LOWER YUBA RIVER ACCORD MONITORING ANNUAL ROTARY SCREW TRAPPING REPORT AND EVALUATION PLAN OCTOBER 1, 2008 AUGUST 31, 2009

Transcription

1 LOWER YUBA RIVER ACCORD MONITORING AND EVALUATION PLAN ANNUAL ROTARY SCREW TRAPPING REPORT OCTOBER 1, 28 AUGUST 31, 29 Prepared for: The Lower Yuba River Accord Planning Team by Casey Campos and Duane Massa Pacific States Marine Fisheries Commission May, 21

2 The information contained in this annual data report represents study results at the date of publication. Recent analysis using multi-year data have fostered a more up-to-date understanding of lower Yuba River fisheries interactions. The results presented in this annual data report may or may not represent the current understanding stemming from recent analysis using comprehensive multi-year data. Please refer to the M&E Interim Report for a more recent analysis and discussion.

3 Table of Contents LIST OF TABLES... 3 LIST OF FIGURES INTRODUCTION Analytics Overview FIELD METHODS Deviations from the RST Protocols and Procedures DATA ANALYSIS METHODS Trap Efficacy Fish Condition Abundance Diversity RESULTS Trap Efficacy Fish Condition Abundance Diversity DISCUSSION ACKNOWLEDGEMENTS REFERENCES APPENDIX A Yuba Accord Annual RST Report July 8, 211

4 LIST OF TABLES Table 1. Monthly b parameter estimates for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Table 2. Monthly b parameter estimates for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Table 3. Length distributions and descriptive statistics for juvenile Chinook salmon captured at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Table 4. Length distributions and descriptive statistics for juvenile steelhead trout captured at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Table A1. Weekly operational results for RST 1 at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A2. Weekly operational results for RST 2 at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A3. Weekly operational results for RST 3 at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A4. Weekly and monthly estimates and standard deviation (SD) of the computed Fulton s Condition Factor (K) for juvenile Chinook salmon at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Table A5. Weekly and monthly estimates and standard deviation (SD) of the computed Fulton s Condition Factor (K) for juvenile steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Table A6. Total fraction of capture by species at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Table A7. Weekly release date, number of marked juvenile Chinook salmon released and daily recaptures observed during capture efficiency trials for RST 1 at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A8. Weekly release date, number of marked juvenile Chinook salmon released and daily recaptures observed during capture efficiency trials for RST 2 at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A9. Weekly release date, number of marked juvenile Chinook salmon released and daily recaptures observed during capture efficiency trials for RST 3 at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A1. Weekly abundance estimates, 95% confidence interval, and total weekly captures of juvenile Chinook salmon at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Yuba Accord Annual RST Report July 8, 211

5 Table A11. Developmental phase, range of dates captured, total fraction of capture, and cumulative total capture for juvenile Chinook salmon and steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Table A12. Length distributions by developmental stage and descriptive statistics for juvenile Chinook salmon and steelhead trout captured at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. LIST OF FIGURES Figure 1. Simple linear regression of the estimated mean weekly Fulton s Condition Factor (K) for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 2. Simple linear regression of the estimated mean monthly Fulton s Condition Factor (K) for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 3. Simple linear regression of the estimated monthly b parameter for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 4. Simple linear regression of the estimated mean weekly Fulton s Condition Factor (K) for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 5. Simple linear regression of the estimated mean monthly Fulton s Condition Factor (K) for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 6. Simple linear regression of the estimated monthly b parameter for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 7. Weekly juvenile Chinook salmon abundance at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 8. Cumulative temporal distribution of estimated juvenile Chinook salmon abundance at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 9. Weekly observed catch of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Figure 1. Cumulative temporal distribution of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 11. Cumulative temporal distribution of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to March 31, 29. Figure 12. Cumulative temporal distribution of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from April 1, 29 to August 31, 29. Figure 13. Mean fork length of Chinook salmon through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Yuba Accord Annual RST Report July 8, 211

6 Figure 14. Weekly frequency and observed fork lengths of juvenile Chinook salmon lifestages at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 15. Mean fork length of steelhead trout through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from April 1, 29 to August 31, 29. Figure 16. Mean fork length of steelhead trout through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to March 31, 29. Figure 17. Mean fork length of steelhead trout through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from April 1, 29 to August 31, 29. Figure 18. Weekly frequency and observed fork lengths of juvenile steelhead trout lifestages at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A1. Weekly Chinook salmon abundance and average weekly turbidity values at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A2. Weekly Chinook salmon abundance and average weekly flow at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A3. Weekly Chinook salmon abundance and average weekly temperature at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A4. Weekly Chinook salmon abundance and lunar cycle at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A5. Weekly steelhead trout catch and average weekly turbidity values at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A6. Weekly steelhead trout catch and average weekly flow at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A7. Weekly steelhead trout catch and average weekly water temperature at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure A8. Weekly steelhead trout catch and lunar cycle at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Figures A9-A3. Semi-monthly length frequency histograms of Chinook salmon at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Figures A31-A52. Semi-monthly length frequency histograms of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. Yuba Accord Annual RST Report July 8, 211

