2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River

Transcription

1 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River Prepared for: Yuba County Water Agency 1402 D Street Marysville, CA Contact: Curt Aikens 530/ Prepared by: Jones & Stokes 2600 V Street Sacramento, CA Contact: Bill Mitchell 916/ January 2006

2 Jones & Stokes Fall-run Chinook salmon spawning escapement in the Yuba River. January. (J&S ) Sacramento, CA.

3 Contents Page Executive Summary... 1 Introduction... 1 Methods... 2 Results... 4 River Conditions... 4 Spawning Escapement, Timing, and Distribution... 5 Run Composition... 6 Hatchery Fish... 6 Recovery Rates... 7 Prespawn Mortality... 7 Recent Trends in Abundance... 8 Additional Studies Acknowledgments References Cited Printed References Personal Communications Appendix A Aerial Photographs Appendix B Weekly Population Estimates Appendix C Hatchery Recovery Data 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River i January 2006 J&S

4 Tables and Figures Table Page Yuba River Chinook Salmon Spawning Escapement Estimates by Reach and Age Class Summary of Prespawn Mortality of Females in the Lower Yuba River in Annual Fall-Run Chinook Salmon Spawning Escapement in the Yuba River during Pre ( ) and Post (1972 Present) New Bullards Bar Reservoir Periods Figure Follows Page 1 Lower Yuba River Chinook Salmon Spawning Escapement Survey Reaches Length Frequencies of Chinook Salmon Collected Throughout the 2004 Season Daily Yuba River Flows Measured at the Smartville and Marysville Gauges, September 1 December 20, Mean Daily Yuba River Water Temperatures Measured at Smartville, Parks Bar, Daguerre Point Dam, and Marysville, September 1 December 31, Weekly Counts of Fresh Salmon Carcasses by Survey Reach, Annual Fall-Run Chinook Salmon Spawning Escapement in the Lower Yuba River during Pre- ( ) and Post- ( ) New Bullards Bar Reservoir Periods Annual Hatchery and Natural Spawning Escapement of Sacramento River Chinook Salmon Annual Ocean Landings of Central Valley Chinook Salmon and CVI Harvest Index Fall-Run Chinook Salmon Spawning Escapement in the Yuba River ii January 2006 J&S

5 Executive Summary The Yuba County Water Agency (YCWA) with assistance from Jones & Stokes has performed annual Chinook salmon spawning escapement surveys on the lower Yuba River since Spawning escapement refers to the number of Chinook salmon (Oncorhynchus tshawytscha) that return to the lower Yuba River to spawn each year. Three reaches of the lower Yuba River (Rose Bar, Parks Bar, and Daguerre) downstream of Englebright Dam were surveyed 3 days per week from October 7 to December 22, 2004, by a four-person crew. These surveys also served to recover coded-wire-tagged (CWT) hatchery strays that originated from hatcheries outside the lower Yuba River. The Pacific States Marine Fisheries Commission (PSMFC) provided an additional crewmember to increase the search effort for CWT fish. The 2004 survey resulted in an estimate of 14,586 Chinook salmon. Since 1996, average spawning escapement in the Yuba River ( : 23,454 fish) has been substantially higher than the average for the preceding years ( : 13,809 fish) of the post New Bullards Bar Reservoir period 1. Overall, average spawning escapement for the pre- and post-reservoir periods ( and ) was 12,906 and 16,004 fish, respectively. Additional information obtained from the 2004 survey included timing and distribution of spawning, age and sex composition of spawners, number and origin of tagged hatchery strays recovered, and the percentage of females that died before spawning. Yuba River flows, water temperatures, and turbidity were also monitored during the 2004 spawning season. Introduction Annual surveys of Chinook salmon carcasses have been conducted on the lower Yuba River since 1953 to estimate fall-run Chinook salmon spawning escapement (i.e., the number of salmon that return to spawn each year). DFG conducted annual surveys of Chinook salmon carcasses on the lower Yuba River from 1953 to 1989 but suspended its surveys because of budget cuts. In response, YCWA retained Jones & Stokes in 1991 to conduct the escapement surveys and has continued these surveys each year since. DFG assisted Jones & Stokes from 1992 through Beginning in 2002, additional funding was provided by the California Department of Water Resources (DWR) and the PSMFC to ensure complete examination for tagged hatchery strays. The main objective of these surveys is to estimate annual spawning escapement of fall-run Chinook salmon in the lower Yuba River (downstream of Englebright Dam). Additional information obtained from the surveys includes timing and distribution of spawning, age and sex composition of spawners, number and origin of tagged hatchery strays recovered, and the percentage of females that 1 Spawning escapement during the post-reservoir period (1972-present) includes those runs that coincided with the period of operation of New Bullards Bar Reservoir Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 1 January 2006 J&S

