Residency, Growth, and Outmigration Size of Juvenile Chinook

RESIDENCY, GROWTH, AND OUTMIGRATION SIZE OF JUVENILE CHINOOK

SALMON (ONCORHYNCHUS TSHAWYTSCHA), ACROSS REARING LOCATIONS

IN THE SHASTA RIVER, CALIFORNIA

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

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.

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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

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 screw trap at RKM 0 from March-July for both years. .. 39

Table 4. ANOVA summary statistics for the linear model with residence time (number of days between date tagged and date of outmigration) as the dependent variable, and tag group, fork length at tagging (mm), and tag year (either 2012 or 2013) as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.4326; residual sum of squares = 94083, and residual standard error = 14.27, with d.f.=462...... 40

Table 5. QAICc ranking results of the top three models, with apparent survival (Phi) to outmigration and recapture probability (p) of juvenile Chinook salmon in the Shasta River in 2012, using a Cormack-Jolly-Seber model in Program MARK and corrected for ĉ = 2.7. “Location” is the spatial variation in survival or recapture probability, “FL” is fork length of fish at tagging (mm), and “tag group” is either fish that were captured, tagged and released in the upper river (UP-SH), fish that were captured in the lower river, tagged and transplanted to the upper river (T-BSC), or transplanted to the lower river (T- CAN). Models are in order from best supported to least supported...... 41

tagged and released in the upper river (UP-SH), fish that were captured in the lower river, tagged and transplanted to the upper river (T-BSC), or transplanted to the lower river (T- CAN). Models are in order from best supported to least supported...... 42

Table 8. Estimated proportion, and standard errors, of tagged fish that out-migrated by the end of July, per year for each tag group, based on Phi 1from the real parameter estimates in Program MARK where Phi(location+tag group)p(location). “Tag group” is either fish that were captured, tagged and released in the upper river (UP-SH), fish that were captured in the lower river, tagged and transplanted to the upper river (T-BSC), or transplanted to the lower river (T-CAN)...... 44

Table 9. Total growth (mm, rounded to the nearest integer) of juvenile Chinook in the Shasta River for each tag group per year. Tag groups were defined as groups of juvenile Chinook salmon 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 in-hand recaptures at the rotary screw trap at RKM 0 from March-July for both years. .. 45

Table 10. ANOVA summary statistics for the linear model with total growth (mm) as the dependent variable, and tag group, fork length at tagging (mm), residence time (number of days between date tagged and date of outmigration), tag year (either 2012 or 2013), and the interaction term of tag group and residence time ([tag group]*Residence time) as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.9038; residual sum of squares = 2886.8, and residual standard error = 4.085, with d.f. =173...... 46

Table 11. Growth rate (mm/day, rounded to two decimal places) for juvenile Chinook salmon for each tag group per year. Tag groups were defined as groups of juvenile Chinook salmon 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 in- hand recaptures at the rotary screw trap at RKM 0 from March-July for both years...... 47

Table 12. ANOVA summary statistics for the linear model with growth rate (mm/day) as the dependent variable, and tag group, fork length at tagging (mm), residence time (number of days between date tagged and date of outmigration), and tag year (either 2012 or 2013), as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.13; residual sum of squares = 46.6, and mean squared error = 0.26, with d.f.=176...... 48

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Table 13. Outmigration fork length (mm, rounded to the nearest integer) for each tag group per year. Tag groups were defined as groups of juvenile Chinook salmon 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 in-hand recaptures at the rotary screw trap at RKM 0 from March-July for both years...... 50

Table 14. ANOVA summary statistics for the linear model with outmigration size (mm) as the dependent variable, and tag group, fork length at tagging (mm), residence time (number of days between date tagged and date of outmigration), tag year (either 2013 or 2013), and the interaction term of tag group and residence time([tag group]*Residence time) as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.9086; residual sum of squares = 2886.8, and residual standard error = 4.085, with d.f.=173...... 51

Table 15. Summary statistics for 87Sr/86Sr values measured for each stream water sample site within the Shasta River basin, organized from top to bottom as most upstream to most downstream...... 53

Table 16. ANOVA summary statistics for the linear model with water 87Sr/86Sr values as the dependent variable and sample location as the explanatory variables. Adjusted R2= 0.99; residual sum of squares = 1.03e-08; mean squared error = 2.07e-09, with d.f = 5. 54

Table 17. Counts of juvenile Chinook salmon otoliths, collected from the rotary screw trap at the mouth of the Shasta River (RKM 0), and categorized with either a lower basin rearing location (ID: Low-SH) or an upper basin rearing location (ID: Up-SH)...... 63

Table 18. Summary of results for the logistic regression with rearing location as the dependent variable (0= lower basin, 1= upper basin), and out-migration Julian week and fork length as the explanatory variables. Full model likelihood ratio test p-value= 0.039...... 65

LIST OF FIGURES

Figure 1. Map of the Shasta River, select influential tributaries, and locations of Dwinnell and Iron Gate Dams for reference...... 19

Figure 2. Map showing the locations of the seasonal CDFW rotary screw traps, the antenna arrays, (black circles), and transplantation sites (grey triangles) within (a) the lower Shasta and (b) the upper Shasta. Note: The antenna array at RKM 12 was installed in March 2013; all other arrays were installed prior to the 2012 field season...... 24

Figure 3. Schematic showing the locations of the PIT antenna arrays and the rotary screw trap on the Shasta River at RKM 0. Corresponding Cormack-Jolly-Seber apparent survival (Phi) and recapture probabilities (p) for each location are labeled, where p(location 1) is the tagging event. Note: “PIT Antenna RKM 0 A” was installed prior to the 2012 tagging season, and uninstalled prior to the 2013 tagging season. Figure adapted from Adams 2013...... 27

Figure 4. Map of stream water collection sites (symbolized as black circles)...... 30

Figure 5. Example of the laser beam line transect location (solid black line on otolith), drawn from the primordial core to the outer edge, on a juvenile Chinook otolith. The solid black arrow indicates the exogenous feeding check growth increment on this otolith...... 35

Figure 6. Example of 87Sr/86Sr values derived from a juvenile Chinook salmon otolith collected from RKM 51 in the upper basin. Each solid black circle is the averaged 87Sr/86Sr values that were sampled per every 10 µm. Distance along transect is from the core to the outer edge of the otolith. Horizontal lines indicate average water 87Sr/86Sr values for the lower basin (dotted line) and upper basin (dashed line)...... 55

Figure 7. Example of 87Sr/86Sr values derived from a juvenile Chinook salmon otolith collected from RKM 0 and later categorized with an upper Shasta rearing location. Each solid black circle is the averaged 87Sr/86Sr values that were sampled per every 10 µm. Distance along transect is from the core to the outer edge of the otolith. Horizontal lines indicate average water 87Sr/86Sr values for the lower basin (dotted line) and upper basin (dashed line)...... 58

Figure 8. Example of 87Sr/86Sr values derived from a juvenile Chinook salmon otolith collected from RKM 0 and later categorized with a lower Shasta rearing location. Each solid black circle is the averaged 87Sr/86Sr values that were sampled per every 10 µm. Distance along transect is from the core to the outer edge of the otolith. Horizontal lines

indicate average water 87Sr/86Sr values for the lower basin (dotted line) and upper basin (dashed line)...... 59

Figure 9. Examples of 87Sr/86Sr values derived from juvenile Chinook salmon otoliths from figures 10, 11, & 12 on the same graph for comparison. Distance along transect is from the core to the outer edge. “ID: Low-SH” (black solid line) is an example of 87Sr/86Sr values derived from a juvenile Chinook salmon otolith collected at RKM 0 and categorized with a lower basin rearing location. “ID: Up-SH” (black dashed line) is an example of 87Sr/86Sr values derived from juvenile Chinook salmon otolith collected at RKM 0 and categorized with an upper basin rearing location. “Known Up-SH” (black dotted line) is an example of 87Sr/86Sr values derived from juvenile Chinook salmon otolith collected at RKM 51 in the upper basin. Each solid black circle is the averaged 87Sr/86Sr values that were sampled per every 10 µm. Horizontal lines indicate average water 87Sr/86Sr values for the lower basin (gray dash-dot line) and upper basin (gray solid line)...... 60

Figure 10. Example of 87Sr/86Sr values derived from a juvenile Chinook salmon otolith collected from RKM 0 and later categorized with an upper Shasta rearing location, with distance along transect being from the core to the outer edge. This fish is the only example in which it was categorized with an upper basin rearing location, but later also reared in the lower basin. Each solid black circle is the averaged 87Sr/86Sr values that were sampled per every 10 µm. Horizontal lines indicate average water 87Sr/86Sr values for the lower basin (dotted line) and upper basin (dashed line)...... 61

Figure 11. Frequency histograms of otolith post-exogenous feeding check 87Sr/86Sr values measured from juvenile Chinook salmon otoliths collected from the rotary screw trap at the mouth of the Shasta River (RKM 0) in (a) 2011 and (b) 2012, and (c) from the rotary screw trap at RKM 51 in the upper basin in both 2011 and 2012. Stream water 87Sr/86Sr values for the upper basin (dashed vertical line) and lower basin (dotted vertical line) are shown...... 62

