Upper Columbia Spring Chinook Salmon, Steelhead, and Bull Trout Recovery

Acknowledgments ix

Dedication xi

Executive Summary xii

1 Introduction 1

2 Species Status 24

3 Factors for Decline 81

4 Delisting Criteria 109

5 Strategy for Recovery 133

6 Social/Economic Considerations 247

7 Relationship to Other Efforts 254

8 Plan Implementation 255

9 Acronyms 274

10 Glossary 278

11 References 286

12 Appendices 298

Table 2.1 Adult (age >3) spawner-to-spawner return estimates and 12-year geometric means (GM) of spawners (S) and returns per spawner (R/S) for Upper Columbia spring Chinook. Return levels for brood years 1960-1969 were adjusted to reflect historical average harvest. Spawner numbers include both hatchery and naturally produced fish. Data are from T. Cooney (NOAA Fisheries). 47

Table 2.2 Goals, associated mechanisms, factors, and levels of risk (L-low; M-medium; H-high) for diversity and spatial structure of Upper Columbia spring Chinook and steelhead. Table was developed following guidance from ICBTRT (2005a) (see Appendix B). Wen = Wenatchee, Ent = Entiat, Met = Methow, and Okan = Okanogan. 50

Table 2.3 Viability ranking of current populations of Upper Columbia River spring Chinook (spatial structure/diversity based on Table 2 .3; Abundance/Productivity based on Figure 2 .10 and Figure 2 .13) (table developed based on guidance from ICBTRT 2005a) (see Appendix B) 51

Table 2.4 Summary statistics for naturally produced (NP) steelhead escapement and run reconstruction for Wenatchee and Entiat populations. GM = 12-year geometric mean; HE = hatchery effectiveness. See Appendix C for a detailed description of run reconstructions. 52

Table 2.5 Viability ranking of current populations of Upper Columbia River steelhead (spatial structure/diversity based on Table 2 .3; Abundance/Productivity based on Figure 2 .20 and Figure 2 .23) (Table developed based on guidance from ICBTRT 2005a; see Appendix B) 54

Table 2.6 Summary statistics for naturally produced (NP) steelhead escapement and run reconstruction for Methow and Okanogan populations. GM = 12-year geometric mean; HE = hatchery effectiveness. See Appendix C for a detailed description of run reconstructions 55

Table 2.7 Bull trout redd counts from streams in the Upper Columbia Basin for years 1983-2003 (data from USFWS and USFS) 57

Table 4.8 Mechanisms, factors, and metrics used to assess spatial structure and diversity of spring Chinook and steelhead populations in the Upper Columbia Basin. Table is from ICBTRT (2005a,b) 123

Table 5.9 Naturally produced Upper Columbia Steelhead run-size criteria and mortality take-limit for recreational harvest fisheries in the Wenatchee River, Methow River, and Okanogan Basin spawning areas. Catch-and-release mortality is assumed to be 5%. From NMFS (2003). 225

Table 5.10 Artificial propagation programs in the Upper Columbia Basin in 2005 listed by release basin, primary hatchery facility association, program operators, and funding source 226

Table 5.11 Summary of artificial anadromous fish production in the Wenatchee subbasin 227

Table 5.12 Summary of artificial anadromous fish production in the Entiat subbasin 228

Table 5.13 Summary of artificial anadromous fish production in the Methow subbasin 228

Table 5.14 Broodstock collection guidelines of the Methow Basin spring Chinook supplementation plan (ESA Section 7 Draft Biological Opinion, Section 10 Permit 1196) 229

Table 5.15 Current artificial anadromous fish production in the Okanogan subbasin 229

Table 5.16 Numbers of different habitat activities implemented within the Upper Columbia Basin within the last 10 years 230

Table 5.17 Habitat action classes and a listing of potential actions associated with each action class. Note that the list of potential actions is not all-inclusive. The list is intended as a guide for local habitat groups in selecting potential actions. Additional potential actions not identified in the list may be appropriate provided they address the action class. None of the actions identified in this table are intended to, nor shall they in any way, abridge, limit, diminish, abrogate, adjudicate, or resolve any authority or Indian right protected by statute, executive order, or treaty. This language shall be deemed to modify each and every section of this recovery plan as if it were set out separately in each section. 231

Table 5.18 Rating of assessment units within each subbasin according to their potential for recovery of listed species in the Upper Columbia Basin. Ratings are from the Biological Strategy (UCRTT 2003) and range from Category 1 (highest) to Category 4 (lowest). Category 1 and 2 assessment units include areas that should be protected (see text) 239

Table 5.19 Summary of possible increases in survival from recommended actions identified in this plan. The numbers in red indicate minimum estimates for Entiat steelhead, because there are no productivity estimates from recommended habitat actions (see Appendix I). 241

Figure 1.1 Subbasins and major tributaries within the Upper Columbia River Subbasin 18

Figure 1.2 Major tributaries within the Wenatchee subbasin 19

Figure 1.3 Major tributaries within the Entiat subbasin 20

Figure 1.4 Major tributaries within the Methow subbasin 21

Figure 1.5 Major tributaries within the Okanogan subbasin 22

Figure 1.6 Logic path, analytical tools, and information sources used to develop the Upper Columbia Basin recovery plan 23

