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Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek, California

USFWS Report

Prepared By: C. Michael Schraml

James T. Earley Laurie A. Earley

California Department of Fish and Wildlife (Game) Agreement P0685505

U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office 10950 Tyler Road Red Bluff, CA 96080

March 2019

U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek ii

Disclaimer

The mention of trade names or commercial products in this report does not constitute endorsement or recommendation for use by the federal government.

The correct citation for this report is:

Schraml, C. M., J. T. Earley and L. A. Earley. 2019. Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek, California. USFWS Report. U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office, Red Bluff, California.


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek iii

Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek, California C. Michael Schraml, James T. Earley and Laurie A. Earley

U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office 10950 Tyler Road, Red Bluff, California 96080

Abstract — On November 9, 2012, the U.S. Fish and Wildlife Service continued an ongoing juvenile salmonid monitoring project on Battle Creek, California, using rotary screw traps. Information about juvenile salmonid abundance and migration in Battle Creek is necessary to guide efforts at maintaining and restoring populations of threatened and endangered anadromous salmonids. From November 9, 2012, through June 30, 2013, spring-run and late-fall-run Chinook Salmon Oncorhynchus tshawytscha, Rainbow Trout / steelhead O. mykiss, and 12 species of non-salmonids were captured in the upper Battle Creek rotary screw trap. During the period of January 22 through February 28, 2013, we conducted six mark–recapture trials at the upper Battle Creek trap to determine rotary screw trap efficiency. Trap efficiencies using naturally reared fall-run Chinook Salmon varied from 4.88% to 11.08% with a season average of 7.58%. Chinook Salmon run designations in the Sacramento River watershed were developed using length-at-date criteria for Sacramento River Chinook Salmon; however, they are not applicable to tributaries with variable and overlapping run timing of spring and fall runs. Preventative measures, such as closing off the Battle Creek Coleman National Fish Hatchery barrier weir in August reduce the potential for fall-run Chinook Salmon to enter the upper watershed (above the Coleman National Fish Hatchery barrier weir). Therefore, captured Chinook, designated as spring-run and fall-run Chinook Salmon were combined and assigned as spring-run for calculating passage indices. The brood year 2012 spring-run Chinook Salmon passage index at the upper Battle Creek trap was 70,044. The juvenile per redd ratio was 219 for spring-run Chinook Salmon and was the lowest since brood year 2002. These ratios produce an expected juvenile passage index range of 225,577 to 351,040 spring-run Chinook Salmon. In August 2012 the Ponderosa fire burned within the Battle Creek watershed. Subsequently, as a result of the fire damage, Battle Creek’s flows became flashier. Two large flows (6,490 and 10,800) occurred in December 2012, potentially scouring redds. The upper Battle Creek trap cannot sample safely at those flows and was pulled from the water. The trap was reinstalled on December 27. Peak out-migration started on December 28. There is a potential that many of the juvenile fish moved out during the flow event that happened from December 21 through December 27. The brood year 2012 late-fall run Chinook Salmon passage index was 103. The passage indices for brood year 2011 age-0+ and brood year 2012 young-of-the-year O. mykiss were 684 and 3,452, respectively.


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek iv

Table of Contents

Abstract ........................................................................................................................................................ iii

Table of Contents ......................................................................................................................................... iv

List of Tables ............................................................................................................................................... vi

List of Figures ............................................................................................................................................. vii

List of Appendices ....................................................................................................................................... ix

Introduction ................................................................................................................................................... 1

Study Area .................................................................................................................................................... 2

Methods ........................................................................................................................................................ 3

Rotary screw trap operations .................................................................................................................... 3

Counting and Measurement ...................................................................................................................... 5

Chinook ................................................................................................................................................. 5

O. mykiss ............................................................................................................................................... 5

Non-salmonid taxa ................................................................................................................................ 6

Genetic and otolith sampling .................................................................................................................... 6

Mark–recapture trials ................................................................................................................................ 6

Marking method .................................................................................................................................... 7

Release and recovery ............................................................................................................................ 7

Trap efficiency .......................................................................................................................................... 7

Interpolated data ........................................................................................................................................ 8

Juvenile passage indices ........................................................................................................................... 8

Results ........................................................................................................................................................... 9

Physical characteristics ............................................................................................................................. 9

Sampling effort ......................................................................................................................................... 9

Mark –recapture efficiency estimates ....................................................................................................... 9

O. Mykiss............................................................................................................................................. 10

Late-fall Chinook ................................................................................................................................ 10

Spring Chinook ................................................................................................................................... 10

Salmonid catch and passage indices ....................................................................................................... 10

O. mykiss ............................................................................................................................................. 10

Chinook ............................................................................................................................................... 10

Non salmonid catch ................................................................................................................................. 11

Mortality ................................................................................................................................................. 11


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek v

Marking mortality ............................................................................................................................... 12

Trapping mortality .............................................................................................................................. 12

Genetic and otolith sampling .................................................................................................................. 12

Discussion ................................................................................................................................................... 12

Sampling effort ....................................................................................................................................... 12

Mark–recapture efficiency estimates ...................................................................................................... 12

Spring Chinook ................................................................................................................................... 12

Salmonid passage indices ....................................................................................................................... 13

O. mykiss ............................................................................................................................................. 13

Late-fall Chinook ................................................................................................................................ 13

Spring Chinook ................................................................................................................................... 14

Acknowledgements ..................................................................................................................................... 15

References ................................................................................................................................................... 16

Tables .......................................................................................................................................................... 19

Figures ........................................................................................................................................................ 25

Appendix A: Rotary Screw Trap Operations .............................................................................................. 42

Appendix B: Weekly Catch and Juvenile Passage Indices ......................................................................... 44

Appendix C: Non-salmonid Species Catch ................................................................................................. 50

Appendix D: Annual Catch and Passage Summaries ................................................................................. 53


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek vi

List of Tables

Table 1. Dates with corresponding week numbers for rotary screw trap operations at river mile 6.2 in Battle Creek, Shasta County. .............................................................................................. 20

Table 2. Summary of efficiency test data gathered by using mark-recapture trials with juvenile naturally reared fall-run Chinook Salmon at the upper rotary screw trap at river mile (RM) 6.2 in Battle Creek, Shasta County from November 9, 2012, through June 30, 2013. ........................... 21

Table 3. Mark-recapture efficiency values used for weekly passage indices of brood year 2012 juvenile Rainbow Trout / steelhead (RBT), late-fall run Chinook Salmon (LFCS) and spring-run Chinook Salmon (SCS) captured in the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1, 2012, through June 30, 2013. ..................................................... 22

Table 4. Brood year 2012 life-stage summary for Rainbow Trout / steelhead, late-fall, winter and spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County. ................................................................................................................... 23

Table 5. The annual passage indices, the April 1 through June 30 passages of juvenile spring-run Chinook Salmon at river mile 6.2 in Battle Creek, Shasta County............................................... 24


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek vii

List of Figures

Figure 1. Battle Creek watershed (dashed lines), the Ponderosa fire perimeter (red), current and historical limits of anadromy and upper rotary screw trap site, Shasta and Tehama Counties, California. ..................................................................................................................................... 26

Figure 2. A 5-ft diameter rotary screw trap similar to the trap operated at river mile 6.2 on Battle Creek, Shasta County, from November 2012 through June 2013. ............................................... 27

Figure 3. Mean daily water temperatures recorded at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from October 1, 2012, through September 30, 2013. ................. 28

Figure 4. Mean daily flows measured at the USGS gauging station (BAT #11376550) at river mile 6.1 and momentary turbidity recorded at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from October 1, 2012, through September 30, 2013. ..................... 29

Figure 5. Sampling effort summarized as the proportion (range: 0 to 1) of each month fished for the upper rotary screw trap for brood year 2012 Rainbow Trout / steelhead and late-fall and spring-run Chinook Salmon. ......................................................................................................... 30