6 died before spawning. Yuba River flows, water temperatures, and turbidity are also monitored during the spawning season. This report presents the results of the 2004 spawning escapement surveys. The results of the surveys were reported in previous documents (Jones & Stokes Associates ). Methods From 1973 to 1989, DFG used a modified form of the Schaefer mark-recovery method to estimate the number of Chinook salmon that spawn each year in the Yuba River (Schaefer 1951). The Schaefer method is a mark-recapture technique designed to estimate the number of fish in a population as a series of distinct units separated by spawning time and location. The sampling methods used during the 2004 spawning escapement surveys on the Yuba River were generally consistent with those used by DFG during past Yuba River surveys with a few modifications. Sampling methods are similar to those used in other Central Valley spawning escapement surveys (Cavallo pers. comm.; Drury pers. comm.). Weekly carcass surveys were conducted during the principal spawning season of fall-run Chinook salmon, from October 7, 2004, to December 22, 2004, in the following reaches (Figure 1): Rose Bar (the downstream end of the Narrows to the State Route [SR] 20 bridge), Parks Bar (SR 20 bridge to Daguerre Point Dam), and Daguerre (Daguerre Point Dam to the Simpson Lane bridge in Marysville). Appendix A presents aerial photos of the lower Yuba River, from Englebright Dam downstream to the confluence with the Feather River, including specific landmarks. The three surveyed reaches include nearly all of the spawning areas used by Chinook salmon in the Yuba River. Spawning may occur between Rose Bar and Englebright Dam, but spawning gravel is scarce in this reach. For many years, DFG did not survey the reach above Parks Bar (Rose Bar Reach). Instead, DFG assumed that 15.5% of the run spawned above Parks Bar. This assumption was based on the average percentage of the total spawning escapement estimated for this reach during the period of (Konnoff pers. comm.). However, most of the surveys conducted since 1994 have revealed that up to 37% of the run spawns in the Rose Bar Reach. DFG s practice on the lower Yuba River was to tag only adult salmon carcasses (age 3 and older) and estimate the number of grilse (age 2) by multiplying the adult estimate by the ratio of fresh grilse carcasses to fresh adult carcasses. This assumes that grilse carcasses are recovered at a rate similar to that of adult carcasses. However, by separating the counts between adults and grilse in recent years, Jones & Stokes found that grilse are often recovered at significantly lower 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 2 January 2006 J&S

7 Englebright Reservoir Parks Bar Smartville Gage 20 Marysville Gage Daguerre Point Dam River Parks Bar Reach Rose Bar Reach Rose Bar Feather 20 Marysville Yuba Daguerre Reach River Simpson Lane (12-05) Miles Figure 1 Lower Yuba River Chinook Salmon Spawning Escapement Survey Reaches

8 rates than adults. Boydstun (1994) also made this observation and suggested that grilse may be more easily overlooked and disappear faster from the stream because of their smaller size. To avoid this potential bias, adults and grilse are recorded separately. This allowed separate estimates of adults and grilse for each reach. Salmon carcasses were classified as adults if they had fork lengths greater than 64.5 centimeters (cm) (25.5 inches) or as grilse if they were less than 64.5 cm long. This cutoff length was determined from previous years classification size. Because the size of Feather River Hatchery salmon may not be truly comparable to Yuba River salmon, future surveys will no longer rely on length-frequency data from Feather River Hatchery salmon. As was discussed in the August 2002 Spawning Escapement Project Working Team (SEPWT) meeting, similar size fish would be expected to have similar recovery rates from year to year; therefore, the break between adult and grilse classification, for field purposes only, can be the same every year. The 64.5-cm size is comparable to the 63 and 66-cm size use in previous years and will be the standard size used for measuring grilse in future years. Survey crews consisted of a boat operator, one to two additional persons in the boat retrieving salmon from deep pools and deep edge waters, and one to two surveyors on foot searching the banks of the lower Yuba River and shallower margins. Gaffs measuring 6 to 8 feet long, and a gig measuring up to 16 feet were used to retrieve and handle the carcasses from both the shore and boat. Carcasses were classified as either fresh or decomposed, based on overall condition. Fresh carcasses had a firm body, at least one clear eye, and pink gills. Decomposed carcasses typically had cloudy eyes, fungus-covered soft bodies, and white gills. Hog rings with colored flagging were clipped to the lower jaw of nearly all the fresh carcasses. Each section of river had a specific color each week, so that each recovered salmon could be identified by the reach and the week in which it was tagged. Carcasses were classified first by size (adult versus grilse) and then by their state of freshness. Fresh adults were further separated by sex (male or female). All fresh carcasses were also examined for the presence of adipose fins. Each carcass with no adipose fin had its fork length recorded and head removed, labeled, and sent to DFG for CWT recovery and decoding. Because in most cases the entire head was removed, these fish could not be tagged, so they were included in the count of decomposed fish. All tagged fish were placed back in the current to simulate the movement of a dying fish that has already spawned. Decomposed fish were first checked for a jaw tag and then counted and chopped using a machete (decomposed carcasses that could not be chopped were tagged with white flagging and treated as a chopped fish). Decomposed carcasses that were found in the water were placed back in the water, and those carcasses found on the banks were left on the banks. Previously tagged fish were counted and chopped and then marked as recovered fish, specifying the color of the tag. Fork lengths were recorded on 110 fresh fish early in the season to create a length-frequency histogram. These data are presented in Figures 2a and 2b Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 3 January 2006 J&S

9 Number of Fish Fork Length (cm) Figure 2a Length Frequencies of Chinook Salmon Collected in the Beginning of the 2004 Season 6 Male Female 5 4 Number of Fish (12-05) Fork Length (cm) Figure 2b Length Frequencies of Males and Females in 2004 Figure 2 Length Frequencies of Chinook Salmon Collected Throughout the 2004 Season