Figure 2.7 Spring Chinook spawners and returns per spawner (R/S) and their 12-year geometric means (GM) in the Wenatchee subbasin during the period 1960 to 1999. Spawner numbers include both hatchery (minus those in Icicle Creek) and naturally produced fish. 59

Figure 2.8 Annual smolts per redd for Wenatchee River spring Chinook. The numbers to the right of the lines are the geometric means (± 1 SD). 60

Figure 2.9 Current and potential distribution of spring Chinook in the Wenatchee subbasin 61

Figure 2.10 Viability curve for Wenatchee and Methow spring Chinook salmon. For the Wenatchee and Methow populations to be viable, their abundance/productivity scores must fall above the viability curve. Variability should be considered as the abundance/productivity estimates approach viability criteria. Viability curve is from the ICBTRT (2005a). This plan recognizes that as abundance and productivity values approach the minimum viability thresholds it will be necessary to incorporate uncertainty and measurement error regarding the status of each population. 62

Figure 2.11 Spring Chinook spawners and returns per spawner (R/S) and their 12-year geometric means (GM) in the Entiat subbasin during the period 1960 to 1999. Spawner numbers include both hatchery and naturally produced fish. 63

Figure 2.12 Current and potential distribution of spring Chinook in the Entiat subbasin 64

Figure 2.13 Viability curve for Entiat spring Chinook. For the Entiat population to be viable, its abundance/productivity score must fall above the viability curve. Variability should be considered as the abundance/productivity estimates approach viability criteria. Viability curve is from the ICBTRT (2005a). This plan recognizes that as abundance and productivity values approach the minimum viability thresholds it will be necessary to incorporate uncertainty and measurement error regarding the status of each population. 65

Figure 2.14 Spring Chinook spawners and returns per spawner (R/S) and their 12-year geometric means (GM) in the Methow subbasin during the period 1960 to 1999. It is assumed that all spawners in 1996 and 1998 were collected for hatchery broodstock. Spawner numbers include both hatchery and naturally produced fish. 66

Figure 2.15 Current and potential distribution of spring Chinook in the Methow subbasin 67

Figure 2.16 Escapement of naturally produced steelhead in the Wenatchee subbasin 68

Figure 2.17 Returns per spawner (R/S) of naturally produced steelhead in the Wenatchee and Entiat subbasins. Returns per spawner are shown for hatchery fish that are as reproductively successful as naturally produced fish (H = 1) and hatchery fish that have no reproductive success (H = 0) 69

Figure 2.18 Current and potential distribution of steelhead in the Wenatchee subbasin 70

Figure 2.19 Viability curve for Wenatchee and Methow steelhead. This figure is based on the assumption that hatchery fish have no reproductive success. Variability should be considered as the abundance/productivity estimates approach viability criteria. Viability curve is from the ICBTRT (2005a). This plan recognizes that as abundance and productivity values approach the minimum viability thresholds it will be necessary to incorporate uncertainty and measurement error regarding the status of each population. 71

Figure 2.20 Escapement of naturally produced steelhead in the Entiat subbasin 72

Figure 2.21 Current and potential distribution of steelhead in the Entiat subbasin 73

Figure 2.22 Viability curve for Entiat and Okanogan steelhead. Assumes hatchery fish have no reproductive success. Variability should be considered as the abundance/productivity estimates approach viability criteria. Viability curve is from the ICBTRT (2005a). This plan recognizes that as abundance and productivity values approach the minimum viability thresholds it will be necessary to incorporate uncertainty and measurement error regarding the status of each population. 74

Figure 2.23 Escapement of naturally produced steelhead in the Methow subbasin 75

Figure 2.24 Returns per spawner of naturally produced steelhead in the Methow and Okanogan subbasins. Returns per spawner are shown for hatchery fish that have no reproductive success (H = 0) and hatchery fish that are as reproductively successful as naturally produced fish (H = 1). 76

Figure 2.25 Current and potential distribution of steelhead in the Methow subbasin 77

Figure 2.26 Escapement of naturally produced steelhead in the Okanogan subbasin 78

Figure 2.27 Current and potential distribution of steelhead in the U.S. portion of the Okanogan subbasin 79

Figure 2.28 Current and potential distribution of bull trout in the Upper Columbia Basin 80

Figure 3.29 Returns per spawner for three levels of productivity (average smolts/redd) and smolt-to-adult return rates (SAR) for spring Chinook in the Wenatchee River, Washington. The SAR of 0.63% was the 8-yr geometric mean from 1993-2000 for naturally produced Chiwawa River spring Chinook (WDFW, unpublished data). The 1% SAR was modeled at the same productivity values for a theoretical comparison. This simple arithmetic model does not account for variance, autocorrelation, or density dependence and should not be used to determine targets for either metric. 107

Figure 3.30 A density-dependent relationship between Chinook salmon smolts per redd and the number of redds in the Chiwawa River, a relatively pristine tributary of the Wenatchee River, Washington. Brood years (BY) are only specified for extreme values 108