Figure 6. Individual releases, pooled and season average (0.1007) trap efficiencies for trials conducted using naturally reared juvenile Chinook Salmon at the upper rotary screw trap at river mile 6.2 in Battle Creek Shasta County from January 23 through February 28, 2013. ................ 31

Figure 7. Fork length and life stage distribution by date and life stage for brood year 2012 and brood year 2011 age-0+ juvenile Rainbow Trout / Steelhead captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1 to December 31, 2012. .... 32

Figure 8. Weekly passage indices with 95% confidence intervals for brood year 2012 juvenile Rainbow Trout / steelhead captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1 through December 31, 2012. ............................................ 33

Figure 9. Weekly passage indices with 95% confidence intervals for brood year 2011 age 0+ juvenile Rainbow Trout / steelhead captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1 through December 31, 2012. ................................. 34

Figure 10. Fork length and life stage distribution by date, life stage, and run for all juvenile Chinook Salmon captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from November 9, 2012, through June 30, 2013. ............................................................ 35

Figure 11. Weekly passage indices with 95% confidence intervals of brood year 2012 juvenile late-fall run Chinook Salmon captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from April 1, 2012 through March 31, 2013. ............................................ 36

Figure 12. Weekly passage indices with 95% confidence intervals of brood year 2012 juvenile spring-run Chinook Salmon captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from November 9, 2012 through June 30, 2013. ...................................... 37


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek viii

Figure 13. Percent cumulative catch young-of-the-year of Rainbow Trout / steelhead captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County, for brood years 1999–2000, 2002–2005, and 2008–2012. ..................................................................................... 38

Figure 14. Map of Battle Creek showing the North Fork, South Fork, and main stem, depicting the location of the Coleman National Fish Hatchery barrier weir and stream survey reaches used by the RBFWO adult monitoring team during snorkel surveys conducted from August to October 2012 (Bottaro et al. 2013). ............................................................................................................ 39

Figure 15. Annual and mean juveniles per redd and number of observed redds for spring-run Chinook Salmon in Battle Creek, Shasta County, for brood years 2001–2012. ........................... 40

Figure 16. Interpolated passage and catch for spring-run Chinook Salmon for brood years 2000–2012 captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County. . 41


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek ix

List of Appendices

Appendix A: Trap Operations Table A. 1. Summary of days the upper rotary screw trap did not fish for approximately 24 hours during the brood year 2012 Rainbow Trout / steelhead (RBT), late-fall run Chinook Salmon (LFCS) and spring-run Chinook (SCS) out-migration period. ........................................ 43

Appendix B: Weekly Catch and Juvenile Passage Indices Table B. 1. Weekly catch, mortality and passage indices with the upper (UCI) and lower (LCI) 95% confidence interval and SE of the weekly strata for brood year 2012 juvenile Rainbow Trout / steelhead captured at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1 through December 31, 2012. ................................................................... 45

Table B. 2. Weekly catch, mortality and passage indices with the upper (UCI) and lower (LCI) 95% confidence interval and SE of the weekly strata of brood year 2011+ age-0+ juvenile Rainbow Trout / steelhead captured at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1 through December 31, 2012. ............................................ 46

Table B. 3. Weekly catch, mortality and passage indices with 95% lower (LCI) and upper (UCI) confidence intervals and SE of the weekly strata of brood year 2012 juvenile late-fall run Chinook Salmon captured at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from April 1, 2012, through March 31, 2013. .................................................................. 47

Table B. 4. Weekly catch, mortality and passage indices with the upper (UCI) and lower (LCI) 95% confidence interval and SE of the weekly strata of brood year 2012 juvenile spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from November 9, 2012, through June 30, 2013. ............................................................ 48

Appendix C: Non-Salmonid Species Catch Table C. 1. Name key of non-salmonid fish taxa captured by the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from November 9, 2012, through June 30, 2013. ......... 51

Table C. 2. Monthly catch of non-salmonid species in the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from November 9, 2012, through June 30, 2013. ................. 52

Appendix D: Annual Catch and Passage Summaries Table D. 1. Brood year (January 1 through December 31) passage indices (in grey) of young-of-the-year Rainbow Trout / steelhead with the upper (UCI) and lower (LCI) 95% confidence interval and SE for brood years 1999–2012 captured by upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County. Adult escapement was measured by video at the Coleman National Fish Hatchery barrier weir (Bottaro et al. 2013). ........................................................... 54

Table D. 2. Brood year (January 1 through December 31) passage indices (shaded in grey) of age-0+ juvenile Rainbow Trout / steelhead with upper (UCI) and lower (LCI) 90% and 95% confidence intervals and SE for brood years 1998+ to 2011+ captured by upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County. .......................................................................... 55


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek x

Table D. 3. Brood year (generally April 1 through March 31) passage indices (shaded in grey) of juvenile late-fall run Chinook Salmon with upper (UCI) and lower (LCI) 95% confidence intervals and SE for brood years 1999–2012 captured by upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County. .................................................................................................... 56

Table D. 4 Brood year passage indices of juvenile spring-run Chinook Salmon with upper (UCI) and lower (LCI) 95% confidence intervals and SE for brood years 1999–2012 captured by upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County. ............................................. 57


Brood Year 2012 Juvenile Salmonid Monitoring in Battle Creek 1

Introduction

In recent decades California has experienced declines in several of its wild salmon and steelhead populations. These declines have been linked to a variety of factors, but the development of federal, state, municipal, and private water projects is likely a primary contributing factor (Jones and Stokes 2005). Battle Creek is important to the conservation and recovery of federally listed anadromous salmonids in the Sacramento River watershed because of its unique hydrology, geology, and habitat suitability for several anadromous species (Ward and Kier 1999; Jones and Stokes 2005). These species include the endangered winter-run Chinook Salmon (winter Chinook) Oncorhynchus tshawytscha, threatened spring-run Chinook Salmon (spring Chinook), and threatened Central Valley steelhead trout O. mykiss. We use the term O. mykiss to refer to both the stream resident (Rainbow Trout) and anadromous (steelhead) life histories, because of the difficulties in differentiating the anadromous and resident forms in the field. Restoration actions and projects that are planned or underway in Battle Creek focus on providing habitat for winter, spring Chinook and O. mykiss. Currently the geographic range of the winter Chinook Evolutionary Significant Unit is small and limited to the main stem of the Sacramento River between Keswick Dam and the town of Red Bluff, California, where it may be susceptible to catastrophic loss. Establishing a second population in Battle Creek could reduce the likelihood of extinction. Battle Creek also has the potential to support significant, self-sustaining populations of spring Chinook and O. mykiss.

Since the early 1900's a hydroelectric project comprised of several dams, canals, and powerhouses has operated in the Battle Creek watershed. The hydroelectric project is currently owned by Pacific Gas and Electric Company (PG&E) and has had severe impacts upon anadromous salmonids and their habitat (Ward and Kier 1999). These impacts include a reduction of instream flows, barriers to migration, loss of habitat, flow related temperature impacts, etc.

In 1992 the Central Valley Project Improvement Act (CVPIA), federally legislated efforts to double populations of Central Valley anadromous salmonids. The CVPIA Anadromous Fisheries Restoration Program outlined actions to restore Battle Creek, which included increasing flows past PG&E’s hydroelectric power diversions to provide adequate holding, spawning, and rearing habitat for anadromous salmonids (USFWS 1997).

