Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek, California

USFWS Report

Prepared By: C. Michael Schraml Charles D. Chamberlain Jaclyne R. Knight

Bureau of Reclamation Interagency Agreement R15PG00067 Activity 5

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

April 2020 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

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. R. Knight, and C. D. Chamberlain. 2020. Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek, California. USFWS Report. U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office, Red Bluff, California.

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Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek, California C. Michael Schraml, Jaclyne R. Knight, and Charles D. Chamberlain U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office 10950 Tyler Road, Red Bluff, California 96080 Abstract — The U.S. Fish and Wildlife Service has conducted juvenile salmonid monitoring in Clear Creek, Shasta County, California, using a rotary screw trap at river mile (RM) 1.7 since December 1998. This monitoring project has three primary objectives: (1) calculate an annual juvenile passage index for Chinook Salmon Oncorhynchus tshawytscha and Rainbow Trout/steelhead O. mykiss for inter-year comparisons and analyses of the effectiveness of stream restoration activities; (2) obtain juvenile salmonid life history information including size, emergence timing, emigration timing, and potential factors limiting survival at various life stages; and (3) collect otolith and tissue samples from juvenile salmonids for analyses and to develop genetic baseline markers for Clear Creek salmonid populations. Chinook Salmon run classifications show that late-fall run, winter-run, spring-run, and fall-run Chinook Salmon were captured in the rotary screw traps; however, due to overlapping spawn timing of spring-run and fall- run Chinook Salmon, and presence of both, it was problematic to index the juvenile passage using only the rotary screw trap at RM 1.7. Since 2003 a weir has been installed annually to isolate adult spring-run Chinook Salmon from adult fall-run Chinook Salmon. This season it was placed instream at RM 8.2. To better estimate the passage of juvenile spring-run Chinook Salmon a second rotary screw trap was installed at RM 8.4. The first O. mykiss and late-fall run Chinook Salmon redds were observed on December 7, 2016. The first brood year 2017 juvenile O. mykiss was captured at the lower trap on January 24, 2017. Fry (69.1%) and parr (29.0%) were the most abundant life stages captured and 69% of the O. mykiss were in the 20–29 mm FL range. Based upon length-at-date tables the first late-fall run Chinook Salmon was captured on April 1, 2017 and peak out- migration occurred through early June. Of the late-fall run Chinook Salmon captured, 92% were fry and 93% were in the 30–39 mm FL range. Snorkel surveys were conducted for spring-run Chinook Salmon redds; the first redds were observed on September 25, 2017 and the first juveniles were captured on November 21. Like late-fall run Chinook Salmon, the most abundant life stage was fry and the majority were in the 30–39 mm FL range (91%, both). No redd surveys are conducted for fall-run Chinook Salmon; based upon length-at-date tables, the first fall run juveniles were captured on December 1, 2017. Like the other Chinook Salmon races the most abundant life stage captured was fry. During this sample season 91 tissue samples were collected at the lower trap and 343 were collected at the upper trap. These samples will be submitted to a laboratory for genetic analysis and runs calls at a future date. In addition to the tissue samples, four mortalities > 50 mm FL were retained for otolith microchemistry analysis. Factors affecting survivorship and the data collected for condition factor will be analyzed and discussed in a separate report in the future. Passage indices and 95% confidence intervals were generated for brood year 2017 late-fall run, spring-run, and fall-run Chinook Salmon; O. mykiss passage indices were calculated for brood years 2017 and 2016 age-0+. The spring-run Chinook Salmon passage index for brood year 2017 from the upper Clear Creek rotary screw trap was 12,381. All redds observed during snorkel surveys were upstream of the upper rotary screw trap site. The indices of passage for

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brood year 2017 from the lower Clear Creek rotary screw trap were 14,383 late-fall run, 8,342 spring-run, and 757,003 fall-run Chinook Salmon. The O. mykiss indices from lower Clear Creek were 86 brood year 2016 age-0+, and 12,386 brood year 2017. Mark– recapture trials were conducted from early December 2017 through mid-March 2018 to determine rotary screw trap efficiency at both locations. The efficiency ranged from 2.41% to 12.98%. No paired mark trials or interval sampling were conducted during the 2017-2018 sample season.

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Table of Contents

List of Tables ...... vii List of Figures ...... viii List of Appendices ...... x Introduction ...... 1 Study Area ...... 2 Methods...... 3 Rotary screw trap operations ...... 3 Counting and measurement ...... 5 Tissue and otolith sampling...... 6 Mark–recapture trials ...... 7 Trap efficiency ...... 8 Interpolated data ...... 8 Juvenile passage indices ...... 10 Mortality ...... 10 Results ...... 11 Trapping conditions...... 11 Sampling effort ...... 11 Mark–recapture efficiency estimates ...... 12 Salmonid catch and passage indices...... 13 Non-salmonid catch...... 16 Tissue and otolith sampling...... 16 Trap year mortality ...... 16 Discussion ...... 17 Sampling effort ...... 17 Salmonid passage indices ...... 17 Non salmonid catch ...... 19 Upcoming projects ...... 19 Acknowledgements ...... 21 References ...... 22 Tables ...... 25

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Figures...... 37 Appendices ...... 60

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List of Tables

Table 1. Dates with corresponding week numbers for rotary screw trap operations at river mile 1.7 and 8.4 in Clear Creek, Shasta County...... 26 Table 2. The mean proportion of the daily catch from 24-h interval sampling events conducted during the 2011-2012 and 2012-2013 sample seasons (Schraml et al. 2018; Schraml and Chamberlain 2019a) at the lower Clear Creek (LCC) rotary screw trap located at river mile 1.7 in Shasta County...... 27 Table 3. The mean proportion of the daily catch from 24-h interval sampling events conducted during the 2013-2014, 2015-2016, and 2016-2017 sample seasons (Schraml and Chamberlain 2019b, 2019c, 2020) at the upper Clear Creek (UCC) rotary screw trap located at river mile 8.4 in Shasta County...... 28 Table 4. Summary of efficiency trial data gathered by using mark–recapture trials with natural- origin juvenile Chinook Salmon at the upper rotary screw trap in Clear Creek, Shasta County, from December 6, 2017, through December 18, 2017...... 29 Table 5. Mark–recapture efficiency values used for weekly passage indices of brood year 2017 juvenile Rainbow Trout/steelhead (RBT), and spring-run Chinook Salmon (SCS) captured in the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1, 2017, to June 30, 2018...... 29 Table 6. Summary of efficiency trial data gathered by using mark–recapture trials with natural- origin juvenile fall-run Chinook Salmon at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 11, 2018, through March 16, 2018...... 30 Table 7. Mark–recapture efficiency values used for weekly passage indices of brood year 2017 juvenile Rainbow Trout/steelhead (RBT), late-fall run (LFCS), spring-run (SCS), and fall-run Chinook Salmon (FCS) captured in the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1, 2017, through June 30, 2018...... 31 Table 8. Brood year 2017 life stage summary for Rainbow Trout/steelhead, late-fall run, winter- run, and spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County...... 32 Table 9. Brood year 2017 life stage summary for Rainbow Trout/steelhead, late-fall run, winter- run, spring-run, and fall-run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County...... 32 Table 10. The 2017 Clear Creek, Shasta County, snorkel survey reach numbers, locations, and river miles (RM) for reference...... 33 Table 11. The proportion (%) of the annual juvenile passage indices that were calculated using interpolated catch data for days the rotary screw traps did not fish for each brood year...... 34 Table 12. Length of the sample season, the annual passage index, and the passage and proportion of the annual passage index that passed the lower rotary screw trap for late-fall run

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Chinook Salmon (LFCS) and Rainbow Trout/steelhead (RBT) during the July 1 through November 15 time period...... 35 Table 13. The number of juvenile O. mykiss held, marked, released, and recaptured, the types of mortalities, and the percent mortality of fish held (shaded in gray) during mark–recapture trials conducted at the lower rotary screw (river mile 1.7) in Clear Creek, Shasta County...... 36

List of Figures

Figure 1. Locations of the upper (UCC) and lower (LCC) rotary screw trap sampling stations used for juvenile salmonid monitoring at river mile 8.4 (UCC) and 1.7 (LCC) in Clear Creek, Shasta County, from November 2017 through June 2018...... 38 Figure 2. A 5-ft diameter rotary screw trap similar to the traps operated at river mile 1.7 and 8.4 on Clear Creek, Shasta County, from November 2017 through June 2018...... 39 Figure 3. Mean daily flow measured at the United States Geological Survey IGO station and momentary turbidity recorded at the upper (UCC) and lower (LCC) Clear Creek rotary screw trap sampling stations at river mile 8.4 and 1.7 in Clear Creek, Shasta County, from October 1, 2017, through September 30, 2018...... 40 Figure 4. Mean daily water temperatures recorded at the upper (UCC) and lower (LCC) Clear Creek rotary screw trap sampling stations at river miles 8.4 and 1.7 in Clear Creek, Shasta County, from October 1, 2017, through September 30, 2018...... 41 Figure 5. Sampling effort summarized as the proportion (range: 0 to 1) of days fished each month for the upper rotary screw trap for brood year 2017 Rainbow Trout/steelhead (RBT), late- fall run (LFCS), and spring-run Chinook Salmon (SCS)...... 42 Figure 6. Sampling effort summarized as the proportion (range: 0 to 1) of days fished each month for the lower rotary screw trap for brood 2017 Rainbow Trout/steelhead (RBT), late-fall run (LFCS), spring-run (SCS), and fall-run Chinook Salmon (FCS)...... 43 Figure 7. Fork length and life stage distribution by date and life stage for brood year 2017 and brood year 2016 age-0+ juvenile Rainbow Trout/steelhead captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1 to December 31, 2017. .... 44 Figure 8. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile Rainbow Trout/steelhead captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1 through December 31, 2017...... 45 Figure 9. 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 8.4 in Clear Creek, Shasta County, from November 20, 2017, through June 30, 2018...... 46 Figure 10. Weekly passage indices with 95% confidence intervals of brood year 2017 juvenile spring-run Chinook Salmon captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from November 20, 2017, through June 30, 2018...... 47

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Figure 11. Fork length and life stage distribution by date and life stage for brood year 2017 and brood year 2016 age-0+ juvenile Rainbow Trout/steelhead captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1 to December 31, 2017. .... 48 Figure 12. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile Rainbow Trout/steelhead captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1 through December 31, 2017...... 49 Figure 13. Fork length and life stage distribution by date, life stage, and run for all juvenile Chinook Salmon captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from November 21, 2017, through June 30, 2018...... 50 Figure 14. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile late-fall run Chinook Salmon by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from March 26, 2017, through March 31, 2018...... 51 Figure 15. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile spring-run Chinook Salmon by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018...... 52 Figure 16. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile fall-run Chinook Salmon by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018...... 53 Figure 17. Interpolated passage and catch for young-of-the-year Rainbow Trout/steelhead for brood years 1998–2017 captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County...... 54 Figure 18. Interpolated passage and catch for late-fall run Chinook Salmon for brood years 1998–2017 captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County...... 55 Figure 19. Interpolated passage and catch for spring-run Chinook Salmon for brood years 2003– 2017 captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County. .. 56 Figure 20. Interpolated passage and catch for fall-run Chinook Salmon for brood years 1998– 2017 captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. .. 57 Figure 21. Pacific Lamprey ammocoete and macropthalmia captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from 2003–2017...... 58 Figure 22. Peak daily flow (cfs) and Pacific Lamprey ammocoete and macropthalmia daily catch by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 19, 2017, to June 30, 2018...... 59

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List of Appendices

Appendix A: Rotary Screw Trap Operations Table A.1. Summary of days the upper rotary screw trap did not fish for approximately 24 hours during the brood year 2017 Rainbow Trout/steelhead (RBT), late-fall run Chinook Salmon (LFCS), and spring-run Chinook (SCS) out-migration period...... 62 Table A.2. Summary of days the lower rotary screw trap did not fish for approximately 24 hours during the brood year 2017 Rainbow Trout/steelhead (RBT), late-fall run Chinook Salmon (LFCS), spring-run Chinook (SCS), and fall-run Chinook Salmon (FCS) out-migration period. 64

Appendix B: Weekly Catch and Juvenile Passage Indices Table B.1. Weekly catch, mortality and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile Rainbow Trout/steelhead captured at the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1 through December 31, 2017...... 67 Table B.2. Weekly catch, mortality and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from November 20, 2017, through June 30, 2018...... 68 Table B.3. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile Rainbow Trout/steelhead captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1 through December 31, 2017...... 70 Table B.4. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile late-fall run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from April 1, 2017, through March 31, 2018...... 72 Table B.5. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile spring-run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018...... 73 Table B.6. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile fall-run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018...... 74

Appendix C: Annual Catch and Passage Summaries Table C.1. Annual catch and brood year passage indices (highlighted in gray) of juvenile spring- run Chinook Salmon with the lower (LCL) and upper (UCL) 95% confidence limits and SE for brood years 2003–2017 captured by upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County...... 77

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Appendix D: Non-salmonid Species Catch Table D.1. Name key of non-salmonid fish taxa captured by the upper (river mile 8.4) and lower (river mile 1.7) rotary screw traps in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018...... 82 Table D.2. Summary of non-salmonid fish taxa captured by the upper Clear Creek rotary screw trap at river mile 8.4, Shasta County, from November 20, 2017, through June 30, 2018...... 83 Table D.3. Summary of non-salmonid fish taxa captured by the lower Clear Creek rotary screw trap at river mile 1.7, Shasta County, from September 13, 2017, through June 30, 2018...... 84

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Introduction

Clear Creek is a west side tributary of the Sacramento River in Shasta County, CA. Whiskeytown dam, constructed in 1963, acts as a total barrier to the upstream passage of anadromous fishes. The U.S. Fish and Wildlife Service (USFWS) Red Bluff Fish and Wildlife Office (RBFWO) has seasonally monitored juvenile salmonids in Clear Creek since December 1998 using a rotary screw trap (RST) placed at river mile (RM) 1.7 above the confluence with the Sacramento River (lower Clear Creek [LCC]). Since 2003 a second trap has been seasonally operated at RM 8.4 (upper Clear Creek [UCC]). Our monitoring efforts focus on three federally listed species: 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. Spring Chinook were listed as threatened in 1999 under the Federal Endangered Species Act (ESA) (64 FR 50394). Sacramento winter Chinook were listed as endangered in 1994 (59 FR 440). Winter Chinook are occasional visitors to Clear Creek; however, a self-sustaining population does not exist in Clear Creek. The California Central Valley steelhead population has been listed as threatened under the ESA since March 1998 (63 FR 13347). Additionally, our monitoring provides us the capability to generate estimates for the other salmonids found in the system: late-fall run Chinook Salmon (late-fall Chinook) and fall-run Chinook Salmon (fall Chinook). Late-fall Chinook migrate into Clear Creek November through April, with peak migration in December and peak spawning occurring in January. These fish primarily utilize the lower portions of Clear Creek for all instream life history phases. Spring Chinook generally migrate into Clear Creek before late August and spawn in the upper anadromous portion of Clear Creek in September and October (Figure 1). Fall Chinook spawning occurs soon after and often overlaps in time with that of spring Chinook with 98-99% taking place in Reaches 6 and 7 below the Gorge Cascade (Giovannetti et al. 2008). A picket weir is utilized each August to November to prevent fall Chinook from spawning in the upper reaches (Bottaro and Chamberlain 2019). Restoration of anadromous salmonid populations in Clear Creek is an important element of the Central Valley Project Improvement Act (CVPIA). The CVPIA has a goal to double populations of anadromous fishes in the Central Valley. The Clear Creek Restoration Program, authorized by Section 3406 (b)12 of the CVPIA, has funded many anadromous fish restoration actions which were outlined in the CVPIA Anadromous Fisheries Restoration Program Working Paper (USFWS 1995) and Final Restoration Plan (USFWS 2001). Since 2010 increased water releases from Whiskeytown Reservoir have occurred during the months of April and June to provide spring attraction flows, also referred to as “pulse flows.” The pulse flows were designed to fulfill “Action I.1.1. Spring Attraction Flows” of the 2009 National Marine Fisheries Service’s (NMFS) Biological Opinion for the Bureau of Reclamation’s Operations Criteria and Plan for the Central Valley Project (NMFS 2009). The objective of the flow increases is to encourage adult spring Chinook to move to upstream Clear Creek habitats for holding and spawning. In these habitats spring Chinook have access to colder water temperatures, large and remote holding pools, and newly-provided and clean spawning gravel. In addition, this limits hybridization and competition with fall Chinook. Ideally, the