7 1. INTRODUCTION The lower Yuba River Accord (Accord) consists of a Fisheries Agreement and several other elements. The Fisheries Agreement includes descriptions of the River Management Team (RMT), the River Management Fund (RMF), and the Monitoring and Evaluation Plan (M&E Plan). The Fisheries Agreement in its entirety can be found on the Accord RMT website 1. The RMT Planning Group includes representatives of the California Department of Fish and Game (CDFG), National Marine Fisheries Service, Pacific Gas and Electric, U.S. Fish and Wildlife Service, Yuba County Water Agency, and one representative for the four non-government organizations (Friends of the River, South Yuba River Citizen s League, The Bay Institute and Trout Unlimited) that are parties to the Fisheries Agreement. The RMT planning group has developed the M&E Plan to guide study efforts through the efficient expenditure of RMF funds. The M&E Plan will provide monitoring data necessary to evaluate whether flow schedules described in the Accord are maintaining fish in good condition as defined by the Viable Salmon Population (VSP) concept developed by McElhany et al. (2). The VSP conceptual architecture utilizes measures of abundance, productivity, diversity, and spatial structure to assess the long-term sustainability of salmonid populations. The M&E Plan uses the VSP framework to evaluate the efficacy of flows prescribed in the Accord to keep fish in good condition and to maintain sustainable populations of Chinook salmon and steelhead trout in the lower Yuba River. Performance indicators and associated analytics were developed for each parameter to assess Chinook salmon and steelhead trout populations on an annual and multi-year basis. Multiple survey techniques will be utilized to address the specific analytics that are necessary to evaluate the performance indicators detailed in the M&E Plan. Juvenile Chinook salmon and steelhead trout abundance will be monitored via rotary screw trapping. The rotary screw trap (RST) was developed by biologists in the 198s (Volkhardt et al. 27) to capture juvenile salmonids. RSTs have been utilized on the lower Yuba River near Hallwood Boulevard since This sampling method has been used to monitor annual abundance and temporal distributions of juvenile Chinook salmon throughout the California Central Valley. The purpose of this Annual Yuba Accord Rotary Screw Trapping Data Report is to: 1) document findings for the analytics in the M&E Program that are dependent on annual data collection from RSTs;, 2) document any deviations from the RST sampling protocols and procedures described in the M&E Program;, and 3) provide recommendations for changes in following year s RST field protocols and procedures Analytics Overview Several analytic applications have been identified in the M&E Plan framework associated with data collected from the RSTs. The major categories to be addressed in this annual report include juvenile fish community composition, abundance, and diversity. In addition, an evaluation of current trapping methods will provide insight into the effectiveness and potential for improved capture procedures. A brief description of each category is described below. 1 Yuba Accord Annual RST Report July 8, 211

8 Trap Efficacy Examine the annual operation of the RSTs to determine if current methods are maximizing the potential for juvenile fish capture and effectively observing temporal distributions. Fish Condition Evaluate the condition of juvenile Chinook salmon and steelhead trout using length-weight relationships and the presence of visually observable abnormalities. Evaluate lower Yuba River flows and water temperatures with various measures of fish condition. Document the species composition and associated temporal distributions of fish captured in the RSTs. Evaluate fish species richness, diversity, dominance and evenness. Abundance Estimate weekly and annual abundances of juvenile Chinook salmon and steelhead trout emigrating from the lower Yuba River at the Hallwood Boulevard site. Examine intra-annual trends in abundances of juvenile Chinook salmon and steelhead trout emigrating from the lower Yuba River at the Hallwood Boulevard site. Estimate abundances of over-summer rearing spring-run Chinook salmon and steelhead trout juveniles emigrating during fall from the lower Yuba River. Distinguish spring-run and fall-run Chinook salmon emigrating juveniles using associated juvenile developmental phases (i.e., yolk-sac fry, fry, parr, silvery parr, and smolt). Estimate the annual abundance of juvenile spring-, fall- and late fall-run Chinook salmon emigrating from the lower Yuba River. Compare lower Yuba River flows and water temperatures with the timing of Chinook salmon and steelhead juvenile emigration. Compare lower Yuba River water temperatures during the Chinook salmon and steelhead trout juvenile rearing and emigration life stages with indices of water temperature suitability. Diversity Evaluate time period-specific size structure during Chinook salmon and steelhead trout emigration. Document the seasonal presence of multiple developmental phases (i.e., yolk-sac fry, fry, parr, silvery parr, and smolt) of juvenile Chinook salmon and steelhead trout. Yuba Accord Annual RST Report July 8, 211

