of this Plan. Thus, the information provided below focuses on CV spring-run Chinook Salmon and CV steelhead, though information for other runs is also provided.
2.1 CV SPRING-RUN CHINOOK SALMON Central Valley spring-run Chinook Salmon in the Yuba River are included in the CV spring-run Chinook Salmon ESU that was listed as threatened in 1999, a status upheld during the recent 2011 review. Spring-run Chinook Salmon in basins outside of the Central Valley generally exhibit a stream-type life history in which adults enter freshwater in the spring, hold over the summer, and spawn in the fall with the resulting juvenile progeny typically spending a year or more in freshwater before emigrating (Healey 1991). In the Central Valley, adult spring-run Chinook Salmon begin migrating upstream in late January and early February and enter the Sacramento River between March and September with a peak in May and June, then enter spawning tributaries primarily between mid-April and mid-June. CV spring-run Chinook Salmon generally evolved to use mid- to high-elevation streams with appropriate temperatures and sufficient flow, cover, and pool depth to allow over-summering. In the California Central Valley these historical habitats are largely not accessible, primarily because of the presence of dams without fish passage capabilities. Spring-run Chinook Salmon holding in these streams are thought to prefer water temperatures below 60ºF but can tolerate temperatures up to 65ºF before
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becoming susceptible to disease. Spawning occurs between September and October and is dependent on water temperatures. Spring-run Chinook Salmon fry emerge from the gravel from November to March and can exhibit considerable variability, migrating downstream as young-of- the-year or yearlings. Immediately after emergence, juveniles seek areas of shallow water and low velocities but can also disperse downstream during high flows. Juvenile outmigration extends from November to early May.
Information from California Department of Fish and Wildlife’s (CDFW) and NMFS’ biologists, as well as data in MWH (2010) and USACE (2012), was used to summarize all runs of juvenile and adult CV Chinook Salmon migration periods in the Lower Yuba River. This information is presented in Table 2-1.
2.2 CV STEELHEAD Central Valley steelhead in the Yuba River are included in the California CV steelhead DPS that was listed as threatened in 1998, a status upheld during the recent 2011 review. CV steelhead life histories can be described as two types, summer-run steelhead and winter-run steelhead, which are defined by the state of sexual maturity upon river entry and the duration of the spawning migration. Only winter-run steelhead currently exist in the rivers and streams of the Central Valley. CV steelhead typically enter freshwater from August through April and spawn from December through April. Spawning peaks from January through March in small streams and tributaries that have cool and well oxygenated water year round. Upstream migration is generally correlated with high flow events and lower water temperatures. Unlike CV spring-run Chinook Salmon, CV steelhead can spawn more than once (iteroparity), though one-time spawners (semelparity) represent the majority. Juvenile CV steelhead outmigration from natal streams takes place episodically from fall through spring during high flows. Outmigrating CV steelhead may use the lower sub-basins of the Sacramento River and the Delta for rearing and as a migration corridor to the ocean.
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Table 2-1. Migration periodicity for CV Chinook Salmon and CV steelhead in the Lower Yuba River. Source: MWH (2010). Fish Species Life Stage Months Peak Months Spring-run Chinook Adult – Upstream March–late May mid-May–late May Salmon migration Fall-run Chinook salmon Adult – Upstream mid-July–mid-December mid-October–beginning migration of November Late fall-run Chinook Adult – Upstream late December–late mid–January salmon migration February Chinook salmon (spring-, Juvenile – Outmigration mid-November–June end of December–March fall-, and late-run) and May Steelhead Adult – Upstream mid-September–March Bimodal distribution with migration first peak during mid- October and second peak during January–February Rainbow Trout/Steelhead Juvenile – Outmigration Year–round April–July (O. mykiss) Source: Department of Fish and Game biologist Duane Massa and National Marine Fisheries Service biologist Brian Elliott. Notes: 1 Species most likely to reach furthest upstream (Yoshiyama et al. 2001) 2 Period represents the combined juvenile outmigration for spring-run, fall-run, and late-run Chinook salmon because it is difficult to distinguish between the three species.
2.3 GREEN STURGEON The southern Distinct Population Segment (DPS) of North American Green Sturgeon (Acipenser medirostris) was listed by NMFS as a threatened species under the federal Endangered Species Act on June 6, 2006 (71 FR 17757). Critical habitat was designated October 9, 2009 (74 FR 52300).
Understanding of the biology of the southern Distinct Population Segment (sDPS) of Green Sturgeon is evolving. Green Sturgeon are long lived, iteroparous, anadromous fish. They may live up to 60-70 years. Until recently, it was believed that the Green Sturgeon sDPS was limited to a single spawning population on the Sacramento River. However, Adams et al. (2007) summarizes information that suggests Green Sturgeon may have been distributed above the locations of present-day dams on the Sacramento and Feather rivers. In addition, Mora et al. (2009) investigated the likelihood that impassable Central Valley dams, combined with modern day flow regulation, constrain the distribution the distribution of Green Sturgeon in the Sacramento River watershed.
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In the California Central Valley, sDPS Green Sturgeon range from the Delta to the Sacramento River up to Keswick Dam, and in the Feather River up to the fish barrier structure below Oroville Dam, and in the Yuba River up to Daguerre Point Dam. Additional habitat may have historically existed in the San Joaquin River basin. Recent research conducted by California Department of Water Resources (DWR) revealed spawning activity in the Feather River. Additionally, there is some empirical evidence of spawning in the Yuba River downstream of Daguerre Point Dam (Cramer Fish Sciences 2011). This suggests the possibility of more than one population of sDPS Green Sturgeon, but further research is needed.
With respect to the management importance of Green Sturgeon in the context of a reintroduction plan for andromous salmonids on the Yuba River, several related points are salient. First, the ESA-listing status of Green Sturgeon sDPS means that they are protected under federal law and recovery actions are required under the Endangered Species Act. Second, since Green Sturgeon have been identified in the lower Yuba River below Daguerre Point Dam, management and recovery actions are appropriate to consider in the larger strategy of fisheries conservation and management in the Yuba River watershed. Third, Green Sturgeon are currently prevented from further upstream migration by the passage barrier at Daguerre Point Dam; and the design of the current salmonid fishways is not conducive for upstream passage of Green Sturgeon. However, if passage for Green Sturgeon were accommodated by dam removal or fish passage facilities at Daguerre Point in the future,9 the cold water habitats upstream would likely be highly beneficial for Green Sturgeon spawning and juvenile rearing. This leads to questions about managing the spatial distribution and density of fishes that compete for space and resources below impassable dams, in this case – Englebright Dam. To benefit all anadromous and resident species, habitat exspansion and connectivity of upstream habitats is highly desirable to relieve the pressure on low elevation, “valley floor habitats.” In particular, a reintroduciton action that would allow spring-run Chinook Salmon and steelhead to occupy higher elevation habitats upstream of Englebright Dam would allow additional productive use of the lower Yuba River for Green Sturgeon, fall-run Chinook salmon, and other resident fishes like Rainbow Trout. By expanding habitats to include the upper Yuba River for spring-run Chinook Salmon and steelhead, there would be less competition and a greater probability for co-existence and productivity of all managed species of concern. In this manner, the reintroduction action can be seen as a benefit to not only spring-run Chinook Salmon and steelhead, but other managed anadromous fishes (i.e., Green Sturgeon, fall-run Chinook salmon) in the Yuba River as well.
9 See Yuba River Fish Passage Improvement, Gathard Engineering Consulting (2014) for conceptual engineering options for retrofitting or removing Daguerre Point Dam in a manner that allows both fish passage and continuity of existing water diversion operations.
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2.4 OTHER SPECIES The presence of other species in the reintroduction area is important in terms of both potential predation and competition with juvenile salmonids. A significant portion of the current species assemblage in upper Yuba reservoirs and adjacent tributaries are the result of years of supplementation with hatchery stocks to increase sport fishing opportunity. Bass (including largemouth, smallmouth and Spotted Bass) and Sacramento Pikeminnow are known predators of juvenile salmonids and are present in both New Bullards Bar and Englebright reservoirs. Resident Rainbow Trout (O. mykiss) and Brown Trout in stream sub-basins may also hinder reintroduction through competition with juvenile CV spring-run and CV steelhead. Downstream of Daguerre Dam in the lower Yuba River (below the Reintroduction Plan’s Action Area), there are also Green Sturgeon, Sacramento striped bass, and American shad (USACE 2012, Chapter. 5, pps. 5-14).
Creel surveys conducted in Englebright Reservoir documented 12 sport fish species: Spotted Bass, Smallmouth Bass, Largemouth Bass, Bluegill, Brown Trout, Rainbow Trout, Carp, Channel Catfish, crappie, kokanee salmon, sucker, Yellow Perch, and Sacramento Pikeminnow (YWCA 2010). The most abundant fish caught were unspecified bass species (28 percent) and Rainbow Trout (56 percent) (DWR 2006). The largest bass documented in creel surveys were in the 12- to 15-inch range, though the apparent popularity of bass fishing in the reservoir suggests that larger specimens may be present. The USACE (2012) BA noted that,
“CDFG stocking records indicate that fish plantings in Englebright Reservoir have taken place from 1965 through 2007. During this period, over 756,000 Rainbow Trout, 228,320 kokanee salmon, 6,973 lake trout (Salvelinus namaycush), nearly 28,000 Brown Trout, 4,000 Eagle Lake Rainbow Trout, 2,640 brook trout, 45 white crappie, and 80 black crappie were planted.”
New Bullard’s Bar Reservoir has been stocked by CDFG since at least 1959. The YCWA’s (2010) Pre-Application Document (PAD) noted that,
“Based on actual CDFG stocking records, between 1969 and 2007 over 4.9 million kokanee salmon, nearly 1.6 million Rainbow Trout, over 310,000 Eagle Lake Rainbow Trout, 40,000 brook trout, 200 eastern brook trout, 200 cutthroat trout [(Oncorhynchus clarki)], and 185 Spotted Bass were planted in New Bullards Bar Reservoir.”
Snorkel surveys in the Middle Yuba River documented primarily Rainbow Trout, Brown Trout, and suckers, though Sacramento Pikeminnow were also observed in one sub-basin (YCWA 2010). Snorkel surveys in the South Yuba River documented Rainbow Trout, Sacramento
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Pikeminnow, and suckers throughout the sub-basin. In the North Yuba River, popular fisheries exist for Rainbow Trout, Brown Trout, kokanee salmon, as well as brook trout in the upper sub- basins and tributaries. A run of kokanee salmon exists on the main stem upper North Fork Yuba River.
To the extent that any of the other species living in the Yuba River watershed might present predation potential for outmigrating juvenile salmonids, stocking practices should be re- examined to ensure they are compatible with reintroduction goals and objectives. In addition, analysis of predation risks should consider that steelhead and spring-run Chinook Salmon populations from the Sacramento River basin generally outmigrate during high winter and spring flows (Healey 1991, Reynolds et al. 1993, McEwan 2001).
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3. DISTRIBUTION OF EXISTING HABITAT
The distribution of existing habitat for anadromous salmonids in the Upper Yuba River basin is a function of both connectivity between upstream and downstream sub-basins and the quality of available habitat. Englebright Dam blocks upstream fish migration at River Mile (RM) 23.9 on the Yuba River. Assuming fish passage was provided at downstream barriers, New Bullards Bar Dam at RM 2.3 on the North Yuba River prevents upstream migrating fish from accessing the majority of the North Yuba River basin; Our House Diversion Dam prevents the upstream passage of fish at RM 12.0 on the Middle Yuba River; and Log Cabin Diversion Dam prevents the upstream passage of fish at RM 4.1 on Oregon Creek. As reported by Vogel (2006)10 and Yoshiyama et al. (2001), the downstream-most complete natural barriers representing the upper limit to potential anadromy are RM 51.0 in the NY, RM 35.1 in the MY and RM 35.7 in the SY sub-basin. While the success of anadromous fish reintroduction(s) to any or all of these areas would generally depend on the development of effective fish passage facilities, it is certain that providing connectivity to (and from) selected upstream habitats is critical to expanding available habitat for spring-run Chinook Salmon and steelhead. Figure 1-1 shows the distribution of existing habitat in each sub-basin relative to areas upstream of each dam. However, not all habitat is equally suitable due to flow and temperature concerns and the presence of partial barriers affects habitat connectivity. For example, there is a natural barrier (10.8 feet waterfall) to fish passage on Oregon Creek at RM 0.6 (HDR 2012). Additional partial barriers to upstream migration associated with low-flow conditions are also present in the SY (at RM 5.1, RM 5.9, and RM 19.6) and MY (at RM 0.4, RM 32.7, and RM 32.9). The timing of upstream movements that would be exhibited by CV spring-run Chinook Salmon and steelhead in the Upper Yuba River may vary under different flow conditions; therefore, the distribution of existing habitat is reported in the context of what is assumed to be complete passage barriers. Remediation of features classified as partial barriers is feasible, with increased instream flows during migration periods and/or physical alteration for improved fish passage characteristics.
Providing connectivity to upstream habitats is critical to expanding available habitat for spring- run Chinook Salmon and steelhead, but the quality of connected habitat may determine the ultimate success of reintroductions. Under current conditions, the distribution of suitable habitats is limited by flow and water temperature. Such limitations on flow and temperature are largely due to the operations of the three FERC projects within the Yuba watershed: Yuba River Development (P-2246); Yuba-Bear (P-2266); and Drum-Spaulding (P-2310). Flow diversion
10 Reported river miles are those provided by Stillwater Sciences (2012) that were calculated based on coordinates provided by Vogel (2006).
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and regulation of instream flow constrains habitat quantity by reducing the amount of wetted area and increasing water temperature, particularly in SY and MY. Daily fluctuations in flow can also lead to stranding events that could place further limits on the size of reintroduced spring-run Chinook Salmon or steelhead populations. Flow conditions will also determine the ability of returning adults to pass areas that represent natural barriers under low flow conditions. For example, the falls located at Middle Yuba River RM 0.4 may prevent upstream access during flow conditions associated with regulated releases from upstream diversion points, but this same site may be passable under higher instream flow scenarios, or during higher flow conditions in “wet years.” This site is typical of existing natural impediments to fish passage that exist in the South and Middle Yuba River, and in Oregon Creek. If reintroduction programs target any of these river reaches, then a more in-depth hydrologic and site-specific hydraulic analysis should be conducted to inform fish passage engineering designs that could be employed to considerably improve localized passage conditions.
The diversion and transport of flows across sub-basins may also result in false attraction of returning adults to locations other than their natal sub-basin. For example, Our House Diversion Dam diverts water through the Lohman Ridge Tunnel to the Log Cabin pool on Oregon Creek. In turn, Log Cabin Diversion Dam also diverts water through the Camptonville Diversion Tunnel to NBB Reservoir. Reintroduction of anadromous salmonids to some of their historical habitat may require screening of diversions such as the Lohman Ridge Tunnel and the Camptonville Diversion Tunnel, to prevent fish from being distributed to other sub-basins.
Flow diversion and regulation also influence the temperature regimes within the upper Yuba River sub-basins. The rate of warming from upstream to downstream is a function of flow and defines the downstream extent of habitat remaining below critical temperatures for CV spring- run Chinook Salmon and CV steelhead adult holding and juvenile rearing.
Stillwater Sciences (2013a) used the RIPPLE model (Chapter 6) to model current habitat conditions in each of the upper Yuba River sub-basins to predict the amount of suitable habitat available – defined in part by a maximum weekly average water temperature of ≤19°C for spring-run Chinook Salmon and ≤20°C for CV steelhead. They also modeled habitat conditions under two different alternative management scenarios (Chapter 6). Increased flows from these projects into the NBB reach, MY, and SY sub-basins would mean better water temperatures and additional habitat over Current Conditions (Stillwater Sciences 2013a). NMFS recommended flows in the FERC relicensing process that specifically address instream flows necessary to support salmonid reintroduction in the Middle and South Yuba River (NMFS 2009).
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4. HABITAT CONNECTIVITY
Successful reintroduction of spring-run Chinook Salmon and steelhead into the Upper Yuba basin is contingent on reestablishing habitat connectivity in both upstream and downstream directions. Englebright Dam (USACE) and New Bullards Bar Dam, Our House Dam and Log Cabin dams (YCWA/P-2246) are man-made structures that present complete barriers to upstream migration. Several natural features present partial or complete barriers to upstream migration in the SY and MY sub-basins depending on flow conditions and the timing of upstream fish migrations. Downstream migration is currently hindered or blocked by man-made dams or diversions located in NBB, SY and MY sub-basins. Removing or modifying dams may be the most effective option for establishing self-sustaining anadromous fish populations in upstream habitats, but dam removal/modification may, or may not be a viable option in the near term.11 Therefore, we assume that some combination of volitional and non-volitional fish passage facilities may be considered as an initial approach. Providing effective upstream and downstream passage at dams is dependent upon successfully accomplishing attraction, collection, and transport of target species and life stages. At this stage of planning, both volitional and semi-volitional (assisted) fish passage systems are considered for future development and cost-benefit analysis.
Under volitional passage, a barrier is modified or removed such that fish arrive at the site under their own power, swimming through or around and past the former blockage. Dam removal is the means to achieve fully volitional fish passage. For dams that will remain in place because of their function for other beneficial uses, fish ladders or other upstream passage facilities may be retrofitted to allow for volitional (or semi-volitional) passage. Partial barriers may be remediated by adding or removing large boulders to create step pools that transform a waterfall into a lower gradient cascade. In some cases, partial barriers can be made more passable by augmenting flows during the upstream migration period of target fish species. Some combination of physical alteration and strategic flow manipulation may offer the best solution. Flow testing and fish passage assessments should be included in the pilot experimentation phase (Chapter 8), specifically in conjunction with radio-tracking of adult test fish (spring-run Chinook Salmon) during a typical upstream migration period.
11 For more information regarding potential modification or removal of Daguerre and Englebright Dams, including conceptual engineering designs, sediment transport modeling, and cost estimates, refer to Yuba River Fish Passage Improvement Investigation (GEC 2014) and Stillwater Sciences (2013a) which provide in depth analysis of dam removal and dam modification options.
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Examples of constructed volitional facilities include fish ladders for adults, screened bypass facilities for juveniles, and nature-like fishways that may function to provide both upstream and downstream passage. Nature-like fishways, such as rock ramps and bypass channels, are intended to simulate natural river conditions by replacing a waterfall with a longer cascade or riffle that is passable by migrating fish. Volitional fish passage facilities are generally preferred because they operate constantly, require little human interference, and may be mechanically less likely to malfunction. They may be less costly to maintain and operate in the long run (relative to non-volitional passage systems), but they generally represent a larger, up-front capital expenditure. Volitional facilities are often fixed structures that provide little flexibility to adjust to changes in fish behavior, environmental or operating conditions. For this reason, appropriately scaled versions of non-volitional passage facilities might be initially implemented, monitored, and evaluated on an interim basis while more permanent and expansive fish passage systems are being designed. In particular, interim collection, transport, and culture facilities, for both adults and juvenile outmigrants, should be considered in early stages because the lower initial costs afford an opportunity to learn and incorporate the most successful strategies into longer-term facility design decisions. Depending on lessons learned in the earlier stages of reintroduction, and tradeoffs associated with expansion of fish passage capacity, the program may transition to larger scale, volitional facilities over time.
A collection and transport operation is a type of non-volitional fish passage used where volitional passage is not logistically, technically, or biologically possible, and fish must be actively moved upstream and/or downstream around barriers. Large dams, especially when several occur in sequence, are more likely to require collection and transport than small structures. Space or engineering constraints may prevent the design of safe and effective, volitional fish passage facilities. Collection and transport methods allow reintroduction to target specific sites for release. For example, spawning adults could be released into the highest quality habitat or dispersed among several upstream sub-basins. Particularly for juveniles, impoundments may present challenges that cannot be overcome with volitional passage if currents confuse downstream fish navigation or if an abundance of predators would reduce survival below a level consistent with self-sustaining production. In such circumstances, site-specific bioengineering analysis and technology development is needed to safely collect and transport juvenile outmigrants. Emerging technologies currently employed at projects in Oregon and Washington appear suitable for adaptation and application to the Yuba River.12
12 Two notable examples of collection and transport operations for out-migrating anadromous fish are at upper Baker Lake in Washington and Lake Billy Chinook in Oregon.
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In some cases, it may be useful to incorporate selective access or sorting and separation by species and life stages when designing upstream and downstream facilities. This could involve a weir, gate, or trap such that fish would be handled before passed upstream or downstream, and could be used to sort fish before transport. Although such structures increase operation and maintenance costs, they would allow managers to exclude fish that could undermine reintroduction objectives, and reduce impacts to local fish populations. For example, in a reintroduction designed to enhance diversity through the evolution of distinct, locally adapted population subunits, excluding the homogenizing influence of other stocks would be beneficial. Furthermore, without selective access, undesirable non-native fishes may be distributed which may not only decrease the success of native species reintroductions, but also negatively impact pre-existing species. Such structures would also provide a large benefit to research and monitoring because they would permit precise counts and measurements of fish.
4.1 UPSTREAM CONNECTIVITY Upstream fish passage systems are typically designed around two primary considerations: 1) Upstream Collection, and (2) Upstream Passage. These components are described as follows:
“Upstream Collection” defines the ability to attract and collect fish from downstream of a barrier dam or weir. This characteristic includes the ability to behaviorally or hydraulically attract or guide the fish from the river into a fish collection chamber. Typical features of an upstream collection facility include a fishway entrance (weir, orifice, slot, etc.), attraction flow to draw fish into the entrance, and a collection pool that encourages fish to stay, or traps fish in the facility to prepare for transport past the dam. In addition, design of upstream collection facilities should include consideration of the capability to conduct scientific monitoring and assessment, appropriate to the scale and complexity of the program objectives.
“Upstream Passage” defines the means to move fish from the collection pool to a release site upstream of the dam. Typical features of the upstream passage feature include various styles of fish ladders, fish lifts, fish locks, or collection and transport systems. This aspect of passage may involve the use of specially designed transport vessels, and facilities at release locations to provide for acclimation of fish to new conditions. The Upstream Collection component is typically the most challenging upstream passage feature to locate and design such that it will reliably draw fish from the river into the collection pool. This is because the collection component must accommodate the target species, interact well with the other flow control operations, river hydrology, site hydraulics, and water quality. Experience shows that the ability to design the entrance component for the desired collection
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performance typically varies more among water control structures than any other fishway feature. As a result, fishway entrances are often modified after their initial construction to help improve their attraction performance. Once fish are collected, the means to transport them past the dam is more straightforward to address; but technical sophistication in both fish passage processes is needed to minimize handling stress, and to maximize program performance.
With respect to upstream passage, effective attraction requires sufficient flows to attract upstream migrants away from other competing flows due to spill or generation releases. Thus, the frequency, magnitude, and location of spill and generation releases (for hydropower dams) plays an important role in determining appropriate attraction flow designs and the feasibility of effective attraction. Effective attraction to fish passage facilities may be further complicated by the span of extremely wide dams or situations where multiple generating facilities exist. In the case of Daguerre Point Dam (see Figure 1-5), upstream collection conditions are not optimal under the current configuration of fishways. The dam is only 24-ft high but 575 feet wide with a complex downstream channel; therefore fish have difficulty finding entrances constructed at the north and south banks. This drawback is likely to persist even if a new ladder is constructed at the north bank abutment of the Daguerre facility. Collection of fish would be limited to a single, bank side operation that will likely fail to attract those fish that accumulate in other areas downstream of the dam face. On the other hand, it is worth noting that the hydraulic and geophysical characteristics near the discharge of Narrows 2 power plant generally offer optimal attraction flow opportunities for siting of an upstream fish ladder and collection facility nearby. A possible confounding circumstance in the Englebright Dam reach is the change in hydraulics that results when the flows are adjusted between Narrows 1 and 2, and the power plant bypasses.
Upstream migrants that are successfully attracted to a passage facility must then be effectively collected in such a way that minimizes migratory delay, stress, and injury. Transport of collected fish can be accomplished through a variety of technologies, such as a technical fish ladder, fish lift/tram, or through a collection and transport approach. Dam height, the degree of water surface elevation fluctuations in the upstream reservoir, and other site specific characteristics usually dictate the relative feasibility of various transport options. Where there are significant uncertainties about fish facility design and performance, pilot experiments might be employed to provide proof of concept before investing in permanent infrastructure.
Fish ladders have been typically used to pass fish over dams, the majority of which are less than 100 feet high. Tests of Chinook salmon passage at the Bonneville Dam fish ladders showed that adult fish collected at the exit of the ladder and re-circulated to the entrance could swim for long periods of time. Another example is the Carmel River re-route channel design (part of the San
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Clemente Dam removal project), which is a nature-like fishway whose longitudinal distance is more than one-half mile, with an elevation drop exceeding one hundred feet. Also, the fish ladder at Faraday Diversion Dam on the Clackamas River operates from June through mid- October to facilitate passage of salmon upstream of North Fork Dam. Fish first enter a holding pen and are counted; then they are allowed to continue migration upstream. The 1.9-mile fish ladder runs from the lower diversion dam to above North Fork Dam, and is the longest operating fish ladder in the world. Nevertheless, ladder height and water quality remain paramount challenges for design of upstream fishways. Since fish ladders are typically constructed at a slope of 1 foot vertical for every 10 feet horizontal, a full length fish ladder at 260-foot high Englebright Dam would be 2,300 to 2,600 feet long depending on how the ladder passed through the dam face. Ladders of this height and length present additional technical and biological concerns due to extended fish passage times and the possibility of the water warming up during transit through the ladder. Excessive temperature differences could introduce stress in fish, potentially affecting their physiology, behavior, and ultimately reducing survival. This may be a seasonal phenomenon that needs careful study and design consideration. It may be possible to reduce or eliminate apparent fish stressors through innovative facility design, systems analysis, and operational protocols. These important concerns, and some potential ideas for addressing them at Yuba River Dams, are further discussed in Section 4.4 Phased Fish Passage Facilities.
The combination of long ladder length, construction along a steep slope, auxiliary water supply, and water temperature control issues raise questions about the viability of a conventional fish ladder as a design option at Englebright Dam. As an alternative, tramways can be used at high head dams where fish ladders are judged infeasible. However, any significant differences between water temperature in the downstream entrance pool and the release location at the reservoir surface would stress fish and may reduce survival. A separate fish ladder or tramway from the base of 635-feet high New Bullards Bar Dam would encounter significant challenges of construction along a steep slope, auxiliary water supply, long ladder length, and water temperature control issues. In addition, the reservoir at NBBD is subject to annual water level fluctuations of up to 150 feet, which would add to the complexity of a fish ladder or tramway at that site.
A collection and transport facility constructed at Englebright Dam or Daguerre Point Dam would allow fish to be released into cool water stream environments upstream of the reservoirs where the difference in water temperature between the collection and release sites can be minimized. Constructing a collection and transport facility at Daguerre Point Dam would allow fish to be released above Englebright Dam to continue their upstream migration to the natal stream. However, unless fish destined for the North Yuba River can be separated at a Daguerre Point
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collection facility, a second upstream fish passage facility would be needed to pass fish upstream into the NY from below NBBD.
4.2 DOWNSTREAM CONNECTIVITY Under existing conditions, juvenile salmonids passing downstream from the Upper Yuba to below Englebright Dam are exposed to mortality factors much different than would be encountered in a free-flowing system. Depending on their migratory pathway, juvenile fish may encounter reservoirs, dams, turbines, spillways, and bypass facilities, in addition to stream sub- basins with reduced flows and higher water temperatures than encountered under unregulated conditions. The survival of fish encountering these features depends on a variety of factors including flow conditions, and the size, features, and operational characteristics of water control structures and associated reservoirs. Juvenile salmonid survival may also be affected by the size and number of outmigrants, capacity and efficiency of fish facilities, timing of outmigration, and the size and species of potential predators. Determining a robust estimate of juvenile salmonid survival passing downstream through each migratory pathway is beyond the scope of this effort; however, a conceptual-level estimate may be useful to identify reintroduction strategies that have the highest likelihood of success. Conceptual-level estimates of juvenile salmonid survival by life stage are provided for the primary migratory pathways for planning purposes only. These assumptions of juvenile salmonid survival will be incorporated into fish passage modeling runs as described in Chapter 7.
4.2.1 Reservoirs Fish outmigrating downstream from the Upper Yuba must successfully navigate through a series of reservoirs and dams. In general, smaller migrants, such as estuary-bound fry (efry) or age-0 smolts (smolt0) will typically be more vulnerable than larger migrants, such as age-1 smolts (smolt1) in reservoirs, where predation is often size selective. Smaller, younger fish may also suffer greater injury or mortality than larger fish when navigating through reservoirs due to swimming speed limitations. Combined, these observations suggest that the smolt1 proportion of the outmigrating population is more likely to successfully pass downstream through reservoirs than the efry or smolt0 outmigrants.
Reservoirs with straight linear shorelines – like Englebright Reservoir, and to some extent New Bullards Bar Reservoir – are more conducive to downstream migration than reservoirs with multiple arms and coves (e.g., Shasta Reservoir, Don Pedro Reservoir) which may cause shoreline-oriented outmigrants to delay their downstream progress. Englebright reservoir, in particular, is relatively narrow and riverine-like, with limited water volume, relatively short residence time, and few discernible alcoves that might cause out-migrants to be delayed or lost.
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However, rapid reservoir refill during the downstream migration period may affect the ability of juvenile salmonids to successfully migrate through the reservoir and locate the route of egress. These assumptions are critical to investigate prior to selecting preferred engineering designs. Reservoir transit studies (i.e., juvenile fish radio-tagging and tracking experiments in the downstream direction) are needed at an early stage to help determine the best approaches for potential reservoir-based, juvenile collection and transport systems.
The following ranges of reservoir survival values for spring-run Chinook Salmon are based on professional judgment, as informed by a review of published information from other hydropower projects and river systems. Estimates of reservoir survival vary as a function of factors that include thermal conditions, reservoir velocities, and predator density. Likewise, estimates of dam survival are highly site-specific and vary as a function of factors including hydraulic conditions, passage facilities (and their design, operation, etc.), and predation. Thus, without details regarding reservoir conditions or the feasibility or performance of various passage facility alternatives, it is difficult to determine the degree to which the survival values reported here could be expected in the Upper Yuba. Nevertheless, as a starting point for analysis, the following estimates and assumptions are presented as a range of survival efficiencies in both New Bullards Bar and Englebright reservoirs:
Assumed Survival of Juvenile Salmonids Passing through New Bullards Bar Reservoir Life Stage Low Mid High Efry (emergent) 0% 5% 10% Smolt0 (subyearling) 2% 20% 40% Smolt1 (yearling) 5% 35% 60%
Assumed Survival of Juvenile Salmonids Passing through Englebright Reservoir Life Stage Low Mid High Efry (emergent) 2% 20% 40% Smolt0 (subyearling) 20% 45% 70% Smolt1 (yearling) 40% 70% 95%
Assumptions
Reservoir survival is lower for smaller life stages. This assumption is supported by studies showing that reservoir predation on juvenile salmon can be size-selective, with
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greater predation on smaller size classes (e.g., Poe et al. 1991). Size-specific differences in reservoir survival may be a function of poorer swimming capabilities for smaller fish (reducing predator avoidance or prolonging reservoir transit times), alleviation of predator gape limitations, or an increased likelihood of attempted reservoir rearing for earlier life stages (USACE 1998) and a corresponding increase in predation risk.