In 1999 PG&E, California Department of Fish and Wildlife (CDFW), U.S. Fish and Wildlife Service (USFWS), U.S. Bureau of Reclamation (USBR), and National Marine Fisheries Service (NMFS) signed a memorandum of understanding to formalize the agreement regarding the Battle Creek Salmon and steelhead Restoration Project (Restoration Project). The Restoration Project is to be completed in three phases (1A, 1B, and 2). The majority of phase 1A has been completed including the removal of Wild Cat Dam, the installation of fish screens and ladders at North Fork Feeder and Eagle Canyon Dams on the North Fork, and the construction of the Baldwin Creek barrier weir. Even though the ladders and screens at North Fork Feeder and Eagle Canyon Dams are installed, the ladders remain closed because the designs do not meet the specified criteria for upstream and downstream passage. Phase 1B is under way and concentrates on the Coleman Canal and Inskip powerhouse and tailrace. The final phase (Phase 2) will continue with the work being done on the South Fork. During this phase of the project Coleman, South, Lower Ripley Creek Feeder, Soap Creek Feeder dams and the South Canal will be removed. The South powerhouse connector tunnel will be constructed, and a fish screen and ladder will be installed at Inskip dam. The planning, designing, and permitting phases of the



Restoration Project have taken longer than originally anticipated. The USBR projected completion in 2016; however, the Restoration Project is now expected to be completed by the end of 2023 (USBR 2018).

PG&E is required under its current Federal Energy Regulatory Commission (FERC) license to provide minimum instream flows of 3 cubic feet per second (cfs) downstream of diversions on the North Fork Battle Creek (North Fork) and 5 cfs downstream of diversions on the South Fork Battle Creek (South Fork). Beginning in 1995, the CVPIA Water Acquisition Program (1995 to 2000) and Ecological Restoration Program (ERP) of CALFED (2001 to present) contracted with PG&E to increase minimum instream flows in the lower reaches of the North Fork and South Fork. In general, flows are increased to 30 cfs ± 5 cfs below Eagle Canyon Dam on the North Fork and below Coleman Diversion Dam on the South Fork. Increased flows were not provided on the South Fork in 2001 and most of 2002 due in part to lack of funds. Based on an agreement in 2003, flows can be redistributed between the forks to improve overall conditions for salmonids, based on water temperatures and the distribution of live Chinook and redds. The intent of the Interim Flow Project is to provide immediate habitat improvement in Battle Creek to sustain current natural salmonid populations while implementation of the more comprehensive Restoration Project moves forward. This has helped to provide adequate temperatures for all juvenile salmonid life history stages ranging from incubation to rearing in most years.

In September 1998 the RBFWO began using rotary screw traps (RST) to monitor downstream passage of juvenile salmonids on Battle Creek, Shasta and Tehama Counties, California (Whitton et al. 2006). Two traps were deployed, one in the upper watershed above the Coleman National Fish Hatchery (CNFH) barrier weir (BW) to estimate spring Chinook and O. mykiss passage and a second in the lower watershed to target fall-run Chinook Salmon (fall Chinook) passage. During the current report period, the RBFWO only operated the upper Battle Creek (UBC) trap to estimate downstream passage. The lower Battle Creek (LBC) trap was used to capture fall Chinook for mark–recapture trials. The purpose of this report is to summarize RST data collected during the period from November 9, 2012, through June 30, 2013 (hereafter, sample period). This ongoing monitoring project has three primary objectives: (1) determine an annual juvenile passage index (JPI) for Chinook and O. mykiss, for inter-year comparisons; (2) obtain juvenile salmonid life history information including size, condition, emergence, emigration timing, and potential factors limiting survival at various life stages, and (3) collect tissue samples for genetic analyses. In this report we discuss the passage indices and life history information. The genetics results, condition factor and survival factors will be covered individually in future reports.

Study Area

Battle Creek is located in Shasta and Tehama counties California. The creek and its tributaries drain the western volcanic slopes of Mount Lassen in the southern Cascade Range. The creek has two primary tributaries, the North Fork, which originates near Mt. Huckleberry and the South Fork, which originates in Battle Creek Meadows south of the town of Mineral, California. In June of 2013, the RBFWO updated the river miles (USFWS, unpublished data) using recently collected Light Detection and Ranging (LiDAR) data (Watershed Sciences 2011). The river miles presented in this report reflect the new river mile system. The North Fork is approximately 29.5 mi long from the headwaters to the confluence with the South Fork. There is a natural barrier waterfall located at river mile (RM) 13.2 and is the Restoration Project



boundary. South Fork Battle Creek is approximately 30 mi long, and has a natural barrier waterfall (Angel Falls) 22.5 miles from the confluence. The main stem of Battle Creek flows approximately 16.8 mi west from the confluence of the two forks to the Sacramento River east of Cottonwood, California. The entire watershed encompasses an area of approximately 369 mi² . The length of the current anadromous fishery in Battle Creek is 24.6 mi. The current 24.6 mi of anadromous fishery in Battle Creek encompasses 5.2 RM from Eagle Canyon Dam to the forks confluence on the North Fork, 2.5 RM from Coleman Dam on the South Fork, and 16.8 RM of the main stem (Figure 1). Historically, the anadromous fishery exceeded 53 mi.

Battle Creek has the highest base flows of any of the Sacramento River tributaries between Keswick Dam and the Feather River, and flows are influenced by both precipitation and spring flow from basalt formations (Ward and Kier 1999). The average flow at CNFH in Battle Creek is approximately 500 cfs. The South Fork is more influenced by precipitation and likely experiences higher peak flows, whereas the North Fork receives more of its water from snowmelt and spring-fed tributaries. Maximum discharge usually occurs during the period of November to April because of heavy precipitation. Average annual precipitation in the watershed ranges from about 25 in at the Coleman Powerhouse to more than 50 in at the headwaters, with most precipitation occurring between November and April (Ward and Kier 1999). Ambient air temperatures range from below 32ºF in the winter to summer highs in excess of 115ºF.

Land ownership in the Battle Creek watershed is a comprised of private, state, and federal, entities, including: the CDFW, Bureau of Land Management (BLM), and USFWS. Most of the land within the restoration area is private and zoned for agriculture, including grazing. Currently, much of the lower Battle Creek watershed is undeveloped, with scattered private residences, ranching enterprises, and local entities.

On August 18, 2012, a lightning-strike fire named the Ponderosa fire started in the Battle Creek watershed. It burned a total of 27,676 acres and was contained on August 31. The majority of the fire burned very hot and the entire fire boundary was within the Battle Creek watershed (Lewis 2014; Figure 1). There were two large storms in December 2012 that caused significant erosion in the burn scar area.

Methods

Rotary screw trap operations In November 2012 the RBFWO continued the operation of two rotary screw traps on

Battle Creek. The rotary screw traps (RST; E.G. Solutions®, Corvallis, OR) consist of a 5 ft. diameter cone covered with 1/8-in diameter perforated stainless steel screen. This cone acts as a sieve, which separates fish from the sampled water. The cone and live-box are supported between two pontoons and the cone’s auger-type action passes water, fish, and debris to the rear of the trap directly into the live-box. This live-box retains fish and debris passing water through screens located on the back, sides, and bottom (Figure 2).

Each RST is attached to a cable high line and positioned instream with a system of ropes and pulleys. Modifications have been made to reduce potential impacts to the captured fish and to improve our efficiency. Modifications to the traps included increasing the size of the live-boxes and flotation pontoons. Each rotary screw trap cone is divided in half. Our traps have been modified so that the cod-end of one half of the cone can be closed off. The contents of the closed half are discharged back into the creek instead of into the live-box, thus hypothetically cutting the trap’s catch in half. The modification is reversible allowing the trap to be operated in



either the full-cone or half-cone configuration. During the sample season, the UBC trap was operated at full-cone to improve our passage estimate by increasing catch. The LBC trap was always operated at full-cone to ensure sufficient numbers of fall Chinook were available for mark–recapture trials.

The timing of the UBC RST operation is based upon the spring Chinook out-migration period, which is typically from mid-November though the end of June. The LBC trap, which was only used to capture naturally-produced fall Chinook for use in mark–recapture trials to estimate trap efficiency at the UBC trap, was operated for 1 or 2 d prior to marking.