Figure 12. Relationship between Julian week and fork lengths of juvenile Chinook salmon, collected at the rotary screw trap at RKM 0, from which otoliths were sampled in (a) 2011 and (b) 2012. Juvenile Chinook salmon categorized with a lower basin rearing location are symbolized with hollow circles (ID: Low-SH), while those categorized with an upper basin rearing location are symbolized with solid black circles (ID: Up-SH). Refer to Appendix A for Julian weeks and corresponding calendar dates...... 64

LIST OF APPENDICES

Appendix A. Table of Julian weeks with corresponding calendar dates (month/day). ... 82

Appendix B. Water temperature in the Shasta River basin at (a) RKM 0, (b) RKM 51, and (c) BSC RKM 0, from Jan. 2012 to June or July 2013. The thermal tolerance of juvenile Chinook salmon (23°C) is indicated by the dashed horizontal black line...... 83

Appendix C. Hydrograph for the Shasta River (USGS site 11517500) from Jan. 2012 through Dec. 2013. Irrigation season is indicated on the graph by vertical dotted lines and gray arrows (April 1 to Oct. 1)...... 86

Appendix D. Beta estimates and standard errors (1), and real parameter estimates and standard errors (2) for the apparent survival to outmigration of tagged juvenile Chinook in the Shasta River for 2012 from the top Program MARK model Phi(location+FL)p(location), which is corrected for ĉ = 2.7. “Location” is the spatial variation in survival or recapture probability and “FL” is fork length of fish at tagging (mm). Phi is estimated apparent survival for the four recapture events (locations 1-4) and fork length at tagging (FL). Recapture probability is indicated by “p” for each recapture event (location 2-5). Note: Phi (location 3) was fixed at 1...... 87

Appendix E. Beta estimates and standard errors (1), and real parameter estimates and standard errors (2) for the apparent survival to outmigration of tagged juvenile Chinook in the Shasta River for 2013 from the top Program MARK model Phi(location+tag group)p(location+FL), which is corrected for ĉ = 2.6. “Location” is the spatial variation in survival or recapture probability, “FL” is fork length of fish at tagging (mm), and “tag group” is either fish that were captured, tagged and released in the upper river (UP-SH), fish that were captured in the lower river, tagged and transplanted to the upper river (T- BSC), or transplanted to the lower river (T-CAN). Phi is estimated apparent survival for the four recapture events (locations 1-3) and fork length at tagging (FL). Recapture probability is indicated by “p” for each recapture event (locations 2-4). Note: Phi (location 3) was fixed at 1...... 88

Appendix F. Map showing water sample sites in relation to the basic underlying geology of the Shasta River. Geology of the areas in white are not shown in this figure for purposes of simplicity. Hydrology and geology map layers are from USGS.gov...... 89

INTRODUCTION

The life-history of anadromous salmonids encompasses entire watersheds, from

mountain rivers to wide estuaries and the coastal oceans. Because juvenile salmonids are sensitive to changes in water quality, temperature, stream flow, turbidity, and food webs they may be useful indicator species for the condition of habitats in the watershed. A

decline of juvenile salmonid production in a watershed may reflect the extent of

anthropogenic habitat modification throughout the basin. Responses of salmon

populations to changes in habitat are often mediated by changes in life-histories.

Salmonid species with flexible, or plastic, juvenile life-history strategies may be able to persist despite anthropogenic alteration of freshwater rearing habitats, if their life-history response is adaptive in the altered habitat. In this study, I evaluated the life-history response of juvenile Chinook salmon (Oncorhynchus tshawytscha) to habitat conditions in two discrete spawning areas of the Shasta River, a Klamath River, CA, tributary with a history of extensive habitat modification.

Chinook, or king, salmon have one of the most variable life histories of all the

Pacific salmon species. Diversity in juvenile Chinook salmon life histories is well described (Healey 1991), but the circumstances under which juveniles may adopt one life history strategy over another are poorly understood. Generally, juvenile Chinook salmon follow either an ocean-type or stream-type life history (Healey 1991). Ocean-type

Chinook salmon emerge from stream gravel in early spring and spend 3-6 months in fresh

14 water before out-migrating to the estuary as smolts. Stream-type Chinook salmon remain in fresh water for at least a year before emigrating to the marine environment. Post- smolts typically spend 2-6 years in the ocean before migrating back into fresh water to spawn as adults. Evidence of genetic divergence between ocean and stream type Chinook salmon (Carl and Healey 1984, Clarke et al. 1994, Rasmussen et al. 2003) suggests that genetic differences may pre-determine the life history strategy of juveniles. However, environmental factors can also strongly influence residency, growth, and outmigration timing of juvenile Chinook salmon (Wedemeyer et al. 1980, Heming et al. 1982,

Nicholas and Hankin 1988, Taylor 1990, Beckman et al. 2003, Sykes et al. 2009). For instance, temperature and food sources are strongly associated with juvenile growth rate

(Taylor 1990, Heming et al. 1982), and variation in juvenile growth rate can significantly influence smoltification and timing of outmigration, as demonstrated by Beckman et al.

(1998, 2003). Smolt size and timing of outmigration vary widely among individuals and populations, and have long-term implications for ocean survival and the year of return as adults (Zabel & Achord 2004, Scheuerell et al. 2009). For the fall Chinook salmon population in Idaho’s Snake River, Perkins and Jager (2011) proposed that variations in life histories may ultimately be linked to juvenile growth. They suggested that if newly emerged juveniles were too far behind the “typical growth schedule” based on photoperiod cues and temperature, they were more likely to become yearling migrants, or stream-type Chinook salmon.

Historically the Shasta River was an exceptional system in terms of fall-run

Chinook salmon production (Wales 1951, NRC 2004). During the past several decades,

however, a steady decline in salmon populations in the Shasta River has been associated

with reduced in-stream flow, loss of riparian vegetation, and increased sediment inputs

(NMFS 2012). In the 1930s the largest annual spawning count for fall-run Chinook

salmon in the Shasta River was upwards of 80,000, but in recent years that count has

dropped to an average around 5,000 (Deas et al 2003, Chesney and Knechtle 2013).

Most juvenile Chinook salmon in the Shasta basin exhibit an ocean-type life

history. This type of life history requires that juveniles find rearing locations with

abundant prey to be able to rapidly grow to smolt size in a short time span in order to out- migrate before their first winter. There are two primary spawning areas for Chinook salmon in the Shasta: the canyon area in the lower basin, and the Big Springs complex in the valley of the upper basin. Juveniles rear in both areas, but the habitats have dramatically different characteristics. The purpose of this project is to evaluate these two key salmonid habitat areas in the Shasta River by comparing the relative quality (i.e. outmigration size, growth rate) and proportion of Chinook salmon smolts that are produced from the upper and lower basin, and to determine if life history strategies differ between juveniles rearing in the upper or lower basin.

Measuring life history characteristics of free-living fish in the field presents a number of important challenges that can be addressed using new technologies. Passive

Integrated Transponder (PIT) tags are a widely used tool to monitor movement, residency, growth, survival, and timing of outmigration in juvenile salmonids (Prentice et al. 1990, Achord et al. 1996, Skalski et al. 1998, Roussel et al. 2000). Otolith microchemical analysis has become an increasingly popular technique in determining

natal origins and migration patterns in salmonids (Bacon et al. 2004, Barnett-Johnson et al. 2005). Chemical signatures in stream water and prey items are incorporated into the calcified structures of fish (Campana 1999). If water chemistry is sufficiently different across sites, then fish from different rearing sites can be precisely distinguished based on the differences in strontium isotope ratios (87Sr/86Sr) (Ingram and Weber 1999, Kennedy et al. 2000, Campana and Thorrold 2001, Barnett-Johnson et al. 2010). Various environmental factors can influence deposition of elements in otoliths, such as temperature and salinity (Eldson and Gillanders 2004). Barnett-Johnson et al. (2008), however, demonstrated that relating strontium isotopes to landscape geology provides a basic framework in which to identify natal origins and movement of salmonids within freshwater habitats.

A limited number of studies have been conducted on the distribution, residence, and growth of juvenile Chinook salmon in the Shasta River basin. Relative growth, residency, and outmigration size of juveniles in the lower and upper basins has not been previously documented. I addressed three main questions in this study: (1) Do growth, outmigration size, and migration time differ between Chinook salmon from the upper and lower basin? (2) Are these life history differences fixed among individuals born in each location? (3) Are differences in rearing location of individuals reflected in differences in otolith chemistry? To answer these questions, my project uses a combination of mark- recapture field studies using PIT tag technology, and microchemical analysis of juvenile

Chinook salmon otoliths from known and unknown rearing origins within the Shasta

River Basin. Identifying critical rearing locations could provide useful guidance for

17 restoration and conservation efforts in the Shasta River watershed and could help direct restoration efforts to sites which may have greater positive impacts on Chinook production.