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spring Chinook adult population would migrate upstream of the UCC RST not only for spring Chinook habitat and population integrity purposes but also for fish production estimation (juveniles produced per adult or redd) unconfounded by reproduction of spring Chinook downstream where they are not captured by UCC. The RBFWO has used rotary screw traps as the primary method to evaluate trends in juvenile salmon abundance in Clear Creek. While RSTs have limitations (e.g., can be challenging to effectively fish through rapid changes in flow), they can be an effective monitoring tool for providing reasonable estimates of juvenile production and facilitate annual comparisons when used consistently over a number of years (USFWS 2002; Volkhardt et al. 2007). Since 2003 the RBFWO has been using the UCC RST to index passage of spring Chinook. Passage indices of spring Chinook using only the LCC RST were found to be significantly underestimated (Gaines et. al 2003; Greenwald et. al 2003; Brown and Earley 2007). It is difficult to differentiate between spring Chinook and fall Chinook at the LCC RST. Though spring Chinook generally spawn earlier than fall Chinook, their spawning periods overlap significantly rendering them largely indifferentiable based on length or other externally identifiable characteristics. In August 2012 the Clear Creek picket weir was installed instream at RM 7.4 to protect the spring Chinook population spawning upstream of that point from potential superimposition and genetic introgression with fall Chinook as in previous years (Giovannetti and Brown 2013). The juvenile passage index is adjusted for redds identified above the weir at RM 7.5 but below UCC if present, but none were identified in this intermediate reach for the period of this report. This monitoring project has three primary objectives: (1) calculate annual juvenile passage indexes (JPI) for Chinook and O. mykiss for inter-year comparisons and analyses of the effectiveness of stream restoration activities; (2) obtain juvenile salmonid life history information including size, emergence timing, emigration timing, and potential factors limiting survival at various life stages; and (3) collect otolith and tissue samples from juvenile salmonids for analyses and development of baseline markers for the Clear Creek salmonid populations. In this report we discuss the passage indices and life history information. Analysis of survival, genetic, and otolith efforts will be covered in future independent reports. All passage data presented here are from brood year (BY) 2017.

Study Area

Whiskeytown Lake receives supplemental water from a cross-basin transfer sourced from Lewiston Lake in the Trinity River watershed. The Clear Creek watershed below Whiskeytown Dam covers an area of approximately 48.9 square miles, and Clear Creek itself flows 18.3 river miles to the Sacramento River. Clear Creek downstream of Whiskeytown Dam is accessible to anadromous fish. The upper and lower reaches of the anadromous portion transition significantly in geomorphic character at the Clear Creek road bridge, and the two zones support different fish communities. The upper reach flows south from Whiskeytown Dam almost 10.1 river miles. The lower reach heads in an easterly direction to the Sacramento River for a distance of approximately 8.2 river miles (Figure 1). In the upper reach the stream is more constrained by canyon walls and a bedrock channel, has a higher gradient, less spawning gravel, and more deep pools. In the lower reach the stream meanders through a less constrained alluvial flood plain, has a lower gradient, more spawning gravel, and fewer deep pools. The lower reach is managed for fall Chinook and late-fall Chinook and supports species of the foothills fish

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community. The more abundant fishes found in foothills community are Pacific Lamprey Entosphenus tridentatus, Sacramento Pikeminnow Ptychocheilus grandis, Sacramento Sucker Catostomus occidentalis, Hardhead Mylopharodon conocephalus, and Riffle Sculpin Cottus gulosus. Clear Creek’s fish assemblage is comparable to Moyle’s (2002) pikeminnow-hardhead- sucker assemblage except that large numbers of O. mykiss utilize the lower reach as well. The upper reach is managed for spring Chinook, which require cooler summer water temperatures than do the runs downstream. Although it was once anticipated that O. mykiss would predominately be in the uppermost reaches, recent data show greater spawning distributions in Reach 6 of the lower river (Figure 1; Schaefer et al. 2019). Whiskeytown Dam acts as a sediment trap. This combined with an altered flow regime and historic gold and gravel mining operations has impacted the lower portion of Clear Creek by reducing the gravel and other sediments needed for spawning, habitat-forming geomorphological process, and floodplain quality. The resultant reduction in habitat quality in Clear Creek below Whiskeytown Dam has been well documented by various investigators (Coots 1971; Graham Matthews & Associates 2003). Effects of reduced coarse sediment include riffle coarsening, fossilization of alluvial features, loss of fine sediments available for overbank deposition and riparian regeneration, and a reduction in the amount and quality of spawning gravel available for anadromous salmonids (Graham Matthews & Associates and Pittman 2007). In some areas of the Clear Creek stream channel, only clay hardpan or bedrock remains. The Clear Creek Restoration Program is an ongoing effort that has been addressing some of these habitat impacts with floodway restoration projects and gravel injection. Ambient air temperatures ranged from 25℉ in the winter to a summer high of 113℉ at the Redding Municipal Airport Station. Most precipitation falls into this watershed as rainfall, averaging 20 inches in the lowest elevations to more than 60 inches in the highest elevations. Most of the watershed’s rainfall occurs between November and April with little or none occurring during the summer months (McBain and Thrush 2001). The LCC RST is located at RM 1.7 and UCC RST is located at RM 8.4. The RSTs operate in or near the thalweg of the channel at both locations. The stream gradients at these locations range from approximately 1.0 degree to 1.5 degrees.

Methods

Rotary screw trap operations Sampling for juvenile salmonids in Clear Creek was accomplished by using standardized RST sampling techniques. The RSTs deployed in Clear Creek are manufactured by E.G. Solutions, Corvallis, Oregon (Figure 2). This type of trap utilizes a 5 ft diameter cone-shaped auger covered with one-eighth inch 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 while passing water through screens located in its back, sides, and bottom. Because of the high numbers of salmon out-migrating from Clear Creek, modifications have been made to the RSTs to reduce potential negative effects to juvenile salmonids created by high fish densities in the live-box. A “half-cone modification” has been made by placing an aluminum plate over one of the two cone discharge ports and removing an exterior cone hatch cover. This created a condition in which 50% of the collected fish and debris were not passed

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into the live-box, but were discharged from the cone into the creek thereby reducing overcrowding of fish in the live-box. Both traps were fished in the half-cone configuration for the entire season. Other modifications to RST equipment that provided greater protection to collected fish included enlarging the size of the live-box and increasing the size of flotation pontoons (to accommodate the larger live-box). Inside the live-box a midway fish exclusionary screen made of expanded aluminum was added dividing the live-box into two halves: fore and aft. This screen prevents large predatory fish from harassing and preying on smaller salmonids. A panel of clear polycarbonate was attached to the rear screen of the live-box to reduce water velocities within the live-box. Modifications to RST operations have included day and night sampling during the peak out-migration periods for spring Chinook and fall Chinook. To improve JPI computation, an attempt was made to fish high flow events when juvenile salmonids are thought to out-migrate and to increase the frequency of mark–recapture trials during those events except when flows in excess of 2,000 cfs (LCC) or 800 cfs (UCC) were encountered. 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 2017 redd timing data, 2017 water temperature data from redd construction forward, and water temperature data from water year 2013 (for the dates of September 11, 2017, to February 28, 2018) to estimate accumulated thermal units (ATU) for the days not yet realized at the time of calculation. Using these data, we predicted that spring Chinook emergence would occur in late November. The UCC trap was set two weeks 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). The UCC trap started operation on November 19, the LCC trap on September 12, 2017, we ceased trap operations on June 29, 2018. An attempt was made to fish the RSTs continuously from November 19, 2018, until June 29, 2018. The LCC trap was purposely set into operation before predicted emergence of BY17 salmonids to investigate possible Chinook and O. mykiss smolt outmigration during early fall rainfall events. For the period of September 12 to November 19, LCC was continuously fished except during periods of high debris loads when the cone was raised to reduce risk of damaged equipment. Each RST is attached to a cable high line and positioned instream with a system of ropes and pulleys. Fisheries crews typically accessed the RST by wading from the creek bank; however, during higher flows the RST was pulled into shallow water for boarding. After being serviced the RST was returned back to the thalweg as soon as possible to begin fishing again. The RST was serviced daily unless conditions (high flows, heavy debris loads, or high fish densities) required more frequent 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, cone fishing depth, number of rotations of the cone during the 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 cone fishing depth (in) was measured with a gauge that was permanently mounted to the pontoon adjacent to the cone. The rate of rotation (revolutions per min) of the cone was measured with a mechanical stroke counter that was mounted to the RST

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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 onboard the RST in front of the cone using a mechanical flow meter (Oceanic® Model 2030 flowmeter; General Oceanics, Miami). Water turbidity was measured from a grab-sample with Hach Model 2100D turbidimeter (Hach® Company, Ames, IA). Mean daily discharge data were collected at the U.S. Geological Survey’s Igo gauge site (Station #11372000), located at Clear Creek near Igo CA, approximately 2.6 river miles upstream of the UCC trap (Figure 1). All environmental and biological data were entered into a Microsoft Access database at the trap site using a Panasonic Toughbook® (Model CF-19). Dip nets were used to remove the contents of the RST live-box and place them on a sorting table for examination and separation of debris from fish. The captured fish were brought to shore in lidded 5-gal buckets where they were transferred to 10- or 25-gal buckets with aerators. They were then sampled as described further below. Counting and measurement The monitoring team counted and obtained length measurements (to the nearest 1.0 mm) for all fish taxa, dead or alive, that were collected. Live fish to be measured were anesthetized in a 1-qt plastic tub with approximately 1–3 ml of a 100 g/L 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 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, various criteria were used to count salmon, trout, and non-salmonid species. In general during intermediate trap clears that were not at the end of the 24-h sampling period, fish were simply identified, classified to age-class, and counted; however, no length measurements were taken under these circumstances. Chinook — At the end of the sample period when less than approximately 250 salmon were collected in the RST, all were counted, measured to FL, and 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 UCC RST, all Chinook captured that were assigned fall Chinook by Greene were considered instead to be spring Chinook because we installed a picket weir to block fall Chinook from passing upstream of UCC. There is undoubtedly overlap in the fork lengths of adjoining runs of juvenile salmon that are not captured by the dichotomous length-at-date criteria (Harvey et al. 2014). Subsampling was conducted when more than approximately 250 juvenile salmon were captured. This was accomplished by using a cylinder-shaped, one-eighth inch mesh “subsampling net”. The bottom of the subsampling net was constructed with a metal frame that created two equal halves. Each half of the subsampling net bottom was built with a mesh bag

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that was capable of being tied shut. One side of the net was tied shut and the other side 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 resulting in halving of the sample. 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 trap catch was successively subsampled until approximately 150–250 individuals remained. All the fish in the final subsample were then measured. The number of successive splits that were used varied with the number of salmon collected from one split (to create a one-half subsample) up to three splits. O. mykiss — All O. mykiss that were encountered at the end of the sample period were counted, measured, and classified to life stage in much the same manner as salmon: yolk-sac fry (R1), fry (R2), parr (R3), silvery parr (R4), and smolt (R5). Fish that were found in the live-box during supplemental storm sampling were counted and assigned to a life stage classification. All live juvenile O. mykiss greater than 50 mm in FL that were captured during the daytime sample were weighed to the nearest 0.1 g with an electronic scale (Scout Pro SP601; Ohaus Corp, Parsippany, NJ) for condition factor analysis. Non-salmonid taxa — All non-salmonid taxa were counted, and up to 20 randomly selected individuals of each species were measured. Total length 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). Fish that were taken from the live-box during supplemental storm sampling were counted, but no length measurements were obtained. Catch data for all fish taxa were consolidated to represent monthly sums. The LCC trap captures many minute (usually < 25 mm), delicate non-salmonid fry. Many of these fish do not survive the extra handling required for measuring. 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. 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 2017, December 24–31, is eight days long. The first sampling week of the current study was Week 37 in 2017 and the last sampling week was Week 26 in 2018 (Table 1). Tissue and otolith sampling Tissue samples were collected from select Chinook for the purpose of run identification. Samples were taken by removing a 1–2 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 USFWS archive, California Department of Fish and Wildlife (CDFW) archive, and for future analysis. Samples at UCC and LCC were taken when the length-at-date tables designated the Chinook as winter Chinook, late-fall Chinook, or when FL > 100 mm. In addition, at UCC samples were taken proportionately to the anticipated out-migration distribution of spring Chinook. An attempt was made to collect samples from a range of FLs to minimize sampling siblings, which might potentially bias the genetic analysis.

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Mark–recapture trials Since the RST only captures fish from a small portion of the creek cross section, it is necessary to implement a method 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 juvenile salmonids moving downstream during a given time period. Ideally separate mark–recapture trials would be conducted for each species, run, and life stage to estimate species and age-specific trap efficiencies; however, at both traps catch rates for O. mykiss and late-fall Chinook were too low to conduct separate trials. Therefore, all species and life stage passage estimates at LCC were calculated using mark–recapture trials from fall Chinook fry collected at the LCC RST. This was the third sample season that spring Chinook captured at the UCC trap were used for efficiency trials to calculate the JPIs for UCC RST. Four trials were conducted at the UCC trap and seven trials were conducted at the LCC 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 in order to generate reliable estimates (Steinhorst et al. 2004). In an effort to meet that goal, no mark–recapture studies were conducted with less than 100 individuals. All but one of the releases consisted of fish marked with a single mark (see below). One LCC trial was conducted using 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 the RBFWO to distinguish Clear Creek marked Chinook from those marked at the RBDD. The methods used for marking are described below. During Weeks 15 and 16 we captured enough O. mykiss to conduct a mark–recapture trial. The fish were single marked (see Marking procedures below). Because the JPI has historically been calculated using efficiencies from Chinook trials, the single O. mykiss efficiency result is presented here for comparison. We used the Chinook trials in the O. mykiss JPI calculation for consistency with our reports from previous years. Marking procedures — Fish were enumerated and FL was measured on a minimum of 30 individuals. Single marked fish consisted of immersing the salmon in a solution of 1.6 g of Bismarck brown-Y stain in 20 gal of water for a duration of 50 min. This stain can be retained on the fish for up to a week. Dual marked fish were first anesthetized with a 60–80 mg/l solution of MS-222, and surgical scalpels were then used to remove an area of approximately 1–2 mm2 from the corner of either the upper or lower caudal fin lobe. After the clipping process was completed, the salmon were stained with Bismarck brown. Recovery and release — 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 mortalities resulting from the marking procedure. On the following evening weak, injured, and dead fish were removed. The remaining fish were counted and transported for release 0.2 (UCC) or 0.4 river miles (LCC) upstream of the RST sampling site. The fish were released in batches of less than 50 fish, one batch immediately after another, no earlier than 15 min before sunset. The nighttime releases of marked fish were designed to reduce the potential for unnaturally high predation on the marked fish possibly experiencing temporary disorientation by the transportation and to imitate the tendency for natural populations of out-migrating Chinook to move downstream primarily at night (Groot and Margolis 1998; Schraml et al. 2018; Schraml and Chamberlain 2019a). To explore the relationship of trap efficiency to biological and environmental variables we collected flow, water temperature, and

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turbidity data at the time of release. Marked Chinook that were recaptured in the trap were counted, measured, and subsequently released downstream of the trap to prevent them from being recaptured again. In most cases when stream flows were predicted to exceed 2,000 cfs efficiency trials were not conducted, reducing the chance of mortalities and for crew-related safety concerns. Fish being held for a mark–recapture trial were released downstream of the trap. Trap efficiency The number of fish released and recaptured from a trial were used to calculate the weekly trap efficiencies 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 as it performs better with small sample sizes and is not undefined when there are zero recaptures (Carlson et al. 1998; Steinhorst et al. 2004). In addition, Steinhorst et al. (2004) found it to be the least inaccurate of those considered. Weekly trap efficiencies were calculated by use of the equation:

h Êh = (r +1)/(mh + 1),

where

Ê = 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 effectively altering trap efficiency mid-trial, or a trial did not recapture seven fish to generate statistically sound estimates, the trial was excluded and the season average efficiency value was used. Additionally, for the periods preceding the first trial and proceeding a week after the last trial of the season, the season average efficiency was used for those strata. Season average efficiency values were calculated using the equation:

E̅ s = (r̅ + 1)/(m̅ + 1),

where

E̅ = the calculated season average trap efficiency r̅ = the average number of marked fish recaptured from all valid trials at an individual trap during the sample season m̅ = the average number of marked fish released from all valid trials at an individual trap during the sample season

Interpolated data When the trap could not be safely fished or the cone stopped rotating during the sampling period, the daily catch was interpolated. Depending on the creek conditions during the outage and the length of the outage we used one of two methods to interpolate the data.