9 2. FIELD METHODS Field sampling methods are described in the RST Protocols and Procedures (see Appendix K of the Accord M&E Plan) Deviations from the RST Protocols and Procedures RST monitoring described in the Protocols and Procedures occurred at one site (Hallwood Boulevard) for the period of this annual report. Additional juvenile salmonid capture locations above Daguerre Point Dam were not established. Thus, results in this annual report describe data collected solely at the Hallwood Boulevard site. Additionally, trap efficiency tests were not conducted with juvenile steelhead trout due to low capture rates at the Hallwood Boulevard site. No abundance estimates were generated for steelhead trout during this reporting period. 3. DATA ANALYSIS METHODS 3.1. Trap Efficacy Results for each RST at the Hallwood Boulevard site were examined including the dates operated, total number of days fished, fraction of total, and total non-operation days with causal descriptions Fish Condition The condition of juvenile Chinook salmon and steelhead trout was examined weekly, monthly and annually using Fulton s Condition Factor (K) (Ricker 1975; Anderson and Neumann 1996): W 3 1, K ; L where W is weight and L is the length of an individual fish. Using simple linear regression, the mean weekly and monthly estimates of Fulton s Condition Factor were used to examine whether the body condition of juvenile Chinook salmon and steelhead trout changed over time. The growth of juvenile Chinook salmon and steelhead trout was examined using a length-weight relationship (Ricker 1975; Anderson and Neumann 1996): b W al ; where W is weight and L is the length of an individual fish, and a and b are parameters estimated by linear regression of the logarithmically transformed length-weight data. Using simple linear regression, estimates of the monthly b parameter were used to determine if growth of juvenile Chinook salmon and steelhead trout changed over time. The proportion of juvenile Chinook salmon and steelhead trout with visually observable abnormalities was examined. Regression analysis was used to examine whether measures of body condition (K), growth (b parameter) and proportions of visual abnormalities were related to measures of flow and water temperature. Yuba Accord Annual RST Report July 8, 211

10 Fish species richness (S) was examined using total catch at the Hallwood Boulevard site. Fish species diversity was calculated using the Shannon Diversity Index (H ) (Magurran 23): S H p i ln p ; i 1 i where S is the number of species encountered, p i is the relative abundance of species i, which is calculated as: ni pi ; N where n i is the number of species i and N is the total number of individuals. Fish species dominance was estimated using the Simpson s Dominance Index (D) (Birch 1981; Magurran 23): S ni D ; i 1 N 2 where S, n i and N are described above. Fish species evenness was estimated using Simpson s Evenness Index (Magurran 23, Magurran and Phillip 21): 1 E D 1 ; D S where D and S are described above Abundance A simple-stratified design for mark-recapture estimation (Carlson et al. 1998) was used to estimate the weekly (7-day) abundances of juvenile Chinook salmon emigrating from the lower Yuba River. During periods when trap efficiency tests were conducted, the following equation was used to predict weekly abundance of emigrating Chinook salmon: ui M mi i ˆ 1 U i ; 1 The variances of the weekly Chinook salmon estimates were calculated using: ( ˆ ) ( V M U 1)( ui mi 1)( M i mi) ui 2 ( mi 1) ( mi 2) i i ; Confidence intervals (95%) of the estimates were calculated using: Yuba Accord Annual RST Report July 8, 211

11 Uˆ 1.96 V ( Uˆ ) ; where ˆ Ui was the estimated number of unmarked Chinook salmon downstream migrants during period i, u i was the number of unmarked Chinook salmon captured during period i, M i was the number of Chinook salmon marked and released during period i and m i was the number of marked Chinook salmon captured during period i. Weekly RST efficiencies for each trap were combined to create a single efficiency value for each weekly stratum. Weekly abundance estimates of Chinook salmon were then scaled to the sum of available hours during each weekly period and the number of hours the sampling device operated during the weekly period. During periods when trap efficiency tests were not conducted, observed Chinook salmon catch was scaled in the same manner using the following equation: H Nˆ i Nˆ ; ij h i where Nˆ i was the total weekly abundance of juvenile Chinook salmon passing the Hallwood Boulevard site, h i was the total number of hours that the sampling device i operated during the weekly period and H was the total number of hours within the weekly period. Juvenile Chinook salmon abundance and observed steelhead trout catch during the emigration period were examined temporally. Weekly captures of juvenile Chinook salmon were identified by juvenile developmental phase (i.e., yolksac fry, fry, parr, silvery parr and smolt) to evaluate potential temporal modalities corresponding to spring-, fall- and late fall-run Chinook salmon. Juvenile steelhead trout were also identified using these criteria. Weekly abundance estimates of juvenile Chinook salmon and daily observed catch of steelhead trout were examined in relation to environmental variables including measures of water temperature, flow, turbidity, and lunar cycle. Dates associated with percentile expressions (1%, 25%, 5%, 75%, 9%, 95% and 99%) of the cumulative temporal distribution of juvenile Chinook salmon and steelhead trout emigrating from the lower Yuba River were estimated by fitting asymmetric logistic functions to the cumulative temporal distributions of weekly abundance and observed catch. A simple asymmetric logistic function was fitted using the following expression (Richards 1959): j D i n i 1 Y i 1 (%) 1 1 exp α β D i 1 δ ; D i n where Y (%) i 1 i is the percentage of the cumulative temporal distribution of juvenile Chinook salmon and steelhead emigrating past a location from day 1 through time D i, and, and are parameters (i.e., Yuba Accord Annual RST Report July 8, 211