MATERIALS AND METHODS

Study Area

Shasta River

The Shasta River watershed is located in Siskiyou County, California and encompasses approximately 2,000 km2 (Figure 1). It is the fourth largest tributary to the

Klamath River and has an annual average flow of approximately 6.3 cubic meters per second (m3 s-1) during non-irrigation season (Jeffres et al. 2009). The Shasta River flows approximately 97 km northwestward from its headwaters on the north slope of Mt. Shasta and in the Eddy Mountains, to its confluence with the Klamath River. Tributaries of the

Shasta River include streams with flashy hydrographs dominated by precipitation inputs

(e.g. Parks Creek), and more stable spring-fed streams (e.g. Big Springs Creek); the main-stem exhibits characteristics of both. Since 1926, Dwinnell Dam, located at river kilometer (RKM) 58, has blocked access to about 22 percent of anadromous fish habitat in the upper Shasta River (NMFS 2012).

In the upper basin, the Shasta River meanders through the low-gradient Shasta

Valley for 50 km, from Dwinnell Dam to approximately RKM 12, near the confluence with Yreka Creek (Figure 1). The valley floor is primarily composed of volcanic materials deposited from ancient basaltic flows and a catastrophic debris avalanche from an ancestral form of Mount Shasta in the late Pleistocene (Jennings et al. 1977, Jeffres et al. 2010). Agricultural and ranching practices dominate the Shasta Valley and produce

Figure 1. Map of the Shasta River, select influential tributaries, and locations of Dwinnell and Iron Gate Dams for reference.

a heavy influence of run-off water that is returned to the river at elevated temperature and degraded quality. However, several spring-fed tributaries feed into the main-stem and provide cooler refugia with stable water temperatures year-round. Recently, extensive restoration efforts in the upper basin have been undertaken to improve habitat quality, including fencing off riparian areas from livestock, restoring riparian vegetation, and working with irrigators to maintain instream flows (Jeffres et al. 2010, AquaTerra 2011).

Efforts to monitor juvenile salmonid abundance, distribution, and health in relation to these various ongoing restoration projects in the upper basin are currently underway.

The lower 10 km of the Shasta River, before it empties into the Klamath River, wind through a high gradient canyon in the foothills of the Siskiyou Mountains. This canyon area is geologically comprised of intermediate volcanic rock (Jennings et al.

1977). Water temperatures fluctuate seasonally, becoming much warmer in the summer

and often exceeding the lethal thermal tolerance of juvenile Chinook salmon (23°C;

Moyle 2002) by July. In the early 1980s, the California Department of Water Resources

conducted spawning gravel enhancement efforts in the canyon reaches of the Shasta

River (McBain & Trush Inc et al. 2010). The effect this gravel augmentation has had on

juvenile salmonid populations is unclear.

At the mouth of the Shasta River, a seasonal fish weir and rotary screw trap has

been in operation by the California Department of Fish and Wildlife (CDFW) for over a

decade to monitor salmonid populations. As part of a juvenile salmonid monitoring

project, CDFW has also constructed a series of PIT tag remote detection stations, or

antenna arrays, throughout the Shasta River to observe the movement and distribution of

fish. The CDFW has also installed several HOBO U22 Water temp pro v2 loggers (Onset

Corp. Part # U22-001) throughout the Basin to monitor water temperature.

Big Springs Creek

Big Springs Creek (BSC) empties into the Shasta River around RKM 54 (Figure

1). At a total length of 3.7 km, from its spring-fed headwaters to the confluence with the

Shasta River, BSC is a small but influential tributary. An impoundment dam 3.5 km upstream from the mouth of BSC was constructed several decades ago for irrigation purposes. This impounded all the spring sources and created Big Springs Lake.

Temperatures of water discharging from the springs into the creek range from 10°C in the winter to 15°C in the summer (Jeffres et al. 2009). Stream flow contribution from BSC into the Shasta River averages about 2.3 m3 s-1 during the non-irrigation season (October through March), and about 1.5 m3 s-1 during the irrigation season (April through

September) (Jeffres et al. 2009).

Recognizing the importance of BSC production of salmonids in the Shasta River,

The Nature Conservancy purchased over 16 km2 of what is now Shasta Big Springs

Ranch (SBSR) in 2009. The Ranch includes approximately 3.5 km of BSC from its confluence with the Shasta River to the base of Big Springs Lake. Since the purchase of

SBSR, restoration efforts have included cattle exclusion fencing, riparian vegetation enhancement, and various ongoing wildlife and fisheries monitoring projects, while still maintaining an active cattle ranch on the property. As a result of riparian fencing, instream macrophytes have dramatically increased, altering some of the physical and ecological processes of the creek (Jeffres et al. 2010). As part of an ongoing salmonid

22 monitoring project by the CDFW, antenna arrays and water temperature loggers have been installed at various points along the length of BSC.

Capture and Tagging Methods

Fish sampling and handling was permitted under Humboldt State University IACUC

11/12.F103-A. Juvenile Chinook salmon from brood years 2011 and 2012 were PIT tagged. During the spring of 2012 and 2013, fish were captured and tagged between the months of March and May, the primary rearing period for Chinook salmon parr in the

Shasta River (Bill Chseney, CA Dept. of Fish & Wildlife, personal communications).

Juveniles in the lower canyon area were caught using a rotary screw trap (RST) located at the mouth of the Shasta River and operated by the CDFW. Juveniles in the upper basin were caught using hand nets, fyke nets, seines, or a rotary screw trap located at RKM 51.

One of my study goals was to evaluate the life-history response of juvenile

Chinook to habitat conditions encountered in each of the rearing areas. In order to determine if any life-history differences observed between the upper basin and the canyon were plastic, I designed a mark-recapture transplant experiment with three defined groups of tagged fish:

1. Fish caught, tagged, and released in the upper-Shasta, between RKM 51 and

RKM 60. Hereafter this tag group will be referred to as “UP-SH.”

2. Fish caught in the RST at RKM 0, tagged, and transplanted to RKM 2 of Big

Springs Creek. Hereafter this tag group will be referred to as “T-BSC.”

3. Fish caught in the RST at RKM 0, tagged, and transplanted to a site in the canyon

at RKM 9. Hereafter this tag group will be referred to as “T-CAN.”

(refer to Figure 2 for fish tagging and transplantation locations, and for antenna array locations).

To avoid tagging juveniles that were too small to safely implant PIT tags, and those that had already started the irreversible physiological changes associated with smolting, only fish between the fork lengths of 50 mm and 70 mm were tagged. Based on my visual observations, many juvenile Chinook in the Shasta River typically begin to express smolting characteristics, including loss of parr marks, silver coloration, and deciduous scales, once they reach a fork length of 70 mm. Prior to handling and tagging, fish were anesthetized in a small tub with two 2.4 g Alka-Seltzer-Gold™ tablets dissolved in approximately 2 liters of water. A small incision on the ventral left side between the pectoral and pelvic fins was made with the beveled tip of a 12 gauge needle.

A 9 mm PIT tag (134 kHz FDXB, Biomark) was manually inserted into the body cavity.

All PIT tags and syringe needles were disinfected in bleach and rinsed in distilled water prior to use. Fork length was measured to the nearest 1.0 mm for each fish tagged. Fish were allowed to recover in an aerated bucket until normal swimming behavior was observed. To minimize stress, fish were released into assigned locations of the river the same day they were tagged. Fish in the T-CAN group were released into a quarter-mile side channel, instead of the fast-flowing main-stem, at the transplantation site of RKM 9

(Figure 2). Fish in the T-BSC group were released once the temperature difference between water in the release bucket and Big Springs Creek was less than 2°C.

(a)

(b)

This was achieved by gradually exchanging the canyon water in the release bucket with

Big Springs Creek stream water. The fish were then released into an eddy with instream

macrophytes at the transplantation site of BSC RKM 2 (Figure 2).

Residency

From mid-March through July for both the 2012 and 2013 tagging field seasons,

residence time at each location was determined using instream detections from Allflex

antenna systems in place in Big Springs Creek and the main-stem Shasta River (refer to

Figure 2). When a tagged fish swam through an antenna system, the PIT tag’s unique 15- digit number was recorded onto a solar powered data logger on shore, allowing

movements of tagged individuals to be established. I defined residence time as the

number of days between initial date of tagging and date of detection at RKM 0. A more

detailed description of the antenna systems is given in Adams (2013). Antenna arrays

were maintained weekly. All tagging data were stored and organized using a Microsoft

Access database.

A linear model was fit with residence time as the dependent variable, tag group and

tag year as categorical independent variables, and fork length as a covariate, and analyzed

with ANOVA (Type III sums of squares). I used a post-hoc Tukey HSD test for a pair-

wise comparison of mean residence times between tag groups. Fish that resided past July

for either 2012 or 2013 were not included in the analysis.

