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Migrating the Sacramento-San Joaquin Ri

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Migrating the Sacramento-San Joaquin Ri Prepared in cooperation with the U.S. Fish and Wildlife Service Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the Sacramento-San Joaquin River Delta During the Winter of 2009–10 Open-File Report 2012–1200 U.S. Department of the Interior U.S. Geological Survey Cover: Image Courtesy of NASA. Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the Sacramento-San Joaquin River Delta during the Winter of 2009–10 By Russell W. Perry, Jason G. Romine, and Scott J. Brewer, U.S. Geological Survey; Peter E. LaCivita, William N. Brostoff, U.S. Army Corps of Engineers; and Eric D. Chapman, University of California at Davis Prepared in cooperation with the U.S. Fish and Wildlife Service Open-File Report 2012-1200 U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior KEN SALAZAR, Secretary U.S. Geological Survey Marcia K. McNutt, Director U.S. Geological Survey, Reston, Virginia: 2012 For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod Telephone: 1-888-ASK-USGS For an overview of USGS information products, including maps, imagery, and publications, visit http://www.usgs.gov/pubprod To order this and other USGS information products, visit http://store.usgs.gov Suggested citation: Perry, R.W., Romine, J.G., Brewer, S.J., LaCivita, P.E., Brostoff, W.N., and Chapman, E.D., 2012, Survival and migration route probabilities of juvenile Chinook salmon in the Sacramento-San Joaquin River Delta during the winter of 2009–10: U.S. Geological Survey Open-File Report 2012-1200, 30 p. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted material contained within this report. Contents Abstract ........................................................................................................................................................... 1 Introduction ...................................................................................................................................................... 2 Methods ........................................................................................................................................................... 5 Telemetry System ........................................................................................................................................ 5 Fish Tagging and Release ........................................................................................................................... 7 Model Development ..................................................................................................................................... 8 Parameter Estimation ................................................................................................................................ 10 Survival through the Delta .......................................................................................................................... 12 Results ........................................................................................................................................................... 14 River Conditions and Migration Timing ...................................................................................................... 14 Detection Probabilities ............................................................................................................................... 14 Route-Specific Survival through the Delta .................................................................................................. 16 Migration Routing ....................................................................................................................................... 21 Relative Contributions to SDelta ................................................................................................................... 22 Discussion ..................................................................................................................................................... 23 Acknowledgments ......................................................................................................................................... 25 References Cited ........................................................................................................................................... 25 Appendix A .................................................................................................................................................... 28 Figures Figure 1. Maps of the Sacramento-San Joaquin River Delta with shaded regions showing river reaches that comprise survival through the Delta for four different migration routes ................................................... 4 Figure 2. Map showing location of telemetry stations used to estimate survival and migration route probabilities within four major migration routes of the Sacramento-San Joaquin River Delta during the winter of 2009–10 .......................................................................................................................................... 6 Figure 3. Schematic of the mark-recapture model used to estimate survival (Shi), detection (Phi), route entrainment (Ψhl), and joint survival-entrainment (φhi,jk) probabilities of juvenile late-fall Chinook salmon migrating through the Sacramento–San Joaquin River Delta for releases made in winter of 2009–10 ......... 9 Figure 4. River discharge, water exports, and Delta Cross Channel discharge during the migration period of tagged juvenile Chinook salmon migrating through the Sacramento-San Joaquin River Delta during winter of 2009–10 ........................................................................................................................................ 15 Figure 5. Probability of surviving migration through the Sacramento-San Joaquin River Delta (Sh) for each of four migration routes for tagged late-fall juvenile Chinook salmon migrating from the Sacramento River ........................................................................................................................................ 18 Figure 6. Comparison of route-specific survival between the Sacramento River (A), Sutter Slough (B1), and Steamboat Slough (B2) for late-fall Chinook salmon tagged and released in December 2009 (R1 and R2) and February 2010 (R3 and R4) ................................................................................................ 19 Figure 7. Cumulative survival for each migration route as a function of distance traveled for juvenile late- fall Chinook salmon released in December 2009 (R1 and R2) and February 2010 (R3 and R4) ................... 20 iii Tables Table 1. Summary of release dates, locations, and sample size of acoustically tagged late-fall Chinook salmon released into the Delta during the winter of 2009–10 ........................................................................ 8 Table 2. Route-specific survival through the Sacramento–San Joaquin River Delta (Sh) and the probability of migrating through each route (Ψh) for acoustically tagged fall-run juvenile Chinook salmon released December 2–5, 2009 (R1) and December 16–19, 2009 (R2) ....................................................................... 17 Table 3. Ratio (θh) of survival through route h (Sh) to survival through the Sacramento River (SA) for acoustically tagged late fall-run juvenile Chinook salmon released in December 2–5 and December 16–19, 2009 ............................................................................................................................... 21 Table 4. Probability of migrating through each route (Ψh) for acoustically tagged late fall-run juvenile Chinook salmon released in December 2009 as a function of gate position when fish passed the Delta Cross Channel. ............................................................................................................................................ 22 Conversion Factors Multiply By To obtain Length foot (ft) 0.3048 meter (m) mile (mi) 1.609 kilometer (km) Area square foot (ft2) 0.09290 square meter (m2) Volume cubic foot (ft3) 0.02832 cubic meter (m3) Flow rate cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s) Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:°F=(1.8×°C)+32. Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows:°C=(°F-32)/1.8 iv Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the Sacramento-San Joaquin River Delta during the Winter of 2009–10 By Russell W. Perry, Jason G. Romine, and Scott J. Brewer, U.S. Geological Survey; Peter E. LaCivita, William N. Brostoff, U.S. Army Corps of Engineers; and Eric D. Chapman, University of California at Davis Abstract Juvenile Chinook salmon (Oncorhynchus tshawytscha) emigrating from natal tributaries of the Sacramento River may use a number of migration routes to negotiate the Sacramento-San Joaquin River Delta (hereafter, “the Delta”), each of which may influence their probability of surviving. We applied a mark-recapture model to data from acoustically tagged juvenile late-fall Chinook salmon that migrated through the Delta during the winter of 2009–10 (hereafter, 2010). This report presents findings from our fourth year of research.
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