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Central Valley Chinook Salmon In-River Escapement Monitoring Plan

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Central Valley Chinook Salmon In-River Escapement Monitoring Plan State of California The Natural Resources Agency DEPARTMENT OF FISH AND GAME CENTRAL VALLEY CHINOOK SALMON IN-RIVER ESCAPEMENT MONITORING PLAN By Jennifer M. Bergman Fisheries Biologist Pacific States Marine Fisheries Commission Ryan M. Nielson Biometrician/Project Manager Western EcoSystems Technology, Inc. and Alice Low Staff Environmental Scientist California Department of Fish and Game Fisheries Branch Administrative Report Number: 2012-1 January, 2012 NOTE TO READERS The Central Valley Chinook Salmon In-river Escapement Monitoring Plan is a science- based collaborative approach to improve monitoring of adult Chinook salmon returning from the ocean to spawn in CV streams (escapement) and harvested in freshwater. Accurate estimates of escapement are critical to sound management of ocean and inland harvest and monitoring the recovery of listed stocks. A result of requests from fisheries resource managers, the development of this plan was funded in 2007 by the CALFED Ecosystem Restoration Program. From 2008 to 2011, the project team conducted a thorough statistical review of methods currently used in CV escapement surveys. Sampling designs were reviewed and recommendations were made for improvement of the field and analytical methods used in the existing programs. The most appropriate survey/monitoring technique (i.e., mark- recapture carcass surveys, redd surveys, snorkel surveys, and fish device counters) was identified for each watershed. To improve data management and reporting, an online database was reorganized and updated to provide a centralized location for sharing CV Chinook salmon escapement estimates and annual monitoring reports. Various population models have been used to estimate escapement from mark-recapture carcass survey data, without measures of precision and bias. The pooled Petersen, modified Schaefer, and Jolly-Seber models have been used for many years in the CV. Based on a review of the available mark-recapture models and simulation modeling, this plan recommends replacement of the models currently used with the superpopulation modification of the Cormack-Jolly-Seber (ClS) model. Successful implementation of this monitoring plan will rely on continuation of the collaborative and dedicated efforts of multiple agencies and entities throughout the CV. As with all of its products, Fisheries Branch is very interested in ascertaining the utility of this document, particularly regarding to its application to the monitoring and management decision process. Therefore, we encourage you to provide us with your comments. Please be assured that they will help us direct future efforts. Comments should be directed to Dr. Russell Bellmer, Fisheries Branch Monitoring Program Lead, 830 S Street, Sacramento, CA 95814,916327-8840, [email protected]. s~ Chief, Fisheries Branch TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................. 3 EXECUTIVE SUMMARY ............................................................................................. ix ACKNOWLEDGEMENTS ..........................................................................................xiii CHAPTER 1 INTRODUCTION.................................................................................... 1 CHAPTER 2 ESTIMATING CHINOOK SALMON ESCAPEMENT USING FISH DEVICE COUNTERS.................................................................................................... 11 CHAPTER 3 ESTIMATING CHINOOK SALMON ESCAPEMENT USING MARK-RECAPTURE CARCASS SURVEYS ............................................................ 19 CHAPTER 4 RECOVERING CODED-WIRE TAGS AND COLLECTING BIOLOGICAL DATA.................................................................................................... 31 CHAPTER 5 RECOMMENDATION FOR ESTIMATING TOTAL ANGLER HARVEST AND ANGLER EFFORT WITH THE CENTRAL VALLEY ANGLER SURVEY .......................................................................................................................... 36 CHAPTER 6 RECOMMENDED CHINOOK SALMON ESCAPEMENT MONITORING FOR THE BASALT AND POROUS LAVA DIVERSITY GROUP ........................................................................................................................................... 42 1 MAINSTEM SACRAMENTO RIVER................................................................ 42 1.1 WINTER-RUN CHINOOK SALMON................................................................ 42 SUMMARY OF EXISTING PROGRAM(S)....................................................... 42 REVIEW OF EXISTING PROGRAM(S)............................................................ 46 RECOMMENDED MONITORING .................................................................... 47 1.2 FALL-RUN CHINOOK SALMON..................................................................... 49 SUMMARY OF EXISTING PROGRAM(S)....................................................... 49 REVIEW OF EXISTING PROGRAM(S)............................................................ 54 RECOMMENDED MONITORING .................................................................... 55 1.3 LATE FALL-RUN CHINOOK SALMON .......................................................... 57 SUMMARY OF EXISTING PROGRAM(S)....................................................... 57 REVIEW OF EXISTING PROGRAM(S)............................................................ 58 RECOMMENDED MONITORING .................................................................... 58 2 COW CREEK....................................................................................................... 58 2.1 FALL-RUN CHINOOK SALMON..................................................................... 58 SUMMARY OF EXISTING PROGRAM(S)....................................................... 58 REVIEW OF EXISTING PROGRAM(S)............................................................ 59 RECOMMENDED MONITORING .................................................................... 59 3 BEAR CREEK...................................................................................................... 60 3.1 FALL-RUN CHINOOK SALMON..................................................................... 60 SUMMARY OF EXISTING PROGRAM(S)....................................................... 60 REVIEW OF EXISTING PROGRAM(S)............................................................ 61 RECOMMENDED MONITORING .................................................................... 61 3.2 LATE FALL-RUN CHINOOK SALMON .......................................................... 61 RECOMMENDED MONITORING .................................................................... 61 4 BATTLE CREEK................................................................................................. 62 4.1 WINTER-RUN CHINOOK SALMON................................................................ 62 SUMMARY OF EXISTING PROGRAM(S)....................................................... 62 REVIEW OF EXISTING PROGRAM(S)............................................................ 66 RECOMMENDED MONITORING .................................................................... 66 4.2 SPRING-RUN CHINOOK SALMON ................................................................. 66 SUMMARY OF EXISTING PROGRAM(S)....................................................... 66 REVIEW OF EXISTING PROGRAM(S)............................................................ 66 RECOMMENDED MONITORING .................................................................... 66 4.3 FALL-RUN CHINOOK SALMON..................................................................... 67 SUMMARY OF EXISTING PROGRAM(S)....................................................... 67 REVIEW OF EXISTING PROGRAM(S)............................................................ 68 RECOMMENDED MONITORING .................................................................... 68 4.4 LATE FALL-RUN CHINOOK SALMON .......................................................... 68 SUMMARY OF EXISTING PROGRAM(S)....................................................... 68 RECOMMENDED MONITORING .................................................................... 68 CHAPTER 7 RECOMMENDED CHINOOK SALMON ESCAPEMENT MONITORING FOR THE NORTHERN SIERRA NEVADA DIVERSITY GROUP ........................................................................................................................................... 69 5 ANTELOPE CREEK............................................................................................ 69 5.1 SPRING-RUN CHINOOK SALMON ................................................................. 69 SUMMARY OF EXISTING PROGRAM(S)....................................................... 69 REVIEW OF EXISTING PROGRAM(S)............................................................ 69 RECOMMENDED MONITORING .................................................................... 70 5.2 FALL-RUN CHINOOK SALMON..................................................................... 70 RECOMMENDED MONITORING .................................................................... 71 5.3 LATE FALL-RUN CHINOOK SALMON .......................................................... 71 RECOMMENDED MONITORING .................................................................... 71 6 MILL CREEK....................................................................................................... 71 6.1 SPRING-RUN CHINOOK SALMON ................................................................. 71 SUMMARY OF EXISTING PROGRAM(S)......................................................
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