Survival in New Bullards Bar Reservoir is lower than in Englebright Reservoir. This assumption is supported by a greater relative abundance of potential predators (e.g., centrarchids) (YCWA 2012), warmer surface water temperatures, and the larger size and additional shoreline complexity of NBB Reservoir compared to Englebright Reservoir.
For purposes of exploring the juvenile outmigration component in this initial Reintroduction Plan, we focused on the prospects of operating surface collection facilities located in the forebay near Englebright and New Bullards Bar Dams. However, we are aware of proposals to look at a head-of-reservoir floating surface collector (FSC) for New Bullards Bar Dam. This concept is proposed by some to avoid the perceived inability of juveniles to successfully navigate the reservoir (which has not yet been shown). Therefore, reservoir transit (radio-tracking) studies with juvenile fish are proposed in this Plan as a first step to definitively assess this key component of downstream fish passage systems.
4.2.2 Tributary Collector In order to avoid exposing juvenile salmonids to the risks associated with reservoir passage, one option is to collect downstream migrants from each of the tributaries upstream of the reservoir fluctuation zone. Captured outmigrants can be transported downstream and released below the dams. The efficacy of tributary collectors depends on the operational flow range of the facility, the magnitude, timing, duration, and frequency of flows during the outmigration period, the availability of a construction site in a suitable, accessible location of the tributary upstream of the reservoir, and the magnitude and type of debris that are entrained in the stream flow.
Assumed Tributary Collector Juvenile Salmonid Fish Guidance Efficiency
Life Stage Low Mid High Efry (emergent) 30% 55% 80% Smolt0 (subyearling) 50% 70% 85% Smolt1 (yearling) 65% 80% 95%
Assumptions
Screening facility is located in the tributary, upstream of the reservoir inundation zone.
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Collection devices are designed to satisfy NMFS and CDFW engineering design criteria, with potential for application of site-specific criteria to address unique design challenges.
Facilities are sized to screen up to the 5 percent exceedance flow for each tributary.
Screening facilities are sized to the respective tributaries; no other site-specific conditions were considered. Juvenile salmonids transported and released downstream may be exposed to predation within the transport containers, disease transmission, and increased stress. Transport of juvenile salmonids may also impair adult orientation or homing abilities, perhaps by disrupting sequential imprinting processes during juvenile out-migration which represents potential risk to both target and non-target populations.
Assumed transport survival of juvenile salmonids released downstream of the dams
Life Stage Low Mid High Efry (emergent) 50% 70% 90% Smolt0 (subyearling) 60% 72.5% 95% Smolt1 (yearling) 75% 80% 95%
Assumptions
Vehicle access is readily available and optimal at all potential tributary collector sites.
Vehicles are equipped with state-of-the-art, aquacultural life support systems.
Juvenile salmonids are segregated by size within modular transport containers.
Acclimation facilities are provided as necessary to minimize stress during transitions of loading and unloading fish
All fish handling, segregations, and transitions are accomplished through hydraulically- engineered, water-to-water transfer procedures, designed to minimize stress
4.2.3 Forebay Passage Once outmigrants successfully approach a dam forebay, they typically have multiple potential downstream passage routes. They can be attracted to a downstream fish passage system, such as an FSC, pass through the turbines if they do not find or are unwilling to enter the entrance to downstream fish passage facilities, or pass over spillways during high flow events. At small hydroelectric projects it is sometimes possible to screen all fish away from the turbines (full exclusion screen) and divert them through a safe downstream bypass facility under all but flood flow conditions. This can be especially important where the height of the dam and type of
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turbines are not safe for fish passage. However, on larger rivers and dams, or where the reservoir pool level exhibits significant fluctuations, full exclusion screens may not be practical.
Partial flow screens have been employed often in combination with barrier nets that guide downstream migrants to the entrance of a collection facility. An FSC is an example where outmigrating fish are guided to the entrance of the structure by pumps located behind the fish screens (MWH 2010). The success of FSCs typically depends on the use of barrier nets (e.g., Baker Hydroelectric Project, Washington [NMFS 2008, WGI 2006]) or large volumes of flow (e.g., 6,000 cfs at Round Butte Dam, Oregon [NMFS 2005, PGE 2009]) to guide fish to the entrance. Similar to reservoir passage, larger out-migrants (smolt1) may have greater survival than smaller, younger fish when navigating through dam passage facilities due to swimming speed limitations (Ferguson et al. 2007).
Assumed Floating Surface Collector: Combined Collection Efficiency and Facility Survival of Juvenile Salmonids Life Stage Low Mid High Efry (emergent) 45% 65% 85% Smolt0 (subyearling) 50% 70% 90% Smolt1 (yearling) 55% 75% 95%
Assumptions
Facility survival is lower for smaller life stages. This assumption is supported by studies showing lower dam passage survival for subyearling vs. yearling Chinook (e.g., Ferguson et al. 2007). By extension, survival for Efry would be expected to be less than subyearling Chinook.
Maximum collection efficiency/survival of 95%. As a point of reference, Puget Sound Energy (PSE)’s Upper Baker FSC has a collection efficiency performance standard of 95% and a facility survival standard of 98%, resulting in a combined collection efficiency/survival of 93%. Rounding this value up to 95% represents the highest value (for Smolt1). Estimates for Smolt0 and Efry were reduced incrementally based on an expectation of slightly lower facility survival with decreasing size. The Upper Baker FSC has been able to meet or exceed the survivability standard every year since operations began in 2008 (R2 2011).
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4.2.4 Turbines In the absence of effective downstream fish passage facilities, fish passing downstream through a dam will exit through the turbines, conduits/draft tubes, or spillways. The survival of fish passing through turbines depends on the characteristics of the generating equipment (e.g., the type and size of the turbine, head [related to the difference between reservoir pool elevation and elevation of the turbine], and size and species of entrained fish). Pelton-type turbines designed for high-head installations most likely cause complete mortality due to their basic design. In a Pelton or impulse turbine, water is directed at high pressure onto clamshell buckets attached to the periphery of the impeller wheel to impart a torque on the turbine impeller. High rotating speeds and tight clearances mean almost 100 percent fish mortality. Water released from NBBD passes to the new Colgate Powerhouse through two large Pelton turbines, any fish that pass through the long penstock and into the Colgate Powerhouse are assumed not to survive.
The survival of outmigrating fish encountering Francis turbines, such as the ones at the Narrows 1 and 2 Powerhouses, both downstream of Englebright Dam, depends on the head, runner diameter, rotational speed and other factors, but may be 70 percent or greater (Figure 4-1) (Eicher et al. 1987). Other factors being equal, smaller fish exhibit higher survival than larger fish when passing through a Francis turbine (Franke et al. 1997). Latent effects of fish passage through turbines are not completely understood, but it is probable that turbine passage causes latent injuries and mortalities that have an effect on fish populations.
Large Kaplan turbines, such as those used at mainstem Columbia River dams, have shown average fish survival of about 80 to 90 percent (Eicher et al. 1987), but are typically used at projects with less than about 100 feet of head. However, there are no Kaplan turbines currently installed (or proposed) in the Yuba River hydroelectric facilities where reintroduction is projected to occur.
Fish passing downstream through the Upper Yuba dams were assumed to pass through the downstream fish passage facilities or through spillways. For modeling purposes, 87 percent of the time the juveniles pass through the FSC, whereas 13 percent of the time there is spill. When there is spill, 27 percent of the fish go through the surface collector and the other 73 percent pass downstream through the spillways. These rates were based on period of spill of approximately 13 percent annually, with median spill of 1,500 cfs and a surface collector design flow of 410 cfs (MWH 2010).
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Figure 4-1. Relationship of head to mortality for Francis turbines (Eicher et al. 1987).
4.2.5 Spillways Survival of fish passing through spillways is primarily affected by shear and strike. Damaging shear occurs when the plunging spill flow enters a tailrace, and there is a substantial difference in velocities where the two flows come together (Nietzel et al. 2000). Strike can occur if the spill flow comes in contact at high velocity with projections within the spillway chute, or with rock along the bank or the bottom of the plunge pool. Other areas of concern for spillway passage survival may be the minimum gate opening and the bottom conditions downstream of the concrete discharge chute (stilling basin). If the gates are only open a small amount to pass small spill flows, then characteristics of the high-velocity jet through the thin opening below the gate could injure or kill fish. Additionally, passing small spill flow volumes results in a very thin sheet of high-velocity water as the flow passes down the spillway, exposing fish to an increased likelihood that they will ‘scrape’ along the concrete rather than simply ride down in the water column. If the bottom surface downstream of the spillway discharge chute is rough and jagged it could result in fish impacting or scraping on portions of the bottom surface as they move
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downstream at high velocity. Concentrations of predators within a stilling basin can also affect fish survival as noted at Daguerre Point Dam where juveniles passing over the face of the dam can be disoriented and vulnerable to predation in the deep, low-velocity water (Entrix and Monroe 2003).
Assumed Spillway Survival of Juvenile Salmonids at Englebright Dam and New Bullards Bar Dam Life Stage Low Mid High Efry (emergent) 0% 20% 30% Smolt0 (subyearling) 10% 30% 50% Smolt1 (yearling) 10% 30% 50%
In addition to spillways, some dams have bottom release sluiceways that discharge below the dam. The sluiceways are generally used to supplement the spill flow during extreme high-flow events. The sluiceways are submerged on the upstream side of the dam and are rectangular in shape, with a reducing area in the downstream direction through the dam. During flood operations, flow releases at NBBD are made through the spillways and may also be made through the bottom outlet. Due to the depth of submergence of the bottom outlet, juvenile salmonids are not expected to pass through the bottom outlet when they are used to pass flow. Englebright Dam has no low level outlet; but low level outlets are incorporated into the facilities at Our House and Log Cabin Dams.
4.3 TEMPERATURE CONCERNS Maintaining suitable water temperatures at entrance and exit conditions is a critical concern for successful upstream and downstream fish passage facilities. Fish migrating upstream may encounter cold water at the base of a dam and be unwilling to enter an upstream fish passage facility that is discharging water drawn at depth from the upstream reservoir. Engineering design solutions are available to mix warm water from the top of a reservoir with cold water at the bottom; however, the target release temperature may be based on satisfying temperature limits miles downstream of the dam. In addition, tailrace releases that represent a mix of warm surface water and colder bottom water present a potential temperature difference between the downstream collection site and upstream release site. Fish entering the tailrace collection facility would have to be collected, transported, and released to an upstream area with suitable, similar water temperatures. If the upstream reservoir surface water is significantly warmer than the tailrace, volitional fish passage, such as a conventional fish ladder, may not be feasible. Therefore, where temperature issues are part of facility design considerations, advance data
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collection and engineering analysis is warranted prior to final design and construction. This could possibly be the case for assessing summer season fish passage at Englebright Dam. Although there are no known examples, an upstream fishway system designed to release fish at colder depths may be required to overcome the constraints of conventionally designed fish ladders where surface temperature differentials are excessive. However, if these types of engineering design challenges cannot be functionally overcome for whatever reasons, then collection and transport systems may be the most practical alternative. If this is the case, upstream release locations may change depending on the season in order to maintain suitable water temperatures at the release site. Collection and transport options provide a degree of flexibility to adjust release locations, depending on availability of access roads (or development of other means) to deliver fish to specific release locations. Maintaining water quality is also a significant concern with collection and transportation of fish, particularly water temperatures and dissolved oxygen. Fish may experience thermal stress if the water warms up during transport and the water temperature in the transport tanks is not close enough to the water temperatures at the release location. Therefore, much emphasis must go into design and development fish transport vessels, equipped with state-of-the-art, aquacultural life support systems and acclimation facilities.
Fish migrating downstream in the spring must complete their journey while water temperatures remain suitable throughout their migration route. Spring-run Chinook Salmon and steelhead may rear year-round in the upper NY sub-basin, but water temperatures in the middle and lower mainstem Yuba River may begin warming with the onset of summer and present a potential barrier to passage or become a source of additional mortality under current flow releases. Augmenting flows during critical migration periods may mitigate some of these temperature effects and encourage timely outmigration.
4.4 PHASED PASSAGE FACILITIES In this section, an approach toward development of phased fish passage facilities is considered. A clear management vision that describes a specific pathway to guide reintroduction efforts has not yet been agreed upon, but several options have been studied, conceptually designed, and discussed in stakeholder forums. Rather than attempt to prescribe specific fish facilities at this stage, this Plan identifies some of the facility options that can be evaluated and incorporated into a logical sequence within a phased, adaptive management approach.
Engineering feasibility studies and in-depth fish passage analysis are not detailed in this report, but considerable fish passage work has been completed at conceptual engineering level (MWH 2010, GEC 2014), and should be referenced to better understand options and recommendations
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provided here. These engineering studies represent a foundation for planning and design development. Using what is already known to inform more advanced design efforts is consistent with the phased, adaptive management approach.
As stated earlier, removal of certain dams is generally acknowledged as the most efficacious form of fish passage because it completely removes the obstacles that cause fragmentation of riverine habitats. However, where dam removal is considered infeasible, or cannot be accomplished in the early phases of reintroduction, other volitional or non-volitional fish passage facility alternatives provide a means to achieve targeted reintroduction objectives. Careful planning is required to ensure that fish passage objectives can be met and (to the degree possible) avoid the possibility that constructed facilities could be rendered unproductive or obsolete over the long-run.
Decisions about when and where reintroductions can (or will) occur must be taken before a definitive strategy for construction of phased fish passage facilities can be fully articulated. However, at this stage, a dual reintroduction experiment strategy is proposed – based on a hypothesis that there is potential for meaningful reintroductions of both spring-run Chinook Salmon and steelhead in all upper Yuba sub-basins. This notion is grounded in the fact that these species historically occupied the upper basin tributaries; and that models and field studies indicate significant habitat potential could still exist under certain circumstances. The dual strategy is recommended to independently explore reintroduction potential in two distinct candidate regions: (1) the upper North Yuba River (accessed via collection of adults downstream of Englebright Dam, and transported upstream of New Bullards Bar Dam), and (2) the collective tributaries of the NBB, MY, and SY reaches (accessed via fish passage at Englebright Dam).
The first recommended step in a pilot reintroduction program is to implement interim fish testing facilities to support experimental reintroductions of spring-Chinook and steelhead to targeted areas upstream of both Englebright and New Bullards Bar Dams. This dual reintroduction experiment strategy would allow testing of several hypotheses which have been generated by modeled scenarios and other studies. If these experiments yield positive results, then further consideration should be given to expanding the facilities in the short-term reintroduction phase.
A phased approach to the development of fish passage facilities may help address the biological uncertainties associated with the reintroduction of spring-run Chinook Salmon and steelhead into the Upper Yuba watershed. Early phases are designed to gain operational experience and record observed fish behavior that can be used to optimize following phases. An early phase might include temporary or modular facilities to help confirm appropriate concepts and locations of the
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facilities, and to evaluate fish behavior and passage capacities (e.g., streamside fish management stations, fish trapping and handling capabilities in existing fish ladders, basic tributary collection devices, experimental collection facility entrances, etc.). Early phases might also allow transport from a temporary adult collection station to multiple, experimental release locations to evaluate stream-specific performance before committing to full build-out of permanent facilities. Phasing upstream passage efforts would be very beneficial for the Upper Yuba reintroduction program by allowing collection of more site-specific fish behavior and hydraulic data to guide the development of reintroduction strategies that have the highest likelihood of success. For instance, a phased approach to reintroduction of spring-run Chinook Salmon and steelhead into the Upper Yuba could begin by collecting fish at the Daguerre Point Dam (north) fish ladder and releasing them directly into the upper North Yuba River, as a first step in the reintroduction process. While Daguerre Point Dam may or may not be the best choice for a long-term fish collection and management station, a temporary facility could be quickly constructed at relatively low cost by retrofitting the existing fish ladder(s) with provisions to capture fish when transport operations are desired. The Daguerre (north side) location also offers a convenient staging location for an interim facility building where adult and juvenile fish may be held for acclimation, monitoring, counting, and scientific study prior to transport and release to the river. An interim facility at the Daguerre location could also facilitate staging and handling of stocks transported from the FRFH that might be used in early pilot experiments.
Depending on future decisions that reflect a longer-term vision for Yuba River fisheries resources, permanent management facilities for upstream collection, passage, and transportation may be better suited to the area downstream of Narrows 2 powerhouse. This particular location makes sense because it is currently the upstream terminus of fish passage. Favorable river hydraulics and channel geomorphic characteristics make it a good location to build a fish ladder, as well as a multi-use management facility that can provide passage opportunities to targeted points upstream. In addition, collecting spring Chinook and steelhead at the Narrows location makes sense from a biological perspective because it would tend to select for fish that are most likely trying to pass further upstream, rather than those fish that might otherwise choose to spawn in the lower river.
There are many aspects of a pilot reintroduction phase that could be the focus of detailed discussion and facility planning, but the scope of this work does not allow for every aspect of phased passage facilities to be addressed. Instead, the following paragraphs deal with a few important considerations for developing passage facilities that will work successfully at specific points in the Yuba River system.
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Englebright Dam and Narrows Hydroelectric Complex Several upstream passage challenges were outlined earlier in Section 4.1 Upstream Connectivity. In the case of Englebright Dam, the challenges associated with dam height and water quality are paramount in terms of designing a functional upstream fishway system. However, to the extent these issues are revealed in subsequent engineering analysis, they may be potentially overcome with innovative design solutions such as:
incorporation of automated temperature controls,
structural insulation and shading to reduce thermal heat gain in concrete structures,
use of auxiliary cold water systems emanating from reservoir depths,
expanded resting pools, gates and crowding devices to prevent fall back,
subsurface exits from fishways into cooler receiving water,
dam notching to reduce the overall height to be surmounted.
To better assess the chances of success, and if deemed advisable by design team engineers, an upstream volitional fishway system at the Englebright-Narrows 2 location may be developed in stages by incorporating in situ testing to proceed as described below:
Stage one (initial test stage) This stage could begin by examining fish attraction into a short fish ladder test segment (e.g., Denil, or vertical slot-style, 20 vertical feet) that is part of a testing configuration. Test water can be provided by tapping into the Narrows 2 bypass conduit, or piped in from a representative surface reservoir intake at prescribed points. This offers the opportunity to test different “candidate source waters” to see if fish will accept or reject the ladder entry point based on its hydraulic and physical configurations and water quality characteristics. By carefully choosing the sources of test water, real simulations will reveal critical performance characteristics (i.e., ladder acceptance or rejection) that can be expected to prevail in subsequent stages of fish ladder build out.
Stage Two (first fishway segment to collection facility) If fish are successfully attracted to the ladder entrance in stage one, then a fully-functional ladder extension can be built to raise fish from the river (via conventional fish ladder) to an elevated fish collection facility (approximately 60-75 vertical feet) where ample resting pool areas exist at a flat gradient. This “operations platform” could allow operators the option of either loading fish into transport vehicles, or directing fish into a possible fishway extension (e.g., ladder/lift/tram) that allows for passage to Englebright Reservoir.
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Stage Three (second fishway segment from collection facility to reservoir) To test the efficacy of an additional fish ladder extension from the collection station to the reservoir, another short fish ladder segment could be tested, similar to stage one, in which the proposed water source for the upper fish ladder extension is brought in via pumped or gravity fed (or siphon) pipes. By employing these methods, there will be some definitive indication of whether or not fish would enter and swim up into this ladder section: thus providing evidence of how a full-rise fish ladder would likely perform, prior to committing to the expense of a permanent concrete facility.
Notching of Englebright Dam is another design option to consider. If Englebright dam were notched down to a height of 170 or 140 feet, as is described in the engineering report: Yuba River Fish Passage Improvement Investigation (GEC 2014), and an intermediate fish collection station were built, this would result in an upper ladder segment that is approximately 100 feet or less. As an alternative to building an upper ladder extension, fish loaded into transport vehicles at the elevated fish management station could be driven to designated release points upstream (including experimental releases directly into Englebright reservoir just upstream of the dam, or other destinations further upstream according to program management goals). As another alternative, a tramway or railway could be constructed to transport fish from the elevated fish management station to a release point in the reservoir forebay. Test fish could be tagged and tracked to examine their behavior and ultimate fate.
New Bullards Bar Dam and Colgate Powerhouse Some fish passage engineering challenges may be seen as too costly or risky given the state of current technology and practice. For instance, a separate fish ladder (or tramway) from the base of 635-feet high New Bullards Bar Dam would encounter significant challenges of construction along a steep slope, auxiliary water supply, long ladder length, and water temperature control issues. In addition, the reservoir at NBBD is subject to annual water level fluctuations of up to 150 feet, which would add to the complexity of a fish ladder or tramway at that site. Engineering solutions may be available to successfully address volitional passage issues at Englebright Dam and Our House Dam; but the complexities and challenges involved with volitional or semi- volitional upstream passage at New Bullards Bar Dam appear to favor collection and transport operations as a more reliable and cost-effective means to connect the habitats of the upper north Yuba River. A collection and management station built at the base of New Bullards Bar Dam could be developed in a manner that is substantially similar to that proposed for staged development at Englebright Dam. Should passage be established upstream of Englebright Dam (along with habitat restoration actions for the reach downstream of New Bullards Bar dam), then a collection and transport station at New Bullards Bar Dam would make sense to provide adult
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fish access to the upper North Yuba River. Fish migrating all the way to the base of New Bullards Bar Dam would once again provide a clear biological signal that they are seeking further passage to upstream habitats. Radio-tracking of experimental fish, in proper sequence with other steps, would be required to validate the need for an additional fish passage station.
New Colgate Powerhouse Restoring the anadromous fish habitat potential between New Colgate Powerhouse and New Bullards Bar Dam was explored in the habitat assessment modeling conducted by Stillwater Sciences (2013a). In summary, this reach might be extremely productive for spring-run Chinook Salmon and steelhead if: (a) additional cold water flow is released at New Bullards Bar Dam, and (b) gravel supplementation is accomplished to restore spawning substrate in this gravel- starved reach. One of the great fisheries values that might be realized by restoring habitat in this reach is that cold water releases from New Bullards Bar Dam can ensure that water temperature remains suitable for Chinook salmon and steelhead in every water year type. This opportunity is appealing from a salmon and steelhead management perspective because it provides a measure of security against the future risks of climate change that might yield adverse impacts on the CV salmon and steelhead ESU’s as a whole.
New Colgate Powerhouse itself may be an upstream passage barrier to some extent because of its peaking power operations and the unpredictable hydraulic changes that frequently occur when the power plant operates over a range of flows, thus mixing cold water from power plant effluent with warm, low flows from upstream sources in spring and summer. To assess fish passage at the New Colgate site, radio-tagged fish might be released in Englebright reservoir, while flow and water quality conditions are carefully documented at the new Colgate site under a series of experimental flow releases. If the results of these pilot experiments indicate complications, then additional radio-tracking experiments might be conducted. Releasing test fish just upstream of Colgate powerhouse would help assess the efficacy of collection and transport upstream of the Colgate facility- in order to provide adult fish access to this reach while reducing limitations on power plant operations during seasons of migration. Experiments involved with collecting juvenile outmigrants at the same location could also be conducted to offer a more comprehensive assessment of the reintroduction potential of this reach. In the longer-term, if experiments show that fish passage can occur at Colgate without serious compromise to the hydropower operations, then a protocol can be determined that allows for operations that are compatible with fish reintroduction. Phased fish passage facilities will be needed to conduct these key experiments and provide for any short-term or long-term expansions in the overall reintroduction effort.
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Upper North Yuba River According to habitat assessment modeling (Stillwater 2013a) and field studies, the NY sub-basin, when compared to other upper Yuba sub-basins, contains more suitable and productive habitat (as measured by total stream miles and mesohabitat qualities) under current water management conditions. However, under modeled scenarios featuring flow supplementation and habitat restoration actions – the combined habitat productivity of the NBB, MY, and SY rivals the NY, especially in some of the drier water years. From a water resources perspective, it makes sense to look closely at the NY option, if only because it is the only tributary where significant water management changes are unnecessary to the success of a reintroduction. Therefore, the upper North Yuba River might be considered as a possible starting point for a collection and transport style reintroduction program. The most significant unknown that needs to be addressed before making a commitment to this path is the actual fish passage facility performance (i.e., collection and transport efficiencies) that will be realized in moving fish around the NBBD and reservoir. If fish passage can be done to a high level of success, then the benefit of the habitat potential will be maximized. On the other hand, if fish passage efficiencies (especially downstream juvenile migration) are marginal or poor, then the success of the overall effort will be much less productive. Because of this critical consideration, and in acknowledgement of the range of costs accompanying programs of this scale, it is imperative to conduct pilot experiments to compare results of reintroduction options upstream of both New Bullards Bar and Englebright dams. If, for example, pilot reintroduction experiments of anadromous fish passage are highly successful in the NY, then facilities to expand collection and transport of fish to a production level could be built at a Narrows (or Daguerre Point) collection facility. If the program evolves, based on comparative results of pilot experiments, to include fish passage upstream of the current Englebright Dam location, then fish would re-occupy the river reach leading up to NBBD, and an adult upstream collection and transport facility could be constructed below NBBD at a later date. This option may be necessary in the event that a future decision is taken to modify or remove Englebright Dam, or else to provide for the optimal utilization of all suitable habitats in the reaches below and above NBBD.
There is one important caveat, from a fish facilities perspective, about starting with a NY reintroduction effort: it is highly recommended that pilot experiments be initiated at the earliest possible time to test the viability of different methods for collecting out-migrating juvenile fish. This includes experimentation with tributary collection devices and conducting juvenile fish “reservoir transit studies” to help determine the best and most cost-effective approach to collecting out-migrating fish. Studies show that the habitat in the upper north Yuba is generally abundant and productive for anadromous fish; but because of the enormity of the NBBD and
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reservoir, the ability to conduct successful juvenile fish collection operations could make – or break – this particular reintroduction option. In other words, it does no good to transport adult fish to highly productive habitats to spawn if their progeny (out-migrating smolts) cannot make it back out to the estuary and the ocean. Therefore, commencing reservoir and tributary collection studies should be an important early priority to help determine the best adaptive management path for reintroduction plan implementation.
Siting of collection and transport stations is dependent on short-term and long-term program goals. The best formula for making siting decisions is to keep a long-term vision in mind when conceptualizing short term actions and designing interim facilities. How will facilities constructed in pilot and short-term reintroduction phases contribute to the success of the long- term operation? Does siting of a facility in a particular location preclude changes that may be called for through the adaptive management process? Can lower-cost, basic facilities suffice for some parts of the reintroduction program during early experimentation phases to conserve funding until the long-term facility design is established? Additional discussion of phased approaches to reintroduction planning – with emphasis on the biological and genetic aspects – is described in the next sections.
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5. STOCK SELECTION AND GENETIC MANAGEMENT13
5.1 INTRODUCTION There are typically four specific actions associated with reintroduction of anadromous salmonids: (1) donor stock selection and collection, (2) rearing/culture of individuals from the donor stock(s), (3) reintroduction/release of these individuals, and (4) post-introduction monitoring of donor stock populations and reintroduced populations (SJRRP 2011). This section is focused solely on the selection of donor stock for reintroduction to the upper Yuba River watershed, and relies on examples and recommendations used in reintroduction planning for the San Joaquin River Restoration Program (SJRRP) and other relevant stock selection and reintroduction efforts.
5.2 UPPER YUBA RIVER WATERSHED CHARACTERISTICS Reintroduced salmonid populations are expected to have a higher probability of success when they originate from donor populations that are most adapted to environmental conditions of the river systems to which they are being reintroduced (Nielsen and Powers 1995, Huntington et al. 2006). Understanding local environmental conditions of the reintroduction area is important for selecting stocks that have life histories and environmental tolerances most compatible with the existing environment. Factors such as timing and magnitude of flows, locations and seasonality of migration barriers, and water temperature are most relevant to selection of a suitable stock. Key habitat attributes for spring-run Chinook Salmon and steelhead such as pool density and depth, cover, spawning substrate quantity and quality, and overwintering habitat may also influence the likelihood that a reintroduction of a given stock will succeed.
5.2.1 Flow Understanding the timing and magnitude of flows in the upper Yuba River basin in relation to life history timing is important for selecting successful parent stocks for reintroduction. Different source populations of spring-run Chinook Salmon and steelhead are adapted to different flow regimes, and as discussed in the sections that follow, the flow regime has a controlling influence on other key factors such as passage and water temperature. Ideally, the parent stock will be from a population adapted to a similar hydrologic regime as the upper Yuba River basin.
13 Prepared by Stillwater Sciences 2014.
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Steelhead and spring-run Chinook Salmon populations from the Sacramento River basin generally outmigrate during high winter and spring flows (Healey 1991, Reynolds et al. 1993, McEwan 2001). The South and Middle Yuba rivers are highly regulated and generally exhibit relatively lower winter base and summer low flows, and a more truncated snowmelt influence than the unregulated North Yuba River (Figure 1-4). Due to the highly regulated nature of the Yuba River basin, the selection of source stock adapted to a river system where most juveniles outmigrate in spring and early summer before flows recede and water temperatures increase would be favorable. The migration of adult spring-run Chinook Salmon past passage impediments (partial or low-flow barriers) is expected to be more successful during high flows (see section 1.4); thus selecting parent stocks that migrate upstream earlier in the migration period before high flows subside should be prioritized. These priorities assume current flow regimes. Detailed analysis of flows required to attract, pass, and hold spring-run Chinook Salmon into the MY and SY sub-basins is included in the NMFS 10(j) flow recommendations (NMFS 2012, Stillwater 2013a). Potential adjustments to flow releases from upstream dams on the South and Middle Yuba rivers could benefit passage and water temperature conditions. As stated in the Public Draft Recovery Plan (NMFS 2009):
“Reintroduction of fish to historic habitats will require a concerted effort by FERC and other interested parties to align license schedules and develop watershed approaches to developing new stream flow regimes...This approach is especially necessary in the McCloud, upper Yuba, upper Merced, and other watersheds where upstream hydroelectric projects may...affect downstream habitats that are essential for recovery.”
5.2.2 Barriers to Anadromy Natural, impassable barriers to upstream salmonid migration have been identified on the Middle Yuba River at RM 34.4, and on the South Yuba River at RM 35.4 (Vogel 2006, UYRSPST 2007). In addition, for both the South and Middle Yuba rivers, at least three “low flow” barriers- features that block adult passage at lower flows, but not necessarily at higher flows—have been identified downstream of the impassable barriers (Vogel 2006). Data on natural migration barriers in the North Yuba River are not currently available, but Yoshiyama et al. (2001) report that the pre-dam upstream limit of anadromy on the North Yuba was likely Loves Falls, at river mile (RM) 51, about two miles upstream of the Salmon Creek confluence.