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Average method — We used the average method to interpolate (generate) a daily catch on days when a trap was not fished at all during the 24-h sample period and on partially sampled days with a zero catch. Interpolated catch data were generated by use of the equation:

I = (Cb + Ca)/(Dˑ2),

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 RST did not fish Ca = the mean catch of D after the RST did not fish

Hourly proportion of daily catch method — We used the hourly distribution of daily catch to estimate missing data for times when the trap sampled an incomplete portion of the 24-h sample period. This was only applied when at least some catch occurred prior to stoppage and the trap stoppage time could be determined. During the 2011-2102 and 2012-2013 sample seasons we conducted 24-h interval sampling events at the LCC trap (Schraml et al. 2018; Schraml and Chamberlain 2019a). During the 2013-2014, 2015-2016, and 2016-2017 sample seasons we conducted them at the UCC trap (Schraml and Chamberlain 2019b, 2019c, 2020). The traps were sampled on the hour for each hour during the events at LCC and hourly proportion of the daily catch was calculated. The mean hourly proportion of the daily catch was then calculated for each hour of the day from all sampling events (Table 2; Table 3). These distributions of daily catch were used to estimate what the total daily catch would have been had the trap fished a complete 24-h period (actual catch plus the estimated missing catch):

Id = C/P, where

Id = the total daily catch (actual catch plus the estimated missing catch) rounded to the nearest fish C = the actual catch for the time period the trap sampled P = the average proportion of the daily catch (in the 24-h sampling events) for the time the trap sampled

The missing catch was estimated by subtracting actual catch from the estimated total daily catch:

Im = Id – C,

where

Im = the estimated missing catch for the time period that the trap did not sample

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Juvenile passage indices In general the season was stratified by one-week periods for both traps. Weekly juvenile passage indices for Chinook and O. mykiss were calculated by dividing the weekly catch totals by either the weekly trial 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 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. At UCC we split Week 50 and Week 51 into two substrata because we conducted three mark–release trials during that period. Using methods described by Carlson et al. (1998) and Steinhorst et al. (2004), the weekly juvenile passage indices were estimated by:

N̂ h = Uh / Êh,

where

N̂h = the passage during week h Uh = the unmarked catch during week h Êh = the calculated trap efficiency during week h

The variance and 95% CI for each week’s passage (N̂h) were calculated 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 the percentile bootstrap method performed the best as it had the best coverage of a 95% CI. The variance for N̂h is simply the sample variance of the 1,000 iterations of N̂h 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% CIs for the weekly juvenile passage indices were found by producing 1,000 iterations of Nh and locating the 25th and 975th values of the ordered estimates. The 1,000 iterations were produced by using R (version 3.5.0, 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. Juvenile Chinook and O. mykiss passage indices were summarized by brood year. The juvenile passage indices for O. mykiss were calculated from January 1, 2017, through December 31, 2017. The JPIs for late-fall Chinook were calculated for the brood year, which this year started on April 1, 2017, and ran through March 31, 2018. The juvenile passage indices for spring Chinook and fall Chinook were generated from the current trap season catch, September 13, 2017, through June 30, 2018. 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 indirect mortalities that can occur because of trap operations.

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The mortality numbers in this report are for the sample season, 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 our operations. Every fish encountered dead in our live-box is treated here as a mortality.

Results

Trapping conditions During the sample season mean daily flows at the USGS Igo gauge ranged from a minimum of 147 cfs on June 29, 2018, to a maximum of 931 cfs on June 18, 2018. The maximum measured flow (based upon 15-min interval data) was 1,150 cfs on April 7, 2018 (Figure 3). The minimum flows were comprised almost entirely from controlled releases out of Whiskeytown Lake, while the maximum resulted from Whiskeytown releases (“Pulse flows”) plus natural storm flow accretions. Instream water temperatures at each trap site were measured year round, however the temperatures listed below are only for the trap season. Upper Clear Creek — The channel width of Clear Creek at the UCC RST spanned from approximately 30 ft at the lowest flows to more than 130 ft at the highest flows. Measured water depths in Clear Creek at the base of the RST cone ranged from 3.6 to 4.9 ft, with an average depth of 4.2 ft. The shallowest depths were recorded in June 2018 (mean, 3.9 ft), and the deepest depths were recorded in March and April 2018 (mean, 4.3 ft). Measured turbidity levels ranged from 0.46 NTU on May 3, 2018, to 19.5 NTU on March 2, 2018, with a mean turbidity of 1.6 NTU. Turbidity was typically the lowest during the lower flows of summer and highest during the higher flows caused by precipitation runoff (Figure 3). Mean daily water temperature during the sampling season at UCC ranged from a low of 43.8℉ on March 1, 2018, to a high of 63.9℉ recorded in late June 2018 (Figure 4). Lower Clear Creek — The channel width of Clear Creek at the LCC RST spanned from approximately 40 ft at the lowest flows to more than 150 ft at the highest flows. Measured water depths in Clear Creek at the base of the RST cone ranged from 2.5 ft to 4.8 ft, with an average depth of 3.0 ft. The shallowest depths were recorded during September 2017 (mean, 2.7 ft), and the deepest depths were recorded in June 2018 (mean, 4.8 ft). Measured turbidity levels ranged from 0.58 NTU on June 1, 2018, to 43.2 NTU on April 7, 2018, with a mean turbidity of 2.04 NTU (Figure 3). Mean daily water temperature ranged from 42.9℉ on February 23, 2018, to 71.0℉ on June 30, 2018 (Figure 4). Sampling effort Upper Clear Creek — During the sample season we would have liked to fish the UCC trap continuously from November 19, 2017, to June 29, 2018 (224 d). Unfortunately, because of high flow and a limited of staff we could not do so. The trap did not fish from July 1 through November 19, 2017, because trap operations targeted spring Chinook out-migration and this was the trap’s off-season (Figure 5). The UCC RST did not sample for 23 days during the trap season (Table A.1). O. mykiss brood year — Trapping conditions were generally good; however, eight days catch during peak out-migration had to be interpolated because the trap could not fish due to high flow (Table A.1; Figure 5). Of the total catch, 10.2% was interpolated.

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Spring Chinook brood year — The UCC RST did not sample for 4 d because of high flow, which was during the pulse flow in June. The lack of adequate staff, a wildland fire, and training sessions prohibited us fishing another 32 d (Figure 5). There were six partially sampled trap days in which the cone had been stopped by debris, vandalism, or the cone was raised because of high flow partway through a set (Table A.1). Only 1.3% of the catch was interpolated. Lower Clear Creek — The LCC RST was operated from mid-September through the month of June, but didn’t fish continuously until mid-November. O. mykiss brood year — The conditions for rotary screw trapping during BY17 out-migration were very good and catch for only two days had to be interpolated. The LCC trap season targets spring and fall Chinook out-migration and did not sample from July through September 12, 2017, the off-season hours accounted for 20% off the total hours available to fish (Figure 6). The days that LCC did not fish for a full 24-h period are listed in Table A.2. Only 1.4% of the catch was interpolated. Late-fall Chinook brood year — The conditions and off-season hours were the same as described for O. mykiss (Figure 6) and there were only 3 d (1.8% of the catch) that the catch had to be interpolated (Table A.2). Spring and fall Chinook brood year — The LCC RST did not sample for 52 of the 244 d during the sample season. None of the non-sampled days were the result of high flow; however, shortage of staff resulted in RBFWO not fishing the trap a total of 30 d. We did not fish the trap another 22 d in the fall because high debris loads and zero catches (Figure 6). There were only two partially sampled days when the cone was raised because of high flow (Table A.2). Only 1.1% of the spring and 7.1% of the fall Chinook Salmon catch had to be interpolated. Mark–recapture efficiency estimates Upper Clear Creek — Four mark–recapture trials were conducted to estimate UCC RST efficiency. The first release of marked fish occurred on December 7, 2017, and the last on December 19, 2017. During the four trials, 681 marked Chinook were released and 67 were recaptured. The number of individual fish released for each trial ranged from 130 to 237, with an average of 170. Recaptured fish numbers per trial ranged from 12 to 25 (Table 4) with an average of 17. Efficiencies ranged from 8.33% to 12.98% per trial, and the season average efficiency was 10.53%. No mark–recapture trials were conducted from November 21 through December 7, 2017, and from December 19, 2017, through June 30, 2018, because of low fish collection numbers. As described in the methods for the periods when no mark–recapture trials were conducted, the “season” average efficiency was used to calculate passage. O. mykiss — Annual JPI for O. mykiss are for the dates from January 1 to December 31, 2017, requiring trap efficiencies from the same time period. The season average efficiency from the 2016-2017 sample season (Schraml and Chamberlain 2020) and weekly trap efficiencies and the 2017-2018 trap season average were used to calculate the weekly and annual JPIs (Table 5). Actual weekly trial data was used to calculate 7.3% of the annual JPI and the rest was expanded by using the season average efficiency. Spring Chinook — The trap season covers the spring Chinook brood year. As such, the individual trial and season average efficiencies from this sample season were

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used to calculate the spring Chinook weekly and annual juvenile passage indices (Table 5). Actual weekly trial data was used to calculate 51.1% of the annual JPI and the rest was expanded by the season average efficiency. Lower Clear Creek — Seven mark–recapture trials were conducted using Chinook; the first release of marked fish occurred on January 12 and the last on March 17, 2018. During the seven trials 3,229 marked Chinook were released and 139 were recaptured (Table 6). The number of individual fish released for each trial ranged from 272 to 509, with an average of 461. Recaptured fish numbers per trial ranged from 9 to 30 with an average of 20. Efficiencies ranged from 2.41% to 6.26% per trial, and the season average efficiency was 4.55%. No mark–recapture studies were conducted from September 12, 2017, to January 10, 2018, and from March 17 through June 30, 2018, because of low fish collection numbers. For the second trial the fish were dual marked with Bismarck brown and a lower caudal fin clip to distinguish between multiple weekly release groups and trap locations. This year we captured a sufficient number of O. mykiss to conduct one trial. We released 163 fish and recaptured two for a Bailey’s efficiency of 1.83%. Because less than seven fish were recaptured the trial was deemed not valid. O. mykiss — Weekly trial data and season average from the 2016-2017 (Schraml and Chamberlain 2020) and 2017-2018 sample seasons were used to calculate the O. mykiss weekly and JPIs at the LCC trap (Table 7). Actual weekly trial data was used to calculate only 1.1% of the annual JPI; the rest was expanded by the season average efficiency. Late-fall Chinook — The JPI for late-fall Chinook was calculated from April 1, 2017, to March 31, 2018. The season averages from the 2016-2017 (Schraml and Chamberlain 2020) and 2017-2018 sample seasons were used to calculate 100% of the late-fall Chinook weekly and annual JPIs (Table 7). Fall and spring Chinook — The trap season covers the spring and fall Chinook brood year. As such, the individual trials and season average from this sample season were used to calculate the spring and fall Chinook weekly and annual juvenile passage indices (Table 7). Weekly trial efficiencies were used to calculate 3.8% of the spring and 78.4% of the fall Chinook Annual JPIs. Salmonid catch and passage indices Upper Clear Creek — A total of 2,591 fish representing five fish taxa were collected in the UCC RST during the sample season. The most abundant fish taxa collected were Chinook and O. mykiss. O. mykiss — A total of 239 young-of-the-year BY17 O. mykiss were captured in the UCC trap. The first fish was caught on March 17 and the last on December 24, 2017 (Figure 7). Fork lengths ranged from 21 to 244 mm, and the mean and median were 46 and 35 mm, respectively. The life stage composition was 2.5% yolk-sac fry, 47.3% fry, 49.4% parr, and 0.8% silvery parr (Table 8). The official weekly and annual passage indices are calculated using LCC RST data because much of the O. mykiss spawning occurs below the UCC RST. The passage data presented below are for comparison purposes. Passage peaked at 366 on Week 20 (Figure 8). The annual JPI was 2,338 (95% CI: 2,141–2,548; Table B.1). The RBFWO monitored the adult populations of O. mykiss and late-fall Chinook in Clear Creek by kayak surveys in fall 2017 and winter 2018; all

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adult data, for these fish, presented in this report are from Schaefer et al. (report in draft form at the time of publication). There were 20 redds observed above the UCC trap. Based upon passage there were 177 juveniles-per-redd produced. A total of 37 age-0+ O. mykiss from previous brood years were captured at UCC. Three life stages were represented: 73.0% parr, 24.3% silvery parr, and 2.7% smolt. Fork lengths ranged from 79 to 255 mm and the mean and median were 138 mm and 117 mm, respectively. Chinook — Length-at-date tables (Greene, memorandum) indicated that we collected fall, winter, and spring Chinook. The UCC RST captured 1,275 Chinook during the sample season. Seven Chinook length-classified as winter Chinook were captured, the rest length-classified as spring Chinook or fall Chinook. Chinook of all life stages from yolk-sac fry to smolt were collected (Figure 9). The data trends for each size-classified run of Chinook, along with our assumptions and adjustments, are summarized below. Late-fall Chinook — No BY17 late-fall Chinook were captured during the sample season. Winter Chinook — Seven winter Chinook sized fish were caught, one in January 2018, four in February, and two in March (FL: 65, 80, 76, 77, 79, 93 and 92 mm); six were smolt and one a silvery parr. Spring Chinook — All adult spring Chinook data presented in this report can be found in Bottaro and Chamberlain (2019). For spring Chinook estimates at UCC, we did not strictly rely on length-at-date tables. Installation of the picket weir confined adult fall Chinook below the trap, preventing them from spawning upstream. Therefore, we assigned all length-at-date fall Chinook as spring Chinook. A total of 1,268 spring Chinook were captured. Fork lengths for all BY17 spring Chinook captured ranged from 29 mm to 102 mm, with a mean and median FL of 38 and 35 mm, respectively. The majority of measured individuals (91.6%) were ≤ 39 mm in FL. The life stage composition was as follows: 91.6% fry, 0.6% parr, 3.5% silvery parr, and 4.3% smolt (Table 8). Peak passage occurred during Weeks 47–51, when 82.8% of the fish passed (Figure 10); out-migration steadily declined afterwards. The annual JPI was 12,381 (95% CI: 10,595–15,143; Table B.2; Table C.1). Nine spring Chinook redds were observed above the separation weir, and none were below the UCC trap. The juvenile passage index yielded a production of 1,376 juveniles- per-redd. Lower Clear Creek — A total of 33,794 individual fish representing 16 fish taxa were collected in the LCC RST during the sampling period, not including visual non-salmonid fry estimates. The most abundant fish taxa collected were Chinook, followed by O. mykiss. The LCC RST capture data are reported below. O. mykiss — A total of 697 young-of-the-year BY17 O. mykiss were captured in the LCC trap. The first fish was caught on January 24 and the last on December 8, 2017 (Figure 11). Fork lengths ranged from 21 to 130 mm, and the mean and median was 35 and 27 mm, respectively. The life stage frequencies were as follows: 1.1% yolk-sac fry, 69.6% fry, 29.0% parr, and 0.3% silvery parr (Table 9). Peak passage occurred over an eight-week period (Weeks 13–20) and then steadily declined (Figure 12). The annual JPI was 12,386 (95% CI: 11,345–13,441;

