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 ...............................................................................................................................................