Apparent survival to outmigration was estimated using the R Statistical Software

(R Development Core Team 2012) and Program MARK (White and Burnham 1999), to

determine if tag group and fork length affected survival to outmigration. The two field

seasons in 2012 and 2013 were analyzed separately. For each tagged individual, an

encounter history at RKM 0 was constructed. There were five capture events for 2012:

the tagging event, and recapture events at the RKM 0 C antenna, RKM 0 B antenna, the

RST at RKM 0, and RKM 0 A antenna (Figure 3). There were four capture events for

2013: the tagging event, and recaptures at the RKM 0 C antenna, RKM 0 B antenna, and

the RST at RKM 0 (Figure 3). The antenna at RKM 0 A was uninstalled prior to the 2013

field season. For both years, survival (Phi) between the RKM 0 B antenna and the RST at

RKM 0 was assumed equal to one because the antenna are only about 10 meters apart

(Figure 3).

In R, the package “RMark” (Laake and Rexstad 2008; Laake et al. 2012) was

used to construct Cormack-Jolly-Seber (CJS) models that were fit using the logit link

function. The base model was Phi(location)p(location), which allowed apparent survival

(Phi) and recapture probability (p) to vary between recapture intervals and locations.

Simple models were built with tag group and fork length as covariates in order to

determine overall survival (Phi) to outmigration and recapture probability (p) at RKM 0.

For each year, the ĉ of the full model with no continuous covariates was used to

determine if the assumptions for the CJS model were met, where ĉ ≈ χ2/df (Cooch and

White 2013). For both years, the ĉ for the top model was less than 3, which was considered “relatively safe” (Lebreton et al. 1992, White and Burnham 1999). Once the models were built, they were imported into Program MARK for model selection using the Akaike information criterion corrected for small sample sizes (AICc; Burnham and

Phi 1 PIT Antenna RKM 0 C p (location 2)

Phi 2 530 meters

Shasta

PIT Antenna RKM 0 B Flow

p (location 3) Phi 3 = 1 River

10 meters

Rotary Screw Trap p (location 4)

Phi 4 40 meters

PIT Antenna RKM 0 A p (location 5) 180 meters

Klamath River

Anderson 2002). The estimated ĉ for both years was used to convert to QAICc for model

selection: values were ĉ = 2.7 and ĉ =2.6 for 2012 and 2013 respectively. Apparent

survival to outmigration for fish tagged at fork lengths between 50 mm and 70 mm was

estimated for each tag group for each of the two field seasons.

Growth and Outmigration Size

Individual fish growth and size at outmigration were obtained through recapture of PIT-tagged fish in the rotary screw trap (RST) at the mouth of the Shasta River from

mid-March through July for both the 2012 and 2013 tagging seasons. Throughout the same time periods, fyke nets and hand nets were used to recapture juveniles in the upper

Shasta-Big Springs complex to monitor growth rate, and to check for PIT tag retention.

To determine the presence of PIT tags, recaptured fish were scanned with a Biomark FS-

2001 or Pocket Reader EX. Total growth was defined as the difference in fork length (in

mm) between the date a fish was tagged and the date it was recaptured at the RST at

RKM 0. Growth rate was estimated as millimeters per day that a tagged fish grew until it

out migrated. A linear model was fit with total growth as the dependent variable, and tag

group, residence time, fork length, tag year, and the interaction term of tag group and

residence time as the explanatory variables. An ANOVA (Type III sums of squares) was

performed and results reported. A Tukey HSD test was completed to compare mean total

growth between tag groups. Another linear model was fit with growth rate as the

dependent variable, tag group and tag year as categorical explanatory variables, and fork

length as a covariate. An ANOVA (Type III sums of squares) was also performed, and a

Tukey HSD test was completed to compare mean growth rates between tag groups.

Finally, a linear model was fit with outmigration size as the dependent variable, and tag

group, residence time, fork length, tag year, and the interaction term of tag group and

residence time as the explanatory variables. An ANOVA (Type III sums of squares) was performed for this model as well. A Turkey HSD test completed to compare mean outmigration size between tag groups. For the linear models with total growth and outmigration size as the dependent variables, collinearity between tag group and residence time was eliminated by centering residence time on tag group. This allowed for the effect of residence time to represent the difference between the residence time of an individual and the mean residence time of other individuals in the same tag group.

Stream Water Collection and Microchemical Analysis

Stream water samples were collected from five sites: RKM 0, RKM 12, RKM 51,

RKM 56, and BSC RKM 1 (Figure 4). All sites were sampled in mid-March, during the primary rearing time for juvenile Chinook salmon. Samples from sites RKM 0, RKM 56, and BSC RKM 1 were collected in 2012, while samples from sites RKM 12 and RKM 51 were collected in 2013. Two water samples were taken at each site. Fifty ml of stream

water was vacuum-filtered through a 0.45µm membrane that had been prewashed with

distilled water and the filtrate from each site. A blank with distilled water was sampled

in the same manner at each stream water collection site, but without the prewash from the

filtrate. Samples and blanks were stored in polypropylene bottles and acidified to pH 2

with 12 Molar hydrochloric acid until microchemical analysis.

Figure 4. Map of stream water collection sites (symbolized as black circles).

Water samples from sites RKM 0, RKM 56, and BSC RKM 1 were sent to the

College of Oceanographic and Atmospheric Sciences at Oregon State University, and

water samples from sites RKM 12 and RKM 51 were sent to the University of California

Davis Interdisciplinary Center for Inductively-Coupled Plasma Mass Spectrometry to be

chemically analyzed to determine strontium isotope ratios (87Sr/86Sr). For a detailed

description of stream water chemical analysis procedures refer to Courter et al. (2013).

To determine the degree to which water sample sites provided distinct separation of water

87Sr/86Sr values, a one-way ANOVA test was performed with a post-hoc Tukey HSD test to compare mean 87Sr/86Sr values between sample sites.

Otolith Sampling and Preparation

Sagittal otoliths were extracted from mortalities of juvenile Chinook salmon that

were collected in rotary screw traps at RKM 0 and at RKM 51 (refer to Figure 2) during

spring 2011 and 2012 by the CDFW field crew. Once I extracted the otoliths, they were rinsed with laboratory grade distilled water and stored in dry vials.

Otoliths that were collected from RKM 0 were sub-sampled by size and Julian week. For 2011 and 2012, otoliths from three fish, one each from the largest, smallest, and intermediate fork length sizes per Julian week were analyzed (Table 1; refer to

Appendix A for Julian week and corresponding calendar dates). All otoliths collected at

RKM 51 from both years were analyzed (Table 1). Otoliths collected from fish from the

RST at RKM 0 had unknown rearing locations (they could have been caught while out-

Table 1. Number of otoliths analyzed for strontium isotope ratios, per year and location.

Collection Location Year collected RKM 0 RKM 51 Total 2011 43 6 49 2012 28 4 32 Total 71 10 81

migrating from either the upper or lower basin), whereas otoliths collected from fish from

RKM 51 were presumed to have reared in the upper basin.

Otoliths were mounted onto glass slides and sanded by hand in a circular motion

following Stevenson & Campana (1992). Juvenile otoliths were permanently attached,

sulcus side up, to a section of a glass cover slip with Crystal BondTM509. The cover slip with the otolith was then affixed using Crystal BondTM 509 to a glass slide for polishing.

For larger otoliths from fish with fork lengths greater than 80 mm, a single side of the

otolith was polished with 1500 grit wet/dry sand paper and rinsed with deionized water.

A fine polish was then attained with 5 micron and 3 micron lapping films. Smaller

otoliths were polished only with the lapping films and rinsed with deionized water.

Polishing progress was observed with an Olympus BX40 microscope, with an attached

QImaging™ Retiga-2000R digital camera. Polishing was considered complete once a

transect was visible from the primordial core, through the exogenous feeding check, and

to the edge of the otolith. The exogenous feeding check on the otolith indicates when a

fish has depleted its yolk sac and has begun feeding on outside sources (Barnett-Johnson

et al. 2007). In preparation for chemical analysis, the cover slips with the attached

otoliths were cut away with a diamond tipped pen, transferred and affixed onto

petrographic slides (27 x 46 mm) using double-sided tape.

Otolith Microchemical Analysis

Otolith 87Sr/86Sr values were measured by laser-ablation multiple-collection- inductively- coupled-plasma-mass spectrometry (LA-MC-ICPMS technique) at the University of

California, Davis, Interdisciplinary Center for Plasma Mass Spectrometry. A line transect

was drawn with a laser beam of 40 µm in diameter across each otolith from the

primordial core to the edge at a speed of 10 µm per second (Figure 5). As the laser beam

transected the otolith, three discrete 87Sr/86Sr values per second were sampled. Depending

on the size of the otolith, it took 35-70 seconds for the laser beam to complete the transect

along the otolith, producing numerous discrete values sampled per otolith. An in-house

marine coral standard was processed at the beginning of each day that analysis took

place. For a more detailed description of the instrumentation used and strontium isotope

measurement calculations, refer to Barnett-Johnson et al. (2005) and Courter et al.

(2013).