Steelhead in the Sacramento River basin generally migrate, hold, and spawn during periods of higher flow than do spring-run Chinook Salmon (Hallock 1989, Ward et al. 2004). It is therefore important to select Chinook salmon stocks with run timings that maximize passage at low flow
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barriers for this reason, and because their ability to leap or ascend barriers is lesser than that of steelhead. Stocks that migrate earlier in the spring before snowmelt-driven stream flows begin to recede are likely to navigate past low flow barriers most successfully.
5.2.3 Water Temperature Water temperature is a key environmental factor likely to limit the potential distribution of spring-run Chinook Salmon and steelhead in the upper Yuba River basin. Selective pressures related to high summer water temperature can result in local adaptation of populations with higher water temperature tolerances and life history strategies that minimize exposure (Gamperl et al. 2002, Rodnick et al. 2004). If increased flow scenarios are implemented in the upper Yuba River basin, there will be a reduction in water temperatures in some sub-basins, most likely increasing the downstream extent of thermally suitable habitat for adult spring-run Chinook Salmon holding and juvenile rearing. The specific impacts of augmented flow on suitability for various life stages are uncertain, and water temperature would likely continue to limit the distribution of both salmon and (to a lesser extent) steelhead in the upper Yuba River basin following reintroduction. Consequently, source stocks that exhibit higher water temperature tolerances and have life history timings that minimize exposure to high water temperatures should be selected.
5.3 CENTRAL VALLEY SPRING-RUN CHINOOK SALMON AND STEELHEAD LIFE HISTORIES
5.3.1 Central Valley Spring-run Chinook Salmon ESU Spring-run Chinook Salmon adults migrate upstream while sexually immature, hold in deep, cold pools over the summer, and spawn in late summer and early fall. Juvenile outmigration is highly variable, with some juveniles out-migrating in winter and spring (ocean-type), but others over- summering and then emigrating as yearlings (stream-type). Table 5-1 illustrates life history timing for spring-run Chinook Salmon in the Sacramento River basin.
Age of Return Adult spring-run Chinook Salmon may return between the ages of 2 and 5 years. Historically, adult spring-run are believed to have returned predominantly at ages 4 and 5 years at a large size. Most spring-run Chinook Salmon now return at age 3, although some portion returns at age 4 (Fisher 1994, McReynolds et al. 2005), probably due to intense ocean harvest (which removes the largest fish from the population and selects for fish that spend fewer years at sea). In 2003, an estimated 69% of the spring run in Butte Creek returned at age 4 (Ward et al. 2004); however, in most years, the proportion of age 4 adults is much smaller.
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Table 5-1. Life history timing of spring-run Chinook Salmon in the Sacramento River basin.
Month Life stage Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec
Adult entry into Sacramento-San Joaquin Delta Estuary Adult entry into Sacramento River
Adult migration past Red Bluff Diversion Dam Entry into spawning tributaries1
Adult holding
Spawning in Deer, Mill, and Butte creeks2 Incubation
Fry emergence
Fry/juvenile outmigration from tributaries3 Fry/juvenile outmigration in Butte Creek4 Fry/juvenile outmigration in Feather River5 6 Yearling outmigration from tributaries3, 7 Ocean entry of yearlings
1 C. Harvey (CDFG, Redding, pers. comm., as cited in Cramer and Demko 1997), Myers et al. (1998), Vogel (1987a,b), and Hill and Webber (1999) 2 Harvey (1995, as cited in Cramer and Demko 1997); Moyle et al. 1995 3 Some spring-run disperse downstream soon after emergence as fry in March and April, with others smolting after several months of rearing, and still others remaining to oversummer and emigrate as yearlings (USFWS 1995, as cited in Yoshiyama et al. 1998). 4 “patterns in Mill and Deer creeks are very similar to patterns observed in Butte Creek, with the exception that Mill and Deer creek juveniles typically exhibit a later young-of-the-year migration, and an earlier yearling migration” (Lindley et al. 2004). 5 “Data collected on the Feather River suggests that the bulk of juvenile emigration occurs during November and December,” (DWR and Reclamation 1999; Painter et al. 1977, as cited in NMFS 2009). 6 Defined here as juveniles that have oversummered in their natal stream. 7 Based on outmigrant trapping in Butte Creek in 1999 and 2000, up to 69% of age 0+ juveniles outmigrate through the lower Sacramento River and Sacramento-San Joaquin Delta between mid-November and mid-February, with a peak in December and January (CDFG 1998, Hill and Webber 1999, Ward and McReynolds 2001). A smaller number remain in Butte Creek and outmigrate in late spring or early summer, and in both Butte and Mill creeks, some of these oversummer and outmigrate as yearlings from October to March, with a peak in November (Cramer and Demko 1997, Hill and Webber 1999). Period of activity Period of peak activity
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Upstream Migration Timing Adult spring-run Chinook Salmon enter the Sacramento-San Joaquin Delta beginning in January, entering their natal spawning streams from March to July (Myers et al. 1998). Adults enter Deer and Mill creeks beginning in mid-February, peaking in May, and concluding the beginning of July (Vogel 1987a, b; C. Harvey, pers. comm., CDFG, Redding; as cited in Cramer and Demko 1997; Lindley et al. 2004) (Figure 5-2). Their upstream migration is timed to take advantage of spring snowmelt flows, which allow them access to upstream holding areas where temperatures are cool enough to hold over the summer prior to the spawning season (NMFS 1999). In the Sacramento River, upstream migration of spring-run Chinook Salmon overlaps to a certain extent with that of winter Chinook (December through July, peaking in March), and adults from particular runs are not generally distinguishable from one another by physical appearance alone, making it difficult to pinpoint migration timing with precision (Healey 1991). Run size and timing for Central Valley spring-run Chinook Salmon is shown in Figure 5-3.
Spawning Timing The timing of spring-run spawning in the mainstem Sacramento River has shifted later in the year, which is believed to be a result of genetic introgression with the fall run (Cramer and Demko 1997). Populations in Deer and Mill creeks, which do not appear to have significantly hybridized with the fall run, generally spawn earlier than those in the main stem or Butte Creek (Cramer and Demko 1997, Lindley et al. 2004). Rutter (1908) noted that most spawning in the late 1800s/early 1900s in the Sacramento River basin occurred in August. Peak spring-run spawning in Butte Creek now usually occurs during the first week of October, while the peak for the fall run is in mid-to late November (Ward et al. 2003, McReynolds et al. 2005). California Department of Fish and Game’s (CDFG) 1998 status review of spring-run Chinook Salmon reports that spring-run spawning historically peaked in the first half of September, two months earlier than the peak for fall Chinook, as based on Baird Hatchery (McCloud River) records from 1888 to 1901. Parker and Hanson (1944) observed intensive spawning of spring-run Chinook Salmon from the first week of September through the end of October in 1941. Currently, redd counts indicate that spring-run Chinook Salmon spawning typically begins in late August, peaks in September, and concludes in October in both Deer and Mill creeks (Harvey 1995, as cited in Cramer and Demko 1997; Moyle, pers. obs., as cited in Moyle et al. 1995; NMFS 2004).
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Figure 5-2. Weekly migration of spring-run Chinook Salmon into Mill, Deer, and Butte creeks (source: Lindley et al. 2004).
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Figure 5-3. Run size and composition of spring-run Chinook Salmon from 1970 to 2008 (source: NMFS 2009, based on CDFG GrandTab spawning data 2009).
Spawning and rearing habitats that may be accessible to the spring run, but inaccessible to the fall run include (1) areas above falls or obstacles that cannot be negotiated during the low flows of summer and fall, and (2) areas above sub-basins that become too hot for salmon in the summer and fall. During the high spring snowmelt flows, spring-run Chinook Salmon can ascend many obstacles that are barriers to upstream migration at lower flows, and can traverse sub-basins in the spring that will be too warm in the fall for adult salmon.
Under historical conditions, the spring and fall Chinook salmon runs were geographically isolated in terms of where they spawned in the basin, which maintained their genetic integrity. Although spring-run Chinook Salmon spawn earlier than fall-run, the timing of spawning of the two runs overlaps enough that hybridization can occur where they share the same spawning areas. Where the spring run is now forced to share spawning grounds in the mainstem Sacramento River with the fall run, fall Chinook salmon may dominate because of their longer growth period in the ocean, slightly larger size, and less time spent holding in the stream prior to spawning. Hybridization between the two runs has tended to be to the detriment of the spring- run life history.
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In some areas, differences in timing of spawning may still be sufficient to maintain separate runs. Peak spring-run spawning in Butte Creek usually occurs during the first week of October, while the peak for the fall-run is in mid-to-late November (Ward et al. 2003, McReynolds et al. 2005).
Elevation of Holding and Spawning Areas in Streams with Wild Spring-Run Stocks Spring-run Chinook Salmon in Deer Creek hold and spawn primarily in the 30 miles between the Ponderosa Way Bridge (elevation 1,640 ft) and upper Deer Creek falls (3,600 ft), which is apparently a barrier to further upstream movement (Marcotte 1984, Harvey 1994). The sub- basin from the Ponderosa Way Bridge to the lower Highway 32 bridge crossing has been identified as important for summer holding (P. Moyle, pers. comm., as cited in Cramer and Demko 1997). In Mill Creek, spring-run spawning has been observed over 50 miles of stream from near the boundary of Lassen National Park at an elevation of 5,000 ft, downstream to the confluence of Little Mill Creek at an elevation of 800 ft (Harvey 1994). Spawning habitat in Butte Creek is confined to lower elevations than in Deer and Mill creeks, with the highest densities of fish spawning in the approximately 10 miles between the upper limit to migration at Quartz Bowl, located approximately one mile below Centerville Head Dam (elevation 1,130 ft) downstream to Covered Bridge (elevation 400 ft) (Cramer and Demko 1997).
Juvenile Rearing and Outmigration The rearing and outmigration patterns exhibited by spring-run Chinook Salmon are highly variable, with fish rearing anywhere from 3 to 15 months before outmigrating to the ocean (Fisher 1994). Variation in length of juvenile residence may be observed both within and among streams. Some may disperse downstream soon after emergence as fry in March and April, with others smolting after several months of rearing, and still others remaining to oversummer and emigrate as “yearlings” (applied here to refer to any juveniles that remain to oversummer in their natal stream) (USFWS 1995, as cited in Yoshiyama et al. 1998). Scale analysis indicates that most returning adults have emigrated as yearlings (Myers et al. 1998). Calkins et al. (1940, as cited in Myers et al. 1998) conducted an analysis of scales of returning adults and estimated that greater than 90% had emigrated as yearlings at a size of about 3.5 in (88 mm).
Extensive outmigrant trapping in Butte Creek has shown that spring-run Chinook Salmon in this stream outmigrate primarily as juvenile (age 0+) fish from November through June, and that this movement appears largely influenced by flow (Ward et al. 2003). A small proportion remains to oversummer and outmigrate as yearlings beginning in mid-September and extending through March, with a peak in November (Cramer and Demko 1997, Hill and Webber 1999, Ward et al. 2004). Outmigration timing in Deer and Mill creeks is similar (Figure 5-4) except that downstream movements of age 0+ fish typically occur later than in Butte Creek, and yearling
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outmigration earlier (Lindley et al. 2004). Yearling outmigrants tend to be more common in Deer and Mill creeks than in Butte Creek (Cramer and Demko 1997). In the Feather River, the majority of fish outmigrate as juveniles in November and December, possibly because juvenile rearing habitat is limited (Seesholtz et al. 2004).
Figure 5-4. Mean monthly catches of juvenile spring-run Chinook Salmon in rotary screw traps in Mill, Deer, and Butte creeks (source: Lindley et al. 2004).
Populations of spring-run Chinook Salmon in Deer, Mill, and Butte creeks have greatly increased since the period from the mid-1970s to about the year 2000, when substantial increases in escapement began, but have begun to decline again since 2006 (CDFG 2009 GrandTab spawning data). Butte Creek currently has the largest naturally spawning Central Valley spring- run Chinook Salmon population. A few naturally spawning fish are also present in Battle, Clear, Cottonwood, and Big Chico creeks (CDFG 2005 GrandTab spawning data), but records reviewed by Yoshiyama et al. (1996) did not indicate that spring-run Chinook Salmon were abundant in these streams under historical conditions. Lindley et al. (2004) classified spring-run populations in these streams as “dependent populations;” i.e., they are likely dependent on strays from populations in nearby streams such as Mill, Deer, and Butte creeks.
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5.3.2 California Central Valley Steelhead DPS There has been only limited research and monitoring on Central Valley steelhead in comparison with Chinook salmon. Though the upper sub-basins of the Sacramento River support a spawning population of resident Rainbow Trout, the mainstem river habitat used by the species is atypical for steelhead, which usually spawn in higher elevation, steeper, and narrower channels. Management of the species is also complicated by its polymorphism, with individuals being capable of exhibiting either a resident (Rainbow Trout) or an anadromous (steelhead) life history.
O. mykiss once occurred throughout the Central Valley, spawning in the upper sub-basins of tributaries to the Sacramento and San Joaquin rivers. Lindley et al. (2006) recently conducted GIS-based habitat modeling to estimate the amount of suitable habitat to support O. mykiss populations in the Central Valley, and their results suggest that steelhead were widely distributed throughout the Sacramento River basin, but relatively less abundant in the San Joaquin River basin due to natural barriers to migration. Yoshiyama et al. (1996) conducted a thorough review of historical sources to document the historical distribution of Chinook salmon in the Central Valley, which can be used to infer historical distribution of steelhead. The assumption that steelhead distribution in the Sacramento River basin overlapped with, and was likely more extensive than, spring-run Chinook Salmon distribution under historical conditions has been supported by studies conducted in the Klamath-Trinity river basin (CH2M Hill 1985, Voight and Gale 1998). Yoshiyama et al. (1996) concluded that, because (1) steelhead upstream migration occurs during high flows, (2) their leaping abilities are superior to those of Chinook salmon, and (3) they have less restrictive spawning gravel criteria; steelhead in the Sacramento River basin “could have used at least hundreds of miles of smaller tributaries not accessible to the earlier- spawning salmon.” The model created by Lindley et al. (2006) estimates that 80% of historically accessible habitat for Central Valley steelhead is now behind impassable dams; this figure is supported by other research into steelhead and Chinook salmon habitat loss in the Central Valley (Clark 1929, Yoshiyama et al. 1996, 2001).
In the Sacramento River basin, populations of O. mykiss are known to spawn in the upper Sacramento, Yuba, Feather, and American rivers, and in Deer, Mill, and Butte creeks. Saeltzer Dam was removed from Clear Creek in 2000, granting easier access to upstream habitats in the canyon sub-basins of the creek.
Steelhead migrate up the Sacramento River nearly every month of the year, with the bulk of migration occurring from August through November, and the peak in late September (Bailey 1954; Hallock et al. 1961, both as cited in McEwan and Jackson 1996; McEwan 2001).
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Spawning in the upper Sacramento River generally occurs between November and late April, with a peak between early January and late March (USBR 2004). Fry emergence is influenced by water temperature, but hatching generally requires four weeks, with another four to six weeks in the gravels before emergence. Juvenile steelhead typically rear in freshwater from 1 to 3 years before emigrating (McEwan and Jackson 1996). The majority of returning adult steelhead in the Central Valley spend two years in fresh water before emigrating to the ocean (McEwan 2001). A scale analysis conducted by Hallock et al. (1961, as cited in McEwan 2001) indicated that 70% emigrated after two years, 29% after one year, and 1% after three years in fresh water. Juvenile emigration from the upper Sacramento River occurs between November and late June, with a peak between early January and late March (USBR 2004).
5.4 REINTRODUCTION STRATEGY The overall goal for implementation of a reintroduction strategy in the Yuba River basin is to improve the overall viability status for the Central Valley Spring-run Chinook Salmon ESU and California Central Valley steelhead DPS so that they may be removed from federal protection under the Endangered Species Act, and so they will sustain long-term persistence and evolutionary potential. In the NMFS (2009) Draft recovery plan, a strategic framework for recovery efforts is described which includes a description of viability at both the ESU/DPS and population scales, a categorization method for prioritizing watersheds currently occupied, and a mechanism prioritizing unoccupied watersheds for reintroductions.
Based on a number of climatological, hydrological, and geological conditions, the draft recovery plan (NMFS 2009) identifies four population groups (referred to as diversity groups) for which Chinook salmon were historically distributed, and two additional diversity groups for steelhead. The populations of spring-run Chinook Salmon and steelhead historically within the Yuba River basin are considered part of the Northern Sierra Nevada Diversity Group, which is composed of east-side tributaries to the Sacramento River, and the Mokelumne River. Populations from within this Diversity Group are likely to be more suitable as donor populations for reintroduction than populations from other diversity groups due to their genetic and life-history timing characteristics which are more likely to contribute to successful adaptation in the reintroduction area.
5.4.1 Recovery Priorities for Central Valley Spring-run Chinook Salmon and Steelhead NMFS (2009) also developed priority levels (referred to as Core 1, 2, or 3 populations) to help guide recovery efforts for watersheds that are currently occupied by at least one of the three listed Chinook salmon and steelhead species in this region (i.e., Sacramento river winter-run Chinook salmon ESU, Central Valley Spring-run Chinook Salmon ESU, and Central Valley
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steelhead DPS). The lower Yuba River steelhead population belongs to the Core 1 priority level, which is considered the highest priority for recovery efforts. NMFS (2009) uses the following five criteria to classify Core 1 populations:
1. known ability or significant immediate potential to support independent populations 2. role of the population in meeting the spatial and/or redundancy viability criteria 3. severity of the threats facing the populations 4. potential ecological or genetic diversity the watershed and populations could provide to the species, and 5. capacity of the watershed and population to respond to the critical recovery actions needed to abate those threats.
Core 1 populations must also meet a low risk extinction criterion consisting of the following three factors:
1. Census population size is >2,500 adults or effective population size is >500, 2. No productivity decline is apparent, and 3. No catastrophic events occurring or apparent within the past 10 years.
Candidate areas for reintroduction were identified by NMFS (2009) and prioritized as either primary or secondary based on watershed-specific information, and reintroduction of steelhead into the upper Yuba River basin is considered a primary recovery area.
5.4.2 Viable Salmonid Populations For the purposes of NMFS salmonid recovery planning, viable salmonid populations are defined as “the foundational principles of viable salmonid populations, which include measures of abundance, productivity, spatial structure and diversity” (NMFS 2009). These measures are used to determine whether a species or population is categorized as viable and for the purposes of recovery planning, which would include recovery planning and monitoring progress. McElhany et al. (2000) indicates that increased viability of an ESU will occur if populations are spatially extensive but also maintain some connectivity, do not all share the same catastrophic threats, and if they are diverse in their life-history and phenotypes. Based on these criteria, a reintroduction strategy that incorporates donor stocks from multiple source populations that exhibit a certain level of diversity is more likely to be successful. If one source population is not successful, there are still other source populations that might be successful and can adequately serve to fulfill reintroduction goals.
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Based on principles described in McElhany et al. (2000) and Lindley et al. (2007), population recovery criteria in terms of extinction risk were developed by the Central Valley Technical Review Team. Using parameters of population size, population decline, catastrophic event risk and frequency, and hatchery influence, a population is only considered to have a low risk of extinction if the following elements are met (NMFS 2009):
the effective population size must be >500 or the population size must be >2,500,
the population growth rate must show that a decline is not apparent or probable,
there must be no apparent or minimal risk of a catastrophic disturbance occurring, and
hatchery influence must be low, as determined by levels corresponding to different amounts, durations, and sources of hatchery strays. These elements should be considered in donor stock selection.
5.5 POTENTIAL SOURCES OF DONOR STOCK FOR REINTRODUCTION TO THE UPPER YUBA WATERSHED Potential stock sources for reintroduction into the Yuba River basin may be comprised of eggs, juvenile, and adult Chinook salmon and steelhead from one or more source populations, and may either be of natural or hatchery origin. Reintroductions have a greater potential to be successful when the donor populations selected have life histories that are compatible with the habitat and environmental conditions present within the reintroduction area (as modified by other restoration efforts). Stock sources from populations located in closer proximity to the reintroduction area have a greater likelihood for success because they are more liable to be adapted to the environment, and because they are less likely to stray.
We assume that naturally spawning spring-run Chinook Salmon populations within the same ESU Diversity Group and genetically similar to the original wild stock are most likely to be adapted to conditions within the historical habitat where stocks are to be reintroduced. For this reason, all independent populations of Central Valley spring-run Chinook Salmon in the Northern Sierra Nevada Diversity Group are addressed in the discussion of donor stock; including FRFH stock, and naturally spawning spring-run Chinook Salmon in the lower Yuba River. A matrix of characteristics of potential donor stocks for reintroduction to the upper Yuba watershed is provided in Table 5-2.
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Table 5-2. Characteristics of potential donor stocks for reintroduction to the upper Yuba River watershed. Potential donor stock Feather River Fish Stock selection criteria Butte Creek Deer Creek Mill Creek Lower Yuba River Hatchery same watershed, and Geographic location in within same ESU diversity within same ESU diversity within same ESU diversity within same ESU diversity within same ESU diversity relation to receiving group: Northern Sierra group: Northern Sierra group: Northern Sierra group: Northern Sierra group: Northern Sierra watershed Nevada Nevada Nevada Nevada Nevada received adult outplants no hatchery planting, but naturally spawning assumed to be native from upstream of Keswick assumed to be native fish include hatchery spring-run is Origin of stock in relation spring-run stock, with and Shasta dams in 1940s, spring-run stock, with strays from FRFH; maintained by hatchery to receiving watershed little to no hatchery but assumed to be native little to no hatchery may contain some production influence stock with little to no influence genetic legacy from hatchery influence original upper Yuba River basin stock7, 5 Fall-, late-fall-, and Fall-, late-fall-, and Butte Creek genetic Deer and Mill creeks Deer and Mill creeks Feather/Yuba River Feather/Yuba River group1 genetic group1 genetic group1 spring-run genetic spring-run genetic genetically distinct genetically distinct genetically distinct 1 1 group group from Deer and Mill from Butte Creek from Butte Creek genetically similar to genetically similar to Evolutionary/genetic creek stocks6 stocks6 stocks6 FRFH and fall-run lower Yuba River and relatedness Butte, Deer, and Mill Butte, Deer, and Mill Butte, Deer, and Mill stocks6 fall-run stocks6 creek stocks are likely creek stocks are likely creek stocks are likely some component of naturally spawning fish most closely related to most closely related to most closely related to genetic legacy of are slightly, though stocks historically stocks historically stocks historically original spring-run significantly different found in Yuba River found in Yuba River found in Yuba River stock may be present7 from fall-run stocks7 High (assumed similar to FRFH stock) Genetic diversity within largely introgressed Low (SJRRP 2010) Moderate (SJRRP 2010) Moderate (SJRRP 2010) with fall-, late-fall, and High (SJRRP 2010) stock spring-run hatchery stocks6
Low-Medium High abundance Low-Medium High abundance abundance (has been in Low abundance Insufficient data to Relative abundance of abundance Low risk of extinction steep decline since Unknown risk of evaluate extinction risk source population Low-Moderate risk of 4 2006 run) extinction (naturally spawning extinction Moderate to high Feather River fish)
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Potential donor stock Feather River Fish Stock selection criteria Butte Creek Deer Creek Mill Creek Lower Yuba River Hatchery extinction risk 5 Risk of jeopardizing existing spring-run None None None Low Low Chinook Salmon stocks in Central Valley Disease concerns Low Low Low Low Moderate High up to 20% recovered in American River sport 2 Rate of straying Unknown Unknown Unknown Unknown fishery roughly 50% failed to return to hatchery and spawned in Feather River3 1 Lindley et al. (2004); NMFS (2009) 2 Cramer (1996) 3 Cramer and Demko (1997) 4 CDFG GRANDTAB data (2009) 5 NMFS (2009) 6 Lindley et al. (2004) 7 Hedgecock (2002) 8 Lindley et al. (2007)
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5.5.1 Spring-run Chinook Salmon Native spring-run Chinook Salmon populations in the Central Valley ESU were largely extirpated by dams that block access to their historical habitat in the upper portions of the watersheds in which they occurred. Most of the extant spring-run Chinook Salmon populations in the ESU show little genetic differentiation from fall Chinook salmon, primarily due to introgression with hatchery stocks (Lindley et al. 2004). Within the ESU, there are now four principle genetic groups: (1) winter-run Chinook salmon, (2) Butte Creek spring-run Chinook Salmon, (3) Deer and Mill Creek spring-run Chinook Salmon, and (4) fall-, late-fall-, and Feather/Yuba River spring-run Chinook Salmon (Lindley et al. 2004). Spring-run Chinook Salmon in Deer, Mill, and Butte creeks are genetically distinct from fall-run stocks and are considered the only remaining viable native Central Valley spring-run Chinook Salmon populations. Spring-run Chinook Salmon in Butte Creek are genetically distinct from those in Deer and Mill creeks, as well as from other Chinook salmon stocks in the Central Valley (Lindley et al. 2004).
The Feather and Yuba rivers are believed to each have supported independent populations of spring-run Chinook Salmon (Lindley et al. 2004). Spring-run Chinook Salmon in these basins are currently genetically similar to each other and to the fall Chinook salmon in the ESU and have little similarity to fish from Deer, Mill, and Butte creeks. Feather River spring-run Chinook Salmon are maintained by hatchery production, and the stock has hybridized with the fall run to a great extent (Lindley et al. 2004). However, a microsatellite analysis by Hedgecock (2002, as cited in Lindley et al. 2004) suggested that, although spring-run Chinook Salmon naturally spawning in the Feather River are not differentiated from the spring-run hatchery stock, they were slightly, although significantly, different from the fall-run stocks in the basin, even though progeny from spring- and fall-runs may return at either time.
There is no hatchery on the lower Yuba River where spring-run Chinook Salmon spawn, but hatchery strays, most likely from the FRFH, do occur there (NMFS 2009). The fact that Chinook salmon with spring-run life histories still spawn in the Feather and Yuba rivers and the results of Hedgecock’s analysis indicate that some component of the genetic legacy of the original spring-run stocks that occurred in their upper basins may still be present (NMFS 2009). Methods to segregate fall- and spring-run stocks at the FRFH were included in the Settlement Agreement for Licensing of the Oroville Facilities (March 2006 as cited in NMFS 2009).
The possibility remains that there is some genetic component of original upper Yuba River watershed spring-run Chinook Salmon stocks in naturally spawning Feather River and lower
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Yuba River stocks (Hedgecock 2002). This spring-run hatchery stock may be useful in recovering the spring-run populations in the Feather and Yuba rivers above the Oroville and Englebright dams. In addition, given access to their historical upper watershed habitats, natural segregation of spring-run and fall-run stocks may serve to reestablish genetically discrete runs, as well as the development of independent populations both between and within these watersheds (Lindley et al. 2004).
Spring-run Chinook Salmon in Butte Creek, which joins the Sacramento River a substantial distance downstream from Deer and Mill creeks, are genetically distinct from those in Deer and Mill creeks and are considered to be an independent population that may be almost completely isolated from others in the ESU (Lindley et al. 2004). Spawning of spring-run Chinook Salmon in Butte Creek occurs at unusually low elevations (<300 m) where summer water temperatures have been documented to exceed 20°C in the coolest sub-basin (Lindley et al. 2004). The fact that they appear to regularly survive temperatures above those reported for other Chinook salmon may suggest the possibility that they are more adapted to warmer temperatures than most Chinook stocks; a characteristic that historically occurring spring-run Chinook Salmon in the San Joaquin River may have shared.
5.5.2 Steelhead Originally, there were both summer-run and winter-run steelhead in the Central Valley, but the summer run has mostly been extirpated due to dams blocking access to suitable coldwater habitat in the upper watersheds of Central Valley streams and lack of suitable habitat downstream (Lindley et al. 2004). Although there may have been considerable genetic diversity in historical independent populations within the DPS, much of this is believed to have been lost because of the existence of dams (Lindley et al. 2006). Remaining steelhead in Central Valley DPS streams are critically depressed, with the anadromous form of O. mykiss being rare in some systems (CDFG 2008 as cited in NMFS 2009).
5.5.3 Hatchery Stocks Genetic introgression caused by hybridization of naturally spawning or wild fish breeding with FRFH strays is considered a major threat to Central Valley Chinook salmon runs, and has increased the risk for substantial alterations in genetic diversity (NMFS 2009). Similarly, populations of steelhead in the Central Valley have had been substantially influenced by hatchery practices, such as the movement of eggs between basins, that have altered population- and watershed-specific genetic diversity (Busby et al. 1996). Besides the potential for hybridization and genetic introgression caused by hatchery influences on wild fish, there is a potential for altered life-history timing, decreased reproductive success, and increased
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competition, predation, and fishing pressure (Waples 1991, Swanson et al. 2008) which may negatively impact reintroduction efforts. Efforts are underway in the Central Valley to improve hatchery management and genetic practices (SJRRP Technical Advisory Committee 2007); however, there are still potential risks associated with including hatchery fish in recovery planning and reintroduction efforts.
5.6 STOCK SELECTION CONSIDERATIONS The primary goal of source stock selection is to identify the stock(s) with the highest likelihood of establishing a self-sustaining, naturally reproducing population in the upper Yuba River watershed.
5.6.1 Criteria Used by Other Reintroduction Efforts The reintroduction of Chinook salmon stocks to their former range is being considered in several locations as part of establishing viable salmonid populations for recovery of listed Chinook salmon ESUs. In this section, we briefly summarize key elements of two recent reintroduction plans in terms of donor stock selection criteria: the San Joaquin River and the upper Klamath Basin.
The Genetics Subgroup of the SJRRP’s Fisheries Management Work Group identified optimum characteristics for choosing spring-run Chinook Salmon donor population sources for reintroduction to the San Joaquin River (SJRRP 2010). The following optimum source stock characteristics are based on their recommendations and are relevant for upper Yuba River source stock selection:
Stock should be of local or regional origin (Central Valley).
Stock should have life history (behavioral and physiological) characteristics that fit conditions expected to occur in the target river or watershed, thereby maximizing the probability of successful reintroduction.
Stock should have a large effective population size.
Stock should have high within-population genetic diversity with low inbreeding coefficients.
Stock should show adequate representation of overall ESU genetic diversity. The SJRRP Stock Selection Strategy (SJRRP 2010) also acknowledges the numerous variables and uncertainty associated with large scale salmonid reintroduction and emphasizes the importance of adaptive management in the decision-making process.
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Criteria for selecting donor stocks were also developed for reintroducing spring-run Chinook Salmon to the upper Klamath River basin (Huntington et al. 2006; Reintroduction of Anadromous Fish to the Upper Klamath Basin: an Evaluation and Conceptual Plan). The following criteria, many of which are relevant for reintroduction in the upper Yuba River watershed, were used to rate Chinook salmon stocks for the upper Klamath reintroduction efforts:
Size and run strength of the donor population stock: population is either (1) a “large” naturally spawning group of fish, or (2) a hatchery population.
