RESIDENCY, GROWTH, AND OUTMIGRATION SIZE OF JUVENILE CHINOOK SALMON (ONCORHYNCHUS TSHAWYTSCHA), ACROSS REARING LOCATIONS IN THE SHASTA RIVER, CALIFORNIA By Christine Mei Ling Roddam A Thesis Presented to The Faculty of Humboldt State University In Partial Fulfillment of the Requirements for the Degree Master of Science in Natural Resources: Fisheries Committee Membership Dr. Darren Ward, Committee Chair Dr. David Hankin, Committee Member Dr. Margaret Wilzbach, Committee Member July 2014 ABSTRACT Residency, Growth, and Outmigration Size of Juvenile Chinook Salmon (Oncorhynchus tshawytscha), Across Rearing Locations in the Shasta River, California Christine Mei Ling Roddam The Shasta River is one of the most productive tributaries of the Klamath River for Chinook salmon (Oncorhynchus tshawytscha). There are two primary spawning and juvenile rearing areas for Chinook salmon in the Shasta: the lower basin canyon, and the Shasta-Big Springs complex of the upper basin. These two areas of the basin are characterized by dramatically different in-stream habitats. This project evaluated differences in growth, residence time, and size at outmigration between these two critical salmonid habitat areas in the Shasta River using a combination of mark-recapture field studies and otolith strontium isotope ratio analysis of new and archived samples. In spring 2012 and 2013, during the primary rearing time for juvenile Chinook salmon in the Shasta River, three groups of fish were PIT tagged: (1) fish caught, tagged, and released in the upper basin; (2) fish caught at the lower basin, tagged and transplanted to the upper basin; and (3) fish caught, tagged, and released in the lower basin. Results indicate significant differences in residence time (defined as tagging date to date of outmigration), growth, and outmigration size between fish in the upper and lower basin, regardless of whether fish were originally caught in the upper basin or transplanted there. Several tagged fish residing in the Shasta-Big Springs complex ii displayed upstream movement and long residency times more similar to river-type Chinook salmon, than to ocean-type juveniles. Strontium isotope ratios (87Sr/86Sr) in stream water collected in March 2012 and 2013 were measured to be 0.704 (precision of 0.000031) and 0.706 (precision of 0.000019) for the upper basin and the lower basin respectively. Juvenile Chinook salmon that reared in the lower or upper basin are identifiable by the distinct differences in 87Sr/86Sr incorporated into the juvenile region of the otoliths. This creates a unique opportunity to determine the relative contribution of the two rearing areas to juvenile Chinook salmon production and, potentially, adult returns via analysis of juvenile and adult otoliths. Overall, I found consistent difference in the duration of residence, growth, and outmigration size between juvenile Chinook salmon that reared in the upper or lower Shasta River basin, irrespective of the location from which fish were initially sampled. Life history differences reflected differences in habitat conditions between the upper and lower basin. Additionally, this project demonstrated the potential use of otolith isotope analysis to identify the rearing location of juvenile Chinook salmon, which may affect marine survival and adult returns. iii ACKNOWLEDGEMENTS Funding for this project was provided by The National Oceanic and Atmospheric Administration (NOAA), the College of Natural Resources at Humboldt State University, and the Marin Rod and Gun Club. Very special thanks to my advisor, Dr. Darren Ward, whose support, patience, and encouragement were integral to this project. Thanks to my committee members, Dr. Margaret Wilzbach, and Dr. David Hankin for their valuable comments and suggestions on this manuscript. Enormous thanks to Bill Chesney, Chris Adams, Morgan Knechtle, Diana Chesney, Caitlin Bean, and Mike McVey at the California Department of Fish and Wildlife in Yreka, for their continued support, assistance, and encouragement on various aspects of this project. Thanks also to the entire CDFW field crew for their assistance with field work and data collection. Thanks to The Nature Conservancy for essential river access, and in particular Chris Babcock and Ada Fowler. Thanks to Justin Glessner at the University of California, Davis for his help with otolith microchemical analysis. Thanks also to Jim Hobbs at UC, Davis, and George Whitman at UC, Santa Cruz for their help with otolith preparation. Thanks to the HSU stockroom manager, Anthony Desch for providing me with essential field equipment and otolith preparation materials. Huge thanks to Tancy Moore for assistance with data analysis in Program Mark. I am incredibly grateful towards all my fellow graduate students in both the fisheries and wildlife departments at HSU for their friendship, support, and encouragement. And of course, this project would not have been possible without the love and support of my family, Thank you. iv TABLE OF CONTENTS ABSTRACT ........................................................................................................................ ii ACKNOWLEDGEMENTS ............................................................................................... iv TABLE OF CONTENTS .................................................................................................... v LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES .......................................................................................................... 10 LIST OF APPENDICES ................................................................................................... 12 INTRODUCTION ............................................................................................................ 13 MATERIALS AND METHODS ...................................................................................... 18 Study Area .................................................................................................................... 18 Shasta River .............................................................................................................. 18 Big Springs Creek ..................................................................................................... 21 Capture and Tagging Methods ...................................................................................... 22 Residency .................................................................................................................. 25 Growth and Outmigration Size ................................................................................. 28 Stream Water Collection and Microchemical Analysis ................................................ 29 Otolith Sampling and Preparation ................................................................................. 31 Otolith Microchemical Analysis ................................................................................... 33 Data Analysis ............................................................................................................ 34 RESULTS ......................................................................................................................... 37 Tagging ......................................................................................................................... 37 Residency .................................................................................................................. 37 v Growth and Outmigration Size ................................................................................. 43 Stream Water Microchemical Analysis ........................................................................ 52 Otolith Microchemical Analysis ................................................................................... 52 DISCUSSION ................................................................................................................... 66 REFERENCES ................................................................................................................. 75 PERSONAL COMMUNICATIONS ................................................................................ 81 vi LIST OF TABLES Table 1. Number of otoliths analyzed for strontium isotope ratios, per year and location. ........................................................................................................................................... 32 Table 2. Number of juvenile Chinook salmon that were PIT tagged (sample size) and mean fork length (FL), in millimeters, at tagging in groups that were captured, tagged and released in the upper river (UP-SH), and groups that were captured and tagged in the lower river and transplanted to the upper river (T-BSC), or to the lower river (T-CAN), per field season (tag year). ................................................................................................ 38 Table 3. Average residence times (number of days from date tagged to date of outmigration, rounded to the nearest integer) of juvenile Chinook salmon in the Shasta River for each tag group per year. Tag groups were defined as groups of juveniles that were captured, tagged and released in the upper river (UP-SH), and groups that were captured and tagged in the lower river and transplanted to the upper river (T-BSC), or to the lower river (T-CAN). Recapture sample sizes (n) are based on antenna detections and in-hand recaptures at the rotary