Data Analysis

Measurements of 87Sr/86Sr values subsequent to the exogenous feeding check

from each otolith were averaged, and compared to the stream water 87Sr/86Sr values to

assign rearing locations of fish with unknown origins in the Shasta River. The laser beam

transected the exogenous feeding check at approximately the 15 second time-point. To avoid possible marine 87Sr/86Sr values, I averaged 87Sr/86Sr values from the 20 second

time-point onward until the end of the transect to obtain a final 87Sr/86Sr value at which to

assign fish to a rearing location. Additionally, 87Sr/86Sr values of otoliths from fish with a

known upper basin rearing origin were compared to 87Sr/86Sr values of otoliths from fish

with unknown rearing origin. I compared histograms of the frequencies of 87Sr/86Sr

values for 2011 and 2012 for fish with unknown and known rearing origins. Based on

these comparisons, fish from unknown rearing areas were then categorized as

1 millimeter

36 having either reared in the upper or lower basin. To determine if outmigration size and timing could be used to identify fish to their juvenile rearing location, a logistic regression was performed with rearing location assignment from the otolith analysis as the dependent variable (where 0= lower basin, and 1= upper basin), outmigration Julian week as a categorical explanatory variable, and outmigration fork length as a continuous explanatory variable.

RESULTS

Tagging

Residency

Numbers of PIT tagged juvenile Chinook salmon varied little between years for the T-BSC and T-CAN groups (Table 2), but the number of tagged juveniles in the UP-

SH group was increased from 15 fish in 2012 to 191 fish in 2013, due to differences in sampling techniques and increased sampling effort. Mean fork lengths at tagging did not differ considerably among groups or years, and ranged from 55-59 mm (Table 2). On average, residence time for juvenile Chinook salmon that were detected out-migrating was about 5-fold longer for the UP-SH and T-BSC groups than for the T-CAN group

(Table 3). Residence time differed with tag group and fork length, but not with tag year

(Table 4). Mean residence time differed between the T-BSC and T-CAN groups, and the

UP-SH and T-CAN groups (post-hoc Tukey HSD test, p<0.01). Residence time did not differ between the T-BSC and UP-SH groups (p>0.05). Residence time generally decreased with increasing fork length regardless of tag group or transplant location.

For the 2012 tagging season, fork length, but not tag group, seemed to have an effect on apparent survival to outmigration (Table 5). For the 2013 tagging season, tag group had an effect on apparent survival to outmigration, but not fork length (Table 6).

Apparent survival to outmigration generally increased with fork length for all tag groups for both years. The estimated proportion of tagged fish that out migrated by July for both

Non-transplant tag group Transplant tag groups UP-SH T-BSC T-CAN Tag Sample Mean Tag Sample Mean Tag Sample Mean Tag Total Year size FL±SE size FL±SE size FL±SE Tagged 2012 15 55±1.3 315 58±0.3 255 58±0.4 585 2013 191 57±2.2 200 57±1.6 200 59±2.2 591 Total Tagged 206 515 455 1176

95% CI for mean Tag Std. Std. Year Group n Mean Dev. Error Lower Upper Min. Max.* UP-SH 5 36 22 7.07 22 50 2 63 2012 T-BSC 133 29 19 1.35 26 31 2 79 T-CAN 109 4 8 2 0 47 1 47 UP-SH 60 30 17 2.59 25 35 4 70 2013 T-BSC 67 27 18 1.78 24 31 2 63 T-CAN 93 8 10 2.33 3 12 1 45 Years UP-SH 65 30 17 2.16 26 34 2 70 Pooled T-BSC 200 28 19 1.068 26 30 2 79 T-CAN 202 6 9 1.506 3 9 1 47

*Excludes 7 known outliers that resided past July for 2012. There were no known outliers that resided past July for 2013.

Coefficients: Estimate Std. Error F p T-CAN (Intercept) 62.40 7.68 T-BSC 23.84 1.44 159.03 < 0.01 UP-SH 23.82 2.14 Fork length -0.97 0.13 57.02 < 0.01 Tag year 2013 -0.28 1.44 0.04 > 0.05

No. of Δ QAICc Δ QAICc Weight Model Parameters (K) Phi(location+FL)p(location) 0.00 0.33754 8 Phi(location+FL)p(location+tag group) 1.65 0.14778 10 Phi(location+FL)p(location+FL) 1.88 0.13169 9

Table 6. QAICc ranking results of the top three models, with apparent survival (Phi) to outmigration and recapture probability (p) of juvenile Chinook salmon in the Shasta River in 2013, using a Cormack-Jolly-Seber model in Program MARK and corrected for ĉ = 2.6. “Location” is the spatial variation in survival or recapture probability, “FL” is fork length of fish at tagging (mm), and “tag group” is either fish that were captured, tagged and released in the upper river (UP-SH), fish that were captured in the lower river, tagged and transplanted to the upper river (T-BSC), or transplanted to the lower river (T- CAN). Models are in order from best supported to least supported.

No. of Δ QAICc Δ QAICc Weight Parameters Model (K) Phi (location+tag group)p(location+FL) 0.00 0.22453 8 Phi(location)p(location+FL) 0.39 0.18491 6 Phi(location+tag group+FL)p(location) 1.91 0.08642 8

years was extracted from Phi 1 from the real parameter estimates from the model where

Phi(location+tag group)p(location) (Table 8).

Growth and Outmigration Size

Total growth, from date tagged until out-migration, averaged 5 times higher for the UP-SH and T-BSC tag groups, than for the T-CAN group (Table 9). In 2012, relatively high flows and low numbers of juveniles in the upper basin led to a small sample size in the UP-SH group. Of the 15 fish in the UP-SH group that were tagged, only one was recaptured at the RST at RKM 0, thus statistical analysis of growth and outmigration data was not performed for 2012 for that tag group. Given that residence time was not significantly different between the UP-SH and the T-BSC groups for both years, it is reasonable to assume that the mean total growth for the UP-SH group in 2012 was similar to that observed in the T-BSC group for both years and to the UP-SH group in 2013. Total growth of juvenile Chinook salmon was affected by tag group and residence time (Table 10). Total growth of juvenile Chinook salmon differed between the

T-BSC and T-CAN groups, and between the UP-SH and T-CAN groups (p <0.01). Mean total growth for the T-BSC and UP-SH groups was not significantly different (p >0.05).

Total growth generally increased with increased residence time regardless of tag group or transplant location.

Mean growth rates over both years were approximately 3 times higher for the UP-

SH and T-BSC groups than the T-CAN group (Table 11). Mean growth rate of juvenile

Chinook salmon was affected by tag group and fork length at tagging (Table 12).

Table 7. Estimated proportion, and standard errors, of tagged fish that out-migrated by the end of July, per year for each tag group, based on Phi 1from the real parameter estimates in Program MARK where Phi(location+tag group)p(location). “Tag group” is either fish that were captured, tagged and released in the upper river (UP-SH), fish that were captured in the lower river, tagged and transplanted to the upper river (T-BSC), or transplanted to the lower river (T-CAN).

Tag group Year UP-SH T-BSC T-CAN 2012 0.63 ± 0.20 0.68 ± 0.10 0.66 ± 0.11 2013 0.43 ± 0.08 0.47 ± 0.08 0.63 ± 0.08

Table 8. Total growth (mm, rounded to the nearest integer) of juvenile Chinook in the Shasta River for each tag group per year. Tag groups were defined as groups of juvenile Chinook salmon 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 in-hand recaptures at the rotary screw trap at RKM 0 from March-July for both years.

95% CI for mean Tag Std. Std. Year Group n Mean Dev. Error Lower Upper Min. Max. UP-SH 1 28 NA NA NA NA 28 28 2012 T-BSC 52 18 15 1.72 14 21 -3 46 T-CAN 28 2 6 2.9 -4 8 -4 25 UP-SH 28 17 12 2.75 12 23 1 43 2013 T-BSC 34 15 12 1.83 11 18 -4 36 T-CAN 39 4 8 2.5 -1 9 -2 40 Years UP-SH 29 18 12 2.5 13 22 1 43 Pooled T-BSC 86 16 14 1.24 14 19 -4 46 T-CAN 67 3 7 1.87 -1 7 -4 40

Table 9. ANOVA summary statistics for the linear model with total growth (mm) as the dependent variable, and tag group, fork length at tagging (mm), residence time (number of days between date tagged and date of outmigration), tag year (either 2012 or 2013), and the interaction term of tag group and residence time ([tag group]*Residence time) as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.9038; residual sum of squares = 2886.8, and residual standard error = 4.085, with d.f. =173.

Coefficients: Estimate Std. Error F p T-CAN (Intercept) 4.51 3.76 T-BSC 13.18 0.69 216.85 < 0.01 UP-SH 14.95 0.99 Fork length -0.01 0.06 0.04 > 0.05 Residence time 0.79 0.06 178.72 < 0.01 Tag year 2013 -1.10 0.67 2.67 > 0.05 T-BSC*Residence time -0.08 0.06 1.37 > 0.05 UP-SH*Residence time -0.12 0.07

Table 10. Growth rate (mm/day, rounded to two decimal places) for juvenile Chinook salmon for each tag group per year. Tag groups were defined as groups of juvenile Chinook salmon 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 in- hand recaptures at the rotary screw trap at RKM 0 from March-July for both years.