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 14 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.3; Table C.2). The BY17 redd count for adult O. mykiss in Reaches 1–6 was 65 and the juveniles-per-redd production was 191. The reach breaks are described in Table 10. Another 10 redds were observed below the LCC trap, the adjusted population (proportionate to juveniles-per-redd) that includes the redds below the trap was 14,292. Only 5 age-0+ fish were captured; four were parr and one a silvery parr. Chinook — Length-at-date tables (Greene, memorandum) indicated that we collected individuals from all four Chinook runs known from the Sacramento River basin. During the sample season, 29,223 individuals were captured. Fork lengths for all measured fish ranged from 26 mm to 105 mm, with a mean and median of 36 mm and 33 mm, respectively. Few fish (7.6%) measured greater than 39 mm in FL. Chinook of all juvenile freshwater life stages were collected (Figure 13), and 97.2% of those were classified as fry stage fish (n = 28,414). The data trends for each run of Chinook are discussed below: Late-fall Chinook — A total of 812 BY17 late-fall Chinook were captured; fork lengths of measured fish ranged from 29 mm to 105 mm with a mean and median of 38 and 36 mm, respectively. Fry were the most common life stage for late-fall Chinook at 92.0% (n = 747). The life stage composition was 0.6% yolk-sac fry, 92.0% fry, 3.6% parr, 2.2% silvery parr, and 1.6% smolt (Table 9). Passage peaked during Weeks 16–23 when 83.4% of the fish passed the trap (Figure 14). The annual JPI for BY17 late-fall Chinook was 14,383 (95% CI: 12,653–16,431; Table B.4). There were 20 total late-fall Chinook redds observed, 15 of which were above the LCC RST site. The juveniles-per-redd production, for redds above the LCC site was 959. The adjusted population (proportionate to juveniles-per-redd) that includes estimated production from redds below the trap was 19,177 (Table C.3). Winter Chinook — Twenty-four winter Chinook sized fish were captured; 1 fish was a parr, 9 were silvery parr, and 14 were smolts. The FL ranged from 48–101 mm. Spring Chinook — According to length at date tables, 375 spring Chinook were captured at the LCC RST. The passage index for spring Chinook is determined by using the UCC RST. The data presented here for the LCC RST is provided for comparison purposes. Peak out-migration occurred from mid- November through mid-December 2017 (Figure 15). The annual passage index was 8,342 (95% CI: 6,767–10,403; Table B.5). Fork lengths ranged from 29 mm to 91 mm, with a mean and median of 37 and 35 mm, respectively. Fry were the most common life stage for spring Chinook at 91.7% (n = 344). The rest of the life stage composition was: 0.3% yolk-sac fry, 0.5% parr, 6.1% silvery parr, and 1.3% smolt (Table 9). Fall Chinook — A total of 28,765 fall Chinook were captured. Fall Chinook made up 98.4% of all salmon captured. The minimum FL was 26 mm and the maximum was 86 mm with the mean and median 35 and 33 mm, respectively. Of the 8,662 fall Chinook that were measured, 7,984 were in the 30–39 mm FL range. Fry were the most common life stage at 97.5%, then yolk- sac fry at < 0.1%, smolt at 0.2%, silvery parr at 1.1%, and parr at 1.2% (Table 9).

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Peak out-migration occurred during weeks 3–9 and the annual passage index was 757,003 (95% CI: 638,702–948,755; Figure 16; Table B.6; Table C.4). Video monitoring estimated the adult female escapement to be 285. Adult escapement on Clear Creek was very unique this year, with the number of Jills (females ≤ 2 years of age; n = 784) far outnumbering adult females (Killam and Mache 2018). Jills make up part of the female spawning population. In previous reports we have reported the number of juveniles-per-female based upon the annual JPI and the number of adult females (≥ 3 years). This brood year that number was 2,656. Non-salmonid catch Upper Clear Creek — Included in the 569 non-salmonid fish caught were Pacific Lamprey (n = 472; 151 ammocoetes, 321 macropthalmia, and 2 adults), Riffle Sculpin (n = 69), California Roach Lavinia symmetricus (n = 10), unidentified lamprey ammocoetes (n = 12), and Cottus fry (n = 4; Table D.1; Table D.2) Lower Clear Creek — A total of 1,532 individual non-salmonids from 12 taxa were captured by LCC RST. The most abundant non-salmonids were Pacific Lamprey and Riffle Sculpin (Table D.3). Pacific Lamprey — A total of 162 ammocoetes and 1,101 macropthalmia were collected. Both were collected throughout the sampling season with a highs in March when 53 ammocoetes and 862 macropthalmia were captured. Riffle Sculpin — A total of 103 Riffle Sculpin were collected. This species was collected throughout the sampling season. Tissue and otolith sampling Tissue samples collected taken from 313 Chinook during this sampling season. Seventy- eight were collected from LCC and 235 were collected from UCC. Samples from LCC were taken when the FL designated the Chinook as winter Chinook (n = 24), late-fall Chinook (n = 24), or when the FL was > 100 mm (n = 5); an additional 32 samples were collected from fish with FLs 32–43 mm. Four O. mykiss UCC trap mortalities with FL > 95 mm were retained for otolith samples. Trap year mortality Marking mortality — A total of 24 mortalities occurred among the 3,951 marked Chinook at both traps for a marking mortality of 0.6%. Mortalities resulting from the marking procedures for each efficiency trial ranged from zero to eleven (Table 4; Table 6). Mortalities occurred at several stages during the mark–recapture process: 3 died while being held before the mark, 20 died while being held after the mark, and another 3 were found dead in the live-box after the release. This season we conducted one mark–recapture trial with 178 O. mykiss fry; 15 (8.4%) of these fish died while being held in a live-car before the mark occurred. Trapping mortality — A total of 181 mortalities for all salmonids occurred as a result of normal RST sampling during the 2017-2018 sample season. Upper Clear Creek — A total of 1,275 Chinook of all runs were captured at UCC and 17 mortalities were recorded. Below is the breakdown of Chinook races and O. mykiss mortalities.

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O. mykiss — There were 755 O. mykiss captured in the UCC RST and 11 were mortalities (1.5%). The indirect mortality limit set by the permit for O. mykiss of 315 was not exceeded. Winter Chinook — There were seven winter-Chinook-sized fish captured in the UCC RST, and none of those fish died. Spring Chinook — There were 1,268 BY17 spring Chinook captured in the UCC RST. Of these captures 17 (1.3%) were recorded as mortalities. The indirect mortality limit for spring Chinook of 4,275 was not exceeded. Lower Clear Creek — A total of 29,223 Chinook of all runs were captured at LCC and 150 mortalities were recorded. Below is the breakdown of Chinook races and O. mykiss mortalities. O. mykiss — There were 1,173 O. mykiss captured in the LCC RST and 3 died as a result of normal trapping operations (0.3%). The permit limit was exceeded. Late-fall Chinook — There were 59 late-fall Chinook captured in the LCC RST, none were recorded as mortalities. Winter Chinook — Twenty four winter-Chinook-sized fish were captured in the LCC RST and no mortalities were recorded. Spring Chinook — There were 375 BY17 spring Chinook captured in the LCC RST. One spring Chinook mortality was recorded (0.3%). The permit limit was not exceeded. Fall Chinook — There were 28,765 BY17 fall Chinook captured in the LCC RST. Of these captures, 149 were recorded as mortalities (0.5%). No permit limits have been set for fall Chinook.

Discussion

Sampling effort Trapping conditions were very favorable for rotary screw trap operations at both traps and for all target salmonids; there were very few days during the peak out-migration periods that catch had to be interpolated for days the trap did not fish. Starting on March 31, 2018, the traps were not fished on the weekends because of reduced staffing. Because the percent of catch that was interpolated was low for all target salmonids we feel that our annual JPIs are more robust than a typical brood year (Table 11; Figures 17–20). This sample season the LCC trap was deployed on the earliest date since we stopped sampling year round (BY04). We wanted to explore the relationship between fall rainfall events and O. mykiss and late-fall Chinook smolt out-migration. Unfortunately there were no spring storms. Salmonid passage indices O. mykiss — The number of observed redds in Reaches 1–6 (n = 65) and the BY17 annual JPI (n = 12,386) were well below the BY02–16 means of 183 and 24,919, respectively (Table C.2); however, the juveniles-per-redd ratio (n = 191) was higher than the same average (mean, 153). The higher than average juveniles-per-redd could have be the result of better than normal trapping conditions. It could also be attributed to the fact that we set the trap earlier than most seasons. During sample seasons when we sampled year round (BY02–05) the proportion

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 17 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office of the passage that occurred from July 1 through November 15 ranged from 0.2% to 14.2% (mean, 7.9%). This brood year passage that occurred during the period of September 13 through November 15 accounted for 3.2% of the annual JPI (Table 12). Only 1.1% of the annual JPI was calculated using actual weekly efficiency trial data. Mean daily flows fluctuated between 284–733 cfs during peak emigration and the season average trap efficiency was used for that entire period. Changes in flow are known to change trap efficiencies; it is unknown how the use of the season average during changing flow conditions affected the accuracy of the weekly and annual JPIs. Late-fall Chinook — The BY17 late-fall Chinook JPI (n = 14,383) was lower than the previous two years. There were 15 late-fall Chinook redds observed above the LCC RST site. The juveniles-per-redd production, for redds above the LCC site was 959, which was higher than BY15 and BY16 (Table C.3); however, it was nearly half of the BY03–16 mean of 1,863. The annual juveniles-per-redd ratios are highly variable (199–8,080); however, the lower than average juveniles-per-redd could be explained by the potential scouring of redds caused by two extended flow events in February 2017. Like O. mykiss, a proportion of the annual passage (1.7%) occurred from September 13 through November 15. The mean proportion of the annual passage from July 1 through November 15 when the trap was fished year round was 6.0% (0.4– 12.0%). The JPI for late-fall Chinook juveniles generated by length-at-date tables could be inaccurate because of the large number of fall Chinook juveniles present and the lack of differentiation between the two runs in late-March and early April. Of the 20 redds observed, five (25%) were located below the LCC site. Observations made during snorkel surveys indicate that a portion of the late-fall Chinook rear in Clear Creek after the traps are removed (personal observation). Because of the reasons above, it is very difficult to get an accurate JPI for late-fall Chinook. An adjusted production index accounting for the redds below LCC would be 19,177. Winter Chinook — The length-at-date measurements for the different runs of Chinook used in this report were developed by California Department of Water Resources (Greene, memorandum) for the Sacramento River. Based upon genetics results from fish taken at both traps (USFWS, unpublished data), the length-at-date tables do not apply well to Clear Creek Chinook. The winter-sized Chinook captured in both traps displayed a similar size and passage timing to that of the late-fall Chinook, suggesting that they are most likely late-fall Chinook despite meeting the size criteria to be winter Chinook. Spring Chinook — This season the four mark–recapture trial efficiencies were used to calculate 51% of the annual passage at UCC, the rest of the passage was calculated using the season average, whereas in BY15 and BY16 actual trial data was used to calculate 86% and 85%, respectively. Mean daily flows during peak spring Chinook out-migration ranged from 211 to 235 (mean, 215). Because the mean daily flow remained fairly constant, the use of the season average efficiency may not have caused a large error in the annual JPI. Next sample season when spring Chinook catch numbers become too few to allow us to conduct efficiency trials, we will switch to Chinook collected at LCC for efficiency trials at UCC. This will allow for more accurate JPI calculations. From 2013–2016 northern California was under severe drought conditions that affected salmon populations. Because of the drought and poor ocean conditions only an estimated 49 adult spring Chinook returned to Clear Creek and the lowest ever number of redds were observed (n = 9). This resulted in the lowest annual JPI (n = 12,381) since the RBFWO began monitoring.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 18 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

The juveniles-per-redd production (n = 1,376) was below the BY03-16 mean of 1,922; however, creek water temperatures do not appear to be the issue because management decisions kept mean daily temperatures from exceeding the Clear Creek Fish Restoration Program temperature targets (NMFS 2009) at the IGO gauge (RM 11.0; Figure 4). At the time of this report it is not known what caused the low number of juveniles-per-redd. Fall Chinook — Like spring Chinook the JPI was the lowest since monitoring began (n = 757,003; BY03–16 mean, 6,175,696). This is a dramatic reduction in the fall Chinook population in Clear Creek. Because the proportion of Jills (females ≤ 2 years of age) in the female spawning population of fall Chinook on Clear Creek has historically been low (mean 2013–2016; 0.21), their influence on the juveniles-per-female production has not been seriously considered. This year female escapement was dominated by Jills (n = 784) and they outnumbered adults (n = 285) 3:1. If only the adult females were used to calculate the juveniles- per-female ratio, the result would be 2,656/female, the highest in the history of the trap. If Jills were considered equally in the calculation the juveniles-per-female would be 708 and slightly over half the BY03–16 mean of 1,353. The fecundity of fall Chinook Jills is unknown, but surely less than that of adults (≥ 3 years) and the actual number of juveniles-per female lies somewhere between the above two estimates. Non salmonid catch Pacific Lamprey — The ammocoete (n = 151) and macropthalmia (n = 321) catch at UCC were above the means since monitoring began, 134 and 77, respectively; however, the macropthalmia catch at LCC far exceeded the mean. The macropthalmia mean at LCC is 291 and this season we captured 1,101 (Figure 21), the second highest to only sample season 2015- 2016 (n = 1,397). The macropthalmia is the out-migrating life stage of the Pacific Lamprey. Catch and flow data from LCC (which can sample in higher flows than UCC) show that macropthalmia tend to move on the first or second flow event in late fall or early winter (Schraml and Chamberlain 2019c). The latest movement prior to this sample season was in mid-February. This year the first significant flow change was March 14–16 (peak flow was 375 cfs); when 76% of the trap season catch (n = 837) was captured (Figure 22). Marking mortality During preparations for the O. mykiss mark–recapture trail a high percentage (8.4%) of the fish died while being held in a live-car prior to the mark on the following day. It is unknown why these fish perished; there were no anomalous conditions on the creek or in the live-box while they were held. The indirect mortality limit set forth by our permit for O. mykiss mark– recapture trials is 75. We did not exceed this limit. Adding these mortalities to the three that occurred during RST operations would yield a total O. mykiss percent mortality at the LCC RST of 1.5%. Fortunately we did not affect a large portion of the population and the average percent mortality for the prior 14 O. mykiss trials was 2.3% (Table 13). We will continue to hold mark– recapture trials with O. mykiss during future sample season when catch numbers are sufficient unless mortality rates indicate we should not do so. Upcoming projects No interval sampling was conducted at either trap because of limited staff. Interval sampling data and hourly percent of daily catch data from previous sampling years were used to

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 19 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office interpolate days when the traps sampled for only a part of the sampling day (Table 2; Table 3). We will continue collecting hourly catch data when conditions and staffing allow us to conduct these labor intensive monitoring events.