To determine when to begin our trapping season, we estimated emergence timing utilizing an accumulated thermal units method (Murray and Beacham 1986; Murray and McPhail 1988; Brown and Earley 2007). We used redd timing data from fall 2012 (Bottaro et al. 2013), 2012 water temperature data from redd construction forward, and temperature data from water years 2009 and 2010 (to estimate accumulated thermal units (ATU) for the days not yet realized at the time of calculation), we predicted that spring Chinook emergence would not occur until mid-December. The trap was set a month before the estimated emergence to accommodate variation in actual vs model input temperature, and variation in emergence timing not captured by the ATU model (most ATU methods predict the number of days to 50% emergence from a redd).

An attempt was made to operate the UBC trap continuously, but at times high flows limited the ability to operate the trap. The trap was not operated when stream flows exceeded certain levels in order to prevent fish mortality, damage to equipment, and to ensure crew safety. When flows allowed, the crews were able to access the trap by wading from the stream bank; however, during high flows access to the trap required that the crews use the cable and pulley system to move the trap into shallow water. After or during sampling and maintenance, the trap was repositioned in the thalweg.

The RST was serviced daily unless conditions (high flows, heavy debris loads, or high fish densities) required multiple trap checks to avoid mortality of captured fish or damage to equipment. At each trap servicing, crews processed the collected fish, cleared the RST of debris, and provided maintenance. Once per day (at the end of the approximately 24-h sampling period), the crew obtained environmental and RST data. Collected data included: dates and times of RST operation, creek depth at the RST, RST cone fishing depth, number of rotations of the RST cone during sampling period, the amount and type of debris collected, basic weather conditions, water temperature, current velocity, and turbidity. Water depths were measured using a graduated staff to the nearest 0.1 ft. The RST cone fishing depth (in) was measured with a gauge that was permanently mounted to the RST pontoon adjacent to the cone. The number of rotations of the RST (revolutions per min) cone were measured with a mechanical stroke counter that was mounted to the RST railing adjacent to the cone. The amount of debris in the RST was volumetrically measured using a 10-gal plastic tub.

Water temperatures were continuously obtained at 30-min intervals with an instream data logger (HOBO® Water Temperature Pro v2 Logger; Onset Computer Corp, Bourne, MA). The crews uploaded temperatures weekly. Water velocity was measured from on the RST in front of the cone using a mechanical flow meter (Oceanic ® Model 2030 flowmeter; General Oceanics, Miami, FL). Water turbidity was measured from a grab-sample with a Hach Model 2100D turbidimeter (Hach Company, Ames, IA). Mean daily discharge data were collected at the U.S. Geological Survey’s CNFH gauging station (#11376550). The gauge site is located below the CNFH BW and approximately 0.1 miles downstream of the UBC trap. All environmental and



biological data were entered into a Microsoft Access database at the trap site using a Panasonic Toughbook® (Model CF-19). Counting and Measurement

Juvenile sampling at the UBC trap was conducted using standardized techniques that were consistent with the CVPIA’s Comprehensive Assessment and Monitoring Program standard protocol (USFWS 1997; USFWS 2002). The monitoring team enumerated and obtained length measurements (to the nearest 1.0 mm) for all fish taxa that were collected. For both living individuals and mortalities. Fish to be measured were first anesthetized in a 1-qt plastic tub with solution of Tricaine Methanesulfonate (MS-222) at a concentration of 60–80 mg/l. Fish were measured on a wet measuring board, placed in a 10 gal plastic tub filled with fresh creek water and fish protectant, and allowed to recover from the anesthetic effects before being released back into the creek. Water in the tubs was replaced as necessary with fresh creek water to maintain adequate temperature and oxygen levels. Based on project objectives and large numbers of juvenile salmon that were frequently encountered, different criteria were used to count salmon, trout, and non-salmonid species. In general, during trap clears that were not at the end of the 24-h sampling period, fish were identified, classified to age class, and counted, but no length measurements were taken.

Chinook — When less than approximately 250 salmon were collected in the RST, all were counted and measured to fork length (FL). The measured juvenile salmon were assigned to a life stage classification: yolk-sac fry (C0), fry (C1), parr (C2), silvery parr (C3), or smolt (C4). All Chinook that were measured were assigned run designations using length-at-date tables (S. Greene, 1992 memorandum to Randall Brown, California Department of Water Resources, estimated winter-run Chinook Salmon salvage at the State Water Project and Central Valley Project Delta Pumping Facilities). These designations included fall Chinook, late-fall Chinook, winter Chinook, and spring Chinook. At the UBC RST, all Chinook captured that were assigned fall Chinook according to Greene’s run designations were considered to be spring Chinook because management of adult passage allows for passage of spring Chinook, unclipped late-fall Chinook and, O. mykiss above the BW but usually excludes passage of fall Chinook. Fry captured after mid-March by UBC are assigned a run designation of late-fall Chinook.

Subsampling was conducted when more than approximately 250 juvenile salmon were captured. Subsampling was accomplished using a cylinder-shaped 1/8-in mesh “subsampling net”. The bottom of the subsampling net was constructed with a metal frame that created two equal halves. Each half was built with a mesh bag that could be tied shut; one side of the net was tied shut and the other was left open. This subsampling net was placed in a 25-gal bucket that was partially filled with creek water. All collected juvenile salmon were poured into this bucket. The net was then lifted and approximately one-half of the salmon were retained in the side of the net with the closed mesh bag, and approximately one-half of the salmon in the side with the open mesh bag were left in the bucket. The catch was successively subsampled until approximately 150–250 individuals remained.

O. mykiss — All O. mykiss that were collected in the RSTs were counted and FL was measured. All live juvenile O. mykiss > 50 mm FL that were captured during the daytime sample were weighed to the nearest 0.1 g with an electronic scale for condition factor analysis. The juvenile trout were classified to life stage in the same manner as salmon (i.e., yolk-sac fry (R1), fry (R2), parr (R3), silvery parr (R4), and smolt (R5)).



Non-salmonid taxa — All non-salmonid taxa were counted, and up to 20 randomly selected individuals were measured. Total length (TL) was measured for species that do not have a forked caudal fin; otherwise, FL was measured for all other non-salmonid taxa. Lamprey were recorded by life stage (ammocoetes, macropthalmia, or adult). In addition, lamprey ammocoetes were identified to genus using pigment patterns in the caudal fin and caudal ridge as described by Whitton et al. (2010). Catch data for all fish taxa were typically consolidated to represent monthly sums. Sampling weeks were identified by year and number. The weeks mentioned in this report are calendar year weeks, with Week 1 being January 1–7 and Week 52 of 2012, December 23–31, is nine days long. The first sampling week of the current study was during Week 45 in 2012 and the last sampling week was during Week 26 in 2013 (Table 1).

The UBC trap captures many very small (usually < 25 mm) delicate non-salmonid fry. Many of these fish do not survive the extra handling required for measuring. This season we visually estimated the number of these fish in the live-box and designated them as unidentified fry. Once all the measurable fish were removed from the live-box the back screen was removed from the trap and the fry were flushed from the live-box. Genetic and otolith sampling

Genetic samples were taken on selected Chinook for the purpose of run identification. Samples were taken by removing a 1-mm2 tissue sample from the top or bottom lobe of the caudal fin. The samples were divided into three equal parts and placed in 2-ml triplicate vials of the same record number with 0.5 ml of 100% ethanol as a preservative. The triplicate samples were taken for: 1) USFWS archive, 2) California Department of Fish and Wildlife (CDFW) archive, and 3) for future analysis. Samples were taken when the FL designated the Chinook as winter Chinook, late-fall Chinook, or when the FL is > 100 mm. In addition, samples were taken proportionately to the anticipated out-migration distribution of spring Chinook. An attempt was made to collect samples from a range of fork lengths to avoid sampling siblings which might potentially bias the genetic analysis. Additionally, O. mykiss mortalities ≥ 50 mm were collected for otolith microchemistry analysis to determine the maternal origin of trout captured in the trap. Mark–recapture trials

Since the RST only captures fish from a small portion of the creek cross section, it is necessary to project the RST catch numbers to parts of the creek outside of the RST capture zone. Mark–recapture trials were conducted to determine the efficiency of the RST to catch all juvenile salmonid species moving downstream during a given time period.

