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2013 South Delta Chinook Salmon Survival Study

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2013 South Delta Chinook Salmon Survival Study 2013 South Delta Chinook Salmon Survival Study Rebecca Buchanan, University of Washington Pat Brandes, Mike Marshall, Ken Nichols, Jack Ingram and David LaPlante, U.S. Fish and Wildlife Service; Josh Israel, U.S. Bureau of Reclamation; Compiled and edited by Pat Brandes, U.S. Fish and Wildlife Service 22 December 2016 1 Table of Contents Introduction .................................................................................................................................................. 5 Background ............................................................................................................................................... 5 Goals and Objectives ................................................................................................................................. 6 Conceptual Model ..................................................................................................................................... 7 Study Design and Methods ........................................................................................................................... 8 Sample Size Analyses ................................................................................................................................ 8 Study Fish .................................................................................................................................................. 8 Tags ........................................................................................................................................................... 8 Tagging training......................................................................................................................................... 9 Tagging ...................................................................................................................................................... 9 Transmitter Validation ............................................................................................................................ 11 Transport to Release Site ........................................................................................................................ 11 Transfer to Holding Containers ............................................................................................................... 12 Fish Releases ........................................................................................................................................... 13 Dummy-tagged fish ................................................................................................................................. 13 Fish Health Assessment .......................................................................................................................... 14 Tag life tests ............................................................................................................................................ 14 Receiver deployment, retrieval, and receiver database ......................................................................... 14 Data processing and survival model ....................................................................................................... 15 Statistical Methods ..................................................................................................................................... 15 Data Processing for Survival Analysis ...................................................................................................... 15 Distinguishing between Detections of Chinook Salmon and Predators ............................................. 16 Constructing Detection Histories ........................................................................................................ 19 Survival Model ........................................................................................................................................ 20 Model Modifications: Release Group 1 .............................................................................................. 27 Model Modifications: Release Group 2 .............................................................................................. 28 Parameter Estimation ............................................................................................................................. 28 Analysis of Tag Failure ............................................................................................................................. 30 Analysis of Tagger Effects ....................................................................................................................... 30 Analysis of Travel Time ........................................................................................................................... 31 Route Entrainment Analysis .................................................................................................................... 31 2 Survival through Facilities ....................................................................................................................... 35 Results ......................................................................................................................................................... 35 Transport to Release Site ........................................................................................................................ 35 Fish Releases ........................................................................................................................................... 35 Dummy Tagged fish ................................................................................................................................ 36 Fish Health .............................................................................................................................................. 36 Detections of Acoustic-Tagged Fish ........................................................................................................ 36 Tag-Survival Model and Tag-Life Adjustments ....................................................................................... 39 Tagger Effects .......................................................................................................................................... 39 Survival and Route Entrainment Probabilities ........................................................................................ 40 Release Group 1 .................................................................................................................................. 40 Release Group 2 .................................................................................................................................. 42 Pooled Release Groups ....................................................................................................................... 43 Comparison between Release Groups ................................................................................................ 44 Travel Time .............................................................................................................................................. 44 Route Entrainment Analysis at the Head of Old River ............................................................................ 45 Discussion.................................................................................................................................................... 47 Objective 1: Estimating survival in 2013 and the effect of sparse data. ................................................ 47 Objective 2: Comparison Between Release Groups .............................................................................. 49 Objective 3: Determine if travel time could be an explanation for the higher survival with the higher flows. ....................................................................................................................................................... 50 Objective 4: Identify route selection at HOR and Turner Cut and its effect on survival in 2013. ........... 50 Objective 5: Assess the influence of flows and exports on route entrainment ..................................... 50 Objective 6: Determine if there was a reduction in survival without the HORB, and the potential reasons for the reduction, if found. ........................................................................................................ 51 Objective 7: Assess the influence of flow and HORB on survival between Mossdale and Jersey Point. 52 Objective 8: Assess the role and influence of flow and exports on survival in downstream reaches of the Delta.................................................................................................................................................. 53 Conclusions ................................................................................................................................................. 54 References .................................................................................................................................................. 56 Figures ......................................................................................................................................................... 59 Tables .......................................................................................................................................................... 78 3 Appendices ...............................................................................................................................................
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