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Acknowledgements

We would like to thank the following people for their contributions: Greg Aull, RJ Bottaro, Ryan Cook, Laurie Earley, Ryan Mckim, Jacie Knight, Sam Provins, Cameron Reyes, James Smith, Charles Stanley, Ryan Schaefer, Alan Webster, and Travis Webster. We thank the Coleman National Fish Hatchery staff, especially Brett Galyean, for accommodating our program at the Coleman National Fish Hatchery. We would be remiss if we did not thank RJ Bottaro, Jacie Knight, and Charles Stanley for spending their valuable time reviewing this report and for their quality editorial comments and grammatical edits. We thank the Bureau of Land Management for providing creek access on public lands. Additional funding was provided by the CVPIA Clear Creek Fish Restoration Program and the Bureau of Reclamation.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 21 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

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USFWS (United States Fish and Wildlife Service). 1997. Revised Draft Restoration Plan for the Anadromous Fish and Restoration Program. A plan to increase natural production of anadromous fish in the Central Valley of California. Prepared for the U.S. Fish and Wildlife Service under the direction of the Anadromous Fish and Restoration Program Core Group, Sacramento, California.

USFWS (United States Fish and Wildlife Service). 2001. Final Restoration Plan for the Anadromous Fish Restoration Program: A Plan to Increase Natural Production of Anadromous Fish in the Central Valley of California. Prepared for the Secretary of the Interior by the United States Fish and Wildlife Service with assistance from the Anadromous Fish Restoration Program Core Group under authority of the Central Valley Project Improvement Act, Sacramento, California.

USFWS (United States Fish and Wildlife Service). 2002. Comprehensive Assessment and Monitoring Program (CAMP). Annual Report 2000. CH2M-Hill, 2485 Natomas Park Drive, Suite 600 Sacramento, California.

USGS (United States Geological Survey). 2018. National water information system: web interface. Site number 11372000 (Clear Creek at Igo), https://waterdata.usgs.gov/ca/nwis/uv/?site_no=11372000&agency_cd=USGS

Whitton, K. S., J. M. Newton, D. J. Colby and M. R. Brown. 2006. Juvenile salmonid monitoring in Battle Creek, California, from September 1998 to February 2001. USFWS Data Summary Report. U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office, Red Bluff, California.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 24 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Tables

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 25 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 1. Dates with corresponding week numbers for rotary screw trap operations at river mile 1.7 and 8.4 in Clear 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 10/01–10/07 40 04/09–04/15 15 10/08–10/14 41 04/16–04/22 16 10/15–10/21 42 04/23–04/29 17 10/22–10/28 43 04/30–05/06 18 10/29–11/04 44 05/07–05/13 19 11/05–11/11 45 05/14–05/20 20 11/12–11/18 46 05/21–05/27 21 11/19–11/25 47 05/28–06/03 22 11/26–12/02 48 06/04–06/10 23 12/03–12/09 49 06/11–06/17 24 12/10–12/16 50 06/18–06/24 25 12/17–12/23 51 06/25–07/01 26 12/24–12/31 52a a Week 52 (December 24–31, 2017) contains eight days for keeping January 1 as Julian calendar day one.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 26 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 2. The mean proportion of the daily catch from 24-h interval sampling events conducted during the 2011-2012 and 2012-2013 sample seasons (Schraml et al. 2018; Schraml and Chamberlain 2019a) at the lower Clear Creek (LCC) rotary screw trap located at river mile 1.7 in Shasta County. The mean hourly proportion of the daily catch (%) was calculated by taking the average proportion of the daily catch for each hour of each sampling event. These data were used to calculate the missing hourly catch data for days that the LCC trap only sampled a portion of the 24-h sample period. Time Proportion of daily catch (%) 0800 0.4 0900 0.3 1000 0.1 1100 0.2 1200 0.0 1300 0.0 1400 0.0 1500 0.1 1600 0.4 1700 1.3 1800 1.1 1900 6.8 2000 21.1 2100 23.0 2200 14.3 2300 7.3 0000 7.2 0100 5.0 0200 2.7 0300 2.1 0400 2.1 0500 2.3 0600 1.6 0700 0.5

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 27 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 3. The mean proportion of the daily catch from 24-h interval sampling events conducted during the 2013-2014, 2015-2016, and 2016-2017 sample seasons (Schraml and Chamberlain 2019b, 2019c, 2020) at the upper Clear Creek (UCC) rotary screw trap located at river mile 8.4 in Shasta County. The mean hourly proportion of the daily catch for was calculated by taking the average proportion of the daily catch for each hour of each sampling event. These data were used to calculate the missing hourly catch data for days that the UCC trap only sampled a portion of the 24-h sample period. The trap was not sampled from 0900–1600 hours (highlighted in gray). Time Proportion of daily catch (%) 0800 2.6 0900 1000 1100 1200 3.9 1300 1400 1500 1600 1700 0.3 1800 7.0 1900 19.7 2000 13.1 2100 9.7 2200 8.4 2300 4.9 0000 6.4 0100 5.0 0200 3.5 0300 2.1 0400 3.6 0500 3.6 0600 4.9 0700 1.6

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 28 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 4. Summary of efficiency trial data gathered by using mark–recapture trials with natural-origin juvenile Chinook Salmon at the upper rotary screw trap in Clear Creek, Shasta County, from December 6, 2017, through December 18, 2017. The fish for the studies were captured at both the upper (river mile 8.4) and lower rotary screw trap (river mile 1.7). Number Number Number Trial Release date held Mortality Percent mortality released recaptured Bailey's efficiency Run, Origin 1 7-Dec-17 130 0 0.0% 130 16 12.98% SCS, UCC and LCC 2 12-Dec-17 180 0 0.0% 179 14 8.33% SCS, UCC 3 15-Dec-17 137 2 1.5% 135 12 9.56% SCS, UCC 4 19-Dec-17 237 0 0.0% 237 25 10.92% SCS, UCC Total 684 2 0.3% 681 67

Table 5. Mark–recapture efficiency values used for weekly passage indices of brood year 2017 juvenile Rainbow Trout/steelhead (RBT), and spring-run Chinook Salmon (SCS) captured in the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1, 2017, to June 30, 2018. The juvenile passage index column represents to which species or salmon race the efficiency value was applied to calculate the weekly passage index. Light gray shaded rows indicate weeks in which the 2016-2017 season average efficiency was used (Schraml and Chamberlain 2020). Dark gray shaded rows indicate weeks in which the 2017-2018 season average efficiency was used. Dates Week Released Recaptured Bailey's efficiency (%) Juvenile passage index 01-Jan-17 to 30-Jan-17 1-26 322 36 11.46 RBT 20-Nov-17 to 02-Dec-17 47–48 170 17 10.53 RBT, SCS 03-Dec-17 to 09-Dec-17 49 130 16 12.98 RBT, SCS 10-Dec-17 to 14-Dec-17 50a 179 14 8.33 RBT, SCS 15-Dec-17 to 18-Dec-17 50b–51a 135 12 9.56 RBT, SCS 19-Dec-17 to 31-Dec-17 52 170 17 10.53 RBT, SCS 01-Jan-18 to 30-Jun-18 52 170 17 10.53 SCS

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 29 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 6. Summary of efficiency trial data gathered by using mark–recapture trials with natural-origin juvenile fall-run Chinook Salmon at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 11, 2018, through March 16, 2018. Trial Mark date Release date Released Mortality Percent mortality (%) Recaptured Bailey's efficiency (%) 1 11-Jan-18 12-Jan-18 272 0 0.0 9 3.66 2 15-Jan-18 16-Jan-18 509 1 0.2 24 4.90 3 22-Jan-18 22-Jan-18 504 1 0.2 21 4.36 4 31-Jan-18 1-Feb-18 494 1 0.2 30 6.26 5 6-Feb-18 7-Feb-18 496 2 0.4 11 2.41 6 13-Feb-18 14-Feb-18 491 2 0.4 26 5.49 7 16-Mar-18 17-Mar-18 463 11 2.4 18 4.09 Total 3,229 18 0.6 139

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 30 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 7. Mark–recapture efficiency values used for weekly passage indices of brood year 2017 juvenile Rainbow Trout/steelhead (RBT), late-fall run (LFCS), spring-run (SCS), and fall-run Chinook Salmon (FCS) captured in the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1, 2017, through June 30, 2018. The juvenile passage index column represents to which species or salmon race the efficiency value was applied to calculate the weekly passage index. Light gray shaded rows indicate weeks in which the 2016-2017 season average efficiency was used (Schraml and Chamberlain 2020). Dark gray shaded rows indicate weeks in which the 2017-2018 season average efficiency was used. Dates Week Released Recaptured Bailey's efficiency (%) Juvenile passage index 01-Jan-17 to 04-Jan-17 1a 383 34 9.11 RBT 05-Jan-17 to 07-Jan-17 1b 500 33 6.79 RBT 08-Jan-17 to 25-Jan-17 2–4a 534 30 5.79 RBT 26-Jan-17 to 28-Jan-17 4b 552 9 1.81 RBT 29-Jan-17 to 04-Feb-17 5 769 31 4.16 RBT 05-Feb-17 to 30-Jun-17 6-26 534 30 5.79 RBT, LFCS 13-Sep-17 to 31-Dec-17 37–52 461 20 4.55 RBT, LFCS, SCS 01-Jan-18 to 07-Jan-18 1 461 20 4.55 RBT, LFCS, SCS 08-Jan-18 to 14-Jan-18 2 272 9 3.66 RBT, LFCS, SCS 15-Jan-18 to 21-Jan-18 3 509 24 4.90 RBT, LFCS, SCS 22-Jan-18 to 28-Jan-18 4 504 21 4.36 RBT, LFCS, SCS 29-Jan-18 to 04-Feb-18 5 494 30 6.26 RBT, LFCS, SCS 05-Feb-18 to 11-Feb-18 6 496 11 2.41 LFCS, SCS 12-Feb-18 to 18-Feb-18 7 491 26 5.49 LFCS, SCS 19-Feb-18 to 11-Mar-18 4–10 461 20 4.55 LFCS, SCS 12-Mar-18 to 18-Mar-18 11 463 18 4.09 LFCS, SCS 19-Mar-18 to 30-Jun-18 12–26 461 20 4.55 LFCS, SCS

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 31 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 8. Brood year 2017 life stage summary for Rainbow Trout/steelhead, late-fall run, winter-run, and spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County. Rainbow Trout/steelhead Rainbow brood year 2016+ Trout/steelhead Late-fall run Winter-run Chinook Spring-run Chinook age-0+ brood year 2017 Chinook Salmon Salmon Salmon Percent Percent Percent Percent Percent Life Stage Number (%) Number (%) Number (%) Number (%) Number (%) Yolk-sac fry 0 0.0 6 2.5 0 0.0 0 0.0 0 0.0 Fry 0 0.0 113 47.3 0 0.0 0 0.0 1,142 91.6 Parr 27 73.0 118 49.4 0 0.0 0 0.0 7 0.6 Silvery parr 9 24.3 2 0.8 0 0.0 1 14.3 44 3.5 Smolt 1 2.7 0 0.0 0 0.0 6 85.7 54 4.3 Totals 37 239 0 7 1,247

Table 9. Brood year 2017 life stage summary for Rainbow Trout/steelhead, late-fall run, winter-run, spring-run, and fall-run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. Rainbow Trout/steelhead Rainbow brood year 2016+ Trout/steelhead Late-fall run Winter-run Spring-run Fall-run Chinook age-0+ brood year 2017 Chinook Salmon Chinook Salmon Chinook Salmon Salmon Life Stage Number (%) Number (%) Number (%) Number (%) Number (%) Number (%) Yolk-sac fry 0 0.0 8 1.1 5 0.6 0 0.0 1 0.3 10 0.0 Fry 0 0.0 485 69.6 747 92.0 0 0.0 344 91.7 28,036 97.5 Parr 4 80.0 202 29.0 29 3.6 1 4.2 2 0.5 347 1.2 Silvery parr 1 20.0 2 0.3 18 2.2 9 37.5 23 6.1 320 1.1 Smolt 0 0.0 0 0.0 13 1.6 14 58.3 5 1.3 52 0.2 Totals 5 697 812 24 375 28,765

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 32 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 10. The 2017 Clear Creek, Shasta County, snorkel survey reach numbers, locations, and river miles (RM) for reference.In August 2017 the Clear Creek picket weir was placed instream at the Reading Bar site located at RM 8.2 to protect the spring-run Chinook Salmon population from potential spawning superimposition from fall-run Chinook Salmon (Bottaro and Chamberlain 2019). The juvenile passage index is adjusted for redds identified above the weir and below the upper rotary screw trap at RM 8.4. Reach River mile Location 1 18.3–16.1 Whiskeytown Dam to Need Camp bridge 2 16.1–13.2 Need Camp bridge to Kanaka Creek 3 13.2–11.0 Kanaka Creek to Igo gauge 4 11.0–8.6 Igo gauge to Clear Creek Road bridge 5a 8.6–8.2 Clear Creek Road bridge to Reading Bar picket weir site 5b 8.2–7.4 Reading Bar picket weir site to Shooting Gallery picket weir site 5c 7.4–6.5 Shooting Gallery picket weir site to old McCormick-Saeltzer Dam site 6 6.5–1.7 Old McCormick-Saeltzer Dam site to USFWS lower rotary screw trap 7 1.7–0.2 Lower rotary screw trap to USFWS video counting weir

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 33 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 11. The proportion (%) of the annual juvenile passage indices that were calculated using interpolated catch data for days the rotary screw traps did not fish for each brood year. Rainbow Trout/steelhead, late-fall run and fall-run Chinook Salmon data are from the lower screw trap on Clear Creek, Shasta County, at river mile 1.7. The spring-run Chinook Salmon data are from the upper trap at river mile 8.4. Brood Rainbow Trout/steelhead Late-fall run Chinook Salmon Spring-run Chinook Salmon Fall-run Chinook Salmon year (%) (%) (%) (%) 2003 28.6 37.4 11.3 13.0 2004 0.0 0.0 3.4 1.6 2005 3.3 4.1 6.9 7.2 2006 14.0 19.3 19.8 6.8 2007 0.5 1.5 2.1 9.9 2008 0.5 0.0 0.8 10.8 2009 7.1 13.1 3.9 18.7 2010 5.4 6.8 0.1 0.9 2011 6.3 1.6 0.0 0.1 2012 1.9 0.3 25.4 0.2 2013 0.2 0.3 0.7 2.2 2014 26.5 27.5 27.7 32.8 2015 22.3 23.1 3.4 6.5 2016 10.4 13.0 7.5 21.6 2017 1.4 1.8 1.3 6.4