95% CI for mean Tag Std. Std. Year Group n Mean Dev. Error Lower Upper Min. Max. UP-SH 1 0.82 NA NA NA NA 0.82 0.82 2012 T-BSC 52 0.51 0.38 0.08 0.34 0.66 -0.6 0.37 T-CAN 28 0.26 0.87 0.14 -0.01 0.53 -2 2 UP-SH 28 0.61 0.26 0.12 0.37 0.85 0.22 1.4 2013 T-BSC 24 0.51 0.41 0.08 0.35 0.67 -1 1.6 T-CAN 39 0.14 0.62 0.11 -0.08 0.36 -1 1.5 Years UP-SH 29 0.61 0.26 0.12 0.39 0.84 0.22 1.4 Pooled T-BSC 86 0.51 0.38 0.06 0.4 0.62 -1 1.6 T-CAN 67 0.19 0.73 0.09 0.02 0.36 -2 2

Table 11. ANOVA summary statistics for the linear model with growth rate (mm/day) as the dependent variable, and tag group, fork length at tagging (mm), residence time (number of days between date tagged and date of outmigration), and tag year (either 2012 or 2013), as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.13; residual sum of squares = 46.6, and mean squared error = 0.26, with d.f.=176.

Coefficients: Estimate Std. Error F p T-CAN (Intercept) 1.73 0.45 T-BSC 0.37 0.09 13.9 < 0.01 UP-SH 0.56 0.12 Fork length -0.03 0.01 11.79 < 0.01 Tag year 2013 -0.08 0.08 0.85 > 0.05

In 2012, mean growth rates for the T-BSC and T-CAN groups were not significantly different (p > 0.05). However in 2013, and with the two years pooled, the mean growth rates between the T-BSC and T-CAN groups, and between the UP-SH and T-CAN

groups, were significantly different (p < 0.01). Mean growth rates between the UP-SH and T-BSC groups were not significantly different (p > 0.05). The seemingly large range in growth rates for the T-CAN group can most likely be attributed to in-field

measurement errors of recaptured fish. For example, if a fish out-migrated one day after it was tagged, and a recapture fork length was taken that was one millimeter less than or greater than the measured fork length at tagging, then it would seem that fish had a growth rate of ±1.00 mm/day. Realistically, however, that may not be the case.

On average, juvenile Chinook salmon in the UP-SH and T-BSC groups out- migrated at a fork length around 15 mm larger than fish in the T-CAN group (Table 13).

Outmigration size was affected by tag group, residence time, and fork length at tagging

(Table 14). Mean outmigration size of juvenile Chinook salmon between the T-BSC and

T-CAN groups, and between the UP-SH and T-CAN groups, were significantly different

(p <0.01). Mean outmigration size between the T-BSC and UP-SH groups was not significantly different (p >0.05).

Table 12. Outmigration fork length (mm, rounded to the nearest integer) for each tag group per year. Tag groups were defined as groups of juvenile Chinook salmon 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 in-hand recaptures at the rotary screw trap at RKM 0 from March-July for both years.

95% CI for mean Tag Std. Std. Year Group n Mean Dev. Error Lower Upper Min. Max. UP-SH 1 89 NA NA NA NA 89 89 2012 T-BSC 52 78 13 1.54 75 81 54 101 T-CAN 28 59 7 2.61 54 65 51 82 UP-SH 28 78 12 2.76 73 84 56 95 2013 T-BSC 34 73 13 1.84 70 77 52 94 T-CAN 39 61 7 2.51 56 66 52 94 Years UP-SH 29 79 12 2.38 74 83 56 95 Pooled T-BSC 86 76 13 1.18 74 78 52 101 T-CAN 67 60 7 1.78 57 64 51 94

Table 13. ANOVA summary statistics for the linear model with outmigration size (mm) as the dependent variable, and tag group, fork length at tagging (mm), residence time (number of days between date tagged and date of outmigration), tag year (either 2013 or 2013), and the interaction term of tag group and residence time([tag group]*Residence time) as the explanatory variables. Tag groups were defined as groups of juvenile Chinook salmon 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). Adjusted R2 = 0.9086; residual sum of squares = 2886.8, and residual standard error = 4.085, with d.f.=173.

Coefficients: Estimate Std. Error F p T-CAN (Intercept) 4.51 3.76 T-BSC 13.18 0.69 216.85 < 0.01 UP-SH 14.95 0.99 Fork length 0.99 0.06 234.15 < 0.01 Residence time 0.79 0.06 178.72 < 0.01 Tag year 2013 -1.10 0.67 2.67 > 0.05 T-BSC*Residence time -0.08 0.06 1.37 > 0.05 UP-SH*Residence time -0.12 0.07

Stream Water Microchemical Analysis

Mean stream water 87Sr/86Sr ratio values differed between the upper and lower

basin sites, with little variation in values across replicates (Table 15). An ANOVA of the

linear model with water 87Sr/86Sr values as the dependent variable showed the

explanatory variable of sample location to be significant (Table 16). The post-hoc Turkey

HSD test showed that water 87Sr/86Sr values did not differ among upper basin locations

(BSC RKM 1, RKM 56, and RKM 51) and they did not differ between lower basin

locations (RKM 0 and RKM 12).

Otolith Microchemical Analysis

Each juvenile Chinook salmon otolith had its own87Sr/86Sr value profile, which

followed the laser beam line transect from the primordial core to the outer edge.

Typically, the primordial core for each otolith had a 87Sr/86Sr value of 0.708 to 0.709,

signifying a maternal marine strontium signature. As the laser beam transected past the

exogenous feeding check increment, 87Sr/86Sr values gradually decreased and then

leveled out at a value dependent upon where that individual fish reared in the Shasta

basin. I examined each individual otolith 87Sr/86Sr profile and compared it to the stream water analysis results and to the 87Sr/86Sr profiles of otoliths from juveniles that were

collected at RKM 51 in the upper basin. Juvenile Chinook salmon otoliths that were

collected at RKM 51 all had a 87Sr/86Sr profile that leveled out around 0.703-0.704

(Figure 6). Juvenile Chinook salmon otoliths that were collected at RKM 0 and later

Table 14. Summary statistics for 87Sr/86Sr values measured for each stream water sample site within the Shasta River basin, organized from top to bottom as most upstream to most downstream.

Sample site n Mean Range RKM 56 2 0.703930 0.703929 to 0.703931 Upper basin BSC RKM 1 2 0.704062 0.703994 to 0.704129 RKM 51 2 0.704110 0.704108 to 0.704111 Lower basin RKM 12 2 0.705288 0.705285 to 0.705292 RKM 0 2 0.706153 0.706128 to 0.706177

Table 15. ANOVA summary statistics for the linear model with water 87Sr/86Sr values as the dependent variable and sample location as the explanatory variables. Adjusted R2= 0.99; residual sum of squares = 1.03e-08; mean squared error = 2.07e-09, with d.f = 5.

Coefficients Estimate Std. Error F p RKM 0 (Intercept) 0.7062 0.00003216 RKM 12 -0.000864 0.00004548 RKM 51 -0.002043 0.00004548 919.62 < 0.01 RKM 56 -0.002223 0.00004548 BSC RKM 1 -0.002091 0.00004548

0.71 Otolith 87Sr/86Sr

Lower basin water 0.709 Primordial core (Marine) 87Sr/86Sr Upper basin water 87Sr/86Sr 0.708 Start of exogenous feeding

0.707

87 Sr/ 86 Sr 0.706

0.705 Upper Shasta rearing

0.704

0.703 0 100 200 300 400 Distance along transect (µm)

categorized with an upper basin rearing location typically had a 87Sr/86Sr profile that also

leveled out around 0.703-0.704 (Figure 7). On the other hand, juvenile Chinook salmon

otoliths that were categorized with a lower basin rearing location typically had a 87Sr/86Sr

profile that leveled out around 0.706-0.707 (Figure 8). A comparison of the three profile

types onto one graph further illustrated the distinct difference in 87Sr/86Sr profiles of

otoliths from juvenile Chinook salmon that reared in the upper Shasta River, from those that reared in the lower Shasta River (Figure 9). One 87Sr/86Sr profile from a juvenile was

categorized with an upper basin rearing location, but 87Sr/86Sr values derived towards the

outer edge of the otolith indicated that the fish later reared in the lower basin (Figure 10).

This was the only individual with this type of profile. It suggests that the downstream

movement and residency of juvenile Chinook within the Shasta River basin may possibly

be “observed” via otolith microchemistry, given that the fish feeds and resides long

enough in those areas to incorporate the strontium signature.

Frequency histograms were made showing otolith 87Sr/86Sr values, measured after

the exogenous feeding check, from juveniles collected at RKM 0 in 2011 (Figure 11a)

and 2012 (Figure 11b), and from fish collected at RKM 51 in the upper basin for 2011

and 2012 combined (Figure 11c). I found that of the 43 juvenile Chinook salmon otoliths

collected from RKM 0 in 2011, one fish had an otolith 87Sr/86Sr value consistent with

rearing in the upper basin; while of the 28 juveniles collected from RKM 0 in 2012, five

fish had an otolith 87Sr/86Sr value consistent with rearing in the upper basin (Table 17).