12 constants) that describe the shape of the resulting relative cumulative curve. The values of these parameters were obtained through non-linear least squares estimation. Potential relationships between juvenile salmonid movement patterns and flow fluctuations were examined during the sampling period. Changes in weekly abundance of juvenile Chinook salmon or steelhead trout between strata were compared to corresponding changes in weekly average flows. Regression analysis was used to examine potential relationships between the rate of downstream movement of salmonids and rates of flow Diversity Semi-monthly length-frequency histograms were developed to evaluate changes in the size structure of juvenile emigrants from data collected. Length-frequency histograms were compared over the entire emigration period to evaluate intra-annual variation in size structure. Descriptive statistics were used to evaluate the size structure of emigrating Chinook salmon and steelhead trout. Sample mean with 95% confidence intervals were used to describe the central tendency of observed lengths. Standard deviation and variance were used to measure the variability in lengths. Coefficient of variation (CV) was used as a measure of precision and for comparing the variability of lengths (size structure) for each week within the sampling season. Changes in the size of emigrating juvenile Chinook salmon and steelhead trout during the emigration period were examined. Mean lengths of juvenile Chinook salmon and steelhead trout were calculated through each date associated with the percentile expressions (1%, 25%, 5%, 75%, 9%, 95% and 99%) described above. Regression analysis was used to determine if mean length changed over time in relation to the percentile expressions from the cumulative distribution curve. Fork-length distributions of Chinook salmon and steelhead trout were examined for each developmental phase (i.e., yolk-sac fry, fry, parr, silvery parr, and smolt) during the survey period. Developmental phase evaluations for juvenile Chinook salmon and steelhead trout were described using weekly strata. 4. RESULTS 4.1. Trap Efficacy All three RSTs were operated continuously from October 1, 28 through August 31, 29, except during periods of high flows and/or excessive debris and trap damage. Periods of non-operation were frequent during the reporting period. Hallwood RST 1 operated approximately 265 days of 335 possible days during the survey period. RST 1 was inoperative from February 23-25, 29 and March 2-4, 29, due to high flows and excessive debris loading. RST 1 was pulled from the river and inoperative from May 5, 29 to June 18, 29 due to damages sustained during a flow event in excess of 2, cfs. Additionally, the main rotating axle on RST 1 sheared and was inoperable from August 8, 29 to the end of the survey period. Hallwood RST 2 operated approximately 274 days out of 335 possible days during the survey period. RST 2 was inoperative from February 23, 29 to April 16, 29 due to damages sustained during a high flow event. RST 2 was inoperative from May 5-14, 29 due to persistent high flows reaching in excess of 2, cfs. Hallwood RST 3 operated approximately 298 days out of 335 possible days during the survey period. RST 3 was inoperative from February 23, 29 to March 7, 29 and from May 4-29, 29 due to Yuba Accord Annual RST Report July 8, 211

13 persistent high flows and excessive debris loading. Weekly operational results were tabulated for each rotary screw trap including mean, minimum and maximum water velocities observed, water turbidity, cone revolutions per minute before and after servicing, daily cone revolutions, debris load and trap status (Appendix A, Tables A1-A3) Fish Condition The estimated mean Fulton s Condition Factor (K) for Chinook salmon during the entire survey period was.854 (.224 SD) (Appendix A, Table A4). Regression analysis of the weekly and monthly estimates of the mean Fulton s Condition Factor both identified a positive relationship amongst the variables moving through the survey period. The resulting regressions described 47% and 27% of the observations respectively (Figures 1 and 2). By removing single Chinook salmon observations occurring in strata early in the sampling season, the resulting regressions described 92% and 96% of the observations respectively. Figure 1. Simple linear regression of the estimated mean weekly Fulton s Condition Factor (K) for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 2. Simple linear regression of the estimated mean monthly Fulton s Condition Factor (K) for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. The growth of juvenile Chinook salmon was examined and the resulting estimate of the annual b parameter was 3.721, characterizing allometric growth (Table 1). Regression analysis of the monthly b parameter estimates identified a negative relationship amongst variables moving through the survey period and described 22% of the observations (Figure 3). Table 1. Monthly b parameter estimates for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Month Sample Size Estimated (b ) Oct 8 1 N/A Nov Dec Jan Feb Mar 9 1, Apr 9 1, May Jun Jul Aug Entire Year 6, Figure 3. Simple linear regression of the estimated monthly b parameter for juvenile Chinook salmon in the lower Yuba River, CA from October 1, 28 to August 31, 29. Yuba Accord Annual RST Report July 8, 211