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 34 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 12. Length of the sample season, the annual passage index, and the passage and proportion of the annual passage index that passed the lower rotary screw trap for late-fall run Chinook Salmon (LFCS) and Rainbow Trout/steelhead (RBT) during the July 1 through November 15 time period. The trap is located at river mile 1.7 in Clear Creek, Shasta County. Sample Brood 1st Last All LFCSc RBTc season year sample sample year LFCSa RBTa LFCSb RBTb (%) (%) Notes 2001-2002 2001 10/01/01 09/30/02 Yes 2002-2003 2002 10/01/02 09/30/03 Yes 21,017 1,771 175,586 12,479 12.0 14.2 2003-2004 2003 10/01/03 09/30/04 Yes 2,416 1,204 33,041 8,625 7.3 14.0 2004-2005 2004 10/01/04 09/30/05 Yes 542 1,019 12,307 29,771 4.4 3.4 2005-2006 2005 10/01/05 07/06/06 No 73 41 20,707 24,241 0.4 0.2 2006-2007 2006 11/30/06 07/13/07 No 2007-2008 2007 11/27/07 06/30/08 No 2008-2009 2008 11/12/08 07/02/09 No 2009-2010 2009 11/25/09 06/30/10 No 2010-2011 2010 11/02/10 06/30/11 No 78 142 23,058 11,954 0.3 1.2 only 11/02/10–11/15/10 2011-2012 2011 11/01/11 06/30/12 No 149 75 8,703 19,632 1.7 0.4 only 11/01/11–11/15/11 2012-2013 2012 10/26/12 06/30/13 No 142 31 24,935 21,229 0.6 0.1 only 10/26/12–11/15/12 2013-2014 2013 11/05/13 06/30/14 No 98 59 25,996 52,083 0.4 0.1 only 11/05/13–11/15/13 2014-2015 2014 11/06/14 06/30/15 No 24 119 17,922 39,266 0.1 0.3 only 11/06/14–11/15/15 2015-2016 2015 11/02/15 06/30/16 No 42 42 13,940 12,170 0.3 0.3 only 11/02/15–11/15/16 2016-2017 2016 10/18/16 06/30/17 No 34 172 5,713 29,763 0.6 0.6 only 10/18/16–11/15/17 2017-2018 2017 09/13/17 06/29/18 No 242 396 14,373 12,386 1.7 3.2 also 09/13/17–10/24/17 aPassage estimate from July 1 to November 15. bThe annual passage index. cProportion of the annual passage estimate that occurred from July 1 to November 15.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 35 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table 13. The number of juvenile O. mykiss held, marked, released, and recaptured, the types of mortalities, and the percent mortality of fish held (shaded in gray) during mark–recapture trials conducted at the lower rotary screw (river mile 1.7) in Clear Creek, Shasta County. Post- Predation Percent Release Days Number Number Number Pre-mark Marking mark or trap Total Total mortality date held held marked released mortality mortality mortality mortality mortality recaptured (%) 03/17/12 4 77 77 77 N/Aa 1 N/Aa 0 1 1 1.3 03/26/12 4 90 90 90 N/Aa 0 N/Aa 0 0 6 0.0 04/12/12 3 85 88 85 N/Aa 2 N/Aa 0 2 7 2.4 04/24/12 4 103 80 103 N/Aa 3 N/Aa 0 3 7 2.9 03/14/13 3 183 199 174 5 0 3 0 8 10 4.4 03/21/13 3 124 124 123 0 0 1 0 1 2 0.8 03/28/13 4 71 72 67 0 0 4 0 4 5 5.6 04/04/13 4 167 166 162 3 0 4 0 7 6 4.2 04/11/13 3 129 129 124 4 0 1 0 5 0 3.9 04/18/13 3 156 155 155 0 0 1 0 1 12 0.6 05/02/13 4 149 145 141 0 0 6 0 6 5 4.0 03/30/16 4 181 181 175 0 0 3 0 3 5 1.7 04/04/16 4 239 239 239 0 0 0 0 0 8 0.0 04/09/16 4 275 270 270 0 0 2 0 2 8 0.7 04/18/18 2 178 163 163 15 0 0 0 15 15 8.4 Totals 2,207 2,178 2,148 27 6 25 0 58 97 2.6 aThese data were not collected during the 2011-2012 sample season.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 36 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Figures

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 37 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 38 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Figure 2. A 5-ft diameter rotary screw trap similar to the traps operated at river mile 1.7 and 8.4 on Clear Creek, Shasta County, from November 2017 through June 2018.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 39 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

1,400 50 Igo peak daily flow LCC turbidity 45 1,200 UCC turbidity LCC NS 40 UCC NS 1,000 35

30 800 25 600 20 Turbidity (ntu) Turbidity Mean daily flow (cfs) flow daily Mean 400 15 10 200 5

0 0

Date Figure 3. Mean daily flow measured at the United States Geological Survey IGO station and momentary turbidity recorded at the upper (UCC) and lower (LCC) Clear Creek rotary screw trap sampling stations at river mile 8.4 and 1.7 in Clear Creek, Shasta County, from October 1, 2017, through September 30, 2018. Upper and Lower Clear Creek non-sampling dates (LCC NS and UCC NS) are shown at the top of the figure in black and gray, respectively.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 40 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

70 Lower Clear Creek Upper Clear Creek Igo gauging station 65 Temperature target for Igo LCC NS UCC NS 60

50 Mean daily water temperature (ºF) water Mean daily temperature 45

Date Figure 4. Mean daily water temperatures recorded at the upper (UCC) and lower (LCC) Clear Creek rotary screw trap sampling stations at river miles 8.4 and 1.7 in Clear Creek, Shasta County, from October 1, 2017, through September 30, 2018. Clear Creek Fish Restoration Program temperature targets (NMFS 2009) for fish protection and the temperatures recorded at the Clear Creek IGO gauge (river mile 11.0) are provided for comparison. Upper and Lower Clear Creek non-sampling dates (LCC NS and UCC NS) are shown in at the bottom of the figure in black and gray, respectively.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 41 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

1.0

0.9 RBT LFCS 0.8 SCS

0.7

0.6

0.5

Sample effort Sample 0.4

0.3

0.2

0.1

0.0

Month Figure 5. Sampling effort summarized as the proportion (range: 0 to 1) of days fished each month for the upper rotary screw trap for brood year 2017 Rainbow Trout/steelhead (RBT), late-fall run (LFCS), and spring-run Chinook Salmon (SCS). The black lines indicate the expected out-migration time period for the different fishes, the bold portion indicates the peak out-migration period. The trap was located at river mile 8.4 in Clear Creek, Shasta County.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 42 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

1.0

0.9 RBT LFCS SCS 0.8 FCS 0.7

0.6

0.5

Sample effort Sample 0.4

0.3

0.2

0.1

0.0

Month Figure 6. Sampling effort summarized as the proportion (range: 0 to 1) of days fished each month for the lower rotary screw trap for brood 2017 Rainbow Trout/steelhead (RBT), late-fall run (LFCS), spring-run (SCS), and fall-run Chinook Salmon (FCS). The black lines indicate the expected out-migration time period for the different fishes, the bold portion indicates the peak out-migration period. The trap was located at river mile 1.7 in Clear Creek, Shasta County.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 43 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

310 R1 - Yolk-sac fry R2 - fry R3 - Parr R4 - Silvery parr R5 - Smolt UCC NS

260

210

160 Age-0+

Fork (mm) Fork length 110

Brood year 2017 60

Sample Date Figure 7. Fork length and life stage distribution by date and life stage for brood year 2017 and brood year 2016 age-0+ juvenile Rainbow Trout/steelhead captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1 to December 31, 2017. The black line separates age-0+ fish from brood year 2017 fish. Upper Clear Creek non-sampling days (UCC NS) are indicated at the bottom of the figure in gray.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 44 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

600 n = 2,338 ● UCC NS 500 passage 400

300

200 Rainbow Trout/steelhead Trout/steelhead Rainbow

100 Juvenile Juvenile

Sample week

Figure 8. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile Rainbow Trout/steelhead captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1 through December 31, 2017. Non-sampled weeks (UCC NS) are indicated at the bottom of the figure as circles.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 45 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

120 Late-fall Winter Spring Fall C0 - Yolk- 110 sac fry

100 C1 - Fry

90 C2 - Parr 80 Late-fall 70 C3 - 60 Silvery parr Fork (mm) Fork length 50 C4 - Smolt

40 Winter UCC NS 30

Date Figure 9. 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 8.4 in Clear Creek, Shasta County, from November 20, 2017, through June 30, 2018. Upper Clear Creek non-sampling days (UCC NS) are indicated at the bottom of the figure in gray. Spline curves represent the maximum fork lengths expected for each run by date, and are based upon tables of projected annual growth developed by the California Department of Water Resources (Greene, memorandum).

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 46 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

5,000 n = 12,392 4,500 ● UCC NS

4,000

3,500

3,000

2,500

run Chinook Salmon passage Salmon Chinook run 2,000 -

1,500

1,000

Juvenile spring Juvenile 500

Sample week Figure 10. Weekly passage indices with 95% confidence intervals of brood year 2017 juvenile spring-run Chinook Salmon captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from November 20, 2017, through June 30, 2018. Upper Clear Creek non-sampling weeks (UCC NS) are indicated at the bottom of the figure as circles.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 47 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

210 R1 - Yolk-sac fry R2 - fry R3 - Parr R4 - Silvery parr R5 - Smolt LCC NS 190

170

150

130

110 Age-0+ 90 Fork (mm) Fork length 70

50 Brood year 2017 30

Date Figure 11. Fork length and life stage distribution by date and life stage for brood year 2017 and brood year 2016 age-0+ juvenile Rainbow Trout/steelhead captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1 to December 31, 2017. The black line separates age-0+ fish from brood year 2016 fish. Lower Clear Creek non-sampling days (LCC NS) are indicated at the bottom of the figure in black.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 48 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

3,000 n = 13,386 ● LCC NS 2,500 passage

2,000

1,500

1,000 Rainbow Trout/steelhead Trout/steelhead Rainbow

Juvenile Juvenile 500

Sample week Figure 12. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile Rainbow Trout/steelhead captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1 through December 31, 2017. Non-sampled weeks (LCC NS) are indicated at the bottom of the figure as circles.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 49 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

120 Late-fall Winter Spring Fall C0 - Yolk- 110 sac fry

100 C1 - Fry

90 C2 - Parr 80

Late-fall 70 C3 - 60 Silvery parr Fork (mm) Fork length 50 C4 - Smolt

40 Winter LCC NS 30

Date Figure 13. Fork length and life stage distribution by date, life stage, and run for all juvenile Chinook Salmon captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from November 21, 2017, through June 30, 2018. Lower Clear Creek non-sampling days (LCC NS) are indicated at the bottom of the figure in black. Spline curves represent the maximum fork lengths expected for each run by date and are based upon tables of projected annual growth developed by the California Department of Water Resources (Greene, memorandum).

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 50 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

6,000 n = 14,373 ● LCC NS 5,000

4,000

3,000

fall run Chinook Salmon passage run - fall Chinook Salmon 2,000

1,000 Juvenile late Juvenile

Sample week Figure 14. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile late-fall run Chinook Salmon by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from March 26, 2017, through March 31, 2018. Non-sampled weeks (LCC NS) are indicated at the bottom of the figure as circles.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 51 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

4,500 n = 8,351 ● LCC NS 4,000

3,500

3,000

2,500

2,000 run Chinook Salmon passage Salmon Chinook run 1,500

1,000

- spring Juvenile 500

Sample week Figure 15. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile spring-run Chinook Salmon by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018. Non- sampled weeks (LCC NS) are indicated at the bottom of the figure as circles.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 52 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

450,000 n = 757,165 ● LCC NS 400,000

350,000

300,000

250,000

200,000 run Chinook Salmon passage Salmon Chinook run - 150,000

100,000 Juvenile fall Juvenile 50,000

Sample week Figure 16. Weekly passage indices with 95% confidence intervals for brood year 2017 juvenile fall-run Chinook Salmon by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018. Non-sampled weeks (LCC NS) are indicated at the bottom of the figure as circles.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 53 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

70,000 Interpolated passage Interpolated catch 60,000 Expanded passage Actual catch

50,000

40,000

30,000

20,000 Juvenile Rainbow Trout steelhead Trout Juvenile Rainbow

10,000

Brood year Figure 17. Interpolated passage and catch for young-of-the-year Rainbow Trout/steelhead for brood years 1998–2017 captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. The entire bar represents the total passage index for that brood year and the error bars the 95% confidence interval.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 54 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

350,000 Interpolated passage Interpolated catch Expanded passage 300,000 Actual catch

250,000

200,000

fall run Chinook run - fall Chinook Salmon 150,000

100,000 Juvenile late Juvenile

50,000

Brood year Figure 18. Interpolated passage and catch for late-fall run Chinook Salmon for brood years 1998–2017 captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. The entire bar represents the total passage index for that brood year and the error bars the 95% confidence interval.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 55 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

300,000 Interpolated passage Interpolated catch Expanded passage 250,000 Actual catch

200,000

150,000 run Chinook Salmon Chinook run -

100,000 Juvenile spring Juvenile 50,000

Brood year Figure 19. Interpolated passage and catch for spring-run Chinook Salmon for brood years 2003–2017 captured by the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County. The entire bar represents the total passage index for that brood year and the error bars the 95% confidence interval.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 56 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

25,000,000 Interpolated passage Interpolated catch Expanded passage Actaual catch 20,000,000

15,000,000

10,000,000 run Chinook Salmon Chinook - run fall Juvenile 5,000,000

Brood year Figure 20. Interpolated passage and catch for fall-run Chinook Salmon for brood years 1998–2017 captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. The entire bar represents the total passage index for that brood year and the error bars the 95% confidence interval.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 57 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

1,400 Ammocoete Macropthalmia 1,200 Ammocoete mean Macropthalmia mean

1,000

800

600 Pacific Lamprey

400

200

Trap year Figure 21. Pacific Lamprey ammocoete and macropthalmia captured by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from 2003–2017. The 2003–2016 sample season means are also included.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 58 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

1000 400 Peak daily flow 900 LCC NS 350 Ammocoete 800 Macropthalmia 300 700 250 600

500 200

400 150 Peak daily flow (cfs) flow daily Peak 300 100 Daily pacificcatch Lamprey 200 50 100

0 0

Sample date Figure 22. Peak daily flow (cfs) and Pacific Lamprey ammocoete and macropthalmia daily catch by the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 19, 2017, to June 30, 2018. Lower Clear Creek non-sampling days (LCC NS) are indicated at the top of the figure in black.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 59 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Appendices

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 60 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Appendix A: Rotary Screw Trap Operations

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 61 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table A.1. Summary of days the upper rotary screw trap did not fish for approximately 24 hours during the brood year 2017 Rainbow Trout/steelhead (RBT), late-fall run Chinook Salmon (LFCS), and spring-run Chinook (SCS) out-migration period. The table includes sample dates, approximate hours fished, reason for not fishing, and for which fish the juvenile passage index could have been affected. The trap was located at river mile 8.4 in Clear Creek, Shasta County. Sample dates Hours fished (approx.) Reason Species/race affected Jan 6–12, 2017 18.00 High flow RBT Jan 18–24, 2017 18.00 High flow RBT Feb 3–13, 2017 31.00 High flow RBT Feb 17–24, 2017 23.50 High flow, Whiskeytown Lake glory hole spill RBT Mar 17–18, 2017 23.00 Trap repair RBT Mar 21, 2017 10.00 High flow RBT Mar 22–23, 2017 18.50 Trap improperly reset RBT Mar 24–25, 2017 21.00 High flow RBT Mar 27, 2017 18.00 Trap not in thalweg because of dropping flow RBT Apr 6–8, 2017 37.50 High flow RBT, LFCS Apr 16, 2017 16.00 Trap not in thalweg because of dropping flow RBT, LFCS Apr 18–20, 2017 31.50 High flow RBT, LFCS May 7, 2017 20.25 Log stopped cone from rotating RBT, LFCS May 24–25, 2017 26.25 Staff on training assignment RBT, LFCS Jun 4–6, 2017 32.75 First pulse flow event RBT, LFCS Jun 18–21, 2017 24.75 Second pulse flow event RBT, LFCS Jun 23–24, 2017 33.75 Log stopped cone from rotating RBT, LFCS Jun 30, 2017 8.25 End of the 2016-2017 sampling season RBT, LFCS Jul 1–Nov 18, 2017 0.00 Off season RBT, LFCS Nov 19, 2017 11.50 Trap set for 2017-2018 sampling season RBT, LFCS, SCS Jan 3–4, 2018 32.25 Log stopped cone from rotating LFCS, SCS Mar 1–2, 2018 27.25 High flow LFCS, SCS Mar 11, 2018 unknown Trap vandalized, cone raised and counter broken LFCS, SCS Mar 24–25, 2018 27.50 Log stopped cone from rotating LFCS, SCS Mar 30–Apr 1, 2018 24.25 Limited staff LFCS, SCS Apr 6–8, 2018 25.00 Limited staff SCS