Disease concerns: candidate population is (1) resistant to Ceratomyxa shasta, (2) lacks viral diseases, and (3) will not contribute to outbreaks of new diseases in the upper basin if properly managed.
Ecological goodness-of-fit: candidate population/stock is suited to the aquatic environment found in the upper basin, based on an assessment of (1) the basic habitat requirements of the species, (2) migration length, (3) migration and spawn timing, (4) ecological similarity between the source and receiving watersheds, and (5) juvenile life- history patterns.
Evolutionary/genetic relatedness: candidate population is from the same ESU as the extirpated upper basin population or other populations that may be affected by future fish releases, and reflects an emphasis on using geographically proximate versus distant stocks in the reintroduction effort.
History of hatchery influence: candidate population/stock consists of fish adapted to their home watershed and unaffected, directly or indirectly, by conventional fish culture.
Rates at which adults stray: candidate population strays at a low rate that reflects good homing.
5.6.2 Genetics There are three stocks of spring-run Chinook Salmon in the Central Valley that we consider to be the most appropriate donor sources for reintroduction in the upper Yuba River watershed: the Butte Creek stock, the Mill Creek/Deer Creek stock, and the Feather River stock. This conclusion is consistent with the recommendation of the SJRRP Stock Selection Strategy (SJRRP 2010) and is based on many of the same considerations.
Genetics studies evaluating the relative genetic diversity of the aforementioned three potential spring-run Chinook Salmon donor stocks found that all investigated measures of genetic diversity were the lowest for Butte Creek, intermediate for Deer/Mill Creek, and the highest for Feather River spring-run Chinook Salmon (Garza et al. 2008, Banks et al. 2000, Garza
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unpublished; all as cited in SJRRP 2010). The effective population size of the Butte Creek spring-run Chinook Salmon stock is the smallest of the three, since effective size determines the amount of genetic variation maintained in a population (SJRRP 2010). Therefore, the Butte Creek spring-run Chinook Salmon stock would have the highest risk of inbreeding in a reintroduction project. In contrast, the Feather River spring-run Chinook Salmon stock has the highest genetic diversity of the three, and thus the lowest risk of inbreeding in a reintroduction project. As a result, the Feather River stock has the lowest risk of reduced fitness from inbreeding depression. However, the Feather River stock is known to have been affected by hybridization with fall-run Chinook salmon at the FRFH (Garza et al. 2008, as cited in SJRRP 2010). It is also likely that hybridization occurs in the spawning grounds of the lower Feather River (SJRRP 2010) and the lower Yuba River.
The Feather River spring-run Chinook Salmon population is more genetically similar to fall-run Chinook salmon in the Feather River than to the spring-run Chinook Salmon in the Deer/Mill Creek and Butte Creek populations (SJRRP 2010). This raises the potential for outbreeding depression during an introduction, which is unfavorable for the maintenance of phenotypic differentiation (i.e., non-overlapping run timing of spring-run and fall-run Chinook salmon). Tagging studies have found that some offspring from Feather River spring-run Chinook Salmon return as fall-run Chinook salmon, and vice-versa (CDFG 1998).
Banks et al. (2000) and Garza et al. (2008) have shown that the three candidate stocks are genetically distinct, and that the Mill Creek and Deer Creek populations are essentially the same stock. However, a genetic analysis to ascertain the genetic integrity of the potential source populations is a key component for identifying the most suitable stock(s) for reintroduction (SJRRP 2010). Measurement indices that are useful for analysis of potential broodstock(s) include, but are not limited to: within-population genetic diversity and inbreeding levels; effective population size (Ne); among-population genetic diversity; and amount of hatchery influence (SJRRP 2010).
Another aspect of the genetics and demographics of the three candidate spring-run Chinook Salmon stocks that should be considered is the relative influence of hatchery-produced fish on the naturally spawning stock. Whereas the Deer/Mill Creek and Butte Creek spring-run Chinook Salmon stocks appear to be largely free of introgression from hatchery-produced fish, salmon from the FRFH have introgressed extensively with naturally spawning populations in the Feather River and elsewhere (SJRRP 2010).
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A growing body of evidence indicates that hatchery-produced spring-run Chinook Salmon are less fit than natural origin fish (Berejikian and Ford 2004, Myers et al. 2004; as cited in SJRRP 2010). This is at least partly due to hatchery domestication selection, which may cause maladaptation to natural environmental conditions. However, domestication selection from hatchery fish can be counteracted relatively quickly by crossing with natural origin fish and subsequent selection in the natural environment (Quinn et al. 2000, Unwin et al. 2000), as long as the artificial selection has not also caused a loss of genetic variation and an increase in inbreeding (SJRRP 2010).
5.6.3 Recommendations and Additional Considerations Each of the three spring-run Chinook Salmon populations recommended as potential stock sources has both favorable and unfavorable biological characteristics for a successful reintroduction project. Because spring-run Chinook Salmon from different populations vary with respect to important traits such as run timing, spawn timing, and natal fidelity, a reintroduced population with a wide variety of these and other traits would maximize adaptation potential. There is likely significant potential for evolution of traits to occur as a result of the strong, novel selective pressures that would be experienced by fish reintroduced to the upper Yuba River watershed. For these reasons, the SJRRP Stock Selection Strategy (SJRRP 2010) recommends that a simultaneous multiple stock reintroduction experiment be pursued as an adaptive management program. The multi-stock approach would include the Deer/Mill Creek, Butte Creek, and Feather River spring-run Chinook Salmon stocks.
Although there has been much debate on the use of Feather River spring-run Chinook Salmon for the SJRRP reintroduction efforts (SJRRP 2010), the Feather River stock retains valuable genetic and phenotypic diversity worth conserving and should be considered a viable source stock for upper Yuba River reintroduction—either alone or as part of a multi-stock approach.
Additional stock selection factors, including risks and uncertainties, have been identified as part of the SJRRP reintroduction planning process (SJRRP 2010, 2011; SJRRP TAC 2007). Relevant considerations for the upper Yuba River watershed stock selection process are summarized below.
Stocks used should not jeopardize existing salmon or steelhead stocks in the source basin.
A genetic management plan should be developed to guide the reintroduction process. The SJRRP developed a Hatchery and Genetic Management Plan (Börk and Adelizi 2010) that could be used as a guide for the upper Yuba River reintroduction effort.
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It is possible that selected broodstock(s) would not have the genetic variation needed to promote a long-term naturally self-sustaining population in the target river or watershed. An assessment of each potential broodstock’s genetic diversity would ensure that the chosen source population(s) has adequate variation to adapt to changing environmental conditions. Selection of multiple broodstocks could act to reduce risk by increasing overall genetic variation (SJRRP 2010).
Removal of broodstock fishes or eggs from source population(s) could reduce the population viability and recovery potential of the source population(s) and increase the risk of extirpation. To reduce the potential for significant impacts to source population(s), criteria for collection strategies should balance development of reintroduced stocks with minimizing risks to the source population(s) (SJRRP 2010).
It is uncertain what criteria and population thresholds the regulatory fisheries agencies (NMFS and CDFW) will use to determine if fish can be taken from the three source populations and the number of fish that may be taken. If it is determined that the risk to one or more of the source stock(s) is too high, this will narrow the choice of potential source stock and may favor the Feather River stock, as it is the only hatchery-supplemented stock that is recommended for consideration.
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6. PRODUCTION POTENTIAL OF YUBA RIVER14
6.1 MODELING APPROACH AND MANAGEMENT SCENARIOS The upper Yuba River watershed, upstream of Englebright Dam, was divided into four separate sub-basins for modeling purposes: the South Yuba (SY), Middle Yuba (MY), and North Yuba (NY) river watersheds, and the watershed area between New Bullards Bar Dam and Englebright Reservoir (the NBB sub-basin). The sub-basins each have distinct attributes and physical habitat conditions that require different model parameters. Only a portion of the stream channel network in any sub-basin would be accessible to reintroduced spring-run Chinook Salmon and steelhead and provide suitable habitat for these species. The upstream and downstream extent of potential habitat under each modeled scenario was defined for modeling purposes by applying four criteria: (1) known or suspected natural barriers, (2) channel gradient thresholds, (3) channel width thresholds, and (4) water temperature thresholds. For purposes of this assessment it was assumed that passage by salmon and steelhead would be possible in the mainstem rivers of each sub-basin up to existing natural passage barriers, and in smaller tributaries upstream to potential natural barriers or to a point at which either channel gradient is too steep for passage or the channel is too narrow to provide suitable habitat.
Channels with a summer low-flow width less than 8.5 m (28 ft) were assumed to be too narrow to provide suitable holding habitat for spring-run Chinook Salmon. For steelhead, the upstream limit of potentially suitable habitat in tributaries in each sub-basin was defined as any portion of the channel network with a gradient of 20% or greater, or with a sustained (> 300 m [984 ft]) gradient of 8% or greater. In tributaries where the upper distribution of steelhead was not defined by the channel gradient criteria or a physical barrier, suitable steelhead habitat was restricted by minimum channel width thresholds. The upper distribution of steelhead spawning habitat was restricted to 2 m (6.6 ft) winter base flow width, while juvenile summer rearing was restricted to 2 m summer low flow width. For modeling purposes it was assumed that rearing did not occur in sub-basins upstream of spawning.
Because the amount of suitable habitat for each species varies as a function of flow and related environmental conditions such as water temperature, a range of potential conditions, or scenarios, were modeled. The channel gradient and width thresholds described above were used to define the upstream extent of tributary habitat for each spring-run Chinook Salmon and steelhead life stage in all sub-basins under all scenarios. The downstream extent of habitat was
14 Prepared by Stillwater Sciences 2014.
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defined by the summer water temperature tolerances of spring-run Chinook Salmon and steelhead.
In each sub-basin, carrying capacities for spring-run Chinook Salmon and steelhead, and production potential for spring-run Chinook Salmon, were modeled under a Dry Conditions scenario (Scenario D) and two alternative management scenarios. The “Dry Conditions” model scenarios in the SY and MY sub-basins were defined as existing river flows and modeled water temperatures based on 2009 conditions. Because 2009 was a dry water year with below average precipitation and above average summer air temperatures, flows and water temperatures under the Dry Conditions scenario represent the most restrictive (limiting) end of the range of modeled conditions for anadromous salmonids. In the NY sub-basin the Dry Conditions model scenario was defined as existing river flows and water temperatures interpolated from a limited amount of empirical (measured) data collected in 2008 and 2009. In the NBB sub-basin, the Dry Conditions scenario was modeled using existing flows and measured 2010 water temperature data, due to a lack of complete summer water temperature data for 2009.
The alternative scenarios—S3 and S4—were modeled to represent potential future conditions that could be realized by implementing flow and habitat enhancements. Based on previous assessments of habitat conditions in the upper Yuba River watershed, the primary life stages of concern were adult holding for spring-run Chinook Salmon and juvenile rearing for both spring- run Chinook Salmon and steelhead. If reintroduction were to take place, these life stages would be present in the upper Yuba River watershed during the hottest months of the summer when water temperatures under current conditions reach or exceed critical thermal maxima for these species. In the SY, MY, and NBB sub-basins, S3 and S4 therefore represent additional instream flow releases from upstream storage reservoirs to reduce water temperatures and increase suitable habitat in the critical summer months. In the MY and SY sub-basins the alternative management scenarios represent potential flow increases proposed by the U.S. Forest Service and NMFS as part of the Yuba Bear/Drum Spaulding (YBDS) FERC relicensing process that is underway in the upper Yuba River watershed (NMFS 2012). In the NBB sub-basin, S3 and S4 also include the addition of spawning gravel, which is currently limited below New Bullards Bar Dam. Because the North Yuba River upstream of New Bullards Bar Reservoir is unregulated, alternative flow management is not possible and S3 and S4 were therefore based on 2010 and 2011 hydrology and meteorology—years in which summertime flows were higher and air and water temperatures were lower than the Dry Conditions model scenario. The 2010 and 2011 conditions represent above normal and wet water year types, respectively.
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6.1.1 Dry Conditions Scenario The downstream extent of suitable spring-run Chinook Salmon holding and rearing habitat under the Dry Conditions scenario, and the alternative management scenarios, was defined by a water temperature suitability criterion (maximum weekly average temperature, or MWAT) of ≤ 19°C. For RIPPLE modeling purposes, the 19°C MWAT was also used to define the extent of thermally suitable habitat for rearing juvenile spring-run Chinook Salmon. The locations at which these thermal suitability criteria were exceeded were estimated using modeled water temperature data. Where the distance between data collection points was too large to provide useful spatial resolution in the water temperature data, linear interpolation was used to estimate the location at which the 19°C MWAT limit was likely exceeded. The downstream extent of spring-run Chinook Salmon spawning habitat was modeled to extend a fixed distance of 3 miles downstream from holding habitat, based on evidence from the literature (though it was assumed that most post-holding movement will be upstream).
The downstream extent of suitable steelhead rearing habitat under the Dry Conditions scenario was defined as the location in each mainstem river where the MWAT was measured or predicted to exceed 20°C. Where the distance between data collection points was too large to provide useful spatial resolution in the water temperature data, linear interpolation was used to estimate the location at which the 20°C MWAT water temperature threshold was likely exceeded. Tributaries where summer water temperatures exceeded the 20°C MWAT water temperature threshold were excluded from the modeled channel network. Remaining tributaries, including those for which no water temperature data could be located, were assumed to be thermally suitable for steelhead rearing. The downstream extent of potential steelhead spawning habitat in the SY, MY, and NY sub-basins under the Dry Conditions scenario was assumed to be the same as the downstream extent of rearing habitat. This was based on the assumption that successful rearing depends on the availability of (thermally) suitable rearing habitat located downstream of spawning locations. For modeling purposes we assumed that rearing only occurs downstream of spawning. In the NBB sub-basin, potential spawning habitat in the mainstem Yuba River under the Dry Conditions scenario was assumed to be present only downstream of New Colgate Powerhouse because of a lack of spawning gravel from New Bullards Bar Dam downstream to the powerhouse.
6.1.2 Alternative Management Scenarios Alternative Management Scenario S3 assumes that increased releases from dams in the SY, MY, and NBB sub-basins would increase the downstream extent of potential summer habitat for spring-run Chinook Salmon and steelhead in these sub-basins compared with the Dry Conditions
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scenario. Alternative Management Scenario 4 assumes that dam releases in the SY and MY sub- basins would be greater than those under Scenario 3 and would further increase the downstream extent of potential summer habitat for spring-run Chinook Salmon and steelhead in these sub- basins. In the NBB sub-basin, releases from New Bullards Bar Dam under both alternative scenarios are assumed to provide suitable water temperatures for all salmon and steelhead life stages in the entire mainstem channel downstream to Englebright Reservoir. Scenarios S3 and S4 also assume that a gravel augmentation program would be implemented to restore mainstem spawning habitat in the NBB sub-basin downstream of New Bullards Bar Dam to approximately 25% and 75% of its unimpaired extent, respectively.
6.2 POPULATION DYNAMICS (POP)
6.2.1 POP Module Structure The POP module uses sub-basin-specific carrying capacity (K) values for holding, spawning, and summer rearing in conjunction with biological input parameters and life stage-specific stock- production curves15, to estimate equilibrium population sizes for individual channel arcs and the entire watershed. The equilibrium population is reached after multiple iterations of the model are run and a stable, long-term average population structure is reached. Figure 6-1 displays a schematic diagram of the POP module structure, and Table 6-1 describes the life stages used in the spring-run Chinook Salmon model input and output.
The stages escape, holder, spawner, and redd include age-structure information: that is, the model keeps track of the brood-year composition of these stages so that age-specific versions of parameters like sex ratios and fecundities can be applied.
In the POP module, the stage escape represents sexually immature adults leaving the ocean to search for holding habitat. The stage holder represents adults (both male and female) occupying holding habitat. Holder is calculated by distributing the escaped population across accessible arcs of the channel network in proportion to the capacity of these arcs (given by holding_K; Figure 6-1), applying a density-independent survival parameter (holding survival), and truncating any excess to the carrying capacity. Table 6-2 provides a description of each parameter required for input in POP module. The stage spawner represents females at the spawning habitat.
15 Only two stock-production rules are currently used in the Chinook model: (1) the “hockey stick”: if the starting population is x, the ending population is the smaller of rx and K, where K is the arc-specific carrying capacity and r is a density-independent survivorship; and (2) the “Skellam function”: if the starting population is x, the ending population is K(1-exp(-rx/K)). The Skellam function is used only for calculating superimposition losses. All other density-dependent mortality calculations in the model use hockey-stock functions.
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Figure 6-1. Schematic diagram showing the relationships between each life stage in the POP module and the point at which each carrying capacity (K) is applied to the population. BY = brood year.
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Table 6-1. Life stages represented in the spring-run Chinook Salmon POP module. POP module Description life stage escape Total number of all ages of immature adults leaving the ocean to search for holding habitat. holder Male and female adults occupying holding habitat. spawner Females leaving holding habitat in search of spawning habitat. Effective number of redds that contribute to egg production after accounting for the effects of redd superimposition. eggs Total number of eggs produced. swimup Fry emerging from redd gravels. Fry that leave the modeled channel network soon after emergence and rear in the lower efry mainstem river(s) and estuary prior to smolting. The “e” refers to estuary. Juvenile population remaining after efry have left the channel network that survive from fry to summer0 early summer. Component of the juvenile population that smolts during the spring and early summer of their smolt0 first year prior to leaving the channel network or while migrating downstream. Component of the juvenile population remaining, after smolt0 have left the channel network, winter1 that survive from summer to winter. Component of the juvenile population that smolts during the late fall through winter as smolt1 “yearlings.” Efry that survive the spring and early summer in the estuary to become smolts. The “e” refers esmolt0 to estuary. Ocean-resident fish that have spent X years in freshwater before smolting and Y years in oceanXY saltwater after smolting, respectively; “X+Y” is the total age. escapeXY Fish of age X+Y participating in the spawning run, at the time they leave the ocean.
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Table 6-2. Biological parameters input into the POP module for each Chinook salmon model run. Parameter Description of how parameter used in model Value Sources/rationale for selecting value Determines fraction of smolt0 that survive from Englebright Based approximately on survival values of smolt-0-sized juvenile Smolt0 to adult survivala Dam to adult return to freshwater and fraction of esmolt0 0.01 Chinook salmon released at Coleman and Nimbus hatcheries from that survive from the estuary until adult return to freshwater. 1968–1970 (Reisenbichler et al. 1982). Based approximately on survival values of smolt-1-sized juvenile Determines fraction of smolt1 that survive from Englebright Smolt1 to adult survivala 0.05 Chinook salmon released at FRFH from 1967–1970 and Nimbus Dam to adult return to freshwater. Hatchery in 1955 (Reisenbichler et al. 1982). Spawning fraction 2 Fraction of adult spawning run comprised of age-2 fish 0.11 Spawning fraction 3 Fraction of adult spawning run comprised of age-3 fish 0.47 Percent of spawning run in each age class returning to the FRFH Spawning fraction 4 Fraction of adult spawning run comprised of age-4 fish 0.41 (Cavallo et al. 2009). Spawning fraction 5 Fraction of adult spawning run comprised of age-5 fish 0.01 5% mortality was imposed based on pre-spawn mortality observed in Butte Creek in 2004, a year with moderately cool water Determines fraction of the adult population that survives Holding survivala 0.90 temperatures (Ward et al. 2006). An additional 5% mortality was during holding in freshwater. added as an estimate of mortality due to predation and poaching of adults, based on professional judgment. Fraction of the age-2 spawning population comprised of Fraction female 2 0.10 females. Fraction of the age-3 spawning population comprised of Based on sex ratio of coded-wire-tagged spring-run Chinook Fraction female 3 0.55 females. Salmon entering FRFH (Cramer and Demko 1997). The fraction Fraction of the age-4 spawning population comprised of female of all age classes at the FRFH from 1997–2006 was 0.455 Fraction female 4 0.60 females. (Cavallo et al. 2009). Fraction of the age-5 spawning population comprised of Fraction female 5 0.60 females. Eggs per female 2 age-2 spawners 1,000 Calculated from fecundity vs. length regression developed by Eggs per female 3 age-3 spawners 4,000 CDFG (1998a,b). Fork length data for each age class were based Eggs per female 4 age-4 spawners 6,000 on code-wire tagged individuals collected in Butte Creek from 2001–2004 (McReynolds et al. 2005). The Butte Creek data included males and females, so fork lengths for each age class were adjusted downward to more accurately reflect the smaller size of Eggs per female 5 age-5 spawners 8,500 females. For comparison, Cavallo et al. (2009) reports that spring- run Chinook Salmon artificially spawned at the FRFH since 1997 have produced an average of 5,300 eggs per female.
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Parameter Description of how parameter used in model Value Sources/rationale for selecting value SY = 0.54 Based on gravel permeability measurements in the Middle Yuba MY = 0.76 and South Yuba (UYRSPST 2007) and North Yuba (YCWA 2011) Determines fraction of individuals that survive from Embryo survivalb NY = 0.36 and the relationship between permeability and survival (Tagart spawning until emergence from redd gravels. NBB = 1976, McCuddin 1977). The NBB sub-basin was parameterized 0.65 using the mean of the MY and SY values. Based on professional judgment. Outmigrant trapping data from Partitions emergent (swimup) fry into those migrating out of Butte Creek from 2003–2004 indicate that approximately 93% of the Upper Yuba River watershed soon after emergence (late Efry fraction 0.75 outmigrants captured migrated soon after emergence (McReynolds fall and winter) and those remaining to become smolt0 or et al. 2005). Lindley et al. (2004, Figure 25) indicates that this smolt1. value is considerably lower for Mill and Deer creeks. Determines fraction of efry that survive during the period Based on professional judgment. Value is intermediate between Swimup to efry survivala from emergence until leaving the Upper Yuba channel 0.50 "fry colonization" and "0-age transient rearing" survival values network at Englebright Dam. reported by Lestelle et al. (2004). Based on the mean of 7 years of survival estimates (0.0027) from Determines fraction of efry in that survive during time spent release of fry at Red Bluff Diversion Dam to capture in the ocean Efry to esmolt0 survivala in the lower Sacramento river and delta prior to entering the 0.27 fishery (Brandes and McClain 2001). Using a value of 0.27 results ocean. in a combined lower river, delta, estuary and ocean survival of 0.0027 (0.27 * 0.01 smolt0 to adult survival) for efry. Determines fraction of the resident (non-efry) juvenile Based on professional judgment. The value is the same as that Fry to summer0 survivala population that survives during the period from emergence 0.70 reported by Lestelle et al. (2004) for "0-age resident rearing." until outmigration of smolt0. Determines fraction of the oversummering age 0 juvenile Summer0 to winter1 Based on professional judgment. The value is the same as that population that survives during the period from early 0.70 survivala reported by Lestelle et al. (2004) for the “0-age inactive” life stage. summer until outmigration as smolt1. a Survival values account for density-independent mortality such as predation or disease. b Accounts for density-independent mortality but not redd superimposition. Superimposition is accounted for in the stock-recruitment relationship applied in the RIPPLE POP module.
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Spawner is calculated by multiplying by the holder population of each age by the parameter fraction female for each age. The spawning stage females are then distributed across accessible arcs of the channel network in proportion to the capacity of these arcs (given by redd_K; Figure 6-1). The redd stage represents the number of redds that contribute to egg production after accounting for spawning carrying capacity (redd_K) and the effects of superimposition. The number of eggs produced by all redds is calculated by applying the age-specific parameter eggs per female for each successfully spawning female.
The number of emergent fry (swimup) is calculated by multiplying the number of eggs by the embryo survival parameter (Table 6-2). The swimup population is then partitioned into prospective efry (i.e., estuary-bound fry) and resident fry according to the parameter efry fraction. The number of estuary-bound fry that survive to leave the modeled channel network, becoming efry, is determined from the survival parameter, swimup to efry survival (Table 6-2). The efry that survive in the lower river and delta, determined from the parameter efry to esmolt0 survival (Table 6-2), are transformed into to smolts designated as esmolt0.
The swimup fry remaining in the channel network (non-efry) experience density-independent survival (fry to summer0 survival) to become summer0. The summer0 then redistribute downstream in search of available habitat, which is determined by age-0summer_K (Figure 6-1). Summer0 migrants that reach the bottom of the modeled stream network without finding summer rearing habitat become smolt0.
The remaining summer0 (those that find over-summering habitat) experience density- independent survival (summer0 to winter1 survival) to become winter1. All winter1 in the upper Yuba River spring-run Chinook Salmon model leave the channel network as yearlings called smolt1. Survival of smolt0 and smolt1 until adult escapement from the ocean to freshwater is determined using the parameters smolt0 to adult survival and smolt1 to adult survival, respectively (Table 6-2). Survival of esmolt0 until adult return is also determined by the smolt0 to adult survival model parameter.
The POP module recognizes 10 life stages of ocean-resident fish, designated oceanXY for X=0 or 1, Y=0, 1, 2, 3, or 4. The “X” and “Y” indicate the number of years spent in freshwater before smolting and in saltwater after smolting, respectively; thus “X+Y” is the total age. The stages ocean00, ocean10, ocean01, and ocean11 represent fish too small to be harvested or to join a spawning run. The stages oceanXY for Y>1 represent the total populations of fish of age X+Y in the ocean, at a time shortly before the start of the spawning migration. The stages escapeXY represent the fish of age X+Y participating in the spawning run, at the time they leave the ocean.
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These are calculated as the product of oceanXY and the spawning fraction of each age in the spawning run (Table 6-2). For convenience, the model reports the total number of “escapers” of all ages as escape.
6.2.2 POP Module Parameterization The POP module parameter values applied in the model and the data sources and rationale used for their selection are shown in Table 6-2. These parameters were applied to all upper Yuba River watershed model runs and scenarios. Where possible, the biological parameters were specific to spring-run Chinook Salmon populations in the upper Sacramento River basin. For additional detail regarding parameter application, model structure and theory, refer to the following link: http://www.stillwatersci.com/resources/RIPPLE_overview.pdf
6.3 SPRING-RUN CHINOOK SALMON RESULTS
6.3.1 Predicted Distribution of Suitable Habitat In the SY sub-basin, under the Dry Conditions scenario, no suitable spring-run Chinook Salmon holding, spawning, or summer rearing habitat was identified due to water temperature restrictions (Table 6-3). Despite the summer flow increases that would occur under the U.S. Forest Service 4(e) flow recommendations modeled for Scenario 3, only 0.4 miles of mainstem habitat and no tributary habitat was considered thermally suitable in the SY sub-basin under Scenario 3. The lack of suitable tributary habitat for spring-run Chinook Salmon in the SY sub- basin under the Current Conditions scenario and Scenario 3 is due to channel width under the modeled summer low flow conditions for these scenarios, which is predicted to be less than the 8.5m (28 ft) threshold assumed to provide suitable holding habitat. Under Scenario 4, 4 miles of mainstem habitat and 0.9 miles of tributary habitat were predicted due to the substantially higher summer flows, cooler water temperatures, and slightly wider wetted channel that would occur under the NMFS 10(j) flow recommendations (NMFS 2012).
In the MY sub-basin, under the Dry Conditions scenario, 1.4 miles of mainstem habitat were identified as suitable for spring-run Chinook Salmon holding, spawning, and summer rearing (Table 6-3). With increased flows, 4.8 miles of mainstem habitat were predicted to be suitable under S3 and 11.1 miles of mainstem habitat were predicted under S4. No suitable tributary habitat in the MY sub-basin was identified for the Dry Conditions scenario or either of the alternative management scenarios due to channel gradient, channel width, water temperature, or a combination of these factors.
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Table 6-3. Spring-run Chinook Salmon habitat predicted under each modeling scenario in sub-basins of the upper Yuba River watershed. Approximate length of spring-run Chinook Salmon holding and summer rearing habitat (mi)a
Sub-basin Dry Conditions Alternative Scenario 3 Alternative Scenario 4 mainstem 0 0.4 4.0 SY tributaries 0 0 0.9 mainstem 1.4 4.8 11.1 MY tributaries 0 0 0 mainstem 11.3 25.6 34.8 NY tributaries 3.3 3.3 16.7 mainstem 3.2 10.3 10.3 NBB tributaries 0 0 0 a Estimated length only includes portions of the channel network with predicted habitat carrying capacity values > 0. Some portions of the channel network that were predicted to be thermally suitable have channel gradients too steep for holding and rearing and were therefore predicted to have zero carrying capacity. It was assumed for purposes of this assessment that salmon could pass upstream of all low-flow barriers in all water years.
In the NY sub-basin, under the Dry Conditions scenario, 11.3 miles of the mainstem and 3.3 miles of tributary habitat—considerably more than the SY and MY sub-basins—were identified as suitable habitat for spring-run Chinook Salmon holding, spawning, and summer rearing (Table 6-3). The Dry Conditions scenario in the NY sub-basin was defined as existing river flows and water temperatures derived from data collected in 2008 and 2009, both of which were hot, dry years with below average precipitation and above average summer air temperatures. Scenario S3 in the NY sub-basin assumes that stream flows and water temperatures measured in 2010, a year with above average flow and slightly cooler than average air temperatures, would provide approximately 25.6 miles of thermally suitable spring-run Chinook Salmon holding and rearing habitat in the mainstem North Yuba River, and 3.3 miles in tributaries. Scenario S4 assumes that summer stream flows and water temperatures measured in 2011, a year with slightly cooler than average air temperatures and extremely high flows that approached the highest ever recorded, would provide thermally suitable spring-run Chinook Salmon holding and rearing habitat in the entire 34.8 miles of the mainstem North Yuba River and approximately 16.7 miles in tributaries.
In the NBB sub-basin, under the Dry Conditions scenario, 3.2 miles of the mainstem North Yuba River was identified as suitable holding and summer rearing habitat for spring-run Chinook Salmon (Table 6-3). However, due to lack of suitable spawning gravel in the mainstem between New Bullards Bar Dam and the Middle Yuba River confluence, spawning under the Dry
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Conditions scenario was only predicted to occur downstream of New Colgate Powerhouse. Under Alternative Management Scenarios 3 and 4, which assume increased cold water releases from New Bullards Bar Dam and spawning gravel augmentation, the entire 10.3 miles of mainstem channel from New Bullards Bar Dam downstream to Englebright Reservoir were predicted to be suitable for spring-run Chinook Salmon holding, spawning, and summer rearing. No suitable tributary habitat in the NBB sub-basin was identified for spring-run Chinook Salmon under the Dry Conditions scenario or either of the alternative management scenarios.
6.3.2 Carrying Capacity Estimates Results of the HAB module output demonstrate that in all modeled sub-basins and scenarios for spring-run Chinook Salmon, the carrying capacity of holding habitat exceeds that of redd (spawning) carrying capacity in sub-basins with potentially suitable habitat (Table 6-4). In all cases, predicted holding capacity (males and females) was more than twice that of predicted redd capacity (females only). This result suggests that when adult female escapement to freshwater and survival during holding are high enough to produce female spawners in excess of the redd carrying capacity, it is the quantity of spawning habitat that likely limits production of juveniles in the upper Yuba River watershed.