Ideally separate mark–recapture trials should be conducted for each species, run, and life-stage to estimate species and age-specific trap efficiencies. However, catch rates for O. mykiss, spring Chinook, and late-fall Chinook were too low to conduct separate trials. Therefore, all species and life-stage passage estimates were calculated using naturally reared fall Chinook fry collected at the LBC RST. Trials were weather permitted, but were attempted once weekly while there were adequate numbers of Chinook captured by the LBC trap. An attempt was made to mark a minimum of 400 juvenile Chinook for each trial with a goal to recapture at least seven marked individuals (Steinhorst et al. 2004). In an effort to meet that goal, no mark–recapture studies were conducted with less than 100 individuals.

Six efficiency trials were conducted from January 22 through March 3, 2013. Dual marks were used to mark the salmon during the study period. For each trial, the fish were stained with Bismarck brown dye and one group received an upper caudal fin clip and the second group a lower caudal fin clip. The RBFWO also conducts mark–recapture trials at the Red Bluff



Diversion Dam (RBDD) for estimating trap efficiency while monitoring Sacramento River juvenile salmonid populations. The dual mark allowed RBDD to distinguish Battle Creek marked Chinook from those marked at the RBDD. The methods used for marking are described below.

Marking method — Dual marked fish were first anesthetized with a 60–80 mg/l solution of MS-222, and then surgical scalpels were used to remove an area of approximately 1 mm2, or less, from the corner of either the upper or lower caudal fin lobe. After the clipping process was completed, the salmon were marked with Bismarck brown.

Release and recovery — When the marking procedures were completed, the marked juvenile salmon were placed in a live-car and allowed to recover overnight in the RST live-box. This overnight retention allowed for the detection of salmon with latent injuries and delayed mortalities from the marking procedure. On the following evening, weak, injured, and dead fish were removed. The remaining fish were counted and transported 1.0 RM upstream of the RST sampling site to be released. Each group was released in batches of less than 50 fish. The next group was released in the same manner no less than 5 min after the last of the prior group, until all groups were released. The fish were released just below the CNFH’s intake 3 unit no earlier than 15 min before sunset. The nighttime releases of marked fish were designed: 1) to reduce the potential for unnaturally high predation on the marked fish possibly experiencing temporary disorientation by the transportation, and 2) to imitate the tendency for natural populations of out-migrating Chinook to move downstream primarily at night (Groot and Margolis 1998). The stained and marked Chinook that were recaptured later by the RST were counted and measured, and subsequently released downstream of the trap to avoid recapture. To explore the relationship of trap efficiency to biological and environmental variables we collected the following information at the time of release: flow, water temperature, turbidity, moon fraction, light from the moon, cloud cover, rain, wind speed and barometric pressure. In most cases when stream flows were predicted to exceed 2,000 cfs, fish being held for a mark–recapture test were released downstream of the trap and efficiency trials were not conducted, reducing the chance of mortalities and for crew-related safety concerns. Trap efficiency

The number of fish released and recaptured from each group from a trial was pooled to get the weekly trial totals. Weekly trap efficiencies were then generated using a stratified Bailey’s weekly estimator which is a modification of the standard Lincoln-Peterson estimator (Bailey 1951; Steinhorst et al. 2004). The weekly estimator was used because it performs better with small sample sizes and is not undefined when there are zero recaptures (Carlson et al. 1998; Steinhorst et al. 2004). Furthermore, Steinhorst et al. (2004) found it to be the least inaccurate of three estimators. Weekly trap efficiencies were calculated as follows:

( )( )1

1ˆ++

=h

hh m

rE

where E = the calculated trap efficiency in week h rh = the number of marked fish recaptured in week h mh = the number of marked fish released in week h



Although trap efficiency was calculated for all mark–recapture trials, only trials with at least seven recaptures were used to estimate passage, as suggested by Steinhorst et al. (2004). When instream flow fluctuations occurred or a trial did not recapture seven fish to generate statistically sound estimates, the trial was excluded and the “season” efficiency value was used. Season efficiency values were calculated by dividing the mean number of fish recaptured plus one from all valid mark–recapture trials by the mean of all valid trial releases plus one. We also used season efficiency values for the periods preceding the first trial and proceeding a week after the last trial of the season. Interpolated data

When the trap could not be safely fished or time when the cone had stopped rotating during the sampling period, the daily catch must be interpolated. We used an average method to interpolate (generate) a daily catch. Interpolated catch data were calculate by use of the equation:

I = (Cb + Ca) / (D * 2) where I = the interpolated catch for each day the trap did not fish in succession D = the number of days the trap did not fish Cb = the mean catch of D before the RTS did not fish Ca = the mean catch of D before the RTS did not fish

Juvenile passage indices Juvenile passage indices for salmonids were generated by summing the daily catch for

each salmonid species and run, and dividing by the trap efficiency for that week (strata) to determine a weekly passage. Weekly juvenile passage indices for Chinook and O. mykiss were calculated using weekly catch totals and either the weekly trap efficiency or season average trap efficiency. The O. mykiss JPI was calculated for both young-of-the-year and age-0+, which included individuals from all other age classes (not including adult fish). The FL distribution (FL by date) of O. mykiss captured in the trap was used to determine weekly catch of young-of-the-year and age-0+. With few exceptions, graphical display of the FL distribution indicated a distinct separation of the two groups. In addition, age-0+ and young-of-the-year captured during the same week could usually be distinguished by their life-stage classification.

Using methods described by Carlson et al. (1998) and Steinhorst et al. (2004), the weekly juvenile passage indices were estimated by:

h

hh E

UN ˆˆ = ,

where Nh = the passage during week h Uh = the unmarked catch during week h Eh = the calculated trap efficiency during week h

The variance and 95% confidence intervals for each week (Nh) are determined by the percentile bootstrap method with 1,000 iterations (Efron and Tibshirani 1986; Buckland and Garthwaite 1991; Thedinga et al. 1994). Using data with simulated numbers of migrants and trap efficiencies, Steinhorst et al. (2004) determined that the percentile bootstrap method had the



best coverage of a 95% CI. The variance for Nh is simply the sample variance of the 1,000 iterations of Nh produced by bootstrapping Uh, Eh, and mh for each week.

As described by Steinhorst et al. (2004) and demonstrated by Whitton et al. (2006), the 95% confidence intervals for the weekly juvenile passage indices were found by producing 1,000 iterations of Nh and locating the 50th and 950th values of the ordered estimates. The 1,000 iterations were produced by using R (version 3.1.0, www.r-project.org), which used the weekly catch, the calculated efficiency, and the number of marked fish for each trial.

The SE of the sample means of each stratum are also included with the 95% confidence interval. Juvenile Chinook and O. mykiss juvenile passage indices were summarized by brood year (BY). The juvenile passage indices for O. mykiss were calculated from January 1 through December 31, 2012, which in part passed during previous the trap season (2012-2013). The JPI for late-fall Chinook were calculated for the brood year, which this year started on April 1, 2012, and ran through March 31, 2013, some of which also in part passed during the previous trap season. The juvenile passage indices for spring Chinook and fall Chinook were generated from the current trap season catch, November 9, 2012, through June 30, 2013.

Results

Physical characteristics During the period of August 18 to August 30, 2012, a 27,676 acre lightning caused fire

burned entirely with in the Battle Creek watershed. Salvage logging began within the burn scar nearly immediately after the fire was extinguished. There were two large storms in December 2012 that caused significant erosion in the burn scar area. In general turbidity increased with increasing flows. Turbidity was not measured during some high flow events; therefore, turbidity may have been higher during those events.