14 A total of 38,37 juvenile Chinook salmon were examined for visually observable abnormalities; ten juvenile Chinook salmon with visually observable abnormalities were encountered during the survey period with a resultant proportion of.3%. The estimated mean Fulton s Condition Factor (K) for steelhead trout during the entire survey period was 1.6 (.27 SD) (Appendix A, Table A5). Regression analysis of the weekly and monthly estimates of the mean Fulton s Condition Factor both identified a positive relationship amongst the variables moving through the survey period. The resulting regressions described 1% and 4% of the observations respectively (Figures 4 and 5). By removing single fish observations occurring in weekly strata, the resulting weekly regression described 22% of the observations Fulton's Condition Factor (K) y =.3x R 2 =.963 Fulton's Condition Factor (K) y =.3x 9.96 R 2 =.449 Oct 8 Nov 8 Dec 8 Jan 9 Feb 9 Mar 9 Apr 9 May 9 Jun 9 Jul 9 Aug 9 Oct 8 Nov 8 Dec 8 Jan 9 Feb 9 Mar 9 Apr 9 May 9 Jun 9 Jul 9 Aug 9 Figure 4. Simple linear regression of the estimated mean weekly Fulton s Condition Factor (K) for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Figure 5. Simple linear regression of the estimated mean monthly Fulton s Condition Factor (K) for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. The growth of juvenile steelhead trout was examined and the resulting estimate of the annual b parameter was 2.993, characterizing isometric growth (Table 2). Regression analysis of the monthly b parameter estimates identified a weak, slightly positive relationship amongst variables moving through the survey period and described 1% of the observations (Figure 6). Table 2. Monthly b parameter estimates for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Month Sample Size Estimated (b ) Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Entire Year 1, Estimated b parameter Oct 8 Nov 8 Dec 8 Jan 9 Feb 9 Mar 9 y =.2x R 2 =.112 Figure 6. Simple linear regression of the estimated monthly b parameter for juvenile steelhead trout in the lower Yuba River, CA from October 1, 28 to August 31, 29. Apr 9 May 9 Jun 9 Jul 9 Aug 9 A total of 1,317 juvenile steelhead trout were examined for visually observable abnormalities; thirty-two juvenile steelhead trout with visually observable abnormalities were encountered during the survey period with a resultant proportion of 2.43%. Yuba Accord Annual RST Report July 8, 211

15 Regression analysis was used to examine whether measures of body condition (K), growth (b parameter) and proportions of visual abnormalities for juvenile Chinook salmon and steelhead trout were related to measures of flow and water temperature, but were not reported 2. Twenty-eight species of fish were captured during the survey period (Fish Species Richness= S= 28). The Shannon Diversity Index was calculated to be.43, indicating low species evenness. Simpson s Evenness Index was calculated to be.4 also indicating low species evenness. Simpson s Dominance Index was calculated to be.86; indicating one species, juvenile Chinook salmon, dominated the observed community assemblage. Nearly 93% of the total catch throughout the sampling period was comprised of juvenile Chinook salmon. Steelhead trout represented approximately 1.7% percent of the total catch. Fifteen of the 28 species observed were non-native to the lower Yuba River. Summary results were tabulated for each species in Appendix A, Table A Abundance Eighteen trap efficiency evaluations were conducted during the survey period using marked juvenile Chinook salmon. No efficiency tests were conducted on steelhead trout due to low capture rates. Weekly efficiency evaluations were conducted from December 31, 28 to June 1, 29 excluding the week of February 25, 29 and the weeks from May 6, 29 to June 3, 29. Efficiency evaluation results are presented in Appendix A, Tables A7-A9 for each of the three rotary screw traps. Chinook salmon abundance was estimated using methods presented in Carlson et al. (1998). Abundance estimates were generated only during periods when trap efficiency tests were conducted. No expansions were made during periods when trap efficiency evaluations were not completed. Actual observed catch was substituted for expanded estimates when sample strata did not have an associated efficiency value. Chinook salmon estimated abundance for expanded strata was 1,449,272 ± 164,41 (95% CI). Total Chinook salmon abundance to include strata expansions and observed catch from non-expanded periods was 1,463,955 (Appendix A, Table A1). Chinook salmon abundances were characterized by modal peak during the week of January 14, 29 in which an estimated 25,188 Chinook salmon emigrated past the sampling site. A second peak was observed during the week of March 4, 29 in which an estimated 232,939 Chinook salmon emigrated past the RST site. An additional peak was observed during the week of April 29, 29 when an estimated 112,294 Chinook salmon emigrated past the RST site (Figure 7, Appendix A, Table A1). 25, 2, 15, 1, 5, Oct 8 Nov 8 Dec 8 Estimated Abundance Jan 9 Feb 9 Mar 9 Apr 9 May 9 Jun 9 Jul 9 Aug 9 Figure 7. Weekly juvenile Chinook salmon abundance at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, Refer to discussion on page 23. Yuba Accord Annual RST Report July 8, 211