10 Weekly population estimates were calculated based on the proportion of tagged carcasses recovered and the total number of tagged and untagged carcasses observed. Weekly estimates were then added together to obtain the total spawning escapement estimate. Separate population estimates for adult male and female Chinook salmon were not possible because of the difficulty in determining the sex of highly decomposed carcasses (both tagged and untagged) during tag recovery efforts. Therefore, the sex composition of adult salmon was based on the proportion of males and females observed weekly among fresh carcasses. Male and female grilse could not be reliably distinguished by external characteristics (even when fresh), although typically most of the smaller salmon are age 2 males. Streamflows, water temperature, and water clarity were monitored during the spawning escapement surveys to examine the relationship of these variables to spawning timing and distribution. Telemetered daily flow data were obtained from the U.S. Geological Survey (USGS) gage below Englebright Dam near Smartville, California (Station ), and the USGS gage near Marysville, California (Station ). Water temperature was recorded hourly using Onset Optic Stowaway recording thermometers placed near the USGS Smartville gage, at the SR 20 bridge (Parks Bar) crossing, at Daguerre Point Dam, and near the USGS gage near Marysville. Hourly water temperatures were converted to daily averages. Average water clarity was visually estimated each day that the survey was conducted. Results River Conditions Figure 3 presents the daily average Yuba River flows during the 2004 Chinook salmon spawning season. Yuba River flows below Englebright Dam (Smartville gage) ranged from approximately 700 to 1,000 cubic feet per second (cfs) throughout most of the spawning season. Flows near Marysville (Marysville gage) ranged from approximately 500 to 900 cfs throughout most of the season. In the second week of December, flows peaked sharply at approximately 2,200 cfs at Smartville and Marysville in response to storm runoff. Daily water temperatures at Smartville and Parks Bar averaged approximately 55ºF to 56ºF in September and then exhibited a steady decline through December (Figure 4). Daily average water temperatures at Daguerre Point Dam and Marysville ranged from 58ºF to 64ºF in September and then exhibited a steady decline through December (Figure 4). The water was relatively clear during the spawning surveys, with visibility typically averaging 12 feet, making it relatively easy to locate fish in pools Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 4 January 2006 J&S

11 2,500 2,000 Englebright Release Marysville Gage Discharge (cfs) 1,500 1, Sep 5-Sep 9-Sep 13-Sep 17-Sep 21-Sep 25-Sep 29-Sep 3-Oct 7-Oct 11-Oct 15-Oct 19-Oct 23-Oct 27-Oct 31-Oct 4-Nov 8-Nov 12-Nov 16-Nov 20-Nov Survey Date (2004) 24-Nov 28-Nov 2-Dec 6-Dec 10-Dec 14-Dec 18-Dec 22-Dec Figure 3 Daily Yuba River Flows Measured at the Smartville and Marysville Gauges, September 1 December 24, Smartville Parks Bar Daguerre Marysville Water Temperature (F) (12-05) 45 Sep 2 Sep 9 Sep 16 Sep 23 Sep 30 Oct 7 Oct 14 Oct 21 Oct 28 Nov 4 Nov 11 Nov 18 Nov 25 Dec 2 Dec 9 Dec 16 Dec 23 Dec 30 Survey Date (2004) Figure 4 Mean Daily Yuba River Water Temperatures Measured at Smartville, Parks Bar, Daguerre Point Dam, and Marysville, September 1 December 20, 2004

12 Spawning Escapement, Timing, and Distribution An estimated 14,586 Chinook salmon (9,255 adults and 5,331 grilse) spawned in the Yuba River in fall 2004 (Table 1). The spreadsheets used to compute the 2004 spawning escapement estimates are presented in Tables B-1 through B-12 in Appendix B. Table Yuba River Chinook Salmon Spawning Escapement Estimates by Reach and Age Class Survey Reach Adults Grilse Total Percentage of Total Population Rose Bar 2,594 1,219 3, Parks Bar 3,876 1,788 5, Daguerre 2,785 2,324 5, Total 9,255 5,331 14, Percentage of Total Population DFG conducted a redd survey between August 25, 2004, and October 1, 2004 to determine where and when Chinook salmon with spring-run characteristics spawn in the lower Yuba River. Ninety-nine redds were observed. The first redds were observed on September 16, The greatest number of redds were observed from the Narrows pool downstream to the University of California (UC) property (76 redds); 17 redds were observed between the UC property and SR 20; and six redds were observed between SR 20 and Daguerre Point Dam. Redds were constructed in water depths ranging from 0.27 to 1.20 meters (10.6 to 47.2 inches), with a modal depth of 0.60 meters (23.6 inches). Most redds were in glide and riffle habitat. No redds were found in pools, backwater areas or side channel habitat (Massa pers. comm.) It is possible that these early-spawning fish are spring-run Chinook salmon that arrived in the spring and oversummered in the lower Yuba River. In recent years, an automated fish-imaging system operated by DFG in the fish ladders at Daguerre Point Dam has recorded migrating adult salmon during the historical spring-run migration period. However, because of broad spatial and temporal overlap of spring- and fall-run Chinook salmon on the spawning grounds, separate estimates of spawning escapement for these two runs cannot be made. Therefore, estimated spawning escapement includes all Chinook salmon that spawned in fall Chinook salmon typically begin spawning as water temperatures decline below 60ºF. Consequently, spawning activity generally starts and peaks earliest in the Rose Bar reach and latest in the Daguerre Point Dam reach. In 2004, the number of fresh carcasses observed during weekly surveys in the Rose Bar Reach peaked in early November, the Parks Bar Reach peaked from early to mid-november, and the Daguerre Reach peaked in mid-november (Figure 5). It is assumed that spawning occurs approximately 2 weeks before death Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 5 January 2006 J&S