Upper basin juveniles typically out-migrated later in the spring than did lower basin fish.

Additionally, outmigration fork length of upper basin juveniles was generally larger than

57 outmigration fork length of lower basin juveniles (Figure 12). However, outmigration

Julian week and outmigration size could not successfully identify individuals to their rearing location within the basin (Table 18).

0.71 Otolith 87Sr/86Sr

0.709 Primordial core Lower basin water (Marine) 87Sr/86Sr Upper basin water 87Sr/86Sr 0.708 Start of exogenous feeding

0.707

0.706 87 Sr / 86 Sr 87 Sr

0.705 Upper Shasta rearing

0.704

0.703 0 100 200 300 400 500 600 Distance along transect (µm)

0.71 Otolith 87Sr/86Sr

Lower basin water Primordial core 87Sr/86Sr 0.709 (Marine) Upper basin water Start of 87Sr/86Sr exogenous feeding 0.708

0.707 Lower Shasta rearing

0.706 87 Sr / 86 Sr 87 Sr

0.705

0.704

0.703 0 50 100 150 200 250 300 350 400 Distance along transect (µm)

0.71 ID:Low-SH ID:Up-SH Known Up-SH 0.709 Lower basin water 87Sr/86Sr Upper basin water 87Sr/86Sr

0.708

0.707

0.706 87 Sr / 86 Sr 87 Sr

0.705

0.704

0.703 0 100 200 300 400 500 600 Distance along transect (µm)

0.71 Otolith 87Sr/86Sr

Lower basin wter 0.709 87Sr/86Sr Upper basin water 87Sr/86Sr 0.708

0.707

0.706 87 Sr / 86 Sr 87 Sr

0.705

0.704

0.703 0 100 200 300 400 500 Distance along transect (µm)

(a)

(b)

(c)

Table 16. Counts of juvenile Chinook salmon otoliths, collected from the rotary screw trap at the mouth of the Shasta River (RKM 0), and categorized with either a lower basin rearing location (ID: Low-SH) or an upper basin rearing location (ID: Up-SH).

RKM 0 Year collected ID: Low-SH ID: Up-SH Total 2011 42 1 43 2012 23 5 28 Total 65 6 71

(a)

(b)

Table 17. Summary of results for the logistic regression with rearing location as the dependent variable (0= lower basin, 1= upper basin), and out-migration Julian week and fork length as the explanatory variables. Full model likelihood ratio test p-value= 0.039.

Estimate Std. Error (Wald's) z-statistic p-value Intercept -8.239 3.261 -2.527 0.0115 Julian week 0.013 0.036 0.371 0.7106 Fork length 0.046 0.049 0.938 0.3481

Null deviance 41.129 on 70 d.f. Residual deviance 34.652 on 68 d.f.

DISCUSSION

Habitat quality and growth during the freshwater rearing period of juvenile

Chinook salmon are major factors affecting the life-history strategy an individual may

pursue (Taylor 1990, Beckman et al. 1998). Variations in juvenile Chinook salmon life-

histories in the Shasta River basin appear to be influenced by environmental conditions,

particularly by differences in habitat conditions between the upper and lower basin. In

this study, residence time, growth, and outmigration size of juvenile Chinook salmon, between the fork lengths of 50- 70 mm, in the Shasta River differed with rearing location within the basin. In general, juvenile Chinook salmon that reared in the upper basin resided significantly longer, had higher growth, and out migrated at a larger size than those in the lower basin. Travel time from the upper basin to the mouth of the Shasta

River did not seem to determine residence time of juveniles rearing in the upper basin, as indicated by the minimum number of days of residence per tag group in Table 3. The transplantation experiment demonstrated that the differences in juvenile life- history were consistent among the two rearing locations, regardless of whether they had hatched there

(i.e. the UP-SH tag group) or were transplanted there (i.e. the T-BSC tag group).

Life-history differences between the upper and lower basin may be associated with a seasonal decline in habitat quality in the lower basin that potentially forces fish to emigrate. Typically, by early summer, water diversions decrease Shasta River flow to around 1.5 m3 s-1 or lower, and water temperatures in the lower canyon area often reached

near or above the thermal tolerance of juvenile Chinook salmon (Appendices B and C).

This probably forced the majority of juveniles rearing in the lower basin to out-migrate by late spring. On the other hand, juveniles in the upper basin did not experience the same degree of decreased stream flow and resulting increase in temperature, due to the cooler spring-fed tributaries that result from the various groundwater complexes in the upper basin (Appendix B). Consequently, juveniles in the upper basin were able to reside longer, grow larger, and out migrate at a larger size. Outmigration size and timing may have long term implications for post-smolt survival of juvenile Chinook salmon entering the estuary and open-ocean (Zabel & Achord 2004, Scheuerell et al. 2009). More studies are needed on how outmigration size and timing may affect Shasta River juvenile

Chinook salmon rearing in the Klamath River basin and adult returns to the Shasta River.

Gravel augmentation efforts that occurred in the lower Shasta River basin in the

1980s focused primarily on increasing the number of spawning Chinook in the lower basin (McBain & Trush Inc., 2010). Due to a seemingly disproportionate amount of spawning in the lower basin (Morgan Knechtle, CA Dept. of Fish & Wildlife, personal communications), an unintended result may be that a large proportion of the total number of juvenile Chinook salmon rearing in the Shasta River basin out migrate earlier in the season and at a significantly smaller size than is typical for ocean-type Chinook salmon.

Unfortunately, due to a lack of access by researchers to various areas within the Shasta

River basin, the actual proportion of the amount of spawning between the upper and lower basin is unknown. However, a more intensive PIT tag mark-recapture study or otolith microchemistry analysis could potentially be used to quantify the relative

contribution of different juvenile life-history strategies to adult returns, and changes in life-history strategies that may have resulted from anthropogenic habitat alterations.

Several tagged juveniles in the upper basin exhibited residence duration longer than the six months typical of ocean-type juveniles, but shorter than a year that is typical of stream-type juveniles. This suggests more of a continuum of life-history strategies within the freshwater rearing period of juvenile Chinook salmon. Volk et al. (2010) found a similar “continuum” of freshwater and estuarine life-histories of juvenile Chinook salmon through analysis of otolith microchemistry and microstructure. They observed a broad range in migration strategies and demonstrated the plasticity of the juvenile life stage of Chinook salmon.

My project further contributes to the described plasticity in the juvenile life stage of Chinook salmon. Several tagged fish in the T-BSC and the UP-SH tag groups were not included in the residence time analysis due to the extremity of their residence times. For the 2012 tagging field season, at least 5 fish in the T-BSC group, and 2 fish in the UP-SH group, resided in the upper basin through September or October. One fish from the T-

BSC group resided in the upper basin through fall and was detected out migrating in

November, for a total residence time of 175 days. Another fish from the T-BSC group also resided in the upper basin through fall and was detected out-migrating in early

March 2013, for a total residence time of 293 days. This individual evidently adopted a stream-type life history in response to being transplanted to a more suitable juvenile rearing habitat. As of February 2014, no fish from the 2013 UP-SH or T-BSC groups were detected out-migrating after July.

One interesting distinction between fish in the UP-SH group and those in the T-

BSC group was that juveniles in the UP-SH group seemed to re-distribute in the upper basin more often, and thus were more likely to be observed moving into a tributary than fish in the T-BSC group. For instance, in 2012 one fish in the T-BSC group and one fish in the UP-SH group were detected in the main-stem, upstream of their release sites several weeks after release. For the 2013 tagging season, as of August 2013, no fish from the T-BSC group had been detected moving upstream or into another tributary. However, five fish from the UP-SH group, which were tagged at RKM 54, were detected upstream

in the mouth of Big Springs Creek several days or weeks after being tagged. Generally,

juveniles in the T-BSC group reared in Big Spring Creek from a few days to a couple of

weeks, before moving into the Shasta River and rearing in the main stem, upstream of

RKM 46, for several weeks prior to outmigration. Juveniles in the UP-SH group typically

reared in the main stem of the Shasta River, upstream of RKM 46, for several weeks to a

month before out-migrating.