Table 6-4. Predicted habitat carrying capacities (K) of spring-run Chinook Salmon holding, spawning (redds), and summer rearing life stages for each modeled sub-basin and scenario in the upper Yuba River watershed. Carrying Capacity (K) Scenario1 South Yuba2 Middle Yuba North Yuba NBB D 0 914 7,814 4,042 Holding S3 588 3,050 33,976 20,176 S4 3,632 5,710 65,777 20,176 D 0 113 1,347 113 Redd3 S3 163 308 3,641 729 S4 435 807 5,177 2,188 4 Age-0 D 0 5,568 142,940 281,915 summer S3 2,048 22,433 634,715 620,939 rearing S4 75,016 121,985 1,272,247 620,939 1 D = Dry Conditions scenario, S3 = Scenario 3, and S4 = Scenario 4. 2 Under the Dry Conditions scenario the entire SY below the natural fish passage barrier is predicted to be thermally unsuitable for spring-run Chinook Salmon holding and rearing; therefore carrying capacity is zero. 3 Each redd was assumed to support one female spawner. 4 Includes summer rearing carrying capacity of 13,103 from habitat in the thermally suitable sub-basin upstream of the Middle Yuba River confluence. This carrying capacity does not contribute to smolt production due to lack of spawning habitat in that sub-basin, and is not reported in the POP results.
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In the SY sub-basin, predicted spring-run Chinook Salmon redd capacity under S4 is nearly three times that of S3 (Table 6-4). In the MY sub-basin, predicted redd capacity under S3 is nearly three times higher than the Dry Conditions scenario, but only about 40% of S4. The MY sub- basin under S4 is predicted to support approximately seven times more redds than under the Dry Conditions scenario. In each case, the predicted increases are attributable primarily to the increase in suitable holding and spawning habitat that would result from increased summer flow. In the NBB sub-basin, predicted redd capacities under Scenarios 3 and 4 are approximately 6.5 and 19 times higher than the Dry Conditions scenario, respectively. This increase can be attributed to both restoration of spawning habitat and increased summer flows with the concomitant increase in thermally suitable channel. The tripling of redd capacity between Scenarios 3 and 4 in the NBB sub-basin reflects the difference between low and high levels of spawning gravel augmentation assumed under the scenarios.
In the NY sub-basin, predicted redd capacity under S4 is nearly four times that of the Dry Conditions scenario and approximately 1.4 times that of S3 (Table 6-4). Predicted redd capacity under the Dry Conditions scenario is substantially greater than the MY and SY sub-basins, even when compared with predicted MY and SY carrying capacities under the alternative management scenarios. Likewise, predicted redd capacity in the NY sub-basin under Scenarios 3 and 4 far exceeds redd capacity predicted in all other sub-basins under all scenarios. The greater redd capacity of the NY can be ascribed to the greater length of thermally suitable channel and more abundant spawning habitat compared with the other sub-basins. Predicted holding habitat capacity in the NY sub-basin under each scenario exceeds the predicted holding capacity in all other sub-basins.
Carrying capacity for the age-0 summer rearing life stage reflects the relative potential of each sub-basin to provide over-summering habitat and produce yearling spring-run Chinook Salmon smolts. In all sub-basins, age-0 summer rearing capacity increased markedly under the alternative flow scenarios compared with the Dry Conditions scenario (Table 6-4), due to an increased length of thermally suitable channel and greater area of channel inundated during the summer low-flow period. The predicted age-0 summer rearing capacity under the Dry Conditions scenario is greatest in the NBB sub-basin, with nearly twice the predicted capacity of the NY sub-basin under the same scenario and substantially greater capacity than the SY and MY sub-basins under the alternative scenarios. Under Scenarios 3 and 4, predicted habitat for age-0 summer rearing is greater in the NY sub-basin than in the other sub-basins. However, age- 0 summer rearing capacity in the NBB and NY sub-basins are nearly equal under Scenario 3. Age-0 summer rearing capacity in the NBB sub-basin under Scenario 4 is approximately half that of the NY sub-basin under the same scenario. The relatively high age-0 summer carrying
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capacity predicted for the NBB sub-basin compared with the other sub-basins, especially under the Dry Conditions scenario, can be attributed to the significantly wider summer low flow channel, which results in a greater area of rearing habitat per unit length of channel. Age-0 summer rearing capacity did not increase in the NBB sub-basin between Scenarios 3 and 4, since the only difference between scenarios was augmentation of spawning gravels.
6.3.3 Smolt Production Estimates The spring-run Chinook Salmon POP module uses sub-basin-specific carrying capacity values for holding, spawning, and summer rearing in conjunction with biological input parameters and life stage-specific stock-production curves, to estimate equilibrium population size.
At the moderate smolt-to-adult survival parameter values used, predicted adult escapement is sufficient to fully seed available habitat for most model runs (Tables 6-4 and 6-5). Only in the NBB sub-basin under the Dry Conditions scenario is holding habitat not fully seeded. Spawning habitat, which is more limiting than holding habitat, is fully seeded in all model runs. In each sub-basin and each scenario, the predicted number of spawners is greater than redds, indicating that predicted adult escapement is sufficient to fully seed the available spawning habitat (Table 6-5). This result, in turn, indicates that smolt production estimates represent the maximum production potential at the freshwater survival parameter values used.
The POP module results further indicate that, in nearly all model runs, emergent fry production from available spawning gravels was sufficient to fully seed the age-0 summer rearing habitat with individuals destined to become smolts. Only in the NBB sub-basin under the Dry Conditions scenario and S3 was age-0 summer rearing habitat not fully seeded, due to the limited quantity of spawning gravels in these scenarios.
Under the S3 and S4, juvenile production from each sub-basin was predicted to increase substantially compared with the Dry Conditions scenario (Table 6-5). This increased production is a result of a greater amount of available spawning and age-0 summer habitat provided by the increased summer flows and reduced water temperatures under the U.S. Forest Service 4(e) and NMFS 10(j) flows. The POP module output also provides an estimate of the proportion of each juvenile life history type produced in each sub-basin and scenario. The proportion of each juvenile life history type (efry, smolt0, and smolt1) is important to the dynamics and viability of each population due the expected increased survival in the San Francisco Bay-Delta and the ocean with increasing size and age. The relative contribution of efry to juvenile production is similar between all scenarios, comprising between 68% and 75% of the juvenile production. The fraction of the juvenile population composed of smolt0 varied from 0% in the NBB sub-basin to
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30% in the MY sub-basin under the Dry Conditions scenario. The fraction composed of smolt1 varied between 2% in the MY sub-basin under Dry Conditions and 25% in the NBB sub-basin. Within each sub-basin, the percentage of the smolt production composed of smolt1 increased with increasing stream flows and expanded summer rearing distribution.
Table 6-5. Predicted equilibrium population sizes for select spring-run Chinook Salmon life stages for each modeled sub-basin and scenario in the upper Yuba River watershed.
Model Scenario1 egg swimup efry smolt0 smolt1 escape holder spawner redds SY-D2 0 0 0 0 0 0 0 0 0
SY-S3 703,929 380,121 142,546 64,448 1,433 1,101 588 318 139
SY-S4 2,194,102 1,184,815 444,306 132,281 52,491 5,147 3,632 2,025 431
MY-D 566,034 430,186 161,320 69,690 3,896 1,327 914 497 112
MY-S3 1,552,510 1,179,908 442,465 183,990 15,697 3,819 3,050 1,665 307
MY-S4 4,018,695 3,054,208 1,145,328 412,380 85,363 11,484 5,710 3,153 791
NY-D 6,585,187 2,370,667 889,000 275,956 97,155 10,018 7,814 4,349 1,293
NY-S3 18,435,767 6,636,876 2,488,829 530,043 441,827 34,112 30,700 17,280 3,609
NY-S4 26,419,753 9,511,111 3,566,667 395,355 888,186 57,993 52,194 29,615 5,160
NBB-D 577,198 375,179 140,692 0 45,959 2,678 2,410 1,376 113
NBB-S3 3,737,981 2,429,688 911,133 0 297,622 17,341 15,607 8,911 729
NBB-S4 11,103,373 7,217,193 2,706,447 642,033 434,640 35,460 20,176 11,329 2,175
1 D = Dry Conditions, S3 = Scenario 3, and S4 = Scenario 4. 2 Under the Dry Conditions scenario the entire mainstem SY below the natural fish passage barrier is predicted to be thermally unsuitable for spring-run Chinook Salmon holding and rearing; therefore production of each life stage is zero.
The adult escapement estimates generated by the RIPPLE model provide only a rough estimate of the number of adults that likely return to each sub-basin under equilibrium population conditions. However, parameter sensitivity analysis suggests there would be sufficient adult escapement to fully seed the available spawning habitat at much lower smolt-to-adult survival values; thus the juvenile and smolt production estimates used for modeling are not highly sensitive to changes in the number of adults predicted. Notwithstanding these considerations, the primary objective of the model was to predict freshwater habitat capacity of holders, spawners, and juveniles and to estimate production of juveniles and smolts.
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6.3.4 Summary Under the Dry Conditions scenario (with current water management practices), unsuitably high water temperatures would limit access by reintroduced spring-run Chinook Salmon to over 30 miles of otherwise high quality spawning and rearing habitats in the SY, MY, and NY sub- basins, greatly limiting potential smolt production. Similarly, high water temperatures in the NBB sub-basin would restrict spawning and juvenile rearing to a fraction of otherwise suitable habitat, and lack of spawning gravel in thermally suitable sub-basins would further limit juvenile production. Nonetheless, model results indicate that, in the NY sub-basin under all scenarios and the SY, MY, and NBB sub-basins under Scenarios 3 and 4, sufficient spring-run Chinook Salmon holding, spawning, and rearing habitat exists to allow for production of substantial numbers of juveniles and smolts.
6.4 STEELHEAD RESULTS
6.4.1 Predicted Distribution of Suitable Habitat In the SY sub-basin under the Dry Conditions scenario, suitable steelhead spawning and summer rearing habitat would be limited to 11.2 miles of tributary habitat (Table 6-6). The entire mainstem South Yuba River was considered unsuitable for steelhead summer rearing under the Dry Conditions scenario due to modeled temperatures exceeding the 20°C temperature threshold. Under S3, the increased flows and reduced summer water temperatures resulting from the U.S. Forest Service 4(e) flow increases provide 2.2 miles of suitable steelhead habitat in the mainstem South Yuba River. The NMFS 10(j) flows modeled for S4 would further reduce summer water temperatures and provide 5.2 miles of suitable mainstem habitat for steelhead (NMFS 2012). Suitable tributary habitat predicted under S3 and S4 is the same (11.2 miles) as under the Dry Conditions scenario.
In the MY sub-basin under the Dry Conditions scenario, 5 miles of the mainstem and 3.1 miles of tributary habitat are predicted to be suitable for steelhead spawning and summer rearing (Table 6-6). Increased flows in the MY sub-basin under S3 and S4 are predicted to provide 6.7 miles and 13.3 miles of suitable steelhead habitat, respectively. The 3.1 miles of suitable tributary habitat predicted under the Dry Conditions scenario is predicted to be the same under S3 and S4.
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Table 6-6. Steelhead habitat predicted under each modeling scenario in sub-basins of the upper Yuba River watershed. Approximate length of steelhead spawning and age 1+ summer rearing habitat (mi)a,b Alternative Sub-basin Dry Conditions Alternative Scenario 3 Scenario 4 mainstem 0 2.2 5.2 SY tributaries 11.2 11.2 11.2 mainstem 5.0 6.7 13.3 MY tributaries 3.1 3.1 3.1 mainstem 18.2 31.8 34.8 NY tributaries 34.2 34.2 34.2 mainstem 3.7c 10.3 10.3 NBB tributaries 0 0 0 a Estimated length only includes portions of the channel network with predicted habitat carrying capacity values > 0. Some portions of the channel network predicted to be thermally suitable have channel gradients too steep to provide suitable habitat and were therefore predicted to have zero carrying capacity. b Actual length of spawning habitat in tributaries is predicted to be slightly greater than rearing habitat due to greater upstream extent of suitable habitat (increased channel width) during winter spawning flow conditions (see Section 4.2.1.2). c This value represents summer rearing habitat only. For the Dry Conditions scenario, there is no suitable spawning gravel in the NBB sub-basin upstream of the Middle Yuba River confluence and therefore spawning only occurs downstream of the New Colgate Powerhouse(approx. 2 miles).
In the NY sub-basin, under the Dry Conditions scenario, 18.2 miles of the mainstem and 34.2 miles of tributary habitat—considerably more than the SY and MY sub-basins—were identified as suitable habitat for steelhead spawning and summer rearing (Table 6-6). Suitable steelhead habitat in the mainstem North Yuba River is predicted to increase to 31.8 miles under S3 and 34.8 miles (the entire mainstem North Yuba River from New Bullards Bar Reservoir upstream to the natural barrier at Love’s Falls) under S4. Predicted tributary habitat under S3 and S4 remains the same (34.2 miles) as under the Dry Conditions scenarios.
In the NBB sub-basin under the Dry Conditions scenario, 3.7 miles of the mainstem North Yuba River was predicted to be suitable summer rearing habitat for steelhead (Table 6-6). However, due to lack of suitable spawning gravel in the mainstem between New Bullards Bar Dam and the Middle Yuba River confluence, spawning under the Dry Conditions scenario was only predicted to occur downstream of New Colgate Powerhouse. Suitable winter rearing habitat in the NBB sub-basin was assumed to be present under all scenarios in the entire mainstem channel. Under S3 and S4, which assume increased cold-water releases from New Bullards Bar Dam and spawning gravel augmentation, the entire 10.3 miles of mainstem channel from New Bullards
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Bar Dam downstream to Englebright Reservoir were predicted to be suitable for steelhead spawning and summer rearing.
6.4.2 Carrying Capacity Estimates Results of the RIPPLE HAB module indicate that, for each model sub-basin and scenario, there is sufficient steelhead spawning habitat (redd capacity) to fully seed the thermally suitable age 1+ summer rearing habitat. Redd capacity predicted for the NY sub-basin is substantially higher than the other sub-basins (regardless of scenario) due to a greater length and area of thermally suitable mainstem channel and the presence of extensive tributary habitat relative to other sub- basins (Table 6-7).
Table 6-7. RIPPLE-predicted habitat carrying capacities for steelhead life stages for each modeled sub- basin and scenario in the upper Yuba River watershed. Model Scenario1 Redd2 Summer 1+ Winter 1+ SY-D 313 5,936 4,051,334 SY-S3 588 11,401 4,051,334 SY-S4 1,062 21,390 4,051,334 MY-D 547 6,463 2,709,801 MY-S3 841 10,001 2,709,801 MY-S4 1,909 25,971 2,709,801 NY-D 4,393 101,401 5,970,183 NY-S3 8,172 182,161 5,970,183 NY-S4 9,137 202,901 5,970,183 NBB-D 120 18,8143 2,674,907 NBB-S3 1,256 66,537 2,674,907 NBB-S4 3,755 66,537 2,674,907 1 D = Dry Conditions, S3 = Scenario 3, and S4 = Scenario 4. 2 Each redd was assumed to support one female spawner. 3 Includes summer 1+ rearing carrying capacity of 3,367 from habitat in the thermally suitable sub-basin upstream of the Middle Yuba River confluence. Because there is no suitable spawning habitat in this sub-basin, this capacity was not used in calculation of smolt production.
Steelhead HAB module results also indicate that age1+ summer steelhead habitat is considerably more limiting than winter habitat. Under the Dry Conditions scenario, predicted age1+ winter habitat capacity ranged from 59 times higher than summer rearing habitat capacity in the NY sub-basin to 683 times higher in the SY sub-basin (Table 6-7). These results indicate that the quantity of age 1+ summer habitat would limit the potential size of the steelhead population in the upper Yuba River watershed.
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These pronounced summer rearing habitat limitations are, in part, attributable to the greater extent of thermally suitable channel in the winter than in the summer. Even in model runs where summer habitat was predicted to be thermally suitable in the entire mainstem study sub-basin (NY sub-basin under S4 and NBB sub-basin under S3 and S4), winter carrying capacity was still higher than summer carrying capacity due to the larger area of channel inundated during winter flows. Parameter sensitivity analysis suggests that juvenile winter rearing density and/or the fraction of usable habitat would need to be reduced substantially before winter habitat becomes limiting.
6.4.3 Smolt Production Estimates Unlike spring-run Chinook Salmon, the POP module was not fully parameterized or run for steelhead due to data limitations and the project scope of work. Potential steelhead smolt production in the upper Yuba River watershed was estimated based on carrying capacities predicted for age 1+ juveniles in the summer. Summer 1+ carrying capacity estimates from the HAB module were multiplied by summer and winter density-independent survival for each life stage to estimate smolt production.
For each model run, estimated smolt production mirrors summer 1+ carrying capacity predicted by the HAB module: significantly more smolts were produced under S3 and S4 compared with the Dry Conditions scenario (Table 6-8). Even the modest flow increases modeled under S3 would result in 1.9 times more production in the SY sub-basin and 1.5 times more production in the MY sub-basin, compared with the Dry Conditions scenario. The higher flow releases under S4 would result in 3.6 times more smolt production in the SY sub-basin and 4 times more smolt production in the MY sub-basin than under the Dry Conditions scenario. In the NY sub-basin, smolt production predicted under S3 and S4 is 1.8 and 2.0 times that of the Dry Conditions scenario, respectively. Estimated smolt production in the NBB sub-basin is 3.5 times higher under both increased flow scenarios compared with the Dry Conditions scenario. These increases are driven in part by the increased length of mainstem channels that become thermally suitable and in part by the increased rearing area resulting from increased summer low-flow widths under S3 and S4.
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Table 6-8. Steelhead smolt production estimates based on RIPPLE-predicted summer carrying capacities for age 1+ steelhead for each modeled sub-basin and scenario in the upper Yuba River watershed.
Scenario South Yuba Middle Yuba North Yuba NBB D 4,808 5,235 82,135 12,5121 S3 9,235 8,101 147,550 53,895 S4 17,326 21,037 164,350 53,895 1 Does not include production resulting from summer rearing carrying capacity of 3,367 that occurs in the thermally suitable sub-basin upstream of the Middle Yuba River confluence where spawning habitat is not available.
The RIPPLE model results further indicate that the NY sub-basin has the potential to produce substantially more steelhead than the SY and MY sub-basins (Table 6-8). Under the Dry Conditions scenario the NY sub-basin is predicted to produce 17 and 16 times more steelhead smolts than the SY and MY sub-basins, respectively. Even compared with augmented flow scenarios in the SY and MY sub-basins, the NY sub-basin under the Dry Conditions scenario is predicted to produce more steelhead smolts. The greater smolt production in the NY sub-basin is due not only to the larger channel size and greater extent of accessible tributary habitat than the other sub-basins, but also to a higher frequency of riffles, which support relatively higher age1+ densities than pools in lower gradient, mainstem channels. These results underscore the sensitivity of the model to the amount of suitable summer rearing habitat, as determined primarily by water temperature.
6.4.4 Summary Several factors point to specific areas of the upper Yuba River watershed, particularly the NY sub-basin, as having excellent potential for sustaining healthy steelhead populations. An abundance of high quality rearing habitat currently supports relatively high densities of resident Rainbow Trout in sub-basins with suitable summer water temperatures. Conditions for juvenile steelhead rearing in the upper Yuba River watershed are currently good, but as demonstrated by the model, increased stream flows and lower summer water temperatures would greatly increase smolt production in the SY, MY, and NBB sub-basins.
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7. LIFE-CYCLE AND PASSAGE MODEL
7.1 INTRODUCTION The intent of a reintroduction plan for ESA-listed salmonids is to re-establish a resilient, self- sustaining salmon population to assist in recovery of the species. To further investigate whether this outcome could be realized through a Yuba River anadromous fish reintroduction program, we developed a Life-Cycle and Passage Model (Life-cycle model) which builds on the results of the habitat assessment and biological productivity model (RIPPLE) presented in Chapter 6.
Our overall goal in constructing this model is to provide an additional planning tool for evaluating alternative passage options associated with reintroduction of salmon to particular tributaries, and to examine the sensitivity of the population dynamics to potential hydrologic modification of those tributaries. A general objective of the model is to quantify likely sources of mortality throughout the salmonid life-cycle in order to evaluate the likelihood of a self- sustaining population of CV spring-run Chinook Salmon on the Yuba River.16 Our specific objectives are to construct a life-cycle model that: (1) includes the alternative hydrologic scenarios that alter the production potential of the Yuba system (Chapter 6); (2) includes downstream and upstream passage around NBB and Englebright dams; (3) includes Delta and ocean survival; (4) quantifies the likelihood of self-sustaining populations; and (5) provides initial hypotheses regarding passage and mortality rates that can be targeted through the pilot, short, and long-term phases of data collection. It is important to note that the model was designed to provide inference on the equilibrium (or long-run dynamics) as opposed to short-run specifics and to provide insight on the relative abundances under the hydrologic scenarios as opposed to absolute abundances.
When populations cannot produce enough individuals to replace the spawning stock on average, then the population will not be capable of sustaining itself in isolation. Thus, populations are self-sustaining when they are capable of exceeding replacement. A useful metric for evaluating the likelihood of self-sustainability is the cohort replacement rate (CRR), which is the rate at which the cohort replaces the previous generation. A CRR of equal to 1 will exactly replace the previous generation, whereas a value of less than 1 will decrease and a value of greater than 1 will increase the population. Thus self-sustaining populations will have CRR values that average 1.0 or greater over long time scales.
16 Note that steelhead life-cycle modeling was not part of the scope of this work, but a similar approach could be taken in future studies. The absence of steelhead life-cycle modeling in this initial plan does not infer that consideration of steelhead reintroduction to meet ESA recovery objectives is unwarranted.
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A population that cannot meet or exceed replacement may still persist if it is connected to other stocks that are highly productive. Populations that do not exceed replacement are called sinks (Pulliam 1988) and persist due to the connectivity to other populations. The connectivity to other populations that allows persistence may be volitional through migration, but it may also be accomplished through anthropogenic means such as collection, transport, and outplanting from productive populations. Caution must be taken with using such anthropogenic means of supporting sink populations; it may ultimately be deleterious to the overall ESU by removing individuals from a population that may itself be recovering (McClure et al. 2011).
There are many factors that may contribute to a population that is not self-sustaining; a situation where the level of production of a female spawner is not adequate to overcome the multiple sources of mortality over her progeny’s life-cycle such that one or more female spawners return. Some of the factors responsible for affecting self-sustainability are due to in-basin conditions, such as habitat quality for spawning, incubation, and rearing. Other factors are due to the migration from the natal areas to the ocean, such as juvenile passage, migration, ocean entry, harvest, adult passage and pre-spawn mortality.
On the Yuba River, the production potential for CV spring-run Chinook Salmon in the NY, MY, SY, and NBB sub-basins was modeled via the Yuba RIPPLE model (Chapter 6). This potential is provided for three stages of juvenile migrants: efry are estuary fry which migrate as fry to the estuary where they will rear before smolting and entering the ocean; smolt0 which are parr that will migrate through the system after rearing in the stream for several months; and smolt1 which are yearlings that have overwintered in the tributaries and will migrate out the spring as 1+ year old smolts (Stillwater Sciences 2013a). Yet, for this potential to be realized, fish from the Yuba River must pass downstream through dams and reservoirs, through the San Francisco estuary, to the ocean, and complete the adult migration back through the Yuba River to habitat that is suitable for spawning to complete the life-cycle (Figure 7-1). Such sources of mortality will determine whether the population of CV spring-run Chinook Salmon on the Yuba River can be self-sustaining, and thus meet a key objective of the reintroduction.
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Figure 7-1. Schematic for life-cycle model of spring-run Chinook Salmon in the Yuba River. Production potential in the North Fork Yuba (NY), Middle Fork (MY), South Fork (SY), and New Bullard Bar (NBB) are moved out of the Yuba River through reservoirs and dams (solid lines) to the ocean where juveniles mature and return as spawners to the Yuba River and return (dashed lines) through passage structures at dams and reservoirs.
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7.2 METHODS
7.2.1 The Life-cycle Model The life-cycle model begins with the production of juveniles from spawners in three stages: efry, smolt0, and smolt1. The production of these three juvenile (J) migrant types as a function of spawners in tributary j are given as follows (the time subscript is suppressed for clarity):
efry Jefry,j = Spj * Ffry,j* P
efry smolt0 Jsmolt0,j = Spj * Ffry,j(1- P) * Sfry*( Ps,j) (1)
smolt0 Jsmolt1,j = Spj * Ffry(1-Pefry) * Sfry* (1 - Ps,j)* Ssmolt0
where Spj refers to the number of spawners in tributary j, Ffry, is the number of fry produced per efry smolt0 spawner, P is the proportion of fry that migrate out as efry, Ps,j is the proportion of smolt0 that migrate as smolt0 (as opposed to stay in the stream over the winter to subsequently migrate as smolt1), Sefry is the survival rate from fry to smolt0 in the stream, and Ssmolt0 is the survival from smolt0 to smolt1 in the stream. The Jefy and Jsmolt0,j migrate out in the brood year, whereas the Jsmolt1,j migrate in the year following the brood year from each of their natal sub-basins (Table 7-1).
We are assuming that each spawning sub-basin acts independently for the purposes of the model. While not true in practice due to straying of adults among spawning sub-basins, this assumption allows us to track each sub-basin individually. As a result, the model can evaluate whether the net production of a sub-basin is adequate for a self-sustaining population, or alternatively if the sub-basin will be a population sink. In addition, we assumed that juvenile production in a sub- basin could not surpass the juvenile production identified in the RIPPLE model outputs (Chapter 6).
The juveniles that are produced in each of the NY, MY, SY, NBB sub-basins are then required to pass through specific routes to exit the Yuba River. Each sub-basin has its own passage configuration that must be modeled to provide connectivity from the spawning sub-basins to the ocean for the juveniles and back to the spawning sub-basins for the adults. Furthermore, we track each outmigrant stage from the spawning sub-basins out to the ocean and back to below Englebright Dam to evaluate the relative contribution of each juvenile outmigrant type to the returning adult population.
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We are evaluating sub-basin-specific alternative collection methods in this analysis. The first passage alternative is to provide collection and transport to the North Yuba. On the NY, the production is above NBBD; therefore, juveniles and adults need to be move to and from the spawning sub-basin to below the Englebright or Daguerre Point dams. On the NY, we are evaluating a tributary collector with transport below Englebright Dam for juveniles. Adult collection occurs at Englebright with transport to a location upstream of the reservoir.
Table 7-1. Model abbreviations and their descriptions.
Ad3,i,j,t Adults at age 3 returning to the Yuba River in year t having migrated in stage i from sub- basin j
Ad4,i,j,t Adults at age 4 returning to the Yuba River in year t having migrated in stage i from sub- basin j
AP3,j Adults above project of age 3 that originated in sub-basin j
Fi Number of offspring produced per spawner for stage i = efry, smolt0, smolt1
CJi,MY Collected juveniles on the Middle Yuba at Our House Dam in stage i
Ffry,j Number of fry produced per spawner efryP Proportion of fry that migrate out as efry smolt0 Ps,j Proportion of fingerling in the stream that migrate as sub-yearling (smolt0) i Juvenile life stage = efry, smolt0, smolt1 j Sub-basin = North Yuba (NY), Middle Yuba (MY), South Yuba (SY), or Englebright Dam sub-basin (ED)
Jefry,j Number of efry juveniles from sub-basin j
Jsmolt0,j Number of smolt0 juveniles in sub-basin j
Jsmolt1,j Number of smolt1 juveniles in sub-basin j
Lj Collection and passage rate for adults returning to sub-basin j
Matage3 Maturation rate of age 3 spring-run Chinook Salmon
Oi,j Outmigrants in stage i in sub-basin j
POH,i Passage at Our House Dam for stage i
Peng,i Passage at Englebright Dam for stage i
PSj Pre-spawn survival rate for adults in sub-basin j
Rdam,i,j Reservoir abundance behind dam for stage i in sub-basin j
Reng,i,j Reservoir abundance behind Englebright Dam for stage i from sub-basin j
ROH,i,MY Reservoir abundance behind Our House Dam for stage i from the Middle Yuba
Sdam,,i Survival in a reservoir associated with a dam for stage i
Sfry Survival rate from fry to smolt0 in the stream
Ssmolt0 Survival rate from smolt0 to smolt1
Sspill, i Survival rate during spill for life stage i
SARi,t Smolt to adult ratio for stage i in year t
Spj Spawners in sub-basin j
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The second passage alternative is to provide upstream and downstream passage at Englebright Dam. This passage alternative assumes that supplemental flows will be provided in the New Bullards Bar and lower Middle Yuba River reaches which are sufficient to allow fish to pass New Colgate Powerhouse. On the MY, the spawning sub-basins are located above Our House Dam, a relatively small dam with a small reservoir. As a result, we are evaluating passage at Our House Dam for juveniles and adults, passage through Englebright reservoir and collection by an FSC at Englebright Dam. Finally, on the SY and NBB sub-basins, there are no additional barriers to migration besides Englebright Dam; therefore, we are evaluating the survival of juveniles through Englebright reservoir and collection by FSC at Englebright Dam. Adult passage for sub-basins occurs at Englebright Dam via a fish ladder with subsequent passage at Our House for adults on the MY.
Dam Collection When juvenile salmonids are collected at the dam forebay, they must first transition the reservoir prior to reaching the forebay collection facility. We apply a reservoir passage mortality based on the three classes of outmigrants to obtain the reservoir abundances (Rdam,i,j) in each reservoir associated with dam (dam = Englebright or Our House), stage (i) and sub-basin (j).
Rdam,i,j = Ji,j * Sdam,i (2)
where Sdam,i refers to reservoir survival for stage i.
Fish that arrive at the dam will then be collected and transported to below the dam. Collection efficiency and survival are combined to provide an estimate of passage through the dam. For
Our House Dam on the MY, the number of collected juveniles (CJi,MY) is a function of the collection efficiency at Our House Dam (POH,i) for stage i.
CJi,MY = ROH,i,MY * POH,i (3)
Once fish pass below Englebright Dam they become outmigrants (Oi) and pass out to the ocean
Oi,j = Reng,i,j* Peng,i (4)
where Peng,i is the passage efficiency at Englebright Dam for stage i.
The passage efficiency, Peng,i is a function of the amount of flow moving through the collector facility relative to flow being spilled when there was spill at Englebright Dam. Otherwise, the
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passage efficiency is a function of the collection efficiency of the FSC. Please see Appendix A for details on the collection efficiency calculations.
Tributary Collection The tributary collector has both collection efficiency and a post-collection survival during transport. The collected migrants (Ci,j) are a function of juvenile production in the tributaries and the tributary collection efficiency for stage i (Ti).
