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Status Review of California Coho Salmon North of San Francisco

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Status Review of California Coho Salmon North of San Francisco STATUS REVIEW OF CALIFORNIA COHO SALMON NORTH OF SAN FRANCISCO Report to The California Fish and Game Commission April 2002 California Department of Fish and Game The Resources Agency State of California State of California The Resources Agency Department of Fish and Game STATUS REVIEW OF CALIFORNIA COHO SALMON NORTH OF SAN FRANCISCO Report to The California Fish and Game Commission Prepared by The California Department of Fish and Game Candidate Species Status Review Report 2002-3 April 2002 i ii TABLE OF CONTENTS I. EXECUTIVE SUMMARY ...................................................1 Petition History ..........................................................1 Conclusions .............................................................1 Recommendations ........................................................3 II. INTRODUCTION .........................................................5 Petition History ..........................................................5 Department Review .......................................................6 Previous Coho Salmon Listing Actions .......................................6 III. BIOLOGY ...............................................................9 Species Characteristics ....................................................9 Range ..................................................................9 Taxonomy and Systematics ...............................................13 Genetics ...............................................................14 Life History and Unique Characteristics ....................................21 IV. HABITAT NECESSARY FOR SURVIVAL ..................................25 Adults .................................................................25 Juveniles ...............................................................26 Essential Estuarine Habitat ...............................................29 Summary of Essential Habitat .............................................29 V. STATUS OF CALIFORNIA COHO SALMON POPULATIONS NORTH OF SAN FRANCISCO ...........................................................35 Structure and Function of Viable Salmonid Populations .......................35 Sources of Information ...................................................37 Historical and Current Distribution by Watershed ...........................38 Presence-by-Brood-Year Investigation ......................................53 2001 Presence Survey Information .........................................55 Abundance and Trends ..................................................65 Conclusions ............................................................76 VI. FACTORS AFFECTING THE ABILITY TO SURVIVE AND REPRODUCE .....79 Climatic Variation ......................................................79 Disease ................................................................83 Predation ..............................................................85 Hatcheries .............................................................88 Genetic Diversity ........................................................99 Habitat Condition ......................................................101 Fishing and Illegal Harvest ..............................................133 VII. INFLUENCE OF EXISTING MANAGEMENT EFFORTS ...................139 Disease ...............................................................139 Hatchery Operations ...................................................140 Forestry Activities ......................................................147 Water Diversion and Fish Passage Remediation .............................154 iii Gravel Extraction ......................................................160 Suction Dredging. ......................................................164 Habitat Restoration and Watershed Management ...........................164 Commercial and Recreational Fishing. .....................................181 Research and Monitoring Programs .......................................183 VIII. CONCLUSIONS .......................................................185 IX. RECOMMENDATIONS .................................................189 Petitioned Action .......................................................189 Future Management ....................................................190 X. RECOVERY CONSIDERATIONS .........................................193 Recovery Planning .....................................................194 XI. ALTERNATIVES TO THE LISTING ......................................197 XII. PROTECTIONS RESULTING FROM LISTING ............................201 XIII. LITERATURE CITED AND PERSONAL COMMUNICATIONS .............203 iv LIST OF FIGURES Figure 1. Native range of coho salmon. .........................................10 Figure 2. Historical distribution of coho salmon in California .......................11 Figure 3. Present distribution of coho salmon in California .........................12 Figure 4. Bootstrapped parsimony tree showing the relationship of the six North American Oncorhynchus species that represent Pacific salmon using combined nuclear and mitochondrial DNA data. ............................................14 Figure 5. Coho salmon evolutionarily significant units (ESU) in California. ............20 Figure 6. Generalized life stage periodicity of coho salmon in California Coastal Watersheds. .......................................................23 Figure 7. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of the Smith River watershed. Includes portions of the Chetco River and Illinois River watersheds. .........................................58 Figure 8. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of the Klamath River watershed. ............................59 Figure 9. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of the Trinity River watershed. .............................60 Figure 10. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of the Redwood Creek, Mad River, Eureka Plain, and Trinidad watersheds. .......................................................61 Figure 11. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of the Eel River watershed. ................................62 Figure 12. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of Mendocino County coastal and Russian River watersheds. .....63 Figure 13. Results of the 2001 presence surveys in historical coho salmon streams (Brown and Moyle 1991) of Marin County and San Francisco Bay coastal watersheds. ......64 Figure 14. California coho salmon hatchery production of juveniles vs commercial catch of adults two years later, 1979 to 1990. Both catch and production are numbers of fish. .............................................................66 Figure 15. California commercial and ocean recreational coho salmon catch. ............67 Figure 16. Summer juvenile coho salmon densities in the Central California Coast Coho ESU. ............................................................71 v Figure 17. Juvenile coho salmon densities for: two index sites on Caspar Creek (top left); two index sites on Little River (top right); Pudding Creek (bottom left); two index sites on Hollow Tree Creek, South Fork Eel River (bottom right). ................72 Figure 18. Juvenile coho salmon density at two index sites in Caspar Creek for the 1987 brood year lineage, 1987 to 1999. ...........................................73 Figure 19. Coho salmon outmigration in Caspar Creek and Little River, 1987 through 2001. 73 Figure 20. Time series plots and predictions for coho smolts counts from Caspar Creek and Little River, Mendocino County. ......................................74 Figure 21. Time series plots with > 10 years of data and predictions for coho juvenile indices from Caspar Creek and Little River, Mendocino County. ...................74 Figure 22. Abundance trend indicators in the Southern Oregon/Northern California Coast Coho ESU (from NMFS 2001a). ...........................................75 Figure 23. Conceptual model of effects of declining habitat quality and cyclic changes in ocean productivity on the abundance of coastal natural salmon. ...................82 vi LIST OF TABLES Table 1. Nomenclature for coho salmon. .......................................13 Table 2. Sample locations for genetics studies reviewed in the text. ..................15 Table 3. Freshwater habitats of the different life-stages of northern California coho salmon. ..........................................................30 Table 4. Fundamental habitat elements and suitable ranges for coho salmon life-stages. ..32 Table 5. Historical presence of coho salmon north of San Francisco, as determined by Brown and Moyle (1991), and the Department’s presence-by-brood-year investigation. 54 Table 6. Results of the Department’s 2001coho salmon presence surveys of SONCC Coho ESU streams listed by Brown and Moyle (1991) as historically containing coho salmon. ..........................................................56 Table 7. Results of the coho presence surveys in streams listed by Brown and Moyle (1991) as historically containing coho salmon for CCC Coho ESU streams. ..........57 Table 8. Summary of estimated average coho salmon spawner abundance in California ESUs. Data are for the years 1987 through 1991. .........................70 Table 9. Summary
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