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 62 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office Table A.1. continued Sample dates Hours fished (approx.) Reason Species/race affected Apr 13–15, 2018 26.00 Limited staff SCS Apr 20–22, 2018 22.75 Limited staff SCS Apr 27–29, 2018 23.25 Limited staff SCS May 4–6, 2018 22.75 Limited staff SCS May 11–13, 2018 22.25 Limited staff SCS May 18–20, 2018 20.25 Limited staff SCS May 21, 2018 7.75 Trap vandalized, rope line cut and stolen SCS May 23–29, 2018 23.75 Limited staff and staff training SCS Jun 1–4, 2018 24.25 Limited staff and first pulse flow SCS Jun 8–10, 2018 22.50 Limited staff SCS Jun 15–19, 2018 24.25 Limited staff and second pulse flow SCS Jun 20, 2018 22.50 Log stopped cone from rotating SCS Jun 22–24, 2018 24.00 Limited staff SCS Jun 25–28, 2018 19.00 Clear Fire burning in area SCS Jun 29–30, 2018 9.00 End of the 2017-2018 sampling season SCS

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 63 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table A.2. Summary of days the lower rotary screw trap did not fish for approximately 24 hours during the brood year 2017 Rainbow Trout/steelhead (RBT), late-fall run Chinook Salmon (LFCS), spring-run Chinook (SCS), and fall-run Chinook Salmon (FCS) out- migration period. The table includes sample dates, approximate hours fished, reason for not fishing, and for which fish the juvenile passage index could have been affected. The trap was located at river mile 1.7 in Clear Creek, Shasta County. Sample dates Hours fished (approx.) Reason Species/race affected Jan 6–12, 2017 21.00 High flow RBT Jan 18–19, 2017 39.75 High flow RBT Jan 22, 2017 16.00 High flow RBT Feb 6–13, 2017 58.75 High flow RBT Feb 17–22, 2017 37.25 High flow, Whiskeytown Lake glory hole spill RBT Mar 25, 2017 18.50 Log stopped cone from rotating RBT May 24–25, 2017 26.75 Staff on training assignment RBT, LFCS May 26–27, 2017 34.25 Vandalism RBT, LFCS Jun 15–16, 2017 31.00 Vandalism RBT, LFCS Jun 30, 2017 9.00 End of the 2016-2017 sampling season RBT, LFCS Jul 1–Sep 11, 2017 0.00 Off season RBT, LFCS Sep 12, 2017 12.50 Trap set for 2017-2018 sampling season RBT, LFCS, SCS Oct 24–Nov 2, 2017 24.25 Cone raised, very limited catch RBT, LFCS, SCS Nov 6–19, 2017 44.00 Cone raised, very limited catch RBT, LFCS, SCS Mar 1–2, 2018 29.00 High flow LFCS, SCS Mar 30–Apr 1, 2018 25.00 Limited staff LFCS, SCS Apr 6–8, 2018 25.25 Limited staff SCS Apr 13–15, 2018 26.00 Limited staff SCS Apr 20–22, 2018 22.75 Limited staff SCS Apr 27–29, 2018 23.50 Limited staff SCS May 4–6, 2018 22.75 Limited staff SCS May 11–13, 2018 22.75 Limited staff SCS May 18–20, 2018 22.75 Limited staff SCS May 23–29, 2018 24.25 Limited staff and staff training SCS Jun 1–3, 2018 24.25 Limited staff SCS Jun 8–10, 2018 23.00 Limited staff SCS Jun 12–13, 2018 29.75 Trap vandalized SCS

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 64 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office Table A.2. continued Sample dates Hours fished (approx.) Reason Species/race affected Jun 15–17, 2018 22.25 Limited staff SCS Jun 22–24, 2018 30.00 Limited staff SCS Jun 25, 2018 12.75 Trap vandalized SCS Jun 29, 20189 9.00 End of the 2017-2018 sampling season SCS

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 65 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Appendix B: Weekly Catch and Juvenile Passage Indices

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 66 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.1. Weekly catch, mortality and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile Rainbow Trout/steelhead captured at the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from January 1 through December 31, 2017. Weeks in which no passage occurred are omitted and weeks in which the trap did not sample are highlighted in gray. Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 7 of 7 11 12-Mar-17 1 0 6 9 12 0.05 4 of 7 12 19-Mar-17 2 0 26 35 46 0.17 7 of 7 13 26-Mar-17 3 0 20 26 36 0.14 6 of 7 14 2-Apr-17 13 0 97 131 179 0.65 6 of 7 16 16-Apr-17 2 0 13 17 24 0.09 7 of 7 17 23-Apr-17 10 0 66 87 120 0.42 7 of 7 18 30-Apr-17 19 0 125 166 227 0.81 7 of 7 19 7-May-17 9 0 66 87 120 0.44 7 of 7 20 14-May-17 42 0 277 366 485 1.75 6 of 7 21 21-May-17 27 0 187 253 347 1.25 7 of 7 22 28-May-17 26 0 171 227 311 1.13 6 of 7 23 4-Jun-17 20 0 185 244 335 1.22 7 of 7 24 11-Jun-17 14 0 92 122 167 0.60 4 of 7 25 18-Jun-17 16 0 188 244 335 1.18 6 of 6 26 25-Jun-17 12 0 79 105 138 0.52 0 of 142 27–46 No sampling from 1-Jul-17 to 19-Nov-17 6 of 6 47 20-Nov-17 2 0 12 19 29 0.14 7 of 7 48 26-Nov-17 3 0 20 29 47 0.22 7 of 7 49 3-Dec-17 7 0 37 54 83 0.41 7 of 7 50 10-Dec-17 5 0 38 60 100 0.52 2 of 2 51a 17-Dec-17 2 0 13 21 39 0.18 5 of 5 51b 19-Dec-17 3 0 20 27 40 0.16 8 of 8 52a 24-Dec-17 1 0 7 9 17 0.08 185 of 365 Season 239 0 2,141 2,338 2,548 3.40 a Week 52 (December 24–31, 2017) contains eight days for keeping January 1 as Julian calendar day one.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 67 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.2. Weekly catch, mortality and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile spring-run Chinook Salmon captured at the upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County, from November 20, 2017, through June 30, 2018. Weeks in which no passage occurred are omitted and weeks in which the trap did not sample are highlighted in gray. Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 0 of 50 40–46 No sampling from 1-Oct-17 to 19-Nov-17 6 of 7 47 20-Nov-17 139 0 880 1,320 1,981 9.55 7 of 7 48 26-Nov-17 274 4 1,735 2,602 4,259 20.78 7 of 7 49 3-Dec-17 217 3 1,093 1,672 2,590 12.94 5 of 5 50a 10-Dec-17 223 1 1,432 2,293 3,820 20.39 2 of 2 50b 15-Dec-17 208 2 207 335 622 3.03 2 of 2 51a 17-Dec-17 53 0 654 1,056 1,717 9.32 5 of 5 51b 19-Dec-17 38 0 707 980 1,415 6.08 8 of 8 52a 24-Dec-17 4 0 336 503 824 3.83 7 of 7 1 1-Jan-18 4 3 272 408 668 3.02 7 of 7 2 8-Jan-18 3 0 25 38 57 0.28 7 of 7 3 15-Jan-18 0 0 25 38 62 0.30 7 of 7 4 22-Jan-18 2 0 18 28 43 0.21 7 of 7 6 5-Feb-18 11 0 13 19 31 0.14 7 of 7 7 12-Feb-18 15 0 25 38 62 0.28 7 of 7 8 19-Feb-18 4 0 70 104 157 0.77 7 of 7 9 26-Feb-18 35 3 108 161 264 1.26 7 of 7 10 5-Mar-18 13 0 25 38 57 0.28 7 of 7 11 12-Mar-18 4 0 222 332 499 2.34 5 of 7 12 19-Mar-18 5 1 95 142 233 1.09 5 of 7 13 26-Mar-18 4 0 38 57 93 0.44 5 of 7 14 2-Apr-18 1 0 44 66 109 0.51 5 of 7 15 9-Apr-18 2 0 38 57 93 0.50 5 of 7 16 16-Apr-18 4 0 6 9 16 0.07 5 of 7 17 23-Apr-18 1 0 25 38 62 0.29 5 of 7 18 30-Apr-18 0 0 25 38 62 0.28 5 of 7 19 7-May-18 0 0 6 9 14 0.07

Brood Year 2017 Juvenile Salmonid Sampling in Clear Creek 68 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office Table B.2. continued Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 0 of 91 27–39 No sampling from 1-Jul-18 to 30-Sep-18 183 of 365 Season 1,268 17 10,595 12,381 15,143 35.98 a Week 52 (December 24–31, 2017) contains eight days for keeping January 1 as Julian calendar day one.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 69 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.3. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile Rainbow Trout/steelhead captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from January 1 through December 31, 2017. Weeks in which no passage occurred are omitted and weeks in which the trap did not sample are highlighted in gray. Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 4 of 4 4a 22-Jan-17 2 0 25 35 51 0.20 3 of 3 4b 26-Jan-17 2 0 61 110 221 1.25 7 of 7 5 29-Jan-17 1 0 17 24 35 0.14 5 of 7 6 5-Feb-17 2 0 25 35 47 0.18 4 of 7 7 12-Feb-17 1 0 25 35 49 0.20 4 of 7 8 19-Feb-17 2 0 76 104 146 0.56 7 of 7 9 26-Feb-17 10 0 124 173 243 1.02 7 of 7 10 5-Mar-17 13 1 166 224 316 1.29 7 of 7 11 12-Mar-17 9 0 109 155 229 0.93 7 of 7 12 19-Mar-17 20 0 249 345 510 2.06 7 of 7 13 26-Mar-17 51 1 635 880 1,186 4.66 7 of 7 14 2-Apr-17 65 0 809 1,122 1,581 6.43 7 of 7 15 9-Apr-17 38 0 473 656 924 3.79 7 of 7 16 16-Apr-17 41 0 510 708 954 3.93 7 of 7 17 23-Apr-17 54 2 672 932 1,313 5.31 7 of 7 18 30-Apr-17 54 1 672 932 1,313 5.20 7 of 7 19 7-May-17 55 0 684 949 1,401 5.67 7 of 7 20 14-May-17 107 3 1,331 1,847 2,602 10.77 6 of 7 21 21-May-17 33 1 438 621 875 3.61 7 of 7 22 28-May-17 42 0 523 725 1,021 4.21 7 of 7 23 4-Jun-17 34 0 423 587 827 3.38 7 of 7 24 11-Jun-17 7 0 112 155 219 0.88 7 of 7 25 18-Jun-17 27 1 336 466 657 2.65 6 of 6 26 25-Jun-17 6 0 75 104 146 0.59 0 of 74 27–36 No sampling from 1-Jul-17 to 12-Sep-17 4 of 4 37 13-Sep-17 6 0 89 132 231 1.05 7 of 7 38 17-Sep-17 5 0 80 110 178 0.79 7 of 7 40 1-Oct-17 2 0 31 44 71 0.35

Brood Year 2017 Juvenile Salmonid Sampling in Clear Creek 70 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office Table B.3. continued Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 7 of 7 41 8-Oct-17 2 0 31 44 71 0.35 7 of 7 42 15-Oct-17 2 0 31 44 71 0.32 3 of 7 43 22-Oct-17 1 0 15 22 36 0.16 6 of 7 47 19-Nov-17 1 0 15 22 36 0.16 7 of 7 49 3-Dec-17 2 0 31 44 71 0.35 256 of 365 Season 697 10 11,345 12,386 13,441 18.89

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 71 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.4. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile late-fall run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from April 1, 2017, through March 31, 2018. Weeks in which no passage occurred are omitted and weeks in which the trap did not sample are highlighted in gray. Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 1 of 1 13 1-Apr-17 2 0 25 35 49 0.19 7 of 7 14 2-Apr-17 31 0 386 535 721 2.91 7 of 7 15 9-Apr-17 18 0 219 311 459 1.83 7 of 7 16 16-Apr-17 58 0 722 1,002 1,410 5.63 7 of 7 17 23-Apr-17 9 0 115 155 219 0.90 7 of 7 18 30-Apr-17 40 0 498 691 973 3.96 7 of 7 19 7-May-17 69 1 879 1,192 1,678 6.58 7 of 7 20 14-May-17 126 2 1,532 2,176 3,064 12.39 6 of 7 21 21-May-17 86 0 1,197 1,623 2,286 9.03 7 of 7 22 28-May-17 98 0 1,219 1,693 2,497 9.78 7 of 7 23 4-Jun-17 201 1 2,444 3,472 4,888 19.93 7 of 7 24 11-Jun-17 20 2 331 449 662 2.60 7 of 7 25 18-Jun-17 30 0 373 518 764 3.00 7 of 7 26 25-Jun-17 3 1 51 69 97 0.37 0 of 74 27–36 No sampling from 1-Jul-17 to 12-Sept-17 4 of 4 37 13-Sep-17 3 0 43 66 99 0.46 7 of 7 38 17-Sep-17 1 0 15 22 36 0.16 7 of 7 39 24-Sep-17 3 0 46 66 99 0.45 7 of 7 40 1-Oct-17 2 0 30 44 66 0.33 7 of 7 41 8-Oct-17 1 0 15 22 33 0.16 7 of 7 42 15-Oct-17 1 0 14 22 33 0.15 7 of 7 48 26-Nov-17 7 0 101 154 249 1.15 7 of 7 49 3-Dec-17 2 0 30 44 66 0.30 7 of 7 51 17-Dec-17 1 0 15 22 36 0.16 268 of 365 Season 812 7 12,653 14,383 16,431 29.4

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 72 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.5. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile spring-run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018. Weeks in which no passage occurred are omitted and weeks in which the trap did not sample are highlighted in gray. Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 6 of 7 47 19-Nov-17 120 0 1,788 2,637 3,960 18.02 7 of 7 48 26-Nov-17 121 1 1,803 2,659 4,300 20.18 7 of 7 49 3-Dec-17 76 0 1,133 1,670 2,701 12.10 7 of 7 50 10-Dec-17 28 0 417 615 995 4.61 7 of 7 2 8-Jan-18 1 0 15 27 55 0.30 7 of 7 3 15-Jan-18 2 0 28 41 60 0.26 7 of 7 4 22-Jan-18 1 0 16 23 36 0.16 7 of 7 5 29-Jan-18 1 0 12 16 22 0.09 7 of 7 7 12-Feb-18 1 0 13 18 27 0.12 7 of 7 8 19-Feb-18 1 0 14 22 33 0.15 7 of 7 9 26-Feb-18 3 0 45 66 107 0.48 7 of 7 10 5-Mar-18 3 0 45 66 99 0.46 7 of 7 11 12-Mar-18 8 0 128 196 286 1.43 7 of 7 12 19-Mar-18 1 0 15 22 36 0.16 5 of 7 13 26-Mar-18 2 0 30 44 66 0.30 5 of 7 14 2-Apr-18 0 0 29 44 66 0.30 5 of 7 15 9-Apr-18 4 0 89 132 198 0.93 5 of 7 16 16-Apr-18 2 0 30 44 71 0.33 0 of 92 27–40 No sampling from 1-Jul-18 to 30-Sep-18 240 of 384 Season 375 1 6,767 8,342 10,403 30.47