Ci,j = Ji,j * Ti (6)
The numbers of outmigrants are a function of the stage-specific transport survival (Strans,i) and the collected migrants in each stage
Oi,j = Ci,j * Strans,i (7)
Outmigration and Adult Return The outmigrants move down the Yuba River through the delta and out to the ocean, where they remain for 1 to 2 years. Central Valley spring-run Chinook Salmon return predominantly as 3 and 4 year olds (Cavallo et al. 2009) and the model tracks age 3 and age 4 returning adults (subscript t for year added for clarity)
Ad3,i,j,t = Oi,j,t-3* SARi,t* Matage3 (8)
Ad4,i,j,t = Oi,j,t-4* SARi,t * (1- Matage3)
where Ad3,i,j,t is the number of returning age 3 adults in stage i from sub-basin j in year t, SARi,t is the smolt to adult return rate for stage i in year t, and Matage3 is the maturation rate of age 3 fish.
After adults return to the Yuba River, they must pass the existing dams to sub-basin spawning habitats. Passage efficiency for adults around the dams was calculated as
AP3,j = ∑ d3,i,,j *Lj (9)
where AP3,j refers to adults above the project and Lj is the collection and passage rate for adults age 3 associated with either transport (NY) or survival through a fish ladder at Englebright (SY,NBB), whereas for fish returning to MY, passage of adults at Our House Dam is also
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included in the calculation of passage for adults. A similar equation was developed for age 4 adults.
Finally, spawners in each of the Yuba tributaries (Spj) are composed of both age 3 and age 4 adults above the associated dams and reservoirs in the spawning habitat after experiencing pre- spawn mortality.
Spj = PSj*(AP3,j +AP4,j) (10)
In the absence of passage-related survival issues, the CRR of the populations is approximately 2.2 (the exact rate depends upon the distribution of sub-yearling and yearling smolts, which varies by hydrologic alternative). This value of CRR for our hypothetical population on the Yuba River is consistent with CRRs calculated for Chinook populations in watersheds with less urban influence e.g., the Yukon River and Chena/Salcha Rivers in Alaska, which can have CRRs ranging from approximately 0.9 to 6 (AYK SSI 2012). Biological parameters are described in Appendix A, whereas passage-related parameters are described in Chapter 4 and summarized in Appendix A.
Incorporating Uncertainty Many of the biological parameters and passage parameters needed to simulate the possible reintroduction of CV spring-run Chinook Salmon to the Yuba River are unknown. Yet, through analysis of data, published studies for Chinook in the Central Valley and elsewhere in their west coast distribution, and expert opinion, we can provide informed initial values for parameterizing the life-cycle model. The purpose of the parameter values at this stage is to summarize existing knowledge with the goal of expressing uncertainty in a manner that reflects our current knowledge, or ignorance, of particular parameter values.
We provide estimates of model parameter values using a triangular distribution, which can be defined by the low, mode, and high values of the distribution (Figure 7-2). This distribution provides an intuitive way to go from literature-derived values and expert opinion to a probability distribution by specifying the low, high, and mode as the worst possible case, the best possible case, and the moderate case, respectively. The low, hi, and mode values associated with passage related parameters are described in Appendix A.
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7.2.3 Evaluating Passage Alternatives and Hydrologic Scenarios
Passage Alternatives The life-cycle model was used to simulate the production potential of the NY, MY, and SY into adults returning to the Yuba River. Multiple passage scenarios were evaluated to understand how the different passage alternatives would lead to different levels of adult abundance below Englebright Dam. We modeled two passage alternatives that provided connectivity from each of the spawning sub-basins (NY, MY, SY, and NBB) to the ocean: 1. Collection and transport program to the North Yuba. 2. Construction of a fish ladder and juvenile downstream passage facilities at Englebright
Dam and upstream and downstream passage at Our House on the MY.
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Figure 7-2. Example of triangular probability distribution. The triangular distribution is defined by the lower bound, upper bound, and mode or peak: therefore, the distribution can be either symmetric or asymmetric.
Hydrologic Scenarios We ran three different hydrologic scenarios. These scenarios are defined in detail in Stillwater Sciences 2013a (see Chapter 6), but here we provide the salient features of each scenario (Table 7-2).
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Table 7-2. Hydrologic scenarios evaluated with the passage model for the Upper Yuba. July–Sept Water Sub-basin Modeling Scenario Stream Flow Temperature South Yuba Dry conditions (D) Existing releases 2009 (modeled) River (SY) USFS 4(e) augmented releases (dry Scenario 3 (S3) 2009 (modeled) water year) Scenario 4 (S4) NMFS 10(j) augmented releases 2009 (modeled) Middle Yuba Dry conditions (D) Existing releases 2009 (modeled) River (MY) USFS 4(e) augmented releases (dry Scenario 3 (S3) 2009 (modeled) water year) Scenario 4 (S4) NMFS 10(j) augmented releases 2009 (modeled) 2008–2009 North Yuba Dry conditions (D) Existing flows (unregulated) (measured, with River (NY) interpolation) Scenario 3 (S3) Existing flows (unregulated) 2010 (measured) Scenario 4 (S4) Existing flows (unregulated) 2011 (measured) Yuba River below New Dry conditions (D) Existing releases 2010 (measured) Bullards Bar Dam (NBBD) Scenario 3 (S3) (25% Augmented releases (unimpaired N/A (not limiting) gravel restoration) conditions) Scenario 4 (S4) (75% Augmented releases (unimpaired N/A (not limiting) gravel restoration) conditions)
Running the Life-cycle Model To initiate a model run, we assumed that production would occur at target levels as defined by the production potential model summarized in Chapter 6 (Stillwater Sciences 2013a) for each of the tributaries and each of the life stages for a 10-year period. Thus, production of efry, smolt0, and smolt1 followed assumptions defined in Appendix A. After this period of population establishment, the population was allowed to run for another 90 years in the absence of supplementation. During those later 90 years, juvenile production was capped at the maximum values for that tributary and hydrologic scenario obtained from the RIPPLE production model (Chapter 6, Appendix A). Setting an upper bound to the juvenile production was equivalent to
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implementing a “hockey-stick” stock production relationship (i.e., linear increase until reaching carrying capacity at which point the production is constant at the carrying capacity), which was consistent with the methods employed in the RIPPLE production model (Chapter 6, Stillwater Sciences 2013a).
To understand how the populations would respond to a period of poor ocean conditions, we constructed a “stress test”. We constructed a time series of smolt to adult return ratio (SAR) rates, in which the SAR rates were stable at their nominal values (Appendix A) for the first 50 years of the time series. For the three years from 51 to 53, the SAR rates were halved to indicate poor ocean conditions and thus “stress” the populations. The populations were then allowed to respond to this 3-year period of poor ocean conditions to understand how well the populations could recover from this event.
To reflect uncertainty in model parameters, we used Monte Carlo simulation (Manly 2006) to evaluate alternative possible model parameter combinations. Monte Carlo simulation uses random numbers sampled from some form of a probability distribution (triangular in this application) as input to a deterministic equation or model to derive an outcome under conditions of uncertainty. Thus, uncertainty in model inputs can be translated into uncertainty in model outputs. The life-cycle model used draws from the triangular distribution to construct a parameter set via random draws from all the parameters in the model specified by triangular distributions for the passage parameters (Appendix A). Once the parameter set was drawn, the model ran through the 100-year time series and saved the results of that model trajectory. We used 1,000 Monte Carlo simulations to provide an estimate of the range of outcomes due to uncertainty in the model parameters.
Metrics We used several metrics to understand both the response to the stress test under each of the passage alternatives and the equilibrium population dynamics under each of the hydrologic scenarios. We computed the modeled abundances under each of the hydrologic alternatives for each sub-basin to provide a comparison of relative population size. In addition, we computed the distribution of abundances under each scenario for two reasons: 1) to identify any trajectories that had values of approximately 0 (i.e., < 1 spawner) to indicate reintroduction failure, and 2) to evaluate the uncertainty in the distribution of outcomes under different hydrologic scenarios to observe the relative abundances at equilibrium and their associated uncertainty. Finally, we computed the cohort replacement rate (CRR) or alternatively described as the adult recruits per spawner for two years: 1) brood year 54, which was the first fully impacted year by the stress test and 2) brood year 95, which was at the end of the time series when the CRR indicates
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whether the modeled trajectory is self-sustaining (CRR > 1) or not self-sustaining (CRR < 1). Furthermore, we calculated the probability of a self-sustaining population under each hydrologic scenario and sub-basin as a function of the 1000 model trajectories.
7.2.4 Model Assumptions Several assumptions were made in order to develop the life-cycle model:
The parameter values used in the model are representative of the CV spring-run Chinook Salmon population dynamics. This model is not intended to forecast absolute estimates of abundance, but instead it was developed to understand how hydrologic scenarios would perform under two passage alternatives. As a result, the results are most robust when viewed as relative performance among hydrologic scenarios.
The triangular distributions capture the uncertainty in passage parameters.
Natural variability in the populations was not included as a model parameter, which has important implications for forecasting population abundances. Modeled population sizes of 10 to 20 spawners may theoretically persist for 90 years, yet such a population would likely not be sustainable under actual field conditions due to annual variation in survival in the ocean and estuary.
The survival through the estuary and out into the ocean is based on recent historical estimates of Chinook survival rates (Appendix A), and does not incorporate changes in those rates in the future.
A “hockey stick” functional relationship was used to reflect density dependence in juvenile production. Other density dependent relationships could also be implemented (such as Beverton-Holt, Ricker, etc.), which would provide different estimates of equilibrium stock size and different estimates of CRR.
The distribution of migrants among efry, smolt0, and smolt1 was developed by Stillwater Sciences (2013a). The distribution is assumed to reflect the population that would eventually become established in the Yuba River. Proportions of efry, smolt0, and smolt1 varied by sub-basin and hydrologic scenario and can be found in Appendix A.
7.3 RESULTS AND CONCLUSIONS
7.3.1 North Yuba Passage We ran multiple trajectories under each of the three alternative hydrologic scenarios; however the model runs on the NY, MY, SY, and NBB had a similar shape (Figure 7-3). There is an initial stage of introduction with donor-stock supplementation for the first 10 years (years 1 to 10). Spawner abundance increases from low levels during this period starting at 3 years following the initial reintroduction period. After the supplementation period ends, the population
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equilibrates to a specific abundance depending upon the parameter set that was drawn via Monte Carlo simulation (years 13 through 20). The stress test begins in year 51 and the SAR rate drops by 0.5 through year 53. In year 54, the population responds initially with a brood year composed partly of unaffected age 4 fish along with affected age 3, whereas in year 55 the returning adults are composed of age 3 and 4 fish that were both impacted by the stress test. In the following several years there is a recovery from the stress test, the duration of which depends upon the parameter set drawn via Monte Carlo simulation. After recovery from the stress test each model trajectory stabilizes and continues through the remainder of the modeled time series to year 100 (Figure 7-3).
In the NY, the hydrologic scenarios refer to different hydrologic years, thus representing different climatic conditions leading to different flow levels through the NY. As a result, the results from the model indicate the range of production and relative rates of production that could be expected under different water year types as exemplified by the 2008 through 2011 climatic conditions (Table 7-2). The mean equilibrium modeled abundance under the Dry Conditions scenario (Scenario D) was approximately 1,080 adults, whereas modeled abundance under intermediate flow conditions (S3) was 3,778 (3.5 times higher) and the modeled abundance under wetter conditions (S4) was 6,433 (6.0 times higher) (Figure 7-4).
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Equilibrium population sizes among the hydrologic scenarios indicate that there were no modeled trajectories that had values close to 0, even under the low flow conditions in Scenario D (Figure 7-5). The distribution of modeled abundances ranged from 900 (the lower 2.5% of Scenario D) to 7,322 (the upper 97.5% of the S4).
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The population response to the stress test indicated that population trajectories were recovering from the event (i.e., all CRR values were greater than 1) in all scenarios (Figure 7-6). Scenario D had higher CRR in year 55 relative to the S3 and S4, because the Scenario D had more scope for recovery in year 55. The other two scenarios were already close to their equilibrium population size by year 55; therefore, their CRR was constrained to lower values. By year 95, modeled trajectories in all scenarios had CRR values of approximately 1 (Figure 7-6). The modeled trajectories had values of 1 because there was no change in the adult abundances, which occurred when juvenile production was restricted by the capacity limitation via the RIPPLE model outputs (Chapter 6).
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D S3 S4 Scenario Figure 7-6. Cohort replacement rate (CRR) for two periods on the North Yuba. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1.
7.3.2 Englebright Dam Passage Providing upstream and downstream passage at Englebright Dam opens habitat on the SY, and NBB sub-basins for production. In addition, providing passage at Our House Dam on the MY provides access to spawning and rearing habitat in the Upper MY (Chapter 5). Under Scenario D, NBB had the highest mean modeled levels of spawner abundance (119) relative to MY (23) and SY (0) (Figure 7-7). Under augmented flows on the MY, S3 flows increased the spawner abundance 3.5 fold increase over the Scenario D abundance (82), and S4 flows provided a 19.5
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fold increase (448). On the SY, a model population of 7 spawners could be initiated under S3 augmented flows; S4 flows would increase the spawner abundance approximately 35 fold (246). On the NBB sub-basin, the difference among scenarios included both flow augmentation and gravel supplementation on S3 and S4 relative to Scenario D (Table 7-2). Average modeled spawner abundance in the NBB sub-basin increased 10.7 fold under scenario S3 relative to Scenario D, whereas average abundance increased 20 fold under scenario S4 relative to Scenario D.
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Figure 7-7. Estimates of mean CV spring-run Chinook Salmon spawner abundance in the Middle Yuba (top), South Yuba (middle), and Englebright Dam sub-basins (bottom) under three hydrologic scenarios. Scenario D (red solid line) has the lowest mean abundance relative to either scenario S3 (black dashed line) or scenario S4 (blue dotted line).
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Middle Yuba In the Middle Yuba, the hydrologic scenarios included the Dry Conditions (Scenario D), the augmented releases under USFS 4(e) flows (S3) and the augmented releases under NMFS 10(j) flows (S4) (Table 7-2). Under Scenario D, the distribution of MY spawner abundance in the year 100 was bimodal with a 1.9% chance that spawner abundance would be less than 1 fish at the end of the 100-year time frame (Figure 7-8). There was a marked increase in the modeled equilibrium abundance of the population in the MY by implementing scenario S4 and S3 relative to Scenario D (Figure 7-8). The increase in abundance for S3 relative to Scenario D was approximately 2.4 times and the increase in abundance under S4 was approximately 4.5 times S3.
The cohort replacement rate (CRR) at the end of the time series provides an indication of the proportion of model trajectories that are self-sustaining. All trajectories with CRR values greater than or equal to 1 would be self-sustaining, whereas all those trajectories with CRR values less than one will eventually collapse. Under the Scenario D, there was a 9.6% chance that the MY population would not be self-sustaining, whereas under S3 and S4 there was a 0.2% chance that the MY population would not be self-sustaining (Figure 7-9).
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Figure 7-9. Cohort replacement rate (CRR) for two periods on the Middle Yuba. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1.
South Yuba In the South Yuba, CV spring-run Chinook Salmon juvenile production cannot occur under Scenario D (Stillwater Sciences 2013a). As on the MY, S3 includes USFS 4(e) augmented flows, whereas S4 includes NMFS 10(j) augmented flows (Table 7-2). Under S3 few spring-run Chinook Salmon would be expected to return after 100 years, whereas approximately 3.5 times the S3 levels would be expected under S4 (Figure 7-10). Under S3, there was a 6.8% chance that the reintroduction would result in failure after 100 years (spawner abundance <1), whereas this rate dropped to 0.3% under S4 (Figure 7-10). The life-cycle model indicated that the SY could potentially support a population at higher abundances under S4 than under S3. Yet, the size of
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this population is somewhat uncertain and the modeled spawner abundance ranged from 0 to 450 (Figure 7-10).
The distribution of CRR after the stress test and at the end of the modeled time series was similar for scenarios S3 and S4 on the SY (Figure 7-11). Despite higher relative abundances in year 100 for the S4 alternative, the overall productivity of the SY population was similar for S3 and S4. Response following the stress test was similar with 94.6% of trajectories under S3 and 94.2% of trajectories under S4 showing recovery from the stress test (i.e., CRR > 1). Furthermore, the probabilities of self-sustaining populations were similar between alternatives; there was an 86.5% chance that the CRR > 1 under S3 and an 84.6% chance under S4 in year 100 (Figure 7-11).
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Figure 7-10. Distribution of the modeled spawner abundance in year 100 in the South Yuba. Hydrologic scenario S3 (black) and S4 (blue) are plotted.
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S3 S4 Scenario Figure 7-11. Cohort replacement rate (CRR) for two periods on the South Yuba. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1.
Englebright Dam Sub-basin (NBB) In Englebright Dam sub-basin, Scenario D consisted of existing releases (measured 2010 flows) and existing gravel conditions for spawning habitat (Table 7-2). In contrast, S3 and S4 assumed supplemental flow conditions with 25% gravel augmentation for S3 and supplemental flows with 75% gravel augmentation for S4.
Under Scenario D (i.e., current FERC license conditions for 5 cfs water releases from New Bullards Bar Dam), there were multiple trajectories in which the abundance of the reintroduced population was approximately 0 by year 100 (Figure 7-12). The probability of less than 1 spawner was 12.8% in year 100 indicating failure of the reintroduction. The probability of success is not the converse (i.e., 87.8%), because many of the trajectories had low abundances that almost certainly would have gone extinct under natural population dynamics. Compared to Scenario D, no model trajectory was less than 1 spawner under S3 and S4.
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Figure 7-12. Distribution of the modeled spawner abundance in year 100 in the Englebright Dam sub- basin (NBB). Hydrologic scenario D (red), S3 (black), and S4 (blue) are plotted.
The CRR for NBB also reflects the different relative performances under each hydrologic scenario (Figure 7-13). Under Scenario D, 76.3% of the model trajectories were recovering after the stress test compared to 96.6% under S3 and 100% under S4. The probability that the populations would be self-sustaining under each of the alternatives also varied among alternatives. The proportion of model trajectories indicating a sink population was 49.5% under Scenario D, 1.5% under S3, and 0.0% under S4. These results indicated that the likelihood of a self-sustaining population increases substantially under S3 and S4 relative to Scenario D.
There were some hydrologic scenarios for which the model trajectories were bimodal at the end of the modeled time period (e.g., MY under Scenario D, NBB under Scenario D). The lower mode consisted of population trajectories that were not capable of replacing themselves given passage-related mortality. In contrast, the other mode was composed of model trajectories with CRR values greater than 1, and thus being capable of replacing itself in spite of the mortality due to passage.
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Figure 7-13. Cohort replacement rate (CRR) for two periods on the Englebright Dam sub-basin. CRR for the spawners in year 55, which was after the stress test (top) and spawners in year 95, which was near the end of the 100 year time series (bottom). Boxes indicate median (dark line in center of box), 25th and 75th percentiles (boxes) and whiskers are 1.5 times the interquartile range. Horizontal line indicates a CRR of 1.
The lower mode was composed of model trajectories that had abundances close to 0 by the end of the modeled time period. This group of model trajectories reflected the possibility that the reintroduced population would go extinct and the reintroduction would have failed without additional supplementation beyond the initial 10-year period. Hydrologic scenarios that contained the possibility of reintroduction failure coincided with the possibility that the reintroduction may not be self-sustaining (CRR rates < 1 in year 100). These two processes are linked due to the linear nature of the model. The trajectories with abundances near 0 are the trajectories with the lowest CRR rates. There are other trajectories with CRR rates that are < 1 but that have not gone extinct yet. Within the context of the model, these trajectories would eventually go extinct if the time period was extended beyond 100 years. Thus the proportion of model runs with CRR < 1 at year 100 was always higher than the abundances close to 0 in year 100. Ultimately, the presence of the bimodal set of outcomes indicates the likelihood of a condition in which the sub-basin is straddling two potential outcomes, success or failure. Therefore, the passage rates will determine which of the two outcomes would be most likely.
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7.3.3 Conclusions Given the results of the spring-run Chinook Salmon life-cycle modeling and its associated assumptions, there are several recommendations regarding the locations of reintroductions relative to the hydrologic conditions that would be experienced by the reintroduced population.
The North Yuba can maintain a self-sustaining population under all three modeled hydrologic conditions, and a reintroduction could produce a self-sustaining population when using tributary capture and transport to below Englebright Dam. Since the hydrologic conditions represent alternative unimpaired hydrologic flows from different water year types, the results of the modeling suggests that the population sizes could fluctuate as habitat capacity responds to annual hydrologic conditions.
The Middle Yuba may be able to sustain a population depending upon the hydrologic conditions. Under dry conditions (Scenario D, with current water management practices), there is a non-trivial likelihood of reintroduction failure. Furthermore, the abundances of the modeled self-sustaining trajectories were so low that they may be susceptible to annual variability in delta and ocean conditions leading to failure. The S3 hydrologic scenario improves the performance of the population by improving the likelihood of a self-sustaining population, but the modeled population abundance is still low enough to be vulnerable to annual variability. Under the S4 alternative, the population has a similar CRR as S3, but the abundance is forecasted to be higher, which would provide some additional buffering capacity against annual variability.
The South Yuba could potentially provide some spring-run Chinook Salmon habitat but likely only under S4. Still, under S4 there is some indication that the reintroduction has a high risk of extinction.
The NBB sub-basin could provide self-sustaining populations depending on the hydrologic conditions. Under dry conditions (Scenario D, with current water management practices), there is a non-trivial probability that a reintroduced population would fail over a short time period; furthermore, populations that did become established would likely have a high risk of extinction over a 100-year time period. In contrast, addition of supplemental flows and gravel augmentation under scenarios S3 and S4 reduces the risk of extinction and risk of being a sink population substantially (e.g., Figure 7-13).
The different hydrologic scenarios and passage alternatives may have important but different effects on VSP scoring criteria. The hydrologic scenarios determine the capacity for populations and therefore the levels of abundance that can be obtained by making more or less habitat available. Passage efficiency determines whether the habitats that could produce spring-run Chinook Salmon can be connected to the lower Yuba and ultimately the ocean to complete the life-cycle. Furthermore, the passage
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alternatives can also affect the cohort replacement rate by introducing sources of mortality (e.g., reservoir mortality) prior to the migration out to the ocean. In terms of evaluating VSP scoring, we may expect that the hydrologic scenarios will affect the VSP criteria of abundance (assuming passage has been provided), whereas the type of passage will affect the VSP criteria of productivity. The results of the model presented here for the Yuba are dependent upon the assumptions of production potential for evaluating alternative hydrologic scenarios and assumptions in constructing the passage rates. Here we have only evaluated a single passage alternative for each of the sub-basins; however, if additional passage scenarios were to be evaluated in the future, they could be compared in a similar manner to the methodology used here to understand the trade-offs between passage alternatives and population productivity.
As a final note, it bears repeating that the Life-Cycle Model was not employed for steelhead in the upper Yuba River watershed for reasons described earlier. It would be erroneous to make assumptions about the likelihood of reintroduction success for steelhead based on the model’s output for spring-run Chinook Salmon. Because of migration timing and species-specific life- history differences, steelhead (O. mykiss) may exhibit a unique ability to persist relative to Chinook salmon under prevailing environmental conditions, but the elements of designing and operating fish passage systems for steelhead may also be more complicated.
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8. PHASED PLANNING APPROACH
8.1 CONNECTIVITY The Upper Yuba basin has potential to benefit long term recovery of CV spring-run Chinook Salmon and CV steelhead, but successful reintroduction must address the original and on-going causes of extirpation. Reintroduction of anadromous fish to Upper Yuba basin habitats will be affected by a variety of factors including:
Connectivity;
Harvest;
Ocean conditions;
River flows;
Water temperature;
Disease;
Interactions with pre-existing or introduced species;
Source populations;
Productivity;
Predation; and
Recruitment.
Elimination of access to historical spawning and rearing habitats (i.e., connectivity) above Englebright Dam is considered to be one of the greatest impacts to listed salmonids in the Yuba River watershed. As described in Chapter 7, a life-cycle model can be designed to sequentially evaluate life stage transitions and quantify the effect of these factors on reintroduction success. Alternate reintroduction strategies can be developed to respond to these factors, but the remainder of this section addresses the influence of re-establishing connectivity to spawning and rearing habitats in the Upper Yuba basin.
Opportunities to expand habitat for spring-run Chinook Salmon and steelhead in the Upper Yuba requires fish connectivity to habitats currently blocked by dams, reservoirs, and operations of water control facilities. In lieu of actual dam removal, a successful reintroduction program requires construction of both upstream and downstream fish passage facilities that effectively attract and transport migratory salmonids. The Draft Recovery Plan (NMFS 2009) identified the Yuba River upstream of Englebright Dam as a primary area to reintroduce CV spring-run
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Chinook Salmon and CV steelhead. Implementing successful spring-run Chinook Salmon and steelhead reintroductions will require an evaluation of the relative importance of impacts to different life stages under alternate reintroduction strategies.
The consequences of a reintroduction strategy based on upstream and downstream connectivity at Englebright Dam could be evaluated within the framework of a total life-cycle model (see section 7). A full life-cycle model provides a framework to identify reintroduction benefits to recovery objectives and evaluate alternate connectivity strategies. A life-cycle model can also be used to evaluate the effects of variable conditions (e.g., wet/dry water year, El Niño/La Niña ocean conditions) on transition rates between life stages, in which various connectivity strategies reflect biological risks, uncertainties, costs, and constraints.
Estimates of the reproductive output and survival rates between life stages can be used to evaluate reintroduction strategies and the consequences on population growth. The habitat capacity modeling efforts recently conducted for the Upper Yuba (Stillwater Sciences 2013a) provide an estimate of potential productivity by sub-basin. A separate fish passage modeling component could be used to evaluate the potential survival of outmigrants passing through the Englebright reservoir and dam. Fish migrating through reservoirs must navigate through lacustrine-like, rather than riverine environments, avoiding predation and successfully finding downstream egress routes. Juvenile salmonid outmigration survival through a reservoir is affected by factors such as the size of the smolt, reservoir volume, reservoir refill rate, shoreline complexity, and the population of predators. Successful outmigration also depends on smolts finding and entering safe egress routes associated with downstream fish passage facilities. The size, type, and volume of downstream fish passage facilities affect the effectiveness of the facility and the proportion of outmigrants that pass through the facility versus passing downstream through spill. If fish are unable to find, or are reluctant to enter the downstream fish passage facility, they will pass downstream through spill or turbines, residualize, or be exposed to mortality through predation.
Integrating the results of a habitat capacity model with a fish passage model can provide estimates of the relative number and proportion of the population of juvenile salmon migrating downstream of Englebright Dam. A fish passage model can also be used to evaluate alternate fish passage facilities based on assumptions regarding their efficacy. In their review of Yuba River fish passage, MWH (2010) identified four potential downstream fish passage alternatives for Englebright Dam and three alternatives for NBBD. Fish passage alternatives that will attract and collect fish at different locations – and using different techniques – will affect the percent of fish safely passed downstream through each facility. Downstream migrating fish could be
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captured in the river upstream of the reservoirs or captured at FSCs in the forebay of each dam. Determining which fish passage alternatives provide the greatest opportunity to establish connectivity will be important to developing a successful reintroduction strategy.
In addition to evaluating alternate fish passage facilities at each dam, a fish passage model can also be used to evaluate the efficacy of different combinations of fish passage facilities. The order in which barriers are best removed (or remediated) will be affected by the order in which they occur, quantity and quality of habitat available behind each barrier, and the potential viability of restoring successful passage through each sub-basin.
Constructing upstream and downstream fish passage facilities at Englebright Dam, located at RM 23.9 on the Yuba River, would provide access to habitats in the NBB, SY and MY sub- basins. Although upstream habitats are affected by upstream dam releases and passage may be intermittent under current operations, fish passage facilities would provide access to these sub- basins. Under Dry Conditions, fish passage at Englebright Dam would provide access to 5.5 miles of suitable spring-run Chinook Salmon habitat (Table 3-2, Figure 8-1) and 39.5 miles of suitable steelhead habitat (Table 3-3) (Stillwater Sciences 2013a). However, this calculation assumes that upstream passage is also provided at Our House Dam at RM 12.5 in the MY sub- basin. In addition, 1.2 miles of mainstem habitat in the NBB sub-basin downstream of NBBD is assumed to be suitable for spring-run Chinook Salmon and steelhead holding and rearing, but not spawning because of a lack of suitable spawning substrates. Whether reintroduced fish could effectively establish populations in response to upstream and downstream fish passage at Englebright Dam under Dry Conditions depends on numerous constraints including the incremental survival of fish as they complete each phase of their life-cycle.
Using an upstream collection and transport facility from below Englebright Dam, adult spring- run Chinook Salmon and steelhead could be transported and released upstream of NBB Reservoir to spawn in the 34.7 miles of suitable spring-run Chinook Salmon habitat (Figure 8-2) and 78.2 miles of suitable steelhead habitat available in the NY sub-basin under Dry Conditions. Outmigrating smolts could be captured upstream of NBBD and transported and released downstream of Englebright Dam. This connectivity strategy connects Lower Yuba River populations with habitats in the NY; providing connectivity to the greatest quantity and quality of spring-run Chinook Salmon and steelhead habitat available in the Upper Yuba under Dry Conditions. Downstream transport of Chinook salmon and steelhead smolts has been used to reduce in-river mortality in the Snake River, Washington (Keefer et al. 2006); but study results suggest that juvenile transport reduced adult homing by 10 percent. While juvenile
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transportation has clear short-term survival benefits, the delayed effects manifested in adult stages illustrate the need to assess reintroduction success throughout the life-cycle.
Figure 8-1. Potential connectivity to spring-run Chinook Salmon habitats in the Upper Yuba basin under Current Conditions (i.e., Dry Conditions scenario [Stillwater 2013a]) assuming upstream and downstream fish passage facilities are implemented at Englebright and Our House dams.
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Figure 8-2. Potential connectivity to spring-run Chinook Salmon habitats in the North Yuba Sub-basin under Current Conditions assuming upstream fish passage facilities are implemented at Englebright Dam and downstream passage facilities are implemented above New Bullards Bar Dam. Adult spring-run Chinook Salmon collected below Englebright Dam will be released into suitable habitat above New Bullards Bar Dam, and juvenile outmigrants collected above New Bullards Bar Dam will be released below Englebright Dam.
8.2 DEVELOP OPERATIONAL REINTRODUCTION PLANS This section further elaborates on the subject of goals, objectives, and studies for each of three specific periods of the 3-phased reintroduction plan. The pilot reintroduction phase occurs over the first several years and focuses on obtaining the information to assess changes needed to increase the likelihood of successful reintroduction. Interim fish facilities are designed, constructed, and put into operation during this phase. The short-term reintroduction phase covers evaluations over the following 10 -12 years (3 to 4 generations) and focuses on evaluating population vital rates (survival, reproduction, migration) and passage performance. Advanced or
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permanent fish facilities are designed, constructed, and put into operation during this phase. Finally, the long-term reintroduction phase covers the subsequent 15 + years and focuses on improving performance of the fish passage system, understanding evolutionary and genetic factors, and evaluating long term viability of the reintroduced population.