The mean daily water temperatures at the UBC trap ranged from a low of 41.6ºF on December 21, 2012, to a high of 70.6ºF on June 30, 2013 (Figure 3). During the sample season mean daily flow measured by the U.S. Geological Survey at the CNFH gauging station (#11376550) ranged from a low of 260 cfs on June 17, 2013, to a high of 4,300 cfs on December 2, 2012 (USGS 2018). There were 13 d when flows exceeded 1,500 cfs with a peak flow of 10,800 cfs occurring on December 2, 2012, as measured at 15-min intervals. Turbidity at the UBC trap varied from a low of 1.1 NTU on June 2, 2013, to a high of 541.0 NTU on November 30, 2012 (Figure 4). Sampling effort

During the sample period the UBC trap was operated as continually as possible. The exceptions were during periods of high flow when we could not operate the trap safely. The trap did not fish from July 1 through November 26, 2012 because trap operations targeted spring Chinook out-migration and this was the trap’s off-season. Of the 234 d available during the sample period, the trap was operated 208 full days and 4 partial days. There were 22 d the trap was not operated; of which, 4 d were due to the lack of staff and 16 d due of high flows or predicted storm events (Table A. 1). The monthly sampling effort varied from a low of about 48% in November 2012 to a high of 100% in January, February, April and May 2013 (Figure 5). Mark –recapture efficiency estimates

During the sample period six mark–recapture trials using naturally-produced juvenile fall Chinook were conducted at the UBC trap from January 23 to February 28, 2013. Two thousand



three hundred seventy-two fish were released and 170 were recaptured (Table 2). Weekly trap efficiencies for the valid trials ranged from 4.88% to 11.08%; with a season average trap efficiency of 7.58% (Figure 6). During the six trials we used two different marks to identify groups within a release. The maximum differences in trap efficiency between groups within a trial varied from 0.61% to 4.09%; however, as the groups were released within five minutes of each other, they may not have been independent and were combined.

O. Mykiss — Annual juvenile passage indices for O. mykiss are for the dates from January 1 to December 31, 2012, requiring trap efficiencies from the same time period. Weekly trial and season average efficiencies from the 2011-2012 trap season (Schraml et al. 2018) and the season average from this sample season were used to calculate the weekly and annual juvenile passage indices (Table 3).

Late-fall Chinook — The JPI for late-fall Chinook encompassed the dates from April 1, 2012, to March 31, 2013. The weekly trial and season average efficiencies from both the 2011-2012 (Schraml et al. 2018) and 2012-2013 seasons were used to calculate the weekly and annual juvenile passage indices (Table 3).

Spring Chinook — During the 2011-2012 season the UBC trap was operated in the full-cone configuration for the entire season. The trap season covers the spring Chinook brood year. As such, the individual trials and season average were used to calculate the spring Chinook weekly and annual juvenile passage indices (Table 3). Salmonid catch and passage indices

O. mykiss — A total of 278 young-of-the-year BY12 O. mykiss were captured in the UBC trap. Out migration began later than all other years; the first fish was caught on April 10 and the last on December 31, 2012 (Figure 7). Fork lengths ranged from 23 to 218 mm and the mean and median was 70 and 60 mm, respectively. The life stage frequencies were as follows: 18.7% fry, 73.7% parr and 7.6% silvery parr (Table 4). Passage peaked at 636 on Week 21 (Figure 8). The annual JPI was 3,452 with upper and lower 95% confidence intervals of 3,757 and 3,174, respectively (Table B. 1; Table D. 1). Adult escapement above the CNFH BW was 368 (Bottaro et al. 2013) and from this a juvenile pre adult of production of 9.4 was calculated.

The fork lengths for BY11 age-0+ O. mykiss ranged from 87 to 270 mm with a mean and median of 177 and 190 mm, respectively. The life stage frequencies were as follows: 47.6% parr, 41.3% silvery parr and 11.1% smolt (Table 4). Passage peaked at 248 during Week 17 when 36.3% of the total passage occurred (Table B. 2; Figure 9). The annual JPI was 684 with upper and lower 95% confidence intervals of 766 and 612, respectively (Table D. 2).

Chinook — We captured 4,293 Chinook during the sample period. Length-at-date tables (Greene, memorandum) indicated that we collected spring Chinook, fall Chinook and late-fall Chinook (Figure 10). Fork lengths for all runs ranged from 29 to 115 mm, with a mean and median of 39 and 35 mm, respectively. The life stage distribution was as follows: 1.7% yolk-sac fry, 895% fry, 0.1% parr, 3.5% silvery parr and 5.3% smolt. The data trends for each run of Chinook are summarized below.

Late-fall Chinook — The actual catch of BY11 late-fall Chinook was 10, with a peak catch of three on May 21, 2012, and peak passage during Week 18 (Table B. 4; Figure 11). Fork lengths of late-fall Chinook ranged from 32 to 99 mm with a mean and median of 41 and 35 mm, respectively. The life-stage composition was 90.0% fry and 10.0% smolt (Table 4). The annual JPI for BY11 late-fall Chinook was 103, with an upper and lower 95% confidence intervals of 118 and 89, respectively (Table D. 3).



Spring Chinook — Because the BW at CNFH confined adult fall Chinook below the trap, we assigned all length-at-date fall Chinook (Greene, memorandum) as spring Chinook for the UBC indices. Brood year 2012 spring Chinook were first captured in the UBC trap on November 15, 2012, with a peak weekly catch of 1,119 during Week 1 (Table B. 4; Figure 12). The last BY12 spring Chinook was captured June 27, 2013 and actual catch was 4,286. After adjusting the catch for days the trap was not operated (interpolated catch) the total catch was 5,286 spring Chinook. Fork lengths of spring Chinook measured at the UBC trap ranged from 29 to 115 mm with a mean FL of 39 mm and a median of 35 mm (n = 3,853). The most abundant life stage was fry and the majority of individuals (90.2%) were ≤ 39 mm in FL. The life stage composition of spring Chinook captured at the UBC trap was 1.7% yolk-sac fry, 89.5% fry, 0.1% parr, 3.5% silvery parr, and 5.2% smolt (Table 4).

The annual JPI for BY12 spring Chinook was 70,063 with upper and lower 95% confidence intervals of 78,603 and 62,671, respectively (Table D. 4). The weekly passage indices had a bimodal peak, large passages occurred during Weeks 52, 1 and 2. A smaller peak occurred on Week 16 (n = 1,043) when a majority of the smolts out-migrated (Figure 12).

The RBFWO adult monitoring program estimated that 799 adult Spring Chinook passed above the CNFH BW and observed 320 spring Chinook redds above the UBC RST (Bottaro et al. 2013). Using the number of observed redds and the annual JPI we calculated to juveniles per redd to be 219.

Non salmonid catch Included in the 4,683 non-salmonid fishes caught (not including visually estimated fry)

were 3,174 Sacramento Sucker Catostomus occidentalis, 739 cyprinid fry, 447 Hardhead Mylopharodon conocephalus, 168 Pacific Lamprey Entosphenus tridentatus (165 ammocoetes and 3 macropthalmia), 67 Riffle Sculpin Cottus gulosus, 21 Sacramento Pikeminnow Ptychocheilus grandis, 18 unidentified lamprey ammocoetes , 17 California Roach Hesperoleucus symmetricus, 10 Threespine Stickleback Gasterosteus aculeatus, 7 cottid fry, 3 each centrarchid fry and Speckled Dace Rhinichthys osculus, 2 each Green Sunfish Lepomis cyanellus and Tule Perch Hysterocarpus traski and 1 unidentified Brook Lamprey Lampetra spp. This season we attempted to visually estimate the number of tiny unidentified non-salmonid fry captured by the trap. Approximately 12,000 fry were captured during the months of May and June 2013 (Table C. 1; Table C. 2). Mortality

The RBFWO is authorized by NMFS to take threatened and endangered species under an Endangered Species Act section 10(a)(1)(A) collection permit (permit) for scientific research and enhancement purposes. This permit limits the number of moralities (indirect and incidental mortality) that can occur as a result of trap operations. Indirect mortality is a given number of fish per season, while incidental mortality is a percent of actual total take (catch). The incidental mortality limit for UBC trap operations is 3% for O. mykiss, spring Chinook, and winter Chinook.