16 To examine the cumulative temporal distribution of Chinook salmon abundance, an asymmetric logistic function (Figure 8) was fit to the estimated abundance of emigrating Chinook salmon. The fitted logistic function predicted that 5% had emigrated past the RST site by the week of February 11, 29 and 99% by the week of July 1, 29. Figure 8. Cumulative temporal distribution of estimated juvenile Chinook salmon abundance at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Trap efficiency evaluations were not conducted for juvenile steelhead trout during the survey period. Additionally, no attempt was made to adjust total observed captures for steelhead trout when RSTs were inoperable. Reported abundances for steelhead trout are representative of the total observed steelhead trout catch. Total captures for steelhead trout was 1,317 during the survey period. Most steelhead trout were captured from April 1, 29 to August 31, 29 (n=1,16). Peak weekly captures of steelhead trout (n=169) occurred during the week of June 17, 29 (Figure 2) Oct 8 Nov 8 Dec 8 Observed Catch Jan 9 Feb 9 Mar 9 Apr 9 May 9 Jun 9 Jul 9 Aug 9 Figure 9. Weekly observed catch of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 27 to September 3, 28. To examine the cumulative temporal distribution of juvenile steelhead trout, an asymmetric logistic function (Figure 1) was fit to the observations of emigrating steelhead trout. The fitted logistic function predicted that 5% had emigrated past the RST site by the week of June 17, 29 and 99% by the week of August 19, 29. Yuba Accord Annual RST Report July 8, 211

17 Figure 1. Cumulative temporal distribution of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. For comparison and consistency with the Annual RST Data Report, where a singular logistic function did not fit the observed distribution, the survey period was stratified into two time periods and logistic functions were fit to the data (Figure 11 and 12). Figure 11. Cumulative temporal distribution of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to March 31, 29. Figure 12. Cumulative temporal distribution of steelhead trout at the Hallwood Boulevard site on the lower Yuba River, CA from April 1, 29 to August 31, 29. The relationship between the abundance of emigrating Chinook salmon and steelhead trout was compared to average weekly values of turbidity, flow, temperature and lunar period (Appendix A, Figures A1-A8), however results from these relationships were not reported Diversity The size structure of juvenile Chinook salmon emigrants captured was tabulated to include standard descriptive statistics and showed an increase in the mean size of emigrants moving through the survey period (Table 3). Semi-monthly (15-day interval) length-frequency histograms were also developed (Appendix A, Figures A9-A3). 3 See discussion on page 15. Yuba Accord Annual RST Report July 8, 211

18 Table 3. Length distributions and descriptive statistics for juvenile Chinook salmon captured at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Sampling Period Sample Size Min. (mm) Max. (mm) Mean (mm) Variance Standard Deviation Coefficient of Variation (%) (±) 95% Confidence Oct Oct Nov Nov Dec Dec , Jan , Jan , Feb , Feb , Mar , Mar , Apr , Apr , May May June June July July Aug Aug Chinook salmon fork length was examined using estimated temporal frequencies from a fitted asymmetric logistic function. During the yearly survey period, a positive linear relationship was observed between the estimated fractional passage by date of juvenile Chinook salmon emigration and mean fork length (Figure 13). The coefficient of determination (R²) from a simple linear regression described 8% of the observations. Figure 13. Mean fork length of Chinook salmon through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Chinook salmon yolk-sac fry represented.1% of the observed catch. Eleven Chinook salmon yolk-sac fry were observed during the survey period. Peak observations of Chinook salmon yolk-sac fry occurred during the weeks of March 18, 29 (n=3) and April 15, 29 (n=3). No Chinook salmon yolk-sac fry were observed after April 19, 29. Chinook salmon yolk sac fry ranged in size from 3 to 35 mm, with a mean fork length of 33 mm 1.2 mm (95% CI) (Figure 14, Appendix A, Tables A11-A12). Chinook salmon fry represented.3% (n=44) of the observed catch. Peak observations for Chinook salmon fry occurred during the weeks of November 19, 28 (n=6), December 1, 28 (n=6) and March 4, 29 (n=6). No Chinook salmon fry were observed after May 3, 29. Chinook salmon fry ranged in Yuba Accord Annual RST Report July 8, 211

19 size from 31 to 39 mm, with a mean fork length of 35 mm.66 mm (95% CI) (Figure 14, Appendix A, Tables A11-A12). Chinook salmon parr were the most prevalent lifestage and represented 91.1% (n=12,728) of all Chinook salmon lifestages observed. Peak observations of Chinook salmon parr occurred during the weeks of December 17, 28 (n=82), December 24, 28 (n=796) and January 28, 29 (n=727). No Chinook salmon parr were observed after August 15, 29. Chinook salmon parr ranged in size from 28 to 98 mm, with a mean fork length of 41 mm.15 mm (95% CI) (Figure 14, Appendix A, Tables A11-A12). Chinook salmon silvery parr represented 7.8% (n=1,95) of the observed Chinook salmon catch. Peak observations of Chinook salmon silvery parr occurred during the weeks of June 3, 29 (n=141) and June 17, 29 (n=141). No Chinook salmon silvery parr were observed after August 15, 29. Chinook salmon silvery parr ranged in size from 5 to 143 mm, with a mean fork length of 68 mm.52 mm (95% CI) (Figure 14, Appendix A, Tables A11-A12). Chinook salmon smolt represented.7% (n=92) of the observed Chinook salmon catch. Peak observations of Chinook salmon smolts occurred during the weeks of May 27, 29 (n=21) and June 3, 29 (n=21). No Chinook salmon smolts were observed after August 18, 29. Chinook salmon smolts ranged in size from 57 to 126 mm, with a mean fork length of 82 mm 2.6 mm (95% CI) (Figure 14, Appendix A, Tables A11-A12). Figure 14. Weekly frequency and observed fork lengths of juvenile Chinook salmon lifestages at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Yuba Accord Annual RST Report July 8, 211