General guidelines about the reintroduction process have recently been developed by McClure et al. (2011), and we use their framework for developing the phased planning approach to the reintroduction on the Yuba. The guidelines to reintroduction are somewhat general by design to cover a wide range of reintroductions in different areas of the Pacific Northwest; the authors developed it when faced with proposed reintroductions on the Columbia River. Yet, the McClure et al. (2011) guidelines provide a template that can be used to specify the important components of the planning approach. The McClure et al. (2011) framework is:
1. Establish goals, objectives, and potential benefits a. Goals (e.g., reducing extinction risk) b. Establish objectives that are measurable, time-limited, specific, and scientifically- based c. Potential benefits (e.g., abundance, productivity, spatial structure, and diversity) 2. Evaluate Biological Risks and Constraints a. Biological risks (e.g., disease transmission, mining source population, invasion, and straying) b. Constraints (e.g., barriers, habitat quality, out of basin factors, harvest, natural selection and genetic factors) 3. Execution 4. Monitoring
Multiple reintroductions have taken place over the last decade with the goal of either re- connecting previously separated populations (e.g., Pess 2009, Kiffney et al. 2009) or re- establishing new populations (e.g., SJRRP 2011). These two types of reintroductions may have different goals for reducing extinction risk and thus contributing to recovery of ESA listed salmon. The framework developed by McElhany et al. (2000) provides four dimensions that can be evaluated for understanding the viability of salmonid populations: 1) abundance, 2) productivity, 3) spatial structure, and 4) diversity. Through re-connection to previously blocked habitat, the population may expand into those habitats; therefore, increasing abundance of the existing population. If the habitats are higher quality than those that are currently inhabited, there may be an associated increase in the overall population productivity as well. In contrast, a reintroduction of previously extirpated population attempts to initiate a new population that is spatially distinct from existing populations; thus the goal is to improve the spatial structure of the
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ESU. As stated previously, the goal of the Yuba reintroduction is to improve the overall viability status for the Central Valley Spring-run Chinook Salmon ESU and California Central Valley steelhead DPS so they will sustain long-term persistence and evolutionary potential. The Yuba River reintroduction can improve the viability of the CV spring-run Chinook Salmon ESU by reducing the likelihood that a single catastrophe could affect all existing spring-run Chinook Salmon populations simultaneously (Lindley et al. 2007).
Due to the inherent uncertainties involved with salmon reintroduction planning, an important aspect of the reintroduction process is to ensure that actions early in the reintroduction can be used to inform decisions in later stages of the reintroduction. This process of learning over time will require careful planning, management oversight, and discipline to focus learning toward a finite set of key objectives. There are existing frameworks, such as adaptive management, that can provide informed decision making in light of uncertainty (e.g., Walters 1986). The adaptive management framework is a phased approach requiring several stages: 1) identifying competing hypotheses, 2) formalizing those hypotheses into specific models, 3) collecting data to test which of the competing models is best supported by the available data, 4) updating the hypotheses in light of the collected data, 5) reformulating hypotheses (or removing hypotheses that were not supported by the data), and 6) repeating the process. There are different types of adaptive management, namely passive and active adaptive management.
The process of identifying competing hypotheses, formalizing those hypotheses into specific models, and collecting data to test which of the competing models is best supported by the available data is the process of passive adaptive management (Walters 1986). In contrast, active adaptive management is the process by which specific objectives are identified by stakeholders, and management actions are tied to achieving those objectives a priori (Walters 1986). In either case, we recommend the process of hypothesis generation, hypothesis formalization into expected outcomes from an experiment, conducting the experiment, and reviewing the formalized hypotheses in light of the experimental results.
Finally, given the likelihood of stakeholder involvement in the Yuba reintroduction program, either active or passive adaptive management will provide a quantitative framework for systematically reducing the uncertainty in the reintroduction process. This approach can be particularly valuable for understanding how multiple, possibly competing, objectives such as hydroelectric generation and re-establishment of anadromy may be possible within the Yuba River (e.g., Keeney and Raiffa 1993).
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8.3 PHASE I: PILOT REINTRODUCTION EXPERIMENTS At the writing of this document, there are no Chinook salmon in the Yuba watershed upstream of Englebright dam. All of the statements about populations of spring-run Chinook Salmon and steelhead in the Yuba have therefore been based on historical distributions of Chinook salmon (Yoshiyama et al. 2001), potential for the Yuba to produce spring-run Chinook Salmon and steelhead (Chapter 6, Stillwater Sciences 2013a), and life-cycle modeling of Chinook population dynamics and dam passage (Chapter 7). As a result, it is important to understand what assumptions were made to help us arrive at our current understanding regarding the success of a spring-run Chinook Salmon and steelhead reintroduction, and suggest studies to determine if those assumptions are valid.
The pilot period is focused foremost on assessing whether there are biological or fish passage engineering issues that would cause the reintroduction to fail. Furthermore, the period of the pilot study is on the order of 2-3 years; therefore, studies will need to be completed in this period with a high success of providing the needed information. For some questions, a binary response (yes/no) may suffice. This is a desirable property, because statistical power increases when inference is limited to a binary outcome as compared to estimating a value (Casella and Berger 2002). For this reason, the goals of the pilot experiments are stated to provide inference at the binary level.
The results of the Yuba life-cycle model indicated that establishing self-sustaining populations on the MY, SY, or NBB would be difficult under existing conditions, Scenario D (Dry Conditions, with no additional instream flow supplementation) (Chapter 7); therefore, early reintroduction experiments could be focused on the North Yuba as a logical first step, where model results (Chapter 6, Chapter 7) indicate that a reintroduction under existing conditions could be successful. Still, assuming that flow augmentation could be provided, there are benefits in understanding how adult and juvenile Chinook salmon travel through the Englebright Reservoir, and whether successful passage can be accomplished upstream of Colgate powerhouse. Thus, understanding the conditions necessary for a successful reintroduction on the MY, SY, and NBB could proceed once either USFS 4(e) or NMFS 10(j) flow augmentation was implemented, or if experimental flows were intentionally released from dams in the upper sub- basins to simulate these flows that would likely occur during a reservoir transit study sequence.
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8.3.1 Goals and Objectives The goal of the pilot reintroduction experiment is to assess the viability of spring-run Chinook Salmon and steelhead reintroductions to the North Yuba and above Englebright Dam. Experimental objectives include:
Further assessment of habitat and fish passage conditions in the Yuba River (not already completed) to support a reintroduced spring-run Chinook Salmon and/or steelhead population.17
Conduct experiments with test fish in the upper Yuba River basin to assess suitable habitat by spawning, incubating, and rearing life stages.
Develop a set of testable hypotheses regarding habitat utilization, fish passage efficiency, and survival.
Identify what type of juveniles will be produced in the system and how they behave in response to hydrologic conditions and flow events.
8.3.2 Critical Elements
Can adults that originated elsewhere find spawning habitat above Englebright Dam or in the North Yuba? Are flow alterations needed to promote acceptable passage conditions in the SY, MY, and NBB reaches?
Do spawning salmon/steelhead utilize habitats consistent with the riverine model?
Will spring-run Chinook Salmon utilize the reservoirs as cold water holding habitat prior to ascending to spawning areas in the fall? Will early arriving steelhead also make use of reservoir habitat prior to spawning?
What riverine habitats are utilized for spawning, and when?
Will juveniles rear and survive in the Upper Yuba basin?
What riverine habitats are utilized for rearing?
When do out-migrations occur and what percentages of juveniles at various life stages are moving during storm events?
Do juveniles of different life stages predominantly rear in the river or reservoirs prior to reaching collection stations for outmigration?
17 upper Yuba River habitat assessment studies have been conducted by the Yuba Salmon Forum’s Technical Advisory Team, and modeling and habitat study has been conducted as part of the FERC relicensing processes for Yuba-Bear, Drum-Spaulding, and Yuba River Development.
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What type of fish passage devices (singular or multiple) and collection systems can be employed to successfully capture juvenile salmon/steelhead in tributary environments and where?
8.3.3 Studies Studies would be undertaken to address the critical elements. Using preferred brood stock for pilot reintroduction, experiments could consist of:
Adult Ability to Find Habitat and Spawn
Radio-tagging adults (assuming spring-run Chinook Salmon, steelhead, or surrogate species adults are available to outplant to suitable habitats above Englebright Dam and/or NBBD) to track their distribution and verify adult passage near blockage points and hydropower discharges and at suspected low flow barriers; and use results to evaluate potential effects of Alternative Management Scenario flow releases on fish passage. For instance: o Verify estimated suitability and distribution of holding, spawning and rearing habitats developed using RIPPLE model. o Identify the volitional distribution of adult spring-run Chinook Salmon and/or steelhead (or surrogates) among suitability and availability of upstream habitats.
Radio-tracking of adults to assess their movement above Englebright reservoir. Some potential questions to be addressed are: o Will fish be able to migrate up to Our House Dam and surmount an identified barrier at RM 0.4 on the Middle Yuba? o Will adults leave cold-water releases from Colgate in the mainstem Yuba to migrate up the relatively warmer South Yuba? o Is flow balancing or hydraulic buffering feasible in the Colgate reach? What hydropower peaking operations can be acceptable in this reach to allow satisfactory access and fish productivity upstream? Are there operational procedures or structural modifications (e.g., balancing of flow rates and hydraulic characteristics) that can accommodate safe and effective fish passage? o Will adults hold in Englebright reservoir during the warm summer months and migrate into tributaries in the fall? o Will adults be able to migrate into the sub-basin above Poorman Creek (RM 28) on the South Yuba where there will be suitable holding temperatures and habitat in most years?
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o How will different flow from tributaries affect attraction into each? Will experiments include experimental attraction flow releases (i.e., pulse flows) to assess the ability to promote upstream and downstream migrations?
Radio-tracking of adults to assess their movement in New Bullards Bar reservoir. Some potential questions to be addressed are: o Can adults that are released upstream of New Bullards Bar Dam migrate into the North Yuba to find suitable holding and spawning habitat in dry water years? Is adult release at the NBBD forebay a viable option, or do fish need to be transported further upstream? o Do adults that are released in the North Yuba fall back into the reservoir? Do they subsequently return to the North Yuba to spawn?
If adult salmon are reintroduced (1) above Our House Dam on the Middle Yuba, how far upstream will they be able to migrate? If adult salmon were transported up as far as (2) Milton Dam in the Middle Yuba to avoid warm temperatures in dry years, would they hold in the colder water and later fall back downstream to suitable spawning habitat in autumn?
If adult collection and transport to the South Yuba is considered for spring Chinook salmon (given the stipulation that supplemental flows would be provided in below average water years), what are candidate release locations upstream? If adult salmon are transported to those locations, will they be able to hold and migrate to identified spawning areas successfully? If adult steelhead are released above Englebright Dam during winter months, will they successfully migrate and locate spawning grounds in the South Yuba, New Bullards Bar reach, Oregon Creek, or lower Middle Yuba River?
If passage directly above Englebright Dam is considered for either (or both) spring-run Chinook Salmon and steelhead, would these fish attempt to enter the South Yuba River instead?
Conducting spawning surveys for introduced adults: o Redd counts and carcass counts for distribution.
Juvenile Emergence, Rearing, and Collection
Deploy egg boxes and fry traps into sub-basins with expected adult production to estimate incubation survival in areas identified as high quality habitat as well as areas identified as marginal quality habitat.
Assuming spring-run Chinook Salmon, steelhead, or surrogate species eggs or fry are available to outplant to suitable habitats above Englebright Dam and/or NBBD, electrofish habitats (or devise other means of monitoring) following outplanting to assess
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spring-run Chinook Salmon and/or steelhead (or surrogates) survival when planting into habitats with existing resident populations of rainbow, brown and brook trout. Use results to evaluate alternate outplanting strategies.
Snorkel or electrofish habitats and quantify density of smolts over time to verify production potential density estimates (i.e., RIPPLE model assumption of smolts per square meter), and estimate survival from egg deposition to juvenile migration.
Collect downstream migrants using screw traps to confirm the proportion of each juvenile life history type (e.g., efry, smolt0, smolt1), size-frequency, and outmigration timing.
Collect downstream migrants using screw traps while recording antecedent flow conditions to develop a relationship between juvenile migration patterns and flow. This information will be needed to evaluate the potential fish guidance efficiency flow for downstream collection and transport facilities located immediately upstream of Englebright or NBB reservoirs.
Collect downstream migrants using screw traps installed above Englebright or NBB reservoirs, insert biotelemetry tags, and track downstream migration progress through Englebright and NBB reservoirs. Alternatively, implant outmigrating smolts either captured at Daguerre Point Dam or obtained from the FRFH, with radio-tags and released upstream of Englebright or NBB reservoirs where they may continue their downstream migration. Macro-scale monitoring can identify outmigrant behavior through the reservoirs under Dry Conditions of flow and dam operations.
Fish Passage Evaluation Study a. Convene a fish passage technical panel to estimate the fish guidance efficiency (FGE) and survival of alternate upstream and downstream fish passage facilities at Englebright, New Bullards Bar, and Our House dams. These estimates will only represent educated opinions of the panel; however, they can be used to identify critical assumptions/data gaps regarding timing, size and behavior of migrating spring-run Chinook Salmon and steelhead (or surrogates). b. Using the Panel’s estimates of FGE and survival, develop a spreadsheet-level fish passage model that evaluates tributary and reservoir passage, collection/turbine/spillway guidance and survival under wet, average and dry years for spring-run Chinook Salmon and steelhead (or surrogates) life stages. c. Develop and prioritize alternate connectivity scenarios and quantify the potential contribution to habitat expansion available under each connectivity scenario. For instance, compare the relative performance of a downstream collection and transport facility at the head of a reservoir to an FSC located in the dam forebay under wet, average, and dry water years. These results can be used to identify and prioritize
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uncertainties and potential data gaps related to habitat expansion into the Upper Yuba River. d. Examine in-reservoir predation. e. Identify sites for locating facilities to capture downstream migrants.
f. Devise a biological and engineering protocol for downstream steelhead smolt collection.
8.3.4 Utility of Information The utility of the pilot period is to identify limiting factors in the assumed production potential of the system. In evaluating the likelihood of a successful reintroduction (Chapters 6 and 7), we have assumed that the spring-run Chinook Salmon and steelhead populations would be capable of production at a particular rate. This is dependent on the quality of the habitat and the ability of spring-run Chinook Salmon and steelhead to utilize this habitat for producing offspring. First, the information obtained at the end of the pilot study should be able to identify any factors that would affect the assumed locations of production, i.e., validate habitats identified as suitable under the RIPPLE model and other habitat assessments. The studies outlined above will provide information by indicating whether there are any fatal flaws to certain reintroduction strategy alternatives. Thus, they indicate what critical assumptions will cause the reintroduction to fail in the short term. Some examples of such results would be:
Tagged adults do not find suitable spawning habitat successfully;
Egg survival in sub-basins targeted for reintroduction is extremely low; and
Juveniles cannot successfully outmigrate to hypothesized collection locations. Second, the pilot studies should be designed so that they provide initial estimates of important biological rates for the life-cycle models. For example, estimates of egg survival and fry emergence rates can be used for relating spawner abundance to the fry production parameter
(Ffry, Chapter 7). Furthermore, if abundance estimates of juveniles are obtained at juvenile collection locations (e.g., using rotary screw traps with estimates of trap efficiency on the North Yuba or a temporary surface collector in Englebright Reservoir), these data can be used to estimate the juvenile production per spawner and the distribution of juveniles of different stages. Such estimates can be incorporated directly into the life-cycle model via the efryP (proportion of fry migrating as efry) and smolt0P (proportion of fingerlings in the stream that migrate as sub- yearlings).
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During the pilot experimentation phase, concurrent investigations should begin to test and develop fish facility designs and assumptions as described earlier in section 4.4 Phased Passage Facilities.
8.4 PHASE II: SHORT TERM REINTRODUCTION PLAN IMPLEMENTATION WITH ADAPTIVE MANAGEMENT The goal of the short-term reintroduction is to understand how the vital rates (i.e., fecundity and survival) and the passage efficiencies (collection rates, transportation survival, etc.) will lead to a self-sustaining population on the Yuba River. The short-term period focuses on rates, because there is a trade-off between production of juveniles and the collection and survival rates that a particular cohort can sustain. In short, when the mortality rate becomes too high, the population cannot sustain itself.
The production potential model (Chapter 6), the life-cycle model (Chapter 7) and an evaluation of the possible source stocks (Chapter 5) have provided an initial assessment of the Yuba reintroduction. Furthermore, by explicitly stating the assumptions that were used to model the reintroduction process, we have quantified the biological rates and passage parameters necessary to establish a self-sustaining population. Initial estimates of these rates were used to construct the life-cycle model of the Yuba population (Chapter 7); therefore, studies during this phase should determine whether the rates are consistent with the assumptions in the life-cycle model. In addition, the studies implemented during this period should be capable of evaluating alternative configurations of the reintroduction to identify options that will provide the greatest potential for success. We provide an example of how this can be accomplished in a case study below.
8.4.1 Goals and Objectives
The goal is to understand how the vital rates (i.e., fecundity and survival) and the passage efficiencies (collection rates, transportation survival, etc.) will lead to a self-sustaining population.
The objectives are to: o Verify that the Yuba production is consistent with the rates assumed in the production potential model (Chapter 6) o Verify that the survival rates through reservoirs and in tributaries are consistent with the assumed rates in the life-cycle model (Chapter 7) o Estimate the collection efficiency and transport survival for tributary collectors and FSCs
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o Quantify the effects of out of basin factors (e.g., delta survival, ocean conditions, and harvest) on fish produced in the Yuba River
8.4.2 Critical Elements
Production Potential
What are the levels of juvenile production per spawner?
Can returning adults that originated from fry releases find spawning habitat?
What are the dominant life history stages of juvenile migrants (fry, sub-yearling, and yearling)?
What levels of residualization are expected?
Englebright Dam Passage
Can the SY, NBB reach, Oregon Creek, and MY and provide opportunities for reintroduction if suitable passage, flows, and habitat restoration is provided? Which tributary route will fish choose if released at the forebay of Englebright Dam? Once above Englebright Dam, will spring-run Chinook Salmon and/or steelhead attempt to colonize all accessible stream reaches?
Can the NBB sub-basin provide enough holding, spawning, incubation, and rearing habitat to sustain a population? What level of instream flow and spawning gravel supplementation will be needed to improve the habitat conditions in the NBB sub-basin enough to warrant reintroduction above Englebright Dam?
What is the predation risk in Englebright reservoir? Will piscivorous predators (by species) be actively feeding during colder seasons when outmigrations would be occurring?
What is the guidance efficiency, fish passage scheme, and fish passage route at Englebright Dam under alternate flow conditions?
What operational protocol and instream flow releases could allow migrating fish to enter the New Bullards Bar reach and remain to successfully spawn? Similarly, what instream flows will allow successful egg incubation and early life stage rearing, followed by successful outmigration of juveniles?
New Bullards Bar Reservoir Passage
What is the predation risk in NBB reservoir? Will piscivorous predators (by species) be actively feeding during colder seasons when outmigrations would be occurring?
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What is the guidance efficiency and passage route at NBB Dam under alternate flow conditions or water years?
What is transit time (and rate) of fish released at the head of the reservoirs to a downstream detection point near the dams?
Can reservoir guidance systems provide flow cues that outmigrating salmonids could use to guide to a collection station at NBB Dam?
Passage Topics
Where should downstream migrant collectors be located? What hydraulic and temperature patterns will affect efficiency of collectors? Are there seasonal and diurnal cycles that affect the design and capacity of fish facilities?
What is the feasibility of constructing and operating fish collection facilities (upstream and downstream) at several potential locations? Do benefits warrant the costs? o What variables would affect collection efficiency and to what extent at each of these locations?
What are the effects of handling and transport stress on survival of target life stages?
What state-of-the-art technology can be employed to minimize stress throughout the collection, handling, transport, and release cycle? What type of transport and acclimation facilities are necessary?
How do hydraulics and temperature differentials upstream and downstream of the Colgate powerhouse discharge affect fish passage? What flow split changes would lead to conditions conducive to satisfactory fish passage? Combine this hydraulic analysis with passage studies using radio-tagged fish. Identify operational protocol that would allow peaking operations and still result in acceptable passage conditions. If necessary, use engineering analysis to devise means to moderate hydraulic extremes, or otherwise improve passage conditions, in the area of the Colgate tailrace discharge.
Genetic Issues
What is the performance difference between different brood stocks in terms of smolt to adult return rates?
In terms of genetics and disease, what stocks should be used?
What are the conservation genetic concerns with reintroducing steelhead above dams and how could those be addressed?
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Resident Fish
What are the competition, predation, and genetic effects of anadromous fish production on resident communities?
What future stocking practices are compatible with reintroduction of anadromous fish?
What are the fish disease/pathology concerns in the Upper Yuba River basin and how will those concerns be addressed?
Management/Implementation
How will juvenile productivity in the areas targeted for reintroduction be measured?
What are the magnitude and nature of the potential benefits of a reintroduction that will be used to evaluate success and to compare the relative value of different reintroduction locations and methods? (e.g., abundance, productivity, spatial structure, diversity metrics);
What are realistic time frames for accruing benefits?
What is the duration and biological sequence of studies and reintroduction actions?
What is the timeline and appropriate sequence for studies and reintroduction actions to inform stakeholders and to secure necessary funding and support?
How will fish facilities be incorporated into the reintroduction program? Can interim fish facilities be designed and constructed to allow for early experimentation and validation of concepts, before investing in long-term facilities? What is the proper schedule and sequencing of fish facility development?
What regulatory permits are required? What will be the ESA-status of reintroduced species? Can regulatory programs support reintroduction efforts effectively?
What level of support is required of hydropower and dam operators to make reintroduction scenarios successful? What is the cost of reintroduction in terms of any lost electricity generation or lost water supply? Who will be affected? How can costs be reduced to the maximum extent practicable?
8.4.3 Studies Experiments could consist of:
Stock selection experiments, e.g., spawning success or rearing success from different source populations.
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Constructing temporary collection facilities (upstream and downstream) to test their efficacy using tagged adults (upstream – looking at rates of fall back) and juveniles (downstream).
Developing abundance estimates using screw trap mark recapture experiments (Bonner and Schwarz 2011).
Survey the adult populations (e.g., counting redds, conducting carcass surveys, etc.).
Estimate juvenile production per adult spawner using estimates of spawner populations and estimates of juvenile abundances as described above.
Conduct surveys of resident fish simultaneously to understand changes in abundance of resident communities with increased reintroduction efforts.
Conduct a fish health study
Conduct genetic studies of resident O. mykiss in target areas (below dams we have fish that are of hatchery origin and were derived from out of basin or have ancestors from out of basin resulting in a hybrid stock with uncertain fitness and origin; above the barriers there may be a fairly genetically pristine population of resident O. mykiss that are going to have a fairly high level of success and reproductive fitness and are most representative of the ancestral genetic composition of CV O. mykiss).
Conduct studies to determine whether juveniles successfully navigate Englebright and/or New Bullards Bar Reservoirs to the dams where a potential collection facility (e.g., incline plane trap) could be located; and determine the mortality rate? To provide cost- effective estimates of mortality rate a combination of acoustic tagging and CWT tagging could be used. o Tag smolts and recover at Englebright Dam o Tag smolts and recover at NBB Dam
Conduct predation studies in reservoirs
Assuming stakeholder involvement in modification of flows could be incorporated into the reintroduction process, evaluate modifications of flows on habitat in SY, MY, Oregon Creek, and NBB for understanding flow related improvements in habitat conditions. o Release fry into sub-basins under different flow scenarios and monitor production o Track radio tagged adults during upstream migration at critical junctions like the identified “partial barriers” in SY, MY, Oregon Creek, and New Colgate powerhouse. o Track radio-tagged adults for evaluating passage success/failure at specific natural low-flow barriers that support candidate reintroduction alternatives. Some sites
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for possible study are on the SY, MY, Oregon Creek, Canyon Creek, Lavezzolla Creek.18
8.4.4 Utility of Information The studies in this phase of the reintroduction program are targeted at quantifying the rates at which potential production can be converted to juveniles outmigrating from the system. As a result, the studies should be focused on understanding where the system can become more efficient to maximize the likelihood that the production potential can be converted to smolts leaving the study area. Furthermore, this phase should provide guidance for the construction of passage facilities, i.e., where they should be located and how they should be operated to realize the production potential.
Studies in this period will be used to parameterize and refine hypotheses regarding the range of expected performance of the system from adults captured at the downstream end to outmigrant juveniles.
In addition, this period should identify the likely limitations to production. For example, is collection efficiency at the dam or reservoir survival responsible for low numbers of outmigrating smolts?
The results of the studies in this period should be used to parameterize a population dynamics model to identify the size and extent of supplementation needed to initiate the reintroduction program. The model can be used to determine the duration and level of supplementation needed for the reintroduction.
Studies should address fish pathology concerns that may affect which life stages are used for studies and reintroductions.
Finally, studies should address conservation genetics issues when reintroducing steelhead above dams. There are many questions to be answered during the short-term period due to the number of alternative ways in which the reintroduction could take place. For example, there are many options along different decision axes, such as: 1) which life stages will be reintroduced; 2) which stream sub-basins will be targeted for reintroduction; 3) which collection methods will be employed for which life stages; and 4) where study sites will be located for monitoring and collection. During this period, understanding how studies can be used to inform decisions on each of the various dimensions of the reintroduction will be invaluable.
18 For references to locations of these natural stream features, see MWH (2010), Section 3-Fish Habitat, p.6-10; and, Addley et al. (2011-12), technical memorandum, field studies for Yuba Salmon Forum Technical Work Group.
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While we cannot detail all of the possible combinations of studies, their outcomes and subsequent actions at this point in time, we can provide an example of how studies can be used with life-cycle modeling for resolving a specific question. The question that we have chosen to use as a case study is the possibility of implementing an FSC versus a tributary collector for juvenile collection on the North Yuba sub-basin.
We previously used the life-cycle model to estimate what ranges of NBB reservoir survival rate could potentially lead to a self-sustaining population on the North Yuba. We found that the survival rates through the reservoir would need to be at least 15% for efry, 30% for smolt0, and 45% for smolt1 in order to have a self-sustaining population in 77.4% of the model trajectories. For the purpose of illustration, we set the sub-yearling migrant reservoir survival threshold at 30%. Thus, if the reservoir survival rate is greater than or equal to 30% for sub-yearling migrants, it would be possible to use an FSC at New Bullards Bar Dam. The 30% reservoir survival rate would lead to a self-sustaining population (CRR > 1) on the North Yuba.
The two hypothetical actions that are awaiting study results are: 1) build an FSC if the survival rate is greater than or equal to 30% versus 2) build tributary collector(s) if the survival rate is less than 30%. Note that there could still be other reasons to prefer tributary collector(s) even if the survival rate was found to be greater than the threshold rate, but for the purposes of illustration we will simplify the decision as being dependent upon the results of the reservoir survival studies. While not strictly an adaptive management approach, we use several of the steps in adaptive management to complete the analysis.
The steps to the process as applied to this decision are:
Identify Competing Hypotheses 1. Hypothesis 1: the survival rate of juveniles in NBB is greater than or equal to 30% 2. Hypothesis 2: the survival rate of juveniles in NBB are less than 30%
We also set up a decision matrix to show how one might develop a way of evaluating two different actions in relation to the unknown state of nature, which is the reservoir survival (Table 8-1). While this is a trivial example, these action tables can become more complex as the set of actions become continuous (e.g., setting of flow rates) and the states of nature are multivariate (Walters 1986).
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Table 8-1. Probability of a self-sustaining population under hypothetical states of nature and passage alternatives. Passage Alternative State of Nature Tributary Collector Dam Forebay Surface Collector < 30% survival 1 0.5 > 30% survival 1 1
Note that if we were risk averse, we would simply build the tributary collector, because the modeled probability of a self-sustaining population is 1 under either state of nature. Yet, there may be important reasons for building the surface collector that are not included in the table, such as collection efficiencies, capital cost, debris issues, or additional flexibility with hydrologic operations. This could be captured in a different metric than the one used in Table 8-1; namely, a metric that expressed the loss in value from constructing a tributary collector when in fact reservoir survival was greater than 30%. Still, we continue with the example with the goal of learning about which state of nature is present in the NBB reservoir, as this will affect the decision of which passage alternative to pursue in our hypothetical example.
We design and conduct a study where we acoustically tag 100 fish and evaluate their ability to reach the dam. The relationship of the reservoir survival rates to the decision on which passage alternative can be presented graphically with regions of survival supporting different passage alternatives (Figure 8-3).
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Formalizing the Hypotheses into Specific Models 1. Under hypothesis 1, if 100 fish are tagged, released, and collected at NBB Dam we would expect to collect 30 fish or more on average 2. Under hypothesis 2, if 100 fish are released and collected at the dam we would expect to collect less than 30 fish on average
Under this case study, the formalizing of hypotheses step (although trivial here) is used to translate the hypotheses into predictions of something that can be observed. The role of sample design enters into this step and the next step of the process, because it determines the quality of the data that will be used to differentiate among the competing hypotheses.
Collect Data to Test which of the Competing Models is Best Supported We run the experiment and obtain the information that the mean survival rate is 28% with a 95% confidence interval (CI) of 19.5% to 37.9% (Figure 8-4). The definition of a 95% confidence interval is that if we repeat the experiment many, many, times then this interval will have the true value in it 95% of the time (Casella and Berger 2002).
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Figure 8-4. Graphical display of passage alternative related to reservoir survival after conducting an experiment with 100 fish.
Update the Hypotheses in Light of the Collected Data The results suggest that the survival rate may be less than 30%. Yet, the 95% CI contains the value 30%, suggesting that survival rates greater than 28% may also be probable given the
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observed data. Under a hypothesis-testing scenario, the null hypothesis that the survival rate is greater than 30% cannot be rejected (p-value = 0.70, exact binomial test).
Reformulate Hypotheses (or Remove Hypotheses That Were Not Supported by the Data) There is some indication that the survival rate may be below the target threshold; however, we do not have conclusive evidence that the survival rate is less than 30% as a result of running our first experiment in the hypothetical example. We would want to collect additional information with greater sample size to be able to make a better estimate of the survival rate through the reservoir.
Repeat the Process We increase the sample size to have greater statistical power to discriminate between the two competing hypotheses. We will run the experiment again, and this time we decide to release more fish so that the results may be more clearly interpreted. For example, we could use Passive Integrated Transponder (PIT) tags with a temporary collector installed at the NBB Dam. Thus, for the second experiment, the study consists of releasing 1000 fish.
We find that there were 255 fish collected from the second experiment. The mean survival rate is 25.5% with a 95% CI of 22.8% to 28.3%. We can test the null hypothesis that the survival rate is 30%, and reject this null hypothesis (p-value = 0.0019, exact binomial test). We can update the graphical display with this information (Figure 8-5).
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Figure 8-5. Graphical display of passage alternative related to reservoir survival after conducting an initial experiment with 100 fish and a second experiment with 1000 fish.