13 Rose Bar Reach Grilse Adults Number of Salmon Number of Salmon Oct 12-Oct 19-Oct 26-Oct 1-Nov 9-Nov 16-Nov 22-Nov 30-Nov 7-Dec 14-Dec Survey Date (2004) Parks Bar Reach Grilse Adults Oct 20-Oct 27-Oct 2-Nov 10-Nov 17-Nov 23-Nov 1-Dec 8-Dec 15-Dec 21-Dec Survey Date (2004) Daguerre Reach Grilse Adults Number of Salmon (12-05) 21-Oct 28-Oct 3-Nov 11-Nov 18-Nov 24-Nov 2-Dec 9-Dec 16-Dec 22-Dec Survey Date (2004) Figure 5 Weekly Counts of Fresh Salmon Carcasses by Survey Reach, 2004

14 The Rose Bar Reach is approximately 3.99 miles long. An estimated 26% of the run (3,813 fish) spawned in the Rose Bar Reach (Table 1); therefore, about 971 fish spawned per mile of river. The Parks Bar Reach is approximately 6.34 miles long. An estimated 39% of the run (5,664 fish) spawned in the Parks Bar Reach (Table 1); therefore, about 892 fish spawned per mile of river. The Daguerre Reach is approximately 9.22 miles long; however, the lower portion of the surveyed reach (generally from the Marysville dump downstream to Simpson Lane) is relatively deep, with fine-grained sediments that are generally unsuitable for spawning. About 6 miles of the surveyed portion of this reach contain spawning habitat. An estimated 35% of the run (5,109 fish) spawned in the Daguerre Reach (Table 1); therefore, about 850 fish spawned per river mile of river. Run Composition Adult male and female salmon composed 45% and 55%, respectively, of the fresh adult carcasses observed during the 2004 surveys. Grilse salmon composed 21% of the total number of fresh carcasses observed and 37% of the total estimated population. The sex of grilse could not be reliably determined in the field, but typically the majority of grilse are male. Hatchery Fish An additional field crewmember was added to the survey team to increase the search effort for adipose fin clipped adults (i.e., hatchery strays). The head of every adipose fin clipped fish observed among fresh carcasses was collected. A missing adipose fin indicates that a CWT was implanted in the fish s head when it was a juvenile. Twenty adipose fin clipped fish were recovered during the fall 2004 surveys. Ten adipose fin clipped fish were recovered from the Rose Bar Reach, six from the Parks Bar Reach, and four from the Daguerre Reach. The majority of these fish were collected early in the season, but they continued to be collected throughout the season. The heads of these fish were sent to the Healdsburg DFG office for tag recovery and identification. The results of the decoding and information retrieval are presented in Appendix C. Of the fresh carcasses sampled, 1.6% was hatchery fish (adipose fin-clipped). Most of these fish originated from the Feather River and Mokelumne River hatcheries. Twenty percent had no coded wire tag. Compared to previous years, the increased effort and consistency this year in recovering and identifying hatchery fish likely improved the accuracy of the estimate of the proportion of adipose fin clipped fish in the total spawning population. However, data are insufficient to estimate the total number of hatchery fish in the lower Yuba River 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 6 January 2006 J&S

15 because not all hatchery fish are tagged before being released and because the percentage of hatchery fish that are released from individual hatcheries varies from year to year. Recovery Rates A total of 951 fresh adult salmon carcasses were tagged during the 2004 season in all three reaches (excludes the fresh fish counted on the final survey date that could not be recovered). The weekly recovery rates of tagged adult salmon carcasses (i.e., the percentage of tagged carcasses that were recovered in subsequent weeks) averaged 46% in the Rose Bar Reach, 51% Parks Bar Reaches, and 29% in the Daguerre Reach, with an overall recovery rate of 43% for all reaches. A total of 334 fresh grilse salmon were tagged during the season in all three reaches. The recovery rates of tagged grilse averaged 24% in the Rose Bar Reach, 35% in the Parks Bar Reach, and 17% in the Daguerre Reach, with an overall recovery rate of 26% for all reaches. (Appendix B.) Prespawn Mortality Each year, some salmon die before they spawn. More than 20% of the female carcasses observed in 1998 and 1999 were determined to be unspawned. Therefore, counts were made of all unspawned females throughout the 2004 season. Unspawned female salmon are bright silver; appear to be healthy (i.e., have no apparent signs of disease, trauma, or physical injury); have fins that are in perfect condition, with no signs of wear; and have bodies that are fat from full gonads. There were no checks to identify fish that were only partially spawned. Approximately 0.8% (4 out of 525) of the adult females checked appeared to have died before spawning in the 2004 season (Table 2). Other rivers had substantially higher prespawn mortality rates in % in the Feather River (Seesholtz pers. comm.) and 31% in the American River (Healy pers. comm.). It is believed that in many cases a high prespawn mortality rate is caused by limited spawning habitat or by high water temperatures. However, neither factor was observed in the lower Yuba River; the cause of prespawn mortality in the Yuba River is unknown Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 7 January 2006 J&S