20 The size structure of juvenile steelhead trout emigrants captured was tabulated to include standard descriptive statistics and showed an overall decrease in the mean size of emigrants moving through the survey period (Table 4). Semi-monthly (15-day interval) length-frequency histograms were also developed (Appendix A, Figures A31-A52). Table 4. Length distributions and descriptive statistics for juvenile steelhead trout captured at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, 29. Sampling Period Sample Size Min. (mm) Max. (mm) Mean (mm) Variance Standard Deviation Coefficient of Variation (%) (±) 95% Confidence Oct Oct , Nov Nov Dec Dec Jan Jan Feb Feb Mar Mar Apr Apr May May June June July July Aug Aug Steelhead trout fork length was examined using estimated temporal frequencies from fitted asymmetric logistic functions. During the yearly survey period, a negative linear relationship was observed between the estimated fractional passage by date of juvenile steelhead trout emigration and mean fork length (Figure 15). The coefficient of determination (R²) from a simple linear regression described 73% of the yearly observations. Figure 15. Mean fork length of steelhead trout through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from April 1, 29 to August 31, 29. Steelhead trout fork length was also examined using estimated temporal frequencies from two fitted asymmetric logistic functions used to describe the two distinct modes of steelhead trout passage. A very weak negative linear relationship was observed between the estimated fractional passage by date of Yuba Accord Annual RST Report July 8, 211

21 juvenile steelhead trout emigration and mean fork length (Figures 16 and 17). The coefficients of determination (R²) described.5% of observations for the October 1, 28 to March 31, 29 period, and 7% of observations for the April 1, 29 to August 31, 29 period. Figure 16. Mean fork length of steelhead trout through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to March 31, 29. Figure 17. Mean fork length of steelhead trout through the percentile expressions 1%, 25%, 5%, 75%, 9%, 95% and 99% emigrating at the Hallwood Boulevard site on the lower Yuba River, CA from April 1, 29 to August 31, 29. Steelhead trout yolk-sac fry represented.2% (n=2) of the observed steelhead trout catch. Observations of steelhead trout yolk-sac fry occurred during the weeks of March 11, 29 (n=1) and May 27, 29 (n=1). No steelhead trout yolk-sac fry were observed after May 3, 29. Steelhead trout yolk-sac fry ranged in size from 25 to 36 mm 1.78 mm (95% CI) (Figure 18, Appendix A, Tables A11-A12). Steelhead trout fry represented.2% (n=2) of the observed steelhead trout catch. Observations of steelhead trout fry occurred during the weeks of March 25, 29 (n=1) and July 15, 29 (n=1). No steelhead trout fry were observed after July 13, 29. Steelhead trout fry ranged in size from 24 to 46 mm mm (95% CI) (Figure 18, Appendix A, Tables A11-A12). Steelhead trout parr were the most prevalent life stage observed and represented 78.7% (n=974) of all life stages observed. Peak observations of steelhead trout parr occurred during the weeks of June 1, 29 (n=93) June 17, 28 (n=127) and July 8, 29 (n=76). Steelhead trout parr were observed every month and through the end of the survey period. Steelhead trout parr ranged in size from 23 to 126 mm, with a mean fork length of 63 mm.81 mm (95% CI) (Figure 18, Appendix A, Tables A11-A12). Steelhead trout silvery parr represented 2% (n=247) of the observed steelhead trout catch. Peak observations of steelhead trout silvery parr occurred during the weeks of June 1, 29 (n=32), June 17, 29 (n=37) and July 15, 29 (n=3). Steelhead trout silvery parr were observed during most months of the survey period and through the end of the survey period. Steelhead trout silvery parr ranged in size from 47 to 157 mm, with a mean fork length of 77 mm 1.82 mm (95% CI) (Figure 18, Appendix A, Tables A11-A12). Steelhead trout smolt represented 1% (n=12) of the observed steelhead trout catch. Peak observations of steelhead trout smolt occurred during the weeks of February 18, 29 (n=2) and June 17, 29 (n=2). No steelhead trout smolt were observed after July 29, 29. Steelhead trout smolt ranged in size from 85 to 3 mm, with a mean fork length of 139 mm mm (95% CI) (Figure 18, Appendix A, Tables A11-A12). Yuba Accord Annual RST Report July 8, 211