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 73 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table B.6. Weekly catch, mortality, and passage indices with the lower (LCL) and upper (UCL) 95% confidence limits and SE of the weekly strata for brood year 2017 juvenile fall-run Chinook Salmon captured at the lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018. Weeks in which no passage occurred are omitted and weeks in which the trap did not sample are highlighted in gray. Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 7 of 7 48 26-Nov-17 8 0 119 176 264 1.20 7 of 7 49 3-Dec-17 88 0 1,311 1,934 3,127 14.68 7 of 7 50 10-Dec-17 355 6 5,291 7,802 12,616 56.54 7 of 7 51 17-Dec-17 275 0 4,095 6,044 9,773 45.29 8 of 8 52a 24-Dec-17 176 0 2,541 3,868 6,255 27.47 7 of 7 1 1-Jan-18 146 1 2,176 3,209 4,818 22.38 7 of 7 2 8-Jan-18 731 4 11,739 19,973 39,913 230.22 7 of 7 3 15-Jan-18 4,006 21 56,752 81,755 120,180 537.07 7 of 7 4 22-Jan-18 5,566 30 87,838 127,661 200,774 876.69 7 of 7 5 29-Jan-18 3,367 15 38,760 53,786 75,758 302.70 7 of 7 6 5-Feb-18 5,426 19 134,836 225,145 385,246 2,243.90 7 of 7 7 12-Feb-18 3,671 24 47,530 66,867 95,060 402.45 7 of 7 8 19-Feb-18 2,753 10 39,746 60,505 90,849 418.36 7 of 7 9 26-Feb-18 510 4 37,213 54,879 88,740 402.57 7 of 7 10 5-Mar-18 341 4 5,082 7,495 11,253 51.10 7 of 7 11 12-Mar-18 761 8 12,176 18,606 27,162 134.24 7 of 7 12 19-Mar-18 154 0 2,295 3,385 5,092 24.22 5 of 7 13 26-Mar-18 44 0 715 1,055 1,706 7.75 5 of 7 14 2-Apr-18 5 2 194 286 430 2.06 5 of 7 15 9-Apr-18 29 1 551 813 1,315 6.73 5 of 7 16 16-Apr-18 20 0 656 967 1,452 6.92 5 of 7 17 23-Apr-18 93 0 1,773 2,615 4,229 18.74 5 of 7 18 30-Apr-18 41 0 939 1,385 2,079 9.43 5 of 7 19 7-May-18 49 0 969 1,429 2,145 9.55 5 of 7 20 14-May-18 90 0 1,520 2,242 3,372 15.97 3 of 7 21 21-May-18 20 0 954 1,407 2,274 10.47 3 of 7 22 28-May-18 8 0 626 923 1,493 6.69

Brood Year 2017 Juvenile Salmonid Sampling in Clear Creek 74 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office Table B. 6. continued Days sampled Week Date Weekly catch Weekly mortality 95% LCL Weekly passage 95% UCL SE 5 of 7 23 4-Jun-18 28 0 462 659 990 4.31 5 of 7 24 11-Jun-18 2 0 60 88 132 0.63 5 of 7 25 18-Jun-18 2 0 29 44 66 0.30 0 of 92 27–40 No sampling from 1-Jul-18 to 30-Sep-18 240 of 384 Season 28,765 149 638,702 757,003 948,755 2602.75 a Week 52 (December 24–31, 2017) contains eight days for keeping January 1 as Julian calendar day one.

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 75 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Appendix C: Annual Catch and Passage Summaries

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 76 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table C.1. Annual catch and brood year passage indices (highlighted in gray) of juvenile spring-run Chinook Salmon with the lower (LCL) and upper (UCL) 95% confidence limits and SE for brood years 2003–2017 captured by upper rotary screw trap at river mile 8.4 in Clear Creek, Shasta County. The adjusted passage index (proportionate to juveniles-per-redd) includes redds below the trap (RST), yet above the separation weir. Actual Adjusted Juveniles- Redds Brood annual Passage Standard passage per-redd above Total year catch 95% LCL index 95% UCL error index above RST RST redds 2003 5,157 88,817 108,338 137,672 483 110,422 2,083 52 53 2004 4,045 87,093 107,027 136,366 397 110,000 2,973 36 37 2005 4,499 87,516 104,197 128,418 373 106,241 2,043 51 52 2006 11,618 111,749 127,197 148,539 303 151,162 1,843 69 82 2007 8,153 92,728 110,224 135,069 352 124,295 2,345 47 53 2008 11,623 88,834 96,166 104,402 129 121,622 1,414 68 86 2009 5,333 62,213 68,296 75,384 109 74,084 1,158 59 64 2010 2,059 15,228 17,359 19,910 38 19,288 1,929 9 10 2011 4,614 50,351 55,737 61,085 86 59,453 3,716 15 16 2012 1,610 23,041 25,881 29,746 56 28,038 1,078 24 26 2013 28,529 212,599 228,556 243,300 279 255,132 1,772 129 144 2014 2,852 35,556 41,600 49,286 112 50,844 770 54 66 2015 4,502 45,677 51,010 57,361 100 52,832 1,822 28 29 2016 3,841 34,388 39,117 45,040 86 43,029 1,956 20 22 2017 1,268 10,595 12,381 15,143 36 12,381 1,376 9 9

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 77 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table C.2. Annual catch and brood year (January 1 through December 31) passage indices (highlighted in gray) of juvenile Rainbow Trout/steelhead with lower (LCL) and upper (UCL) 95% confidence limits and SE for brood years 1999–2017 captured by lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. The adjusted passage index (proportionate to juveniles-per-redd) includes redds below the trap in Reach 7. Juveniles- per-redd Brood Actual Standard Adjusted Reaches Reaches Reach 7 year annual catch 95% LCL Passage index 95% UCL error index 1–6 redds 1–6 redds 1999 3,986 4,229 4,506 2000 7,951 8,507 9,162 2001 8,120 8,742 9,424 38 230 2002 986 11,731 12,803 14,193 20 101 127 2003 480 8,758 9,772 10,954 19 78 125 2004 1,001 24,137 28,989 36,746 107 151 192 2005 1,209 22,247 24,791 29,454 57 144 172 2006 406 9,362 10,762 12,632 27 42 256 2007 1,176 27,515 33,910 43,292 127 165 206 2008 1,881 33,284 36,499 40,983 60 148 247 2009 2,219 28,103 30,487 33,599 45 409 75 2010 416 8,172 11,760 17,262 19 233 50 2011 1,117 17,965 19,508 21,612 28 218 90 2012 1,429 19,867 21,229 22,722 23 178 119 2013 3,117 45,097 52,083 60,859 155 66,941 233 160 93 2014 1,447 36,208 39,266 42,312 55 41,289 313 119 17 2015 799 10,990 12,170 13,631 21 13,139 208 54 18 2016 1,843 26,732 29,763 33,613 56 31,874 131 211 10 2017 697 11,345 12,386 13,441 19 14,037 65 165 10

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 78 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table C.3. Annual catch and brood year (April 1 through March 31) passage indices (highlighted in gray) of juvenile late-fall run Chinook Salmon with lower (LCL) and upper (UCL) 95% confidence limits and SE for brood years 1999–2017 captured by lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. The adjusted passage index (proportionate to juveniles-per-redd) includes redds below the trap (RST) in Reach 7. Juveniles Brood Actual 95% Passage 95% Standard Reach 6 Reach 7 per reach Adjusted year annual catch LCL index UCL error redds redds 6 redd index 1999 55,966 272,930 292,323 314,778 55,966 2000 9,496 90,576 101,347 116,274 9,496 2001 12,206 68,446 86,836 112,386 12,206 2002 12,069 156,297 172,708 192,685 298 12,069 2003 1,405 29,432 33,902 39,638 87 24 1,413 1,405 2004 497 9,570 11,906 15,644 48 20 595 497 2005 1,551 17,808 20,401 23,384 45 28 729 1,551 2006 2,825 70,716 86,918 113,960 381 14 6,208 2,825 2007 6,850 149,395 202,011 319,016 1,816 25 8,080 6,850 2008 2,537 39,129 45,903 54,452 127 17 2,700 2,537 2009 4,703 61,181 68,624 79,425 155 122 562 4,703 2010 771 19,929 22,853 27,111 59 33 693 771 2011 554 7,798 8,703 9,546 16 21 414 554 2012 1,643 22,116 24,935 28,146 50 18 1,385 1,643 2013 1,153 19,288 25,996 37,849 147 17 11 1,529 1,153 2014 668 16,240 17,922 19,814 29 15 11 1,195 668 2015 913 12,406 13,940 15,898 27 70 29 199 913 2016 355 4,925 5,712 6,589 13 15 7 381 355 2017 812 12,653 14,383 16,431 29 15 5 959 812

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 79 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table C.4. Annual catch and brood year passage indices (highlighted in gray) of juvenile fall-run Chinook Salmon with the lower (LCL) and upper (UCL) 95% confidence limits and SE for brood years 1999–2017 captured by lower rotary screw trap at river mile 1.7 in Clear Creek, Shasta County. Brood Actual annual Standard Female Juveniles-per- year catch 95% LCI Passage index 95% UCI error spawners female 1998 688,083 5,656,571 6,395,638 7,303,438 2,485 2,573 1999 518,542 5,951,440 6,405,765 7,121,563 4,089 1,567 2000 362,680 13,535,844 14,955,182 16,483,244 3,349 4,466 2001 416,407 5,577,387 5,788,701 6,042,987 3,923 5,615 1,031 2002 227,010 3,560,468 3,858,446 4,174,685 4,783 8,176 472 2003 246,716 5,311,235 6,056,834 7,003,322 14,005 5,435 1,114 2004 195,882 5,361,896 6,190,757 7,216,897 15,604 3,722 1,663 2005 106,173 2,570,162 2,969,321 3,566,470 8,341 9,607 309 2006 163,963 4,275,282 4,929,544 5,832,272 12,915 5,208 947 2007 212,962 4,816,781 5,545,303 6,614,700 14,327 2,634 2,105 2008 298,983 7,129,073 8,451,186 10,397,719 29,879 4,429 1,908 2009 88,121 2,226,170 2,499,990 2,834,759 5,055 1,776 1,408 2010 240,000 3,305,917 3,566,723 3,871,986 4,522 3,697 965 2011 647,145 9,767,159 10,408,622 11,041,760 16,423 3,911 2,661 2012 403,826 6,365,167 7,083,575 7,924,786 12,669 4,693 1,509 2013 884,179 17,609,794 19,800,773 22,681,877 41,639 9,426 2,101 2014 146,823 2,780,989 3,198,623 3,682,269 7,993 6,724 476 2015 289,100 4,218,964 4,735,792 5,409,084 9,491 4,503 1,052 2016 47,655 917,716 1,022,700 1,152,794 1,918 1,401 730 2017 28,765 638,702 757,003 948,755 2,603 1,069 708–2,656a aThe proportion of Jills (females ≤ 2 years of age) in the female spawning population has historically been low (mean 2013–2016; 0.21). During the 2017 spawning season they outnumbered adult females 3:1. The fecundity of Jills is unknown but is lower than that of adults. The lower value is that with Jills included and the high number is calculated with just adults, the true value lays somewhere within the range.

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Appendix D: Non-salmonid Species Catch

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 81 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table D.1. Name key of non-salmonid fish taxa captured by the upper (river mile 8.4) and lower (river mile 1.7) rotary screw traps in Clear Creek, Shasta County, from September 13, 2017, through June 30, 2018. Abbreviation Common name Family Scientific name CAR California Roach Cyprinidae Hesperoleucus symmetricus CATFRY Sacramento Sucker fry Catostomidae Catostomus occidentalis CENFRY Unidentified Centrarchid fry Centrarchidae Centrarchidae spp. COTFRY Unidentified Cottus fry Cottidae Cottus spp. CYPFRY Unidentified Cyprinid fry Cyprinidae Cyprinidae spp. DACE Speckled Dace Cyprinidae Rhinichthys osculus EAMMO Pacific Lamprey ammocoete Petromyzontidae Entosphenus tridentata GSF Green Sunfish Centrarchidae Lepomis cyanellus HH Hardhead Cyprinidae Mylopharodon conocephalus LAMMO Unidentified Lampetra ammocoete Petromyzontidae Lampetra spp. MQF Western Mosquitofish Poeciliidae Gambusia affinis PL Pacific Lamprey adult Petromyzontidae Entosphenus tridentatus PLT Pacific Lamprey macropthalmia Petromyzontidae Entosphenus tridentata RFS Riffle Sculpin Cottidae Cottus gulosus SASU Sacramento Sucker Catostomidae Catostomus occidentalis SPM Sacramento Pikeminnow Cyprinidae Ptychocheilus grandis TP Tule Perch Embiotocidae Hysterocarpus traski TSS Threespine Stickleback Gasterosteidae Gasterosteus aculeatus UAMMO Unidentified lamprey ammocoete Petromyzontidae Lampetra spp. or Entosphenus tridentata UFRY Unidentified fry

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 82 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table D.2. Summary of non-salmonid fish taxa captured by the upper Clear Creek rotary screw trap at river mile 8.4, Shasta County, from November 20, 2017, through June 30, 2018. Species Nov Dec Jan Feb Mar Apr May Jun Totals CAR 2 1 0 1 3 1 0 2 10 COTFRY 0 0 0 0 0 4 0 0 4 EAMMO 13 5 64 13 9 44 1 2 151 PL 0 0 0 2 0 0 0 0 2 PLT 8 11 300 0 0 0 1 1 321 RFS 0 4 6 9 28 21 0 1 69 UAMMO 3 0 2 4 0 3 0 0 12

Brood Year 2017 Juvenile Salmonid Monitoring in Clear Creek 83 U.S. Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Table D.3. Summary of non-salmonid fish taxa captured by the lower Clear Creek rotary screw trap at river mile 1.7, Shasta County, from September 13, 2017, through June 30, 2018. Species Sep Oct Nov Dec Jan Feb Mar Apr May Jun Totals CAR 5 8 2 5 6 0 2 0 2 11 41 CATFRY 1 0 0 0 0 0 0 0 0 0 1 CENFRY 1 0 0 0 0 0 0 0 0 0 1 CYPFRY 3 2 0 0 1 1 1 2 0 1 11 DACE 1 5 0 0 0 0 1 0 0 0 7 EAMMO 2 6 6 6 15 7 53 11 22 34 162 GSF 0 0 0 0 0 0 0 0 0 1 1 HH 4 1 0 7 4 0 6 4 2 8 36 LAMMO 0 0 0 0 0 0 2 0 0 0 2 MQF 0 0 0 0 0 0 2 6 0 4 12 PLT 0 3 4 28 88 112 862 2 1 1 1,101 RFS 20 13 4 6 7 9 21 15 2 6 103 SASU 5 3 1 2 0 0 0 0 1 1 13 SPM 2 1 0 1 1 0 1 1 0 0 7 TP 0 0 0 0 0 0 0 1 0 0 1 TSS 1 2 1 0 0 0 0 0 0 3 7 UAMMO 0 3 0 1 2 1 6 5 2 5 25 UFRYa 0 0 0 0 0 0 0 0 0 1 1 a Visually estimated by rotary screw trap crew.

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