16 Table 2. Summary of Prespawn Mortality of Females in the Lower Yuba River in 2004 Week of: Adult Female Rose Bar Parks Bar Daguerre Prespawn Mortality % Prespawn Mortality Adult Female Prespawn Mortality % Prespawn Mortality Adult Female Prespawn Mortality 10/ % / % % % Prespawn Mortality 10/ % % % 10/ % % % 11/ % % % 11/ % % % 11/ % % % 11/ % % % 11/ % % % 12/ % % % 12/ % % % 12/ % % Totals % % % Recent Trends in Abundance The Yuba River continues to exhibit high rates of natural salmon production, particularly in view of the absence of a hatchery which contributes substantially to salmon populations in other major Central Valley tributaries (e.g., the Feather and American Rivers) and continued commercial harvest. The historical record of fall-run Chinook salmon spawning escapement in the Yuba River indicates that annual spawning escapement has fluctuated from year to year with no apparent long-term trends, although annual escapement has been higher on average in recent years (Table 3 and Figure 6). Before the operation of New Bullards Bar Reservoir, annual spawning escapement averaged about 12,906 fish. Since New Bullards Bar Reservoir began operating (1972 present), average spawning escapement has been approximately 14% higher (14,749) or 24% higher (16,004) than pre New Bullards Bar Dam levels, depending on the estimates or assumptions used in recent years (see below). Much of this increase in the average is a result of relatively large spawning escapements in recent years (Table 3 and Figure 6). Table 3 has two columns for Post-Reservoir Escapement based on different assumptions or methods used to estimate annual spawning escapement in the years 1994 and In these years, YCWA and Jones & Stokes conducted complete surveys of all major spawning reaches, including the Rose Bar reach. In 1995 and the years prior to 1994, spawning escapement surveys 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 8 January 2006 J&S

17 50,000 Pre New Bullards Bar Reservoir Post New Bullards Bar Reservoir 45,000 40,000 35,000 Number of Salmon 30,000 25,000 20, Average = 12,906 Average = 16,004 a Average = 14,749 b 15,000 10,000 5, No surveys 2004 a Average is calculated from estimates for and 1995 (which assume that 15.5% of the total spawning escapement occurred in the Rose Bar Reach) and estimates for 1994 and (which are based on estimates obtained from actual surveys conducted in the Rose Bar Reach). b Average is calculated from estimates for (which assume that 15.5% of the total spawning escapement occurred in Rose Bar Reach) (12-05) Year LEGEND Estimates based on the assumption that 15.5% of the spawning escapement occurred in the Rose Bar Reach during Estimate based on actual surveys conducted in the Rose Bar Reach. SOURCES: : Hallock (n.d.) : Mills and Fisher (1994) : Jones & Stokes ( ). Figure 6 Annual Fall-Run Chinook Salmon Spawning Escapement in the Lower Yuba River during Pre- ( ) and Post- ( ) New Bullards Bar Reservoir Periods

18 conducted by DFG ( ) and YCWA/Jones & Stokes ( and 1995) were limited to the Parks Bar and Daguerre reaches, and estimates of total spawning escapement were based on the assumption that 15.5% of total escapement spawned in the Rose Bar reach. However, surveys of the Rose Bar reach by YCWA/Jones & Stokes in 1994 and have revealed that this percentage is variable and often substantially higher than 15.5%, ranging from 21% to 38% of the total spawning escapement (because complete surveys of the Rose Bar reach were not possible in 1995, it was again assumed that 15.5% of the run spawned in the Rose Bar reach). In the first column labeled Post-Reservoir Escapement (Table 3), the estimates of annual spawning escapement assume that 15.5% of the total spawning escapement occurred in the Rose Bar reach in every year of the post-reservoir period ( ). In the second column labeled Post-Reservoir Escapement, the and 1995 estimates assume that 15.5% of the total spawning escapement occurred in the Rose Bar reach while the 1994 and estimates are based on complete surveys that included the Rose Bar reach. Although the estimates from complete surveys are more accurate, it can be argued that consistent application of the 15.5% assumption over the entire postreservoir period ( ) improves the comparability of recent escapement estimates to earlier estimates. Regardless of which estimates are used, both records indicate that annual spawning escapement in the Yuba River increased substantially after 1995, and was at or above the historical average in most years from 1996 to the present (Table 3 and Figure 6). Average annual spawning escapement for the period was 49% or 79% higher than the average for the preceding years of the post-reservoir period ( ), depending on which estimates are used. Preliminary estimates of annual fall-run Chinook salmon spawning escapement in the mainstem Sacramento River and its major tributaries (including the Yuba River, which contributed approximately 5% to basin-wide escapement [Duran pers. comm.]) over the last decade indicate a trend similar to that observed in the Yuba River. The overall abundance of returning adults to the Central Valley increased dramatically after 1993, reaching a peak of 775,700 adults in 2002 (Figure 7). (Pacific Fisheries Management Council 2005a). Average annual spawning escapement for the period was nearly twice the historical ( ) average. Increases in basin-wide spawning escapement over the last decade can be explained by an increase in the overall abundance of Central Valley salmon and relatively low harvest rates, as reflected by annual ocean landings and the Central Valley Index (CVI) (Figure 8)(Pacific Fisheries Management Council 2005b. The CVI, which provides an annual index of abundance of all Central Valley Chinook salmon stocks, is the sum of ocean landings of Chinook salmon in the area south of Point Arena and the total Central Valley Chinook salmon spawning escapement. The CVI harvest index, which is an annual index of the ocean harvest rate (the percentage of the total population that is harvested in the ocean), is the ocean landings south of Point Arena divided by the CVI. The CVI harvest index declined significantly from 1995 to 2004, reaching a record low in 2001 (PFMC 2005b). Despite this decline in harvest rate, ocean landings remained at low to moderate levels, indicating an overall increase in the abundance of Central Valley Chinook salmon Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 9 January 2006 J&S

19 800, , , ,000 Hatchery Natural 600, , ,000 Number of Salmon 450, , , , , , , ,000 50, (12-05) Year Source: Pacific Fishery Management Council (2004) Figure 7 Annual Hatchery and Natural Spawning Escapement of Sacramento River Chinook Salmon

20 1,200,000 CVI Harvest Index Ocean Chinook Landings 1,000, Number of Salmon 800, , , CVI Harvest Index (Percent) 200, (12-05) Year Source: Pacific Fishery Management Council (2005) 0 Figure 8 Annual Ocean Landings of Central Valley Chinook Salmon and CVI Harvest Index