22 Figure 18. Weekly frequency and observed fork lengths of juvenile steelhead trout lifestages at the Hallwood Boulevard site on the lower Yuba River, CA from October 1, 28 to August 31, DISCUSSION The growth and condition findings for juvenile Chinook salmon and steelhead trout on the lower Yuba River stemming from an analysis of Fulton s Condition Factor (K) revealed the estimated K for juvenile Chinook salmon during the survey period to be.85 (.22 SD). Juvenile steelhead trout were found to have a mean annual K factor of 1.6 (.27 SD). Condition factors for both species improved during the study period and the observations closely follow results reported from available literature in similar studies. Hayden and Pinnix (27) reported K factors for age- Chinook salmon at Willow Creek on the Trinity River, California that increased following emergence and rearing through the spring months, and Chamberlain and Williamson (26) also found that condition factors improved with increasing mean fork length on the Trinity River, California. Additionally, Snider et al. (1998), reported Fulton s Condition Factor (K) for juvenile Chinook salmon to increase with larger fork lengths on the American River, California. Condition factors for juvenile salmonids on the lower Yuba River may be influenced by age and corresponding fork length within the age- size class, resulting in more robust body form and K factors for larger Chinook salmon emigrants observed in latter weekly strata. Prior to full dependence on exogenous feeding, young of the year (YOY) Chinook salmon generally exhibit a low body depth to fork length ratio. As the juveniles develop and become fully dependent on exogenous feeding, condition factors become more reflective of a robust body form. The value of K is based on weight which is highly variable and readily affected by feeding rate, fish health, stock differences, age of Yuba Accord Annual RST Report July 8, 211

23 fish, sex, season, stage of maturity, fullness of gut, type of food consumed, amount of fat reserve and degree of muscular development (Barnham and Baxter 1998, Beeman et al. 1995, Williams 2). A thorough investigation into the available literature concerning salmonid growth (b parameter) found that Chinook salmon and steelhead trout attribute higher growth rates in relation with ocean and estuary residence, and use of off-channel and floodplain habitats (Jeffres et al. 28; Limm and Marchetti 29; MacFarlane et al. 22; Sommer et al. 21). Chinook salmon exhibit complex and varied growth patterns, and the growth of Pacific salmon in freshwater environments varies greatly within and between populations in different river systems (Banks et al. 1971). The prevalence of over-summer rearing Chinook salmon in the lower Yuba River has been anecdotally referenced, and juveniles meeting temporal size criteria for yearling lifestages have been captured during previous RST monitoring at the Hallwood Boulevard site (Massa 25, Massa and McKibbin 26, Campos and Massa 21). Juvenile Chinook salmon captured during the fall and winter months (October-January) with a measured fork length larger than 7 mm are likely employing an extended rearing strategy in the lower Yuba River. Four Chinook salmon that met this criterion were observed during the survey period at the Hallwood Boulevard RST from October 1, 28 to January 31, 29. Previous monitoring efforts at this location observed 33 juvenile Chinook salmon that met this criterion from December 15, 27 through January 31, 28 (Campos and Massa 21); juvenile Chinook salmon ranging in fork length from 78 mm to 134 mm were observed in November 24 and December 24 (Massa and McKibbin 26) and were also observed from October 23 through January 24 with fork lengths ranging from 73 mm to 138 mm (Massa 25). Although the sample size observed for these larger juvenile Chinook salmon from all monitoring efforts has been relatively low, larger sized Chinook salmon have been reported to avoid capture at low stream velocities (Roper and Scarnecchia 2). The lower Yuba River downstream of DPD experiences the lowest flows of the year during the fall months, resulting in relatively low velocities at the Hallwood Boulevard site as compared to the winter and spring months and thus, the actual fraction of the juvenile Chinook salmon population exhibiting an extended rearing strategy may be higher than what was represented from weekly captures as a result of the inherent size selectivity associated with RST sampling during this recent monitoring effort. Furthermore, the relative contribution of these extended rearing strategies on juvenile survivorship and subsequent adult recruitment for juvenile Chinook salmon is largely unknown. A study conducted by CDFG through a USFWS-AFRP grant titled, Yuba River Juvenile Chinook Salmon and Steelhead Trout Life History Study, investigated the relative contribution between these two identified juvenile life history strategies on the lower Yuba River; a fry-dominated exit strategy versus an extended rearing strategy. Native juvenile Chinook salmon were captured via RST, coded-wire tagged and released immediately downstream of the trap from BY23 through BY26. The study tagged and released 68,811 fry and smolt-sized juvenile Chinook salmon to the lower Yuba River. Fourteen of the 68,811 CWT released juvenile Chinook salmon from this project have been recovered to date (Massa et. al 29, 21), two of which were tagged at a larger median fork length (57 mm and 58 mm, respectively). Although these recaptures may represent extended rearing fish, the exact timing of their emigration from the lower Yuba River is unknown. Additionally, both the mark release size (n=68,811) and sample recapture size (n=14) are relatively small, thus robust characterizations from this dataset are difficult to surmise. Results from an ongoing otolith micro-structural study 4 may provide additional information regarding the size, timing and prevalence of extended rearing strategies employed by juvenile salmonids on the lower Yuba River. 4 See Barnett-Johnson, R., Grimes, C.B., Royer, C.F., and Donohoe, C.J. 27. Identifying the contribution of wild and hatchery Chinook salmon (Oncorhynchus tshawytscha) to the ocean fishery using otolith microstructure as natural tags. Canadian Journal of Fisheries and Aquatic Sciences 64: Yuba Accord Annual RST Report July 8, 211