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Given the results of the two studies we would have some information supporting the hypothesis that the survival rate through the reservoir was less than 30%. If needed, we could conduct the second experiment another time to provide a more accurate estimate of the survival rate through the reservoir (Figure 8-6). In the third experiment 260 fish are collected of 1000 released. The mean survival rate for the third experiment is 26.0% with a 95% CI of 23.3% to 28.8%. We can test the null hypothesis that the survival rate is 30%, and reject this null hypothesis (p-value = 0.0057, exact binomial test). In addition we would have three estimates of the survival rate through the NBB reservoir by conducting the studies.
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Figure 8-6. Graphical display of passage alternative related to reservoir survival after conducting an initial experiment with 100 fish, and a second and third experiment with 1000 fish each.
8.5 PHASE III: LONG TERM REINTRODUCTION PLAN IMPLEMENTATION WITH ADAPTIVE MANAGEMENT
8.5.1 Goals and Objectives
Develop a management and operations framework that will enable the reintroduction program to cease supplementation as the population continues in a self-sustaining manner.
Determine how to enhance localized natural recruitment and improve production
8.5.2 Critical Elements
What are the collection facilities needed for a self-sustaining population?
Where should collection facilities be located and how should they be operated to meet the required collection and survival efficiencies for a self-sustaining population?
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What are the most appropriate colonization methods: hatchery supplementation vs. transplanting? What is the time frame for supplementation, if used?
How does the reintroduced population interact with other spring-run Chinook Salmon and steelhead populations? Is it a source or sink in the overall population structure?
How could productivity be enhanced via the potential benefits of habitat restoration (woody debris, gravel augmentation, channel maintenance flows, fish passage facility and systems operations improvements, etc.)?
8.5.3 Studies Studies to address these topics could include:
Monitoring of adult returns relative to juvenile outmigrants of the brood year via CWT or PIT tagging to identify specific cohorts.
Genetic identification of returns to understand who is straying into the Yuba collection facility versus who originated within the Yuba. This information may help identify the inherent production within the Yuba basin versus straying into the basin from other populations.
Otolith microchemistry of returning adults, which would provide information on where fish from the Yuba are rearing after leaving the system. While not directly linked to the production in the Yuba, it would provide information on where spring-run Chinook Salmon and steelhead are rearing in the system.
8.5.4 Utility of Information The information during the long term period would provide opportunities for understanding how the Yuba population was performing relative to other Central Valley spring-run populations. For example, determining how the Yuba population co-varies with the Butte Creek and with the Mill and Deer Creek population (Lindley et al. 2007). This would provide an indication of the degree to which the Yuba population was independent, and therefore providing a reduction in extinction risk through an additional, independent population.
Forecast the long-term sustainability of the reintroduction given production, collection and passage efficiency, outmigration survival, ocean survival, and adult escapement.
Identify the time to self-sustainability when supplementation could cease.
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8.6 HOW TO INCORPORATE ADAPTIVE MANAGEMENT INTO THE PHASES OF THE REINTRODUCTION Adaptive management at its core is a system for evaluating the value of constructing probing experiments for obtaining knowledge about the system relative to the value of allowing the system to run efficiently (Walters 1986). In much of Walters’ (1986) applications, adaptive management was applied to population dynamics of salmon stocks under harvest. Thus, a frequent management tool was to modify harvest as part of the probing experiments. Walters (1986) is quick to point out that too much probing could lead to poor stock performance from a catch perspective, thus potentially harming the revenues to the fishing industry.
In our application, there is also a trade-off between perturbing the system to learn about it relative to maximizing the establishment of the population and allowing it to run as efficiently as possible. This “probing” as it is described by Walters (1986) comes at a cost. In other words, the reintroduction may reach greater abundances in a shorter time period without adaptive management and probing experiments. For example, there may be opportunities to shift production among sub-basins to learn about the carrying capacity of those sub-basins. In order to learn about the carrying capacity of a sub-basin, that carrying capacity must be exceeded. It must be surpassed so that different numbers of spawners (or in the case of supplementation, fry outplants) produce equal numbers of juveniles. It is this number of juveniles that defines the carrying capacity. As a result, any juveniles that were produced above the carrying capacity will not survive due to spatial constraints; they became a cost to learning about the carrying capacity. The cost could be calculated in terms of their ability to survive elsewhere, had they not been part of an experiment that crowded them into a sub-basin with the express intent of exceeding capacity.
A life-cycle model that is capable of expressing uncertainty is an important step in being able to understand the value of information over time, which is an important component to adaptive management. The life-cycle model has many parameters that are defined using existing scientific knowledge based on other systems, but little information that is specific to the Yuba basin. However, as additional information is collected on different rates in the Yuba, a life-cycle model can become a more accurate depiction of the relative benefits of different probing experiments. For example, in attempting to learn about the carrying capacity of a specific sub- basin, the cost to performing such an experiment could be valued by using the life-cycle model. Two future states of the population could be modeled: 1) not performing the experiment and managing the reintroduction without the carrying capacity information; and 2) performing the experiment (and incorporating the lost productivity) along with managing the system with the carrying capacity information in hand. The performance of the population without conducting
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the experiment could then be weighed against the performance of the population once the information on carrying capacity was obtained by comparing their abundances or productivity levels (e.g., CRR).
Over the course of the three phases, much information will be collected with the goal of increasing the probability of a successful reintroduction. The use of adaptive management provides a feedback loop by which such information can be used to improve decision-making. In this way, the use of adaptive management can lead to application of resources in an efficient manner, because the costs associated with experiments are evaluated as part of the process (Walters 1986). As a result, experiments that have low information content or low importance, but may be costly in terms of dollars or foregone production, can be given lower priority to those experiments that can justify their costs.
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Voight, H.N., and D.B. Gale. 1998. Distribution of fish species in tributaries of the lower Klamath River: an interim report, FY 1996. Technical Report, No. 3. Yurok Tribal Fisheries Program, Habitat Assessment and Biological Monitoring Division.
Walters, C. l986. Adaptive management of renewable resources. International Institute for Applied Systems Analysis. New York, NY: Macmillan Publishing Co.
Waples, R.S. 1991. Genetic interactions between hatchery and wild salmonids: lessons from the Pacific Northwest. Can. J. Fish. Aquat. Sci. 48 (Suppl. 1): 124-133.
Ward, P.D., and T.R. McReynolds. 2001. Butte and Big Chico creeks spring-run Chinook Salmon, Oncorhynchus tshawytscha, life history investigation 1998-2000. Inland Fisheries Administrative Report No. 2001-2. California Department of Fish and Game, Sacramento Valley and Central Sierra Region, Rancho Cordova, California.
Ward, P.D., T.R. McReynolds, and C.E. Garman. 2003. Butte and Big Chico creeks spring-run Chinook Salmon, Oncorhynchus tshawytscha, life history investigation 2001–2002. Inland Fisheries Administrative Report. California Department of Fish and Game, Sacramento Valley and Central Sierra Region, Rancho Cordova.
Ward, P.D., T.R. McReynolds, and C.E. Garman. 2004. Butte and Big Chico creeks spring-run Chinook Salmon, Oncorhynchus tshawytscha, life history investigation 2002–2003. Inland Fisheries Administrative Report No. 2004-6. California Department of Fish and Game, Sacramento Valley and Central Sierra Region, Rancho Cordova, California.
Ward, P.D., T.R. McReynolds, and C.E. Garman. 2006. Butte Creek spring-run Chinook Salmon, Oncorhynchus tshawytscha, pre-spawn mortality investigation 2004. Administrative report no. 2006-1. California Department of Fish and Game, Inland Fisheries, Sacramento, California.
Washington Group International (WGI). 2006. Upper Baker River Downstream Fish Passage Facilities – Floating Surface Collector Draft Design Memorandum. Prepared for Puget Sound Energy.
Yuba County Water Agency (YCWA). 2010. Yuba River Development Project, FERC Project No. 2246, Pre-Application Document. Marysville, CA http://www.ycwa-relicensing.com
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NMFS Upper Yuba River Anadromous Salmonid Reintroduction Plan
YCWA. 2011. Study 1.3 North Yuba spawning habitat evaluation. Prepared by YCWA, Marysville, California.
YCWA. 2012. TECHNICAL MEMORANDUM 3-7: Reservoir Fish Populations. Yuba River Development Project, FERC Project No. 2246. September, 2012.
Yoshiyama, R.M., E.R. Gerstung, F.W. Fisher, and P.B. Moyle. 1996. Historical and present distribution of Chinook salmon in the Central Valley drainage of California. Pages 309– 362 in Volume III: Assessments, commissioned reports, and background information. Sierra Nevada Ecosystem Project: final report to Congress. University of California, Center for Water and Wildland Resources, Davis, CA
Yoshiyama, R.M., F.W. Fisher, and P.B. Moyle. 1998. Historical abundance and decline of Chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18:487–521.
Yoshiyama, R., E. Gerstung, F. Fisher, and P. Moyle. 2001. Historical and present distribution of Chinook salmon in the Central Valley drainage of California. Found in: Contributions to the Biology of Central Valley Salmonids. Fish Bulletin 179. Volume 2. Sacramento, CA.
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APPENDIX A
Life-Cycle Model Parameters
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APPENDIX A – LIFE-CYCLE MODEL PARAMETERS
A.1 BIOLOGICAL PARAMETERS The production of juveniles uses parameter values that are taken from the RIPPLE model. This ensured that the life-cycle model results were consistent with the production potential as calculated by the RIPPLE model. The RIPPLE model did not incorporate uncertainty in their modeling; therefore, the juvenile production used in the life-cycle model also did not incorporate uncertainty. The SAR rates also did not incorporate uncertainty. These rates are provided primarily to convert the juveniles leaving the system into adults returning to spawn 3 to 4 years later. While adding uncertainty to the SAR would provide information on how many of the model trajectories were likely to go extinct, it would make inference on the passage and hydrologic scenario evaluations more difficult. Adding uncertainty to the SAR essentially adds white noise to the model results, which obscures the information on system performance. Instead, we chose to construct a period of lower SAR to stress test the populations as described in Chapter 7.
On average, the RIPPLE model assumes that there are 4,392 eggs per female, which equates to 2,572 eggs per spawner if females are not being modeled explicitly (Cavallo et al. 2009, Stillwater Sciences 2013a). These values were derived from the proportions of spring run that return at ages 2 to 5 to the FRFH (Cavallo et al. 2009), the sex ratio for each age of returns (Cavallo et al. 2009), and the fecundity per female at ages 2 through 5 (Stillwater Sciences 2013a). Stillwater Sciences (2013a) defined the egg to fry (swimup) stage survival as 0.76 for the NY, MY, and NBB, whereas it is 0.54 for the SY. Therefore, the value Ffry (fry per spawner) is 1,955 for the NY, MY, and NBB and 1,389 fry per spawner on the SY (Table A-1)
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Table A-1. Biological parameter values used in the Yuba life-cycle model.
Parameter Value Description Source
Ffry,j 1,955 Number of efry per spawner on the NY, Stillwater (2013a) App. G MY,NBB sub-basins
Ffry,SY 1,389 Number of efry per spawner on the SY sub- Stillwater (2013a) App. G basin
efrymax Table A-2* Maximum numbers of efry produced Stillwater (2013a)
smolt0max Table A-2* Maximum numbers of smolt0 produced Stillwater (2013a)
smolt1max Table A-2* Maximum numbers of smolt1 produced Stillwater (2013a) efry P 0.75 Proportion of fry migrating as efry Stillwater (2013a) smolt0 Ps,j Table A-3* Proportion of summer0 (fingerling) that migrate Stillwater (2013a) as smolt0 for hydrologic scenario s and tributary j
PSj (0.78, 0.94, Pre-spawn survival rate for adults in sub-basin j McReynolds and Garman 0.99) (2008)
Sfry 0.7 survival rate from fry to smolt0 in the stream Stillwater (2013a)
Ssmolt0 0.78, 0.94, survival from smolt0 to smolt1 Stillwater (2013a) 0.99)
SARefry 0.001 Smolt to adult ratio for efry Cavallo et al. (2009), Stillwater (2013a)1
SARsmolt0 0.003 Smolt to adult ratio for smolt0 Cavallo et al. (2009)
SARsmolt1 0.009 Smolt to adult ratio for smolt1 Cavallo et al. (2009)
Mage3 0.49 Proportion of adults returning at age 3, based on Cavallo et al. (2009), proportion of females Stillwater (2013a) *These values depend on tributary and hydrologic scenario. 1 Applying approximately 0.27 estuary survival of efry (Stillwater Sciences 2013a) to smolt0 SAR of 0.003 from Cavallo et al. (2009).
Fry can migrate out of the system as efry, smolt0, or smolt1 (Stillwater Sciences 2013a). The proportion of fry that migrate as efry is 0.75, with the remaining 0.25 of the fry migrating as smolt0 or smolt1 after survival to those stages. The fry mature to fingerling size in the stream and survive at a rate of 0.7. The proportion of those fingerlings that migrate as smolt0 is determined by the amount of habitat available. Within the RIPPLE model, all fingerlings that can rear in the stream in existing habitat stay, whereas all fingerlings that do not have rearing habitat migrate as smolt0. The fingerlings that did not migrate out stay and overwinter with a survival of 0.7; these fish subsequently migrate out as smolt1. Because the proportion of smolt0 and smolt1 migrants varies by hydrologic scenario j, we used the values provided in the output of the RIPPLE model (Table A-2) to calculate the proportion of fingerlings migrating as smolt0 smolt0 ( Ps,j) for hydrologic scenario s and sub-basin j.
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We assumed that all spawning spring-run Chinook Salmon had the ability to produce each type of outmigrant; therefore, ratios in Table A-3 were used to predict the proportion of each outmigrant stage.
Table A-2. Production potential values from the Yuba RIPPLE model.
Model Spaw- Scenario egg swimup efry smolt0 smolt1 escape holder ner redds SY-Da 0 0 0 0 0 0 0 0 0 SY-S3 703,929 380,121 142,546 64,448 1,433 1,101 588 318 139 SY-S4 2,194,102 1,184,815 444,306 132,281 52,491 5,147 3,632 2,025 431 MY-D 566,034 430,186 161,320 69,690 3,896 1,327 914 497 112 MY-S3 1,552,510 1,179,908 442,465 183,990 15,697 3,819 3,050 1,665 307 MY-S4 4,018,695 3,054,208 1,145,328 412,380 85,363 11,484 5,710 3,153 791 NY-D 6,585,187 2,370,667 889,000 275,956 97,155 10,018 7,814 4,349 1,293 NY-S3 18,435,767 6,636,876 2,488,829 530,043 441,827 34,112 30,700 17,280 3,609 NY-S4 26,419,753 9,511,111 3,566,667 395,355 888,186 57,993 52,194 29,615 5,160 ED-D 577,198 375,179 140,692 0 45,959 2,678 2,410 1,376 113 ED-S3 3,737,981 2,429,688 911,133 0 297,622 17,341 15,607 8,911 729 ED-S4 11,103,373 7,217,193 2,706,447 642,033 434,640 35,460 20,176 11,329 2,175 a Under the dry conditions scenario the entire SY below the mainstem migration barrier is predicted to be thermally unsuitable for spring-run Chinook Salmon holding and rearing; therefore production of each life stage is zero.
Table A-3. Proportion of smolt0 that stay in the spawning sub-basins to overwinter and migrate out the following year by sub-basin and hydrologic scenario Hydrologic Englebright Dam Scenario South Yuba Middle Yuba North Yuba Sub-basin D 1.00 0.926 0.665 0.00 S3 0.969 0.891 0.456 0.00 S4 0.638 0.772 0.238 0.508
The production model used in Stillwater Sciences (2013a) had sufficient spawners to surpass redd capacity, thus redd capacity became the limiting factor in total production from the system. The numbers of efry, smolt0, and smolt1 provided as output from the production model thus
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reflect the upper levels of production for the North Yuba, Middle Yuba, South Yuba, and Englebright Dam sub-basin under different hydrological alternatives. As a result we used these values to set bounds on the upper limits of juvenile production (Table A-2).
Smolt to Adult Return Ratios The smolt to adult return (SAR) rates are largely outside of the control of the reintroduction; therefore, we did not include uncertainty on the SAR rates. The smolt-to-adult return (SAR) ratios were based on estimates of smolt to adult return ratios for FRFH CWT tagged fish (Cavallo et al. 2009, Palmer-Zwahlen et al. 2004). The smolt0 rate was set at 0.003 as this was the average SAR rate for FRH fish released at the hatchery. The smolt1 rate was set to 0.009 as this was the rate achieved by releases from FRH in San Pablo Bay. Finally, the efry survival rate was set to 0.001, because this value was consistent with the relative survival of efry to smolt0 (0.27) used in developing the RIPPLE production potential estimates (Stillwater Sciences 2013a).
Adult Pre-spawn Mortality Rates Adult pre-spawn mortality rates were calculated from 2001 to 2007 Butte Creek spawning and pre-spawn mortality estimates (McReynolds and Garman 2008), with a low survival rate of 0.78 (2003 survival estimate of 0.35 excluded), mode of 0.94, and maximum of 0.99).
A.2 PASSAGE PARAMETERS We did incorporate uncertainty in the passage parameter values (including reservoir survival) to reflect our uncertainty in these rates. Uncertainty was incorporated via a triangular distribution (Chapter 7), which is defined by low, mode, and hi values. We used the passage rates described in Chapter 4 to define the distribution of passage parameters; the “mid” value presented in Chapter 4 was used as the mode of the triangular distribution.
A.2.1 North Yuba Passage On the North Yuba, juveniles in the efry, smolt0, and smolt1 stages were collected in a tributary collector (Ti) for each stage i (Table A-4). Only those fish that were collected exited the North Yuba and therefore contributed to future spawning abundances. Those fish that were collected were subsequently subjected to transport survival (Strans,i) for each stage i (Table A-5) before being released downstream of Englebright Dam to outmigrate.
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Table A-4. Assumed Tributary Collector Juvenile Salmonid Fish Guidance Efficiency.
Life Stage Low Mode High Efry (emergent) 30% 55% 80% Smolt0 (subyearling) 50% 70% 85% Smolt1 (yearling) 65% 80% 95%
Table A-5. Assumed transport survival of juvenile salmonids released downstream of the dams.
Life Stage Low Mode High Efry (emergent) 50% 70% 90% Smolt0 (subyearling) 60% 72.5% 95% Smolt1 (yearling) 75% 80% 95%
Adult collection at Englebright Dam for transport upstream to the North Yuba was assumed to have a collection efficiency of 95% and a transport survival rate of 95%.
A.2.2 Englebright Dam Passage Passage at Englebright Dam opens the Middle Yuba, South Yuba, and Englebright Dam sub- basins for spring-Chinook production. On the Middle Yuba, habitat for spawning and rearing is located above Our House Dam. We assumed that the juvenile passage at Our House Dam (POH,i) was 95% for all stages. Spring-run Chinook Salmon migrating through Englebright Reservoir had survival rates (Seng,i) that varied with each stage i (Table A-6).
Table A-6. Assumed Survival of Juvenile Salmonids Passing through Englebright Reservoir
Life Stage Low Mode High Efry (emergent) 2% 20% 40% Smolt0 (subyearling) 20% 45% 70% Smolt1 (yearling) 40% 70% 95%
Upon reaching the forebay at Englebright Dam, juveniles were collected at an FSC (Table A-7).
Collection efficiencies at the Englebright Dam (Peng,i) was a function of the amount of flow moving through the collector relative to flow being spilled. The life-cycle model assumed that 87% of the time, the collector was the only attraction for juveniles in the forebay. The other 13% of the time, there was spill and the FSC was competing with the spill for attracting juveniles. During the 13% of the time when there is spill, we assumed that 0.27 of the fish go through the surface collector and the other 0.73 go over as spill. The 0.73 value was based on median spill of
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1500 cfs and the MWH design of surface collector for 410 cfs (MWH 2010). Spill survival
(Sspill,i) was assumed to vary by life history stage (Chapter 4) with survival rates increasing with the age of outmigrant (Table A-8).
Peng,i = 0.87*Reng,i,j *FSCeng,i + 0.13*(0.27*Reng,i,j *FSCeng,i + 0.73*Reng,i,j*Sspill,i)
Table A-7. Assumed Floating Surface Collector: Combined Collection Efficiency and Facility Survival of Juvenile Salmonids Life Stage Low Mode High Efry (emergent) 45% 65% 85% Smolt0 (subyearling) 50% 70% 90% Smolt1 (yearling) 55% 75% 95%
Table A-8. Assumed Spillway Survival of Juvenile Salmonids at Englebright Dam and New Bullards Bar Dam. Life Stage Low Mode High Efry (emergent) 0% 20% 30% Smolt0 (subyearling) 10% 30% 50% Smolt1 (yearling) 10% 30% 50%
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REFERENCES
Cavallo, B., R. Brown, and D. Lee. 2009. Hatchery and Genetic Management Plan for Feather River Hatchery Spring-run Chinook Salmon Program. Prepared by Cramer Fish Sciences for California Department of Water Resources. June 2009.
McReynolds, T.R., and C.E. Garman. 2008. Butte Creek spring-run Chinook Salmon, Oncorhynchus Tshawytscha pre-spawn mortality evaluation 2007. Inland Fisheries Report No. 2008-2.
MWH (MWH Americas Inc.). 2010. Yuba River Fish Passage: Conceptual Engineering Project Options. Prepared for National Marine Fisheries Service, Southwest Region, Habitat Conservation Division, by MWH Americas, Inc., Sacramento, California. February 2010. 110pp.
Palmer-Zwahlen, M.L., A.M. Grover, and J.A. Duran. 2004. Feather River fall Chinook cohort reconstruction – Brood year 1998. Report submitted to DWR. CDFG, Marine Region, Santa Rosa, CA.
Stillwater Sciences. 2013a. Modeling habitat capacity and population productivity for spring- run Chinook Salmon and steelhead in the Upper Yuba River watershed. Revised Technical Report. Prepared by Stillwater Sciences, Berkeley, California for National Marine Fisheries Service, Santa Rosa, California.
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APPENDIX B
Technical Memorandum: Review of MWH 2010 Yuba River Fish Passage, Conceptual Engineering Project Options
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15250 NE 95th Street Redmond, WA98052-2518 Phone: (425) 556-1288 Fax: (425) 556-1290 e-mail: [email protected]
Technical Memorandum
Date: March19, 2013 Project Number: 1782/MM101
Prepared by: P. Hilgert
Subject: Review of Technical Report: MWH Americas, Inc. 2010 Yuba River Fish Passage, Conceptual Engineering Project Options, prepared by MWH Americas, Inc. Sacramento, CA, prepared for NMFS, Southwest Region, Habitat Conservation District.
In support of the development of the Upper Yuba River Anadromous Salmonid Reintroduction Plan, Phil Hilgert reviewed the 2010 MWH report on fish passage alternatives for the Upper Yuba River. Phil Hilgert is a senior fisheries biologist who has served on eight technical review panels evaluating fish passage alternatives at hydroelectric projects in the United States and Canada. Although the MWH report contained information on regulatory considerations and potential fish habitat in the South, Middle and North Yuba rivers, this review concentrated on the upstream and downstream passage alternatives.
SUMMARY
The description of upstream and downstream fish passage facilities presented in the 2010 MWH report covers the suite of facilities typically considered for salmonid fish passage. Estimates of construction costs are conceptual level and are intended to compare alternate facilities rather than provide a site-specific cost estimate. Issues of site-specific constructability or the effects of construction on project operations were not addressed in the MWH conceptual level analysis. The report provides a review of available fish passage designs, but the serviceability of the report is limited by the lack of information on the potential for the facilities to provide safe and effective fish passage. Understanding that a floating surface collector at Englebright Dam is estimated to cost $50 million compared to $79 million for vertical-plate fish screens at Narrows I and II intakes provides a gross understanding of the level of financial commitment associated with fish passage, but does not identify the ability of the facilities to successfully pass fish. Site- specific conditions, such as dam height, topography, intake depth, reservoir volume, water temperature, frequency, timing and magnitude of freshets, debris loading, and the influence of predators all affect the likelihood of a facility to provide safe and effective passage. The cost
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estimates for various facilities were developed at a conceptual level; a similar conceptual level estimate of fish guidance and survival for those facilities is needed to evaluate a comprehensive fish passage program for the upper Yuba River watershed.
UPSTREAM PASSAGE FACILITIES
Fish ladders have been successfully used at many locations to provide volitional fish passage. While dam height alone does not appear to be a limitation to the success of fish ladders, the majority of installations have occurred at dams less than 100 feet high. Since fish ladders are typically constructed at a slope of 1 foot vertical for every 10 feet horizontal, a fish ladder at 260-foot high Englebright Dam would be 2,300 to 2,600 feet long depending on how the ladder passed through the dam face. Ladders of this length present technological and biological challenges, such as the need to maintain appropriate and consistent water quality conditions at the fish ladder entrance, through the ladder, and at the upstream release locations.
The combination of long ladder length, construction along a steep slope, auxiliary water supply, and water temperature control issues affect the viability of a fish ladder as a design option at Englebright Dam. It may be possible to address these fish stressors through innovative design or operations, but the challenges must be considered when evaluating passage alternatives.
Tramways or locks can be used at high head dams where fish ladders are infeasible. However, differences between water temperatures at the downstream entrance pool and the reservoir surface release location may stress fish and reduce survival. Incorporating a subsurface release mechanism into a fish lock would address temperature concerns, but involves other technical challenges. In general, tramways and locks limit the flexibility to alter release locations to address seasonal temperature concerns.
A fish ladder or a tramway at Englebright Dam would provide fish access to the Middle and South Yuba and the reach immediately above Englebright reservoir, but would not provide fish access to the North Yuba which appears to contain the majority of Chinook salmonid habitat under existing conditions (Stillwater 2013a).
Constructing a separate fish ladder or tramway at the base of 635-feet high New Bullards Bar Dam (NBBD) would involve significant challenges due to the steep slope, long ladder length, and water temperature control issues.
A collection and transport facility constructed below Daguerre Point Dam or below Englebright Dam would allow fish to be released into upstream environments where the difference in water temperature between the collection and release sites can be minimized.
Constructing a collection and transport facility below Daguerre Point Dam or below Englebright Dam would allow fish to be released above Englebright Dam to continue their upstream migration to the natal stream. However, unless fish destined for the North
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Yuba can be separated at the Daguerre Point collection facility, a second upstream fish passage facility would be needed to pass fish upstream into the North Yuba from below NBBD.
If gravels are placed below NBBD to improve spawning habitat, locating the entrance to a fish collection facility below NBBD may increase the risk of attracting and transporting fish from the spawning areas below NBBD to upstream non-natal locations.
A phased approach to reintroduction of Central Valley spring-run Chinook Salmon into the Upper Yuba could involve collecting fish below Daguerre Point Dam or below Englebright Dam and releasing them directly into the North Yuba. The North Yuba appears to contain more suitable salmonid habitat than the Middle and South Yuba (Stillwater 2013a). If reintroduction of anadromous fish production was successful in the North Yuba, options to separate fish at the downstream adult collection facility could be considered, or a separate adult upstream collection and transport facility could be constructed below NBBD at a later date.
A temporary collection and transport facility located immediately below Daguerre Point Dam and/or Englebright Dam could be used on an interim basis. If successful, and if other technological challenges can be addressed, collection and transport facilities could be replaced with a volitional fish ladder or lock to provide upstream fish passage on a long-term basis.
DOWNSTREAM PASSAGE FACILITIES
Three potential downstream fish passage designs were evaluated in the MWH 2010 report: fish screening of the intakes at Englebright Dam, floating surface collectors at Englebright Dam, and tributary collectors at Englebright Dam and NBBD. Potential downstream fish passage facilities for each dam are listed in Table 4-2 of the MWH report; however, site specific constraints of the downstream fish passage facilities are not described. For instance, a floating surface collector and screens are listed as options at NBBD, but there is no description of how the facilities could be designed to accommodate water level fluctuations of 150 feet.
As described in the MWH report, the top of the fish screens would be set at “the anticipated minimum operating water surface elevation”. The screens would need to operate over the full range of the reservoir pool level fluctuations.
Vertical-plate fish screens at Narrows I and II intakes would effectively prevent juvenile fish from being entrained, but it is unclear whether the location of the screens along the shoreline would effectively attract downstream migrants and allow them to be collected and passed downstream. The facilities may exhibit poor fish guidance and result in poor downstream survival unless the facilities are sited to intercept downstream migrants.
The floating surface collector at Puget Sound Energy’s Upper Baker Dam, depends on the integration of a guide net and net transition structure (R2 2011, NOAA Fisheries
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2013). The guide nets at Baker Lake are periodically cleaned to prevent biofouling which increased drag on the net and contributes to net failure. The cold water temperatures, low nutrients, and glacially turbid inflow of Baker Lake all serve to limit the rate of biofouling of the guide net leading to the Upper Baker surface collector (PSE 2006). The functionality of a guide net at an Englebright floating surface collector could be compromised by biofouling associated with warmer water, higher nutrient load, and higher ambient light levels in the Yuba River.
Although the intakes could be screened, or downstream passage provided through surface collectors, the rate of reservoir passage and survival would be important considerations in the potential success of the facilities to provide safe and effective downstream fish passage.
The effectiveness of tributary collectors depends on the timing and magnitude of flow that can be screened under NMFS design criteria. If fish are moving downstream during freshets, facilities that screen larger volumes of flow will have higher fish guidance efficiency than smaller volume screens. Debris-loading during freshets may reduce the effectiveness of the screens; salmonid fry are particularly susceptible to impingement and mortality if the screens become partially occluded due to debris loading.
Tributary collector screens on the North Yuba and Middle Yuba are designed to screen flows up to the 5 percent exceedance flow (e.g., North Yuba at 5,000 cfs). The assumption that screens designed to function at the 5 percent exceedance flows can operate within design criteria down to negligible flow in the rivers is unsupported. Screens function to protect and guide fish to bypass facilities through a combination of appropriate through-screen velocities and sweeping velocities. Under low flow conditions, screens may not have a sufficient sweeping velocity to guide juvenile outmigrants into a bypass pipe or collection facility. The design of the tributary collectors will have to incorporate measures to ensure effectiveness over the full range of flows.
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REFERENCES
National Oceanic and Atmospheric Administration (NOAA Fisheries Service). 2013. New Floating Surface Collector at the Baker Hydroelectric Project is a Model for Innovative Fish Passage. NOAA Northwest Region, http://www.nwr.noaa.gov/stories/2012/2013_01_14_floating_surface_collector.html
Puget Sound Energy, Inc. (PSE). 2006. Application for New License, Major Project—Existing Dam, Baker River Hydroelectric Project, FERC No. 2150, Puget Sound Energy, Inc. Bellevue, Washington.
R2 Resource Consultants. March 2011. 2010 Study Report, Biological Evaluation, Upper Baker Downstream Fish Passage Floating Surface Collector.
Stillwater Sciences. 2013a. Modeling habitat capacity and population productivity for spring-run Chinook Salmon and steelhead in the Upper Yuba River watershed. Revised Technical Report. Prepared by Stillwater Sciences, Berkeley, California for National Marine Fisheries Service, Santa Rosa, California.
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