21 Table 3. Annual Fall-Run Chinook Salmon Spawning Escapement in the Yuba River during Pre ( ) and Post (1972 Present) New Bullards Bar Reservoir Periods Year Pre-Reservoir Escapement Year Post-Reservoir Escapement (1) Post-Reservoir Escapement (2) , ,258 9, , ,119 24, , ,809 17, , ,641 5, , ,779 3, , ,722 8, , ,416 7, , ,430 12, , ,406 12, , ,025 14, , ,367 39, , ,256 14, , ,965 9, , ,066 13, , ,406 19, , ,510 18, , ,501 8, , ,837 9, , no survey no survey ,413 14, ,361 6, ,516 6, ,022 10, ,561 14, ,482 27, ,720 25, ,225 30, ,463 23, ,162 14, ,540 22, ,930 23, ,318 28, ,733 14,586 Average 12,906 14,749 16,004 Notes: (1) Estimates from assume that 15.5% of the total spawning escapement occurred in the Rose Bar Reach. (2) This column differs from the first column in that estimates from 1994 and are based on estimates obtained from actual surveys conducted in the Rose Bar Reach. As in the first column, estimates from 1972 to 1993 and 1995 assume that 15.5% of the total spawning escapement occurred in the Rose Bar Reach. Sources: : Hallock (n.d.) : Mills and Fisher (1994) 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 10 January 2006 J&S

22 Additional Studies Additional studies being conducted on the lower Yuba River during the spawning escapement surveys included a virology study by the U.S. Fish and Wildlife Service (USFWS); a DNA tissue collection study by DFG; an ongoing Instream Flow Incremental Methodology (IFIM) study by the USFWS; and a juvenile sampling/tagging study conducted by DFG. Crews from the virology study and the DNA study joined the spawning escapement crew to allow them easier access to the river and provide assistance between surveys. The DFG crew clipped fin tissue of both fresh and decomposing carcasses on October 28, 2004 (Rose Bar Reach). The results of their study are not yet available. A crew of two USFWS employees joined the spawning escapement crew on November 16, 2004 (Rose Bar and Parks Bar Reaches) to conduct fish health work to determine the incidence of viruses in natural returning adult salmon. Kidney samples were extracted from carcasses not yet decomposed and tested for infectious hematopoietic necrosis virus (HNV), infectious pancreatic necrosis virus (IPNV), viral hemorrhagic septicemia virus (VHSV), and oncorhynchus masou virus (OMV). Acknowledgments The success of this project would not have been possible without the full support and enthusiasm of the YCWA, and Curt Aikens, or the thoroughness of the field crew. Tom Dixon and Ron McDaniel, both with the YCWA, saved the crew many hours by transferring vehicles from the upstream to the downstream end of the project sites and retrieving water temperature data. The crew was led by 7- year veteran Darin Clark. The PSMFC hired Darin to ensure a more thorough check for hatchery-tagged fish. Joe Bandel and Greg Brown (first season) of YCWA assisted with data collection. Jones & Stokes crewmembers included Jeff Peters (second season), Kamber Zielke (first season) and Stephanie Theis (tenth season). References Cited Printed References Boydstun, L. B Analysis of two mark-recapture methods to estimate the fall Chinook salmon (Oncorhynchus tshawytscha) spawning run in Bogus Creek, California. California Fish and Game 80(1):1 13. Hallock, R. J. n.d. Status of the Sacramento River system salmon resource and escapement goals. California Department of Fish and Game. Red Bluff, CA Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 11 January 2006 J&S

23 Jones & Stokes Associates fall-run Chinook salmon spawning escapement in the Yuba River. June. (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapement in the Yuba River. February. (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA and 1994 fall-run Chinook salmon spawning escapements in the Yuba River. February. (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. July. (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall Chinook salmon spawning escapements in the Yuba River. July. (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. June 12, (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. March 23, (JSA ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. August (J&S ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. June (J&S ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. May (J&S ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA fall-run Chinook salmon spawning escapements in the Yuba River. June (J&S ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA Draft fall-run Chinook salmon spawning escapements in the Yuba River. April (J&S ) Sacramento, CA. Prepared for Yuba County Water Agency, Marysville, CA. Mills, T. J., and F. Fisher Central Valley anadromous sport fish annual run-size, harvest estimates, and population trends, Inland 2004 Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 12 January 2006 J&S

24 Fisheries Technical Report. California Department of Fish and Game. Sacramento, CA. PFMC (Pacific Fisheries Management Council). 2005a. Review of 2004 ocean salmon fishery. Prepared by the Salmon Technical Team. Portland, OR. February p. 31. Available at: < PFMC (Pacific Fisheries Management Council). 2005b. Stock abundance analysis for 2005; ocean salmon fisheries. Prepared by the Salmon Technical Team. Portland, OR. February Available at: < Schaefer, M. B Estimation of size of animal populations by marking experiments. Volume 52. (Fishery Bulletin 69.) U.S. Fish and Wildlife Service. Washington, DC. Personal Communications Cavallo, Brad. Fisheries biologist. California Department of Water Resources, Sacramento, CA. July 18, 2002 handouts given at the Spawning Escapement Project Working Team (SEPWT) meeting. Drury, Ian. Fisheries biologist. California Department of Fish and Game, Rancho Cordova, CA. July 18, 2002 handouts given at the Spawning Escapement Project Working Team (SEPWT) meeting. Duran, Joe. Fisheries Biologist. California Department of Fish and Game and Pacific States Marine Fisheries Commission. March 30, 2003 presentation given at the Spawning Escapement Project Working Team (SEPWT) meeting. Healy, Mike. Fisheries biologist. California Department of Fish and Game, Rancho Cordova, CA. February 24, 2005 presentation given at the Spawning Escapement Workshop. Konnoff, D. L. Fishery biologist. California Department of Fish and Game, Rancho Cordova, CA. January 27, 1988 memorandum to DFG files regarding 1987 Yuba River Chinook salmon spawning stock estimate. Massa, Duane. Fisheries biologist. California Department of Fish and Game, Rancho Cordova, CA. January 19, to Donna Maniscalco regarding 2004 Chinook salmon redd survey. Seesholtz, Alicia. Fisheries biologist. California Department of Water Resources, Sacramento, CA. February 2, to Donna Maniscalco discussing prespawning mortalities Fall-Run Chinook Salmon Spawning Escapement in the Yuba River 13 January 2006 J&S

