2014 South Delta Chinook Salmon Survival Study Rebecca Buchanan, University of Washington Pat Brandes, Jack Ingram, Mike Marshall, Ken Nichols, David LaPlante, Denise Barnard and Kristen Towne, U.S. Fish and Wildlife Service Josh A. Israel, U.S. Bureau of Reclamation Compiled and edited by Pat Brandes, U.S. Fish and Wildlife Service 3 July 2018 1 Table of Contents Introduction .................................................................................................................................................. 5 Project Goals and Objectives .................................................................................................................... 5 Background ............................................................................................................................................... 6 Conceptual Model and Hypotheses .......................................................................................................... 8 Study Design for 2014 ............................................................................................................................. 11 Update of 2010–2013 Multiyear Covariate Analysis .............................................................................. 12 Methods ...................................................................................................................................................... 13 Study Fish ................................................................................................................................................ 13 Tags ......................................................................................................................................................... 14 Tag Activation ......................................................................................................................................... 14 Tag Life Study .......................................................................................................................................... 15 Surgeon Training ..................................................................................................................................... 15 Fish Sorting .............................................................................................................................................. 15 First tagging week (4/15/2014 - 4/18/2014) ...................................................................................... 15 Second tagging week (4/29/2014 - 5/2/2014) .................................................................................... 16 Third tagging week (5/14/2014 - 5/17/2014) ..................................................................................... 16 Fish Tagging ............................................................................................................................................. 16 Tag Validation ......................................................................................................................................... 17 Fish transport .......................................................................................................................................... 17 Fish holding at release sites .................................................................................................................... 18 Releases .................................................................................................................................................. 18 Dummy-tagged fish ................................................................................................................................. 19 Fish Condition Assessments ................................................................................................................ 19 Fish Health .......................................................................................................................................... 19 Tag Retention Fish ............................................................................................................................... 20 Tag Detection .......................................................................................................................................... 21 Statistical Methods ................................................................................................................................. 21 Data Processing for Survival Analysis .................................................................................................. 21 Survival Model Development .............................................................................................................. 27 Parameter Estimation ......................................................................................................................... 39 Analysis of Tag Failure ......................................................................................................................... 42 2 Analysis of Surgeon Effects ................................................................................................................. 44 Analysis of Travel Time ........................................................................................................................ 45 Route Selection Analysis ..................................................................................................................... 45 Survival through Facilities ................................................................................................................... 45 Update of 2010–2013 Multiyear Covariate Analysis .......................................................................... 46 Results ......................................................................................................................................................... 48 Tagging .................................................................................................................................................... 48 Transport ................................................................................................................................................. 48 Dummy-tagged fish ................................................................................................................................. 48 Fish Health .......................................................................................................................................... 49 Tag Retention Fish ............................................................................................................................... 50 Detections of Acoustic-Tagged Fish ........................................................................................................ 50 Tag-Survival Model and Tag-Life Adjustments........................................................................................ 54 Surgeon Effects ....................................................................................................................................... 55 Survival and Route Entrainment Probabilities ........................................................................................ 56 Release Group 1 .................................................................................................................................. 56 Release Group 2 .................................................................................................................................. 58 Release Group 3 .................................................................................................................................. 60 Pooled Release Groups ....................................................................................................................... 61 Comparison between Release Groups ................................................................................................ 62 Travel Time .............................................................................................................................................. 62 Multiyear Covariate Analysis .................................................................................................................. 64 Route Selection Models ...................................................................................................................... 64 Survival: Mossdale to Head of Old River ............................................................................................. 65 Survival: Head of Old River to Chipps Island ....................................................................................... 68 Discussion ................................................................................................................................................... 71 Study in 2014 .......................................................................................................................................... 71 Fish Health .......................................................................................................................................... 71 Tag Programming Error ....................................................................................................................... 71 Sparse Data ......................................................................................................................................... 72 Survival between Lathrop and Garwood Bridge ................................................................................. 74