The mortality numbers in this report are for the trap year, not brood years, unless otherwise noted. Note that it is impossible to differentiate dead or dying fish that our trap captured as part of the creek’s drift and debris sieved by our trap, from those that expired in our



trap directly due to trapping operations. Every fish encountered dead in our live-box is treated as a mortality.

Marking mortality — A total of 21 mortalities occurred among the 2,372 marked Chinook at the UBC RST (0.3%). Mortalities resulting from our marking procedures for each efficiency trial ranged from zero to nine. All fish used for the mark–recapture trials were naturally reared origin fall Chinook collected at LBC. The indirect marking mortality limit for spring Chinook is 12. Neither limit was exceeded this season.

Trapping mortality — A total of 40 mortalities for all runs of Chinook and five O. mykiss occurred as a result of RST sampling during the 2012-13 sample season.

Spring Chinook — There were 4,286 BY12 spring Chinook handled at the UBC trap this season and 40 of those were recorded as mortalities, or 0.9% of the catch and 0.1% of the passage. The indirect mortality limit for spring Chinook is 5,700. These trap operations did not exceed either mortality limit.

Late-fall Chinook — There were zero moralities among the ten late-fall Chinook captured at UBC. No mortality limits have been placed on late-fall Chinook.

O. mykiss — There were 703 O. mykiss captured in the UBC RST. Five fish were mortalities, or 0.7% of the catch. The indirect mortality limit for O. mykiss is 400. Neither mortality limit was exceeded.

Genetic and otolith sampling Caudal fin genetic samples were collected from 281 of the Chinook captured. Two O.

mykiss were sacrificed for otolith microchemistry analysis.

Discussion

Sampling effort Trap conditions were not ideal this season for sampling the spring Chinook out-

migration. We operated the UBC trap 90% of the sample season. Two December storms forced the trap to be pulled for safety considerations. Peak out-migration at the UBC site generally occurs during late December through early January. The trap did not fish from November 28 through December 8 and from December 21 through December 27, with a partial day on December 29. The latter storm event and partial trap day may have occurred during peak out migration. If out-migration had started during the time when our trap was not in operation then the annual JPI could be negatively biased. Nearly a fifth (18.9%) of the total catch was interpolated for days when the trap did not fish, while only 11.7 % of the O. mykiss and 7.4% of the late-fall Chinook total catch was interpolated.

During BY12 O. mykiss sampling the trap was not fished on 34 days, however the trap fished for majority of the peak out-migration. The same was true for the late-fall Chinook out-migration. Since we were able to sample the entire peak emigration period for these two species, we have high confidence in our passage indices. Mark–recapture efficiency estimates

Spring Chinook — During the past four seasons, no trials have been conducted in December or early January. These are often periods of peak passage for spring Chinook. This season the first trial was conducted on January 23, after 83.7% of the annual JPI had already passed the trap. During the sample season, the season average trap efficiency was used to



estimate 91% of all spring Chinook passage. Because environmental factors, such as flow and turbidity, can affect rotary screw trap efficiencies, it is not possible to know how the use of the season average trap efficiency influenced our annual passage index. It is dependent upon how different the season average trap efficiency was from the actual trap efficiency for each week. If trials could have been conducted for the entire month of January, then 53% of the annual passage index could have been calculated using actual weekly trap efficiencies. If we could use spring Chinook captured in the UBC trap for mark–recapture studies we could apply actual weekly efficiencies to the weekly catch during the majority of the peak out-migration period and improve the accuracy of the weekly and annual juvenile passage indices. Salmonid passage indices

O. mykiss — Fifty percent of the young-of-the-year O. mykiss were captured in the UBC trap after May 26, 2012, which is later than in all but three other years when the trap was operated from January to July (Figure 13). Similar catch distributions were observed in 1999, 2010 and 2011, but in the years 2000–2009, 50% of the annual catch occurred prior to mid-May. In contrast, in 2000 50% of all young-of-the-year trout were captured prior to March 22, 2000. Reasons for the differences in migration timing are unknown, but flow may influence migration patterns as fry typically concentrate in shallow water along stream edges where velocities are lower, but move into faster water as they grow (Moyle 2002). Very few fish < 50 mm (13.9%) were captured in the UBC trap during the BY09 sampling, and flows were higher than observed in the two previous seasons. In addition, there were three storm events between January 19 and February 7, 2010 that produced flows from 3,360 to 4,110 cfs, which may have scoured redds produced prior to or during those dates. In some years, young-of-the-year trout were captured in the trap as early as late February to early March, whereas the first young-of-the-year was captured on April 10 during the current season.

Zimmerman and Ratliff (1999) found that only a small portion of resident Rainbow Trout spawning on the Deschutes River in Oregon occurred when steelhead spawned, and resident trout typically spawned later. In fact, using otolith microchemistry and information collected during spawning surveys, they were able to determine that steelhead and resident trout are reproductively isolated in the Deschutes River. If resident Rainbow Trout spawn later in Battle Creek, the capture distribution observed during BY12 suggests there may be more resident Rainbow Trout spawning in Battle Creek than steelhead, but this cannot be confirmed. It is also possible that steelhead fry are choosing to spend time rearing in Battle Creek before migrating downstream, which may explain the large numbers of young-of-the-year trout > 50 mm observed in the trap in April and May. Otoliths have been collected from O. mykiss donors but have yet to be analyzed. The data from the otolith analysis would provide information allowing us to determine the ratio of resident to anadromous O. mykiss captured in the UBC trap. The RBFWO should obtain funding for a comprehensive otolith study to determine if the ratio of anadromous to resident O. mykiss is changing in Battle Creek as the restoration project moves forward. This will allow us adaptively manage the restoration effort in an attempt to increase the steelhead population.

Late-fall Chinook — Many late-fall Chinook spawn below the CNFH BW and our JPI does not consider those fish and therefore does not represent the entire late-fall Chinook production on Battle Creek. The annual JPI for BY12 late-fall Chinook was 103 and was one of the lowest in the trap’s history (Table D. 3). There were 14 late-fall Chinook adults passed upstream, which was the lowest on record since 2001. Although we may have expected to



observe several more juveniles, we were not surprised to see a low number of out-migrants based on the adult return.

Spring Chinook — The calculated juvenile per redd ratio was the lowest since monitoring began (Table D. 4; Figure 15). The percent of the total catch interpolated was 18.9 and below the 1998–2011 mean of 19.4% (Figure 16). The average juveniles per redd for Battle Creek (BY07–BY11) is 705 and the highest during that time span was 1,097 for BY09. Using these numbers an expected JPI range of 225,600 to 351,040 was calculated. The BY12 JPI was only 72,063.

The adult Spring Chinook escapement estimate was the highest since monitoring began. The 320 spring Chinook redds observed above the UBC RST (Bottaro et al. 2013) were also the highest in our monitoring history. The most redds observed above the CNFH BW prior to this year was 176 in 2003 which likely included fall Chinook redds as several adult fall Chinook passed above the BW in late August. This season 68% of the redds were found in the North Fork, 3% in the South fork and the remaining 19% were located in the main stem. During egg incubation the mean daily temperatures of North and South Forks never ranged high enough to meet Ward and Kier’s (1999) poor suitability rating (> 60ºF). During incubation the furthest downstream temperature monitoring site on the main stem (UBC) reached the poor category on 17 d. However, only six redds were found in Reach 6 (Figure 14). Incubation temperatures were rated good to excellent in the upper reaches where the majority of redds were located (Bottaro et al. 2013). It would appear that water temperatures did not adversely affect production.