25 Appendix A Aerial Photographs

26 Engelbright Dam (4/02) Jones & Stokes Aerial View of Yuba River (1 of 16)

27 Downstream End of Narrows (upper boundary of Rose Bar Reach and Project) (4/02) Jones & Stokes Aerial View of Yuba River (2 of 16)

28 UC Davis Property (4/02) Jones & Stokes Aerial View of Yuba River (3 of 16)

29 Highway 20 Bourdary Boundary between Rose Bar & Parks Bar Reaches (4/02) Jones & Stokes Aerial View of Yuba River (4 of 16)

30 00402 (4/02) Jones & Stokes Aerial View of Yuba River (5 of 16)

31 00402 (4/02) Jones & Stokes Aerial View of Yuba River (6 of 16)

32 00402 (4/02) Jones & Stokes Aerial View of Yuba River (7 of 16)

33 00402 (4/02) Jones & Stokes Aerial View of Yuba River (8 of 16)

34 Daguerre Point Dam Boundary between Daguerre and Parks Bar Reaches (4/02) Jones & Stokes Aerial View of Yuba River (9 of 16)

35 00402 (4/02) Jones & Stokes Aerial View of Yuba River (10 of 16)

36 00402 (4/02) Jones & Stokes Aerial View of Yuba River (11 of 16)

37 00402 (4/02) Jones & Stokes Aerial View of Yuba River (12 of 16)

38 00402 (4/02) Jones & Stokes Aerial View of Yuba River (13 of 16)

39 00402 (4/02) Jones & Stokes Aerial View of Yuba River (14 of 16)

40 Simpson Lane Lower Boundary for Daguerre Reach (4/02) Jones & Stokes Aerial View of Yuba River (15 of 16)

41 Highway 70 Feathre Feather River (4/02) Jones & Stokes Aerial View of Yuba River (16 of 16)

42 Appendix B Weekly Population Estimates

43 Table B-1. Weekly Recoveries of Adult Salmon Carcasses in the Rose Bar Reach, 2004 Week of Week of Tagging (i) Tagged Carcasses Total Carcasses Recovery (j) 7-Oct 12-Oct 19-Oct 26-Oct 1-Nov 9-Nov 16-Nov 22-Nov 30-Nov 7-Dec 14-Dec Recovered (Rj) Recovered (Cj) 12-Oct Oct Oct Nov Nov Nov Nov Nov Dec Dec Tagged Carcasses Recovered (Ri) Total Carcasses Tagged (Mi) Ri/Mi Table B-2. Weekly Population Estimates of Adult Salmon in the Rose Bar Reach, 2004 Week of Week of Tagging (i) Recovery (j) 7-Oct 12-Oct 19-Oct 26-Oct 1-Nov 9-Nov 16-Nov 22-Nov 30-Nov 7-Dec 14-Dec Total 12-Oct Oct Oct Nov Nov Nov Nov Nov Dec Dec Jan Total ,879 Adj. Total 2,594

44 Table B-3. Weekly Recoveries of Grilse Salmon Carcasses in the Rose Bar Reach, 2004 Week of Week of Tagging (i) Tagged Carcasses Total Carcasses Recovery (j) 7-Oct 12-Oct 19-Oct 26-Oct 1-Nov 9-Nov 16-Nov 22-Nov 30-Nov 7-Dec 14-Dec Recovered (Rj) Recovered (Cj) 12-Oct Oct Oct Nov Nov Nov Nov Nov Dec Dec Tagged Carcasses Recovered (Ri) Total Carcasses Tagged (Mi) Ri/Mi Table B-4. Weekly Population Estimates of Grilse Salmon in the Rose Bar Reach, 2004 Week of Week of Tagging (i) Recovery (j) 7-Oct 12-Oct 19-Oct 26-Oct 1-Nov 9-Nov 16-Nov 22-Nov 30-Nov 7-Dec 14-Dec Total 12-Oct Oct Oct Nov Nov Nov Nov Nov Dec Dec Total ,322 Adj. Total 1,219

45 Table B-5. Weekly Recoveries of Adult Salmon Carcasses in the Parks Bar Reach, 2004 Week of Week of Tagging (i) Tagged Carcasses Total Carcasses Recovery (j) 13-Oct 20-Oct 27-Oct 2-Nov 10-Nov 17-Nov 23-Nov 1-Dec 8-Dec 15-Dec 21-Dec Recovered (Rj) Recovered (Cj) 20-Oct Oct Nov Nov Nov Nov Dec Dec Dec Dec Tagged Carcasses Recovered (Ri) Total Carcasses Tagged (Mi) Ri/Mi Table B-6. Weekly Population Estimates of Adult Salmon in the Parks Bar Reach, 2004 Week of Week of Tagging (i) Recovery (j) 13-Oct 20-Oct 27-Oct 2-Nov 10-Nov 17-Nov 23-Nov 1-Dec 8-Dec 15-Dec Total 20-Oct Oct Nov Nov Nov Nov Dec Dec Dec Dec Total ,284 Adj. Total 3,876