The slight dissimilarities between years, in the proportion of juveniles that out-

migrated by July (Table 8, Appendix D and E), may be attributed to differences in the hydrographs for spring 2012 and 2013. During spring 2012 stream flow decreased from

the start of irrigation on April 1, from approximately 10 m3 s-1 to around 1.5 m3 s-1 by late

June (Appendix C). During spring 2013 stream flow decreased more abruptly from the

start of irrigation on April 1, from approximately 6 m3 s-1 to around 1.5 m3 s-1 by late

April (Appendix C). I surmise that several fish in the 2013 UP-SH and T-BSC groups may have been forced to adopt a more stream-type life-history strategy and reside in the

cooler spring-fed tributaries and main-stem in the upper basin through summer and early

fall 2013. This exemplifies how plasticity in the life-history strategies of juvenile

Chinook salmon may allow them, to a certain extent, to adapt to anthropogenic

alterations in freshwater rearing habitats. Williams et al. (2008) suggested that

anthropogenic disturbances may result in evolutionary changes in the life history of salmonids within a few generations, in response to altered natural selection regimes from

these disturbances. They described an observed increase in the stream-type life history strategy for juvenile Chinook salmon in the Snake River, several decades after the construction of a hydropower dam, and a consequent large adult return in the Snake River over the last decade. Crozier et al. (2008) further suggested that the juvenile life history plasticity of salmonids may help to allow fish to persist in the face of climate change, which is likely to affect juvenile freshwater growth, development, thermal tolerance, and disease resistance.

It is important to note that there is another possible life-history strategy in stream- type Chinook, which is the mature male parr (Quinn 2005). Precociously mature male parr have been documented in the upper Shasta River basin (Jeffres, unpublished paper).

Precocious male parr typically undergo an arrested development of smoltification, become sexually mature before they are yearlings, and attempt to spawn during the fall. It is unclear whether some tagged individuals that reside through fall 2013 will attempt to spawn as mature male parr during the fall, or out-migrate as one-year old smolts in spring

2014. Further investigation into the mature male parr life-history strategy for Shasta

River Chinook is needed.

The PIT tagging experiment of this study demonstrated current variations and

differences in juvenile Chinook salmon life-histories within the Shasta River basin, but otolith strontium isotopic ratio analysis may reveal past differences that otherwise might not have been known. The concentration and isotopic ratios of elements in a river is primarily influenced by the underlying geology of the watershed (Barnett-Johnson et al.

2008). Streams within the same watershed can have differing elemental concentrations determined by shifts in the geology of the basin (Ingram and Weber 1999). Natal rearing streams of salmonids can then be determined by the chemical “fingerprint” incorporated into the otolith (Ingram and Weber 1999, Kennedy et al. 2000, Campana and Thorrold

2001, Barnett-Johnson et al. 2010). The difference in geology between the upper and

lower Shasta basin provided a unique opportunity to distinguish rearing locations due to

the distinct stream water 87Sr/86Sr values between two key rearing areas in the basin

(Table 16, Appendix F). Consistent with these results, a preliminary study by Reader and

Chesney (2007) found the concentration of magnesium, phosphorus, manganese, copper, strontium, and barium to be significantly different in stream water between the upper and

lower Shasta River. I found that the distinct chemical signature in stream water from the

upper and lower basin is incorporated into the otoliths of juvenile Chinook salmon

rearing in those respective habitats.

This study also showed that it would be possible to determine the proportion of

juveniles that reared in the upper or lower basin. An estimate of juvenile Chinook salmon

that reared in the upper or lower basin, based on my assignments from the 2011 and 2012

cohorts (Table 17), suggests that most out-migrating juveniles originated in the lower

basin. However, this estimate is based on analysis of otolith microchemistry of moribund

fish collected from rotary screw traps at the mouth of the river. Because of potential biases associated with the collection of moribund fish, these numbers may not accurately

represent the actual proportion of juveniles that reared in the upper or lower basin for

those years.

Curiously, many of the otoliths collected from fish at RKM 0 in 2011 had

elevated 87Sr/86Sr values, many of which were closer to the marine maternal strontium

signature (0.708-0.709) than the lower Shasta basin strontium signature (0.706; Figure

19). The one fish for 2011 that was categorized with an upper basin rearing location also

had a strontium signature elevated slightly above the expected value of 0.704 (Figure 11).

It is unclear if this fish reared near RKM 12 or had an elevated strontium signature like

the rest of the otoliths from 2011 (Table 16, Figure 11). It is possible that the elevation in

87Sr/86Sr values may have been due to contamination in the preparation process.

However, given that all the otoliths were prepared and analyzed in the same manner and

within a short time frame of each other, there may have been other factors affecting the

87Sr/86Sr values of juvenile Chinook salmon otoliths in 2011, such as anthropogenic

impacts specific to 2011. It has been shown that water chemistry and temperature can

affect the ratios of elements incorporated into otoliths (Campana 1999, Eldson and

Gillanders 2004). Further study is needed to determine how the interaction of high

temperatures and specific anthropogenic inputs, such as the seasonal input of fertilizers,

may affect 87Sr/86Sr values in the otoliths of Chinook and other salmonids. Given there

was some discrepancy between the mean stream water 87Sr/86Sr values and the averaged

87Sr/86Sr values for otoliths (Figure 11), individual genetics and anthropogenic influences on stream water microchemistry may also contribute to variations between 87Sr/86Sr values in stream water and those incorporated into the otoliths (Campana 1999, Ingram and Weber 1999, Eldson and Gillanders 2004).Additional study is needed to determine what factors may produce these slight discrepancies.

The freshwater rearing habitat of juvenile Chinook salmon in the Shasta River basin is likely to continue to undergo extensive anthropogenic alterations, both restorative and negative. In response, future changes may be seen in the life-history strategies of juveniles due to the plastic nature of that life stage. There are limits, however, to how much a species can adapt to anthropogenic disturbances in habitat, thus the ongoing restoration and conservation efforts underway in the upper Shasta River, will most likely benefit juvenile Chinook salmon residing in the upper basin that either “willingly” adopt a more steam-type life history, or that may become “stuck” in the upper basin until the early fall.

This project added to our understanding of how different rearing locations within a basin may affect residency and growth of juvenile Chinook salmon in the Shasta River basin. The mark-recapture field portion provided a comprehensive picture of how habitat differences influence the expression of life-history strategies of juvenile Chinook salmon in the Shasta River basin. The microchemical analysis of otoliths was shown to provide a supplemental tool which can be used to identify the proportion of juvenile Chinook salmon that utilize critical rearing areas. These methods and tools combined, demonstrate

74 the importance of life history variations to the survival of Chinook salmon in the Shasta

River.

The flexibility of the juvenile life-history stage of Chinook salmon has allowed them to persist in the Shasta River basin, despite decades of habitat alterations and degradation. Regardless of the potential for salmonids to adapt to anthropogenic disturbances in habitat, it is essential that we realize the consequences our actions may have on the life-history strategies of future generations of salmonids, especially if their historic numbers are ever to be experienced again.

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PERSONAL COMMUNICATIONS

Bill Chesney. 2013. Personal communication. California Department of Fish and Wildlife. 1625 South Main St.. Yreka, CA, 96067.

Morgan Knechtle. 2013. Personal communication. California Department of Fish and Wildlife, 1625 South Main St., Yreka, CA, 96097.

Appendix A. Table of Julian weeks with corresponding calendar dates (month/day).

Calendar dates (month/day) Julian week Start date End date 1 1/1 1/7 2 1/8 1/14 3 1/15 1/21 4 1/22 1/28 5 1/29 2/4 6 2/5 2/11 7 2/12 2/18 8 2/19 2/25 9 2/26 3/3 10 3/4 3/10 11 3/11 3/17 12 3/18 3/24 13 3/25 3/31 14 4/1 4/7 15 4/8 4/14 16 4/15 4/21 17 4/22 4/28 18 4/29 5/5 19 5/6 5/12 20 5/13 5/19 21 5/20 5/26 22 5/27 6/2 23 6/3 6/9 24 6/10 6/16 25 6/17 6/23 26 6/24 6/30 27 7/1 7/7

RKM 0

(a)

RKM 51

) (b

BSC RKM 1

) (c

Irrigation season

(1) Parameter Beta Estimate Standard Error Phi(Intercept) -5.45 2.78 Phi(location 2) 1.15 1.66 Phi(location 3) 0 0 Phi(location 4) 0.85 2.22 Phi(FL) 0.10 0.04 p(Intercept) -1.25 0.27 p(location 3) 0.66 0.39 p(location 4) 0.23 0.39 p(location 5) 0.76 0.76

(2) Parameter Estimate Standard Error Phi 1 0.64 0.06 Phi 2 0.85 0.1

Phi 3 1 0

Phi 4 0.81 0.2 p 2 0.22 0.02 p 3 0.36 0.03 p 4 0.26 0.03 p 5 0.38 0.09

(1)

Parameter Beta Estimate Standard Error Phi(Intercept) -0.03 0.35 Phi(location 2) 2.16 1.91 Phi(location 3) 0 0 Phi(T-CAN) 0.70 0.43 Phi(UP-SH) -0.12 0.40 p(Intercept) -4.71 1.65 p(location 3) 0.73 0.38 p(location 4) 0.10 0.36 p(FL) 0.06 0.02

(2) Parameter Estimate Standard Error Phi 1: T-BSC 0.49 0.05

Phi 2: T-BSC 0.89 0.1

Phi 1: T-CAN 0.66 0.05

Phi 2: T-CAN 0.94 0.05 Phi 1: UP-SH 0.45 0.05 Phi 2: UP-SH 0.88 0.11 Phi 3 1 0 p 2 0.29 0.03 p 3 0.46 0.04 p 4 0.31 0.03