The two major storms that Battle Creek experienced in November and December created high and scouring flows. The low juveniles per redd could be explained by scouring of the redds. Furthermore, the upper Battle Creek trap cannot sample safely at those flows and was pulled from the water. The only way to interpolate the missing data is to take the average of the daily catch from the number of days before and after the trap did not sample. Each time we reset the trap we saw higher catch rates than before the trap was pulled. If, as it appears, emigration had started and/or peaked during the times the trap was not sampling, this would explain the low passage numbers. Because using the average method of interpolation is inaccurate during periods of increasing out-migration the BY 12 JPI may be grossly under estimated.

Passage by the UBC RST typically has a bimodal pattern, the first and largest peak usually occurs in early January and is comprised of fry. The second peak is seen in mid-April and is mostly comprised of silvery parr and smolts. This year’s catch followed the same pattern with a peak catch during Week 1 (n = 1,119) and the second peak occurring during Week 16 (n = 79; Figure 12). If scouring had occurred we would expect that the proportion of smolts to the annual JPI to be near the trap’s historical mean. The BY03–11 mean is 8.03% and this trap season the proportion of fish that out-migrated from April 1 to June 30 was 5.56% (Table 5). Logically, if we missed fish during the storm events, one would expect this percent to be higher than the mean. Because of the above reasons it is unclear if the passage numbers were low because of scour or are negatively biased owing to the difficulty in interpolating data for days when the trap did not fish.



Acknowledgements

We would like to thank the following people for their contributions: Thomas Bland, RJ Bottaro, Colby Crouse, Lance Downing, Sarah Giovannetti, Andrew Kirby, Jacie Knight, Sarah Moffitt, Sam Provins, James Smith, Charles Stanley, William “Rusty” Stark, Andy Trent, and Keenan True. Thank you to Jim Smith, Matthew Brown and Jim Earley for guiding and directing the project. We thank the Coleman National Fish Hatchery staff, especially Scott Hamelberg and Mike Keeler, for accommodating our program at the Coleman National Fish Hatchery. We would be remiss if we did not thank R.J Botarro, Ryan Cook, and Jacie Knight for their hard work in providing excellent input and reviewing this paper. Funding for this project was provided by the California Department of Fish and Wildlife (Game, CDFW) under Agreement Number P0685505.



References

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Tables



Table 1. Dates with corresponding week numbers for rotary screw trap operations at river mile 6.2 in Battle Creek, Shasta County.

Dates Corresponding week Dates Corresponding week 01/01–01/07 1 07/02–07/08 27 01/08–01/14 2 07/09–07/15 28 01/15–01/21 3 07/16–07/22 29 01/22–01/28 4 07/23–07/29 30 01/29–02/04 5 07/30–08/05 31 02/05–02/11 6 08/06–08/12 32 02/12–02/18 7 08/13–08/19 33 02/19–02/25 8 08/20–08/26 34 02/26–03/04 9 08/27–09/02 35 03/05–03/11 10 09/03–09/09 36 03/12–03/18 11 09/10–09/16 37 03/19–03/25 12 09/17–09/23 38 03/26–04/01 13 09/24–09/30 39 04/02–04/08 14 09/30–10/06 40 04/09–04/15 15 10/07–10/13 41 04/16–04/22 16 10/14–10/20 42 04/23–04/29 17 10/21–10/27 43 04/30–05/06 18 10/28–11/03 44 05/07–05/13 19 11/04–11/10 45 05/14–05/20 20 11/11–11/17 46 05/21–05/27 21 11/18–11/24 47 05/28–06/03 22 11/25–12/01 48 06/04–06/10 23 12/02–12/08 49 06/11–06/17 24 12/09–12/15 50 06/18–06/24 25 12/16–12/22 51 06/25–07/01 26 12/23–12/31 52a

a Week 52 (December 23–31, 2012) contains nine days for keeping January 1 as Julian calendar day 1.



Table 2. Summary of efficiency test data gathered by using mark-recapture trials with juvenile naturally reared fall-run Chinook Salmon at the upper rotary screw trap at river mile (RM) 6.2 in Battle Creek, Shasta County from November 9, 2012, through June 30, 2013. Trials that occurred on the same day were trials where multiple groups were released and the results were pooled to calculate weekly trap efficiency. These are grouped by shaded and unshaded rows. The Chinook Salmon used for the studies were captured at the lower rotary screw trap at RM 2.1.

Release date Time of release Released Recaptured Bailey’s efficiency Weekly mean flow, cfs 23-Jan-13 1835 212 17 8.45% 510 23-Jan-13 1830 194 14 7.69% 510 30-Jan-13 1915 160 13 8.70% 541 30-Jan-13 1920 213 15 7.48% 541 6-Feb-13 1835 251 20 8.33% 510 6-Feb-13 1840 258 10 4.25% 510 14-Feb-13 1910 186 8 4.81% 396 14-Feb-13 1905 202 10 5.42% 396 21-Feb-13 1806 175 16 9.66% 374 21-Feb-13 1811 176 22 12.99% 374 28-Feb-13 1755 179 14 8.33% 355 28-Feb-13 1800 166 11 7.19% 355



Table 3. Mark-recapture efficiency values used for weekly passage indices of brood year 2012 juvenile Rainbow Trout / steelhead (RBT), late-fall run Chinook Salmon (LFCS) and spring-run Chinook Salmon (SCS) captured in the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County from January 1, 2012, through June 30, 2013. The juvenile passage index column represents to which species or salmon race the efficiency value was applied to calculate the weekly passage index. Light grey shaded rows indicate weeks in which the 2011-2012 season average efficiency was used (Schraml et al. 2018). Dark grey shaded rows indicate weeks in which the 2012-2013 season average efficiency was used.

Dates Weeks Released Recaptured Bailey's efficiency Juvenile passage index 1-Jan-12 to 7-Jan-12 48–1 585 58 10.07% RBT 8-Jan-12 to 19-Jan-12 2–3a 625 61 9.90% RBT 20-Jan-12 to 24-Jan-12 3b–4a 383 37 9.90% RBT 25-Jan-12 to 28-Jan-12 4b 607 57 9.54% RBT 29-Jan-12 to 31-Jan-12 5a 610 50 8.35% RBT 1-Feb-12 to 4-Feb-12 5b 623 98 15.87% RBT 5-Feb-12 to 8-Feb-12 6a 606 75 12.52% RBT 9-Feb-12 to 11-Feb-12 6b–7a 655 63 9.76% RBT 15-Feb-12 to 21-Feb-12 7b–8a 607 56 9.38% RBT 22-Feb-12 to 28-Feb-12 8b–9a 602 74 12.44% RBT 29-Feb-12 to 6-Mar-12 9b–10a 620 46 7.57% RBT 7-Mar-12 to 10-Mar-12 10b 590 55 9.48% RBT 11-Mar-12 to 30-Jun-12 11–26 585 58 10.07% RBT, LFCS 9-Nov-12 to 21-Jan-13 45–3 395 28 7.58% RBT, LFCS, SCS 22-Jan-13 to 28-Jan-13 4 406 31 7.58% LFCS, SCS 29-Jan-13 to 4-Feb-13 5 373 28 7.86% LFCS, SCS 5-Feb-13 to 11-Feb-13 6 509 30 8.02% LFCS, SCS 12-Feb-13 to 18-Feb-13 7 388 18 6.08% LFCS, SCS 19-Feb-13 to 25-Feb-13 8 351 38 4.88% LFCS, SCS 26-Feb-13 to 4-Mar-13 9 345 25 11.08% LFCS, SCS 5-Mar-13 to 30-Jun-13 10–26 395 28 7.51% LFCS, SCS



Table 4. Brood year 2012 life-stage summary for Rainbow Trout / steelhead, late-fall, winter and spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 6.2 in Battle Creek, Shasta County.

Brood year 2012 Rainbow Trout /

steelhead

Brood year 2011 age-0+ Rainbow Trout / steelhead

Late-fall run Chinook Salmon

Winter-run Chinook Salmon

Spring-run Chinook Salmon

Life Stage Number Percent Number Percent Number Percent Number Percent Number Percent Yolk-sac fry 0 0.0% 0 0.0% 0 0.0% 0 0.0% 72

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