46 Table B-7. Weekly Recoveries of Grilse Salmon Carcasses in the Parks Bar Reach, 2004 Week of Week of Tagging (i) Tagged Carcasses Total Carcasses Recovery (j) 13-Oct 20-Oct 27-Oct 2-Nov 10-Nov 17-Nov 23-Nov 1-Dec 8-Dec 15-Dec 21-Dec Recovered (Rj) Recovered (Cj) 20-Oct Oct Nov Nov Nov Nov Dec Dec Dec Dec Tagged Carcasses Recovered (Ri) Total Carcasses Tagged (Mi) Ri/Mi Table B-8. Weekly Population Estimates of Grilse Salmon in the Parks Bar Reach, 2004 Week of Week of Tagging (i) Recovery (j) 13-Oct 20-Oct 27-Oct 2-Nov 10-Nov 17-Nov 23-Nov 1-Dec 8-Dec 15-Dec Total 20-Oct Oct Nov Nov Nov Nov Dec Dec Dec Dec Total ,912 Adj. Total 1,788

47 Table B-9. Weekly Recoveries of Adult Salmon Carcasses in the Daguerre Point Reach, 2004 Week of Week of Tagging Tagged Carcasses Total Carcasses Recovery (j) 21-Oct 28-Oct 3-Nov 11-Nov 18-Nov 24-Nov 2-Dec 9-Dec 16-Dec 22-Dec Recovered (Rj) Recovered (Cj) 28-Oct Nov Nov Nov Nov Dec Dec Dec Dec Tagged Carcasses Recovered (Ri) Total Carcasses Tagged (Mi) Ri/Mi Table B-10. Weekly Population Estimates of Adult Salmon in the Daguerre Point Reach, 2004 Week of Week of Tagging Recovery (j) 21-Oct 28-Oct 3-Nov 11-Nov 18-Nov 24-Nov 2-Dec 9-Dec 16-Dec 22-Dec Total 28-Oct Nov Nov Nov Nov Dec Dec Dec Dec Total ,991 Adj. Total 2,785

48 Table B-11. Weekly Recoveries of Grilse Salmon Carcasses in the Daguerre Point Reach, 2004 Week of Week of Tagging Tagged Carcasses Total Carcasses Recovery (j) 21-Oct 28-Oct 3-Nov 11-Nov 18-Nov 24-Nov 2-Dec 9-Dec 16-Dec 22-Dec Recovered (Rj) Recovered (Cj) 28-Oct Nov Nov Nov Nov Dec Dec Dec Dec Tagged Carcasses Recovered (Ri) Total Carcasses Tagged (Mi) Ri/Mi Table B-12. Weekly Population Estimates of Grilse Salmon in the Daguerre Point Reach, 2004 Week of Week of Tagging Recovery (j) 21-Oct 28-Oct 3-Nov 11-Nov 18-Nov 24-Nov 2-Dec 9-Dec 16-Dec Total 28-Oct Nov Nov Nov ,257 1, Nov Dec Dec Dec Dec Jan Total , ,423 Adj. Total 2,324

49 Appendix C Hatchery Recovery Data

50 Appendix C. Hatchery recovery data collected from the Yuba River in 2004 Head Tag Number Reach Fork Length (mm) Sex Recovery Date CWT Code Run Brood Year Hatchery Release Site Stock Name Date Released Number of Tagged Fish Released Number of Untagged Fish Released Responsible Agency ROSE 760 F 19-Oct Fall 2001 Feather R Hatchery Wickland Oil Net Pen Feather River CDWR ROSE 930 M 01-Nov Fall 2001 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG DAGU 940 M 21-Oct No Tag ROSE 840 M 01-Nov No Tag ROSE 635 F 07-Oct Spring 2001 Feather R Hatchery Wickland Oil Net Pen Feather River CDWR PARK 860 F 20-Oct Fall 2001 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG ROSE 762 F 12-Oct Fall 2000 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG PARK 925 M 13-Oct Fall 2000 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG DAGU 910 F 03-Dec Fall 2000 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG DAGU 980 F 24-Nov Fall 2000 Mokelumne R Fish Ins West Sacramento Mokelumne River CDFG ROSE 700 F 09-Nov Fall 2001 Mokelumne R Fish Ins Jersey Pt,san Joaq.r Mokelumne River EBMD ROSE 870 F 09-Nov Fall 2001 Mokelumne R Fish Ins Jersey Pt,san Joaq.r Mokelumne River EBMD ROSE 920 M 09-Nov Fall 2001 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG PARK 675 F 17-Nov No Tag PARK 870 M 15-Dec Fall 2001 Mokelumne R Fish Ins Sherman Isl Op Jersy Mokelumne River FWS DAGU 900 M 16-Dec Fall 2001 Mokelumne R Fish Ins Mokelumne River EBMD ROSE 914 M 12-Oct Fall 2000 Feather R Hatchery Wickland Oil Net Pen Feather River CDFG PARK 830 F 01-Dec No Tag ROSE 750 F 22-Nov Fall 2001 Mokelumne R Fish Ins Sherman Isl