Figure 4.31 Viability curves for Upper Columbia spring Chinook. The top figure represents the Wenatchee and Methow Entiat populations and the bottom figure represents the Entiat population. 124

Figure 4.32 Viability curves for Upper Columbia steelhead. The top figure represents the Entiat and Okanogan populations and the bottom figure represents the Wenatchee and Methow populations. 125

Figure 4.33 Distribution of major and minor spawning areas of spring Chinook in the Wenatchee Subbasin 126

Figure 4.34 Distribution of major and minor spawning areas of spring Chinook in the Entiat Subbasin 127

Figure 4.35 Distribution of major and minor spawning areas of spring Chinook in the Methow Subbasin 128

Figure 4.36 Distribution of major and minor spawning areas of steelhead in the Wenatchee Subbasin 129

Figure 4.37 Distribution of major and minor spawning areas of steelhead in the Entiat Subbasin 130

Figure 4.38 Distribution of major and minor spawning areas of steelhead in the Methow Subbasin 131

Figure 4.39 Distribution of major and minor spawning areas of steelhead in the Okanogan Subbasin 132

Figure 5.40 Top graph identifies the proportion of within-subbasin potential for each spring Chinook performance measure realized by each EDT modeling scenario in the Wenatchee subbasin. Scenario 1 (S1) applied the full effectiveness of restoration classes that addressed the primary limiting factors within each assessment unit, regardless of feasibility or cost. Scenario 3 (S3) was 33% the intensity of S1, with full effect of artificial barrier removal and protection. Scenario 2 (S2) is not available at this time. Habitat template indicates the estimated historical condition. Bottom graph represents the predicted abundance (spawners) based on EDT runs for spring Chinook within the Wenatchee subbasin. The dotted and dashed lines indicate the percent increase needed to reach minimum recovery abundance with SARs of 1.34% (used in EDT model runs) and 0.63% (empirical data from the Chiwawa River). See Appendix F for more details. 242

Figure 5.41 Top graph identifies the proportion of within-subbasin potential for each steelhead performance measure realized by each EDT modeling scenario in the Wenatchee subbasin. Scenario 1 (S1) applied the full effectiveness of restoration classes that addressed the primary limiting factors within each assessment unit, regardless of feasibility or cost. Scenario 3 (S3) was 33% the intensity of S1, with full effect of artificial barrier removal and protection. Scenario 2 (S2) is not available at this time. Habitat template indicates the estimated historical condition. Bottom graph represents the predicted abundance (spawners) based on EDT runs for steelhead within the Wenatchee subbasin. The model used an average SAR of 1.26%. See Appendix F for more details. 243

Figure 5.42 Top graph identifies the proportion of within-subbasin potential for each spring Chinook performance measure realized by each EDT modeling scenario in the Methow subbasin. Scenario 1 (S1) applied the full effectiveness of restoration classes that addressed the primary limiting factors within each assessment unit, regardless of feasibility or cost. Scenario 3 (S3) was 33% the intensity of S1, with full effect of artificial barrier removal and protection. Scenario 2 (S2) is not available at this time. Habitat template indicates the estimated historical condition. Bottom graph represents the predicted abundance (spawners) based on EDT runs for spring Chinook within the Methow subbasin. The model used an average SAR of 1.24%. See Appendix F for more details. 244

Figure 5.43 Top graph identifies the proportion of within-subbasin potential for each steelhead performance measure realized by each EDT modeling scenario in the Methow subbasin. Scenario 1 (S1) applied the full effectiveness of restoration classes that addressed the primary limiting factors within each assessment unit, regardless of feasibility or cost. Scenario 3 (S3) was 33% the intensity of S1, with full effect of artificial barrier removal and protection. Scenario 2 (S2) is not available at this time. Habitat template indicates the estimated historical condition. Bottom graph represents the predicted abundance (spawners) based on EDT runs for steelhead within the Methow subbasin. The model used an average SAR of 1.03%. See Appendix F for more details. 245

Figure 5.44 Top graph identifies the proportion of within-subbasin potential for each steelhead performance measure realized by each EDT modeling scenario in the U.S. portion of the Okanogan subbasin. Scenario 1 (S1) applied the full effectiveness of restoration classes that addressed the primary limiting factors within each assessment unit, regardless of feasibility or cost. Scenario 3 (S3) was 33% the intensity of S1, with full effect of artificial barrier removal and protection. Scenario 2 (S2) is not available at this time. Habitat template indicates the estimated historical condition. Bottom graph represents the predicted abundance (spawners) based on EDT runs for steelhead within the Okanogan subbasin. The model used an average SAR of 0.92%. See Appendix F for more details. 246

Figure 8.45 Diagram showing implementation phase relationships 271

Figure 8.46 Diagram showing the flow of information from researchers and monitors in the Upper Columbia Basin to scientific reviewers, public, and decision makers. 272

Figure 8.47 Relationships between biological benefits, costs, and feasibility for prioritizing (sequencing) recovery actions. Tier 1 actions receive the highest priority, while Tier 4 actions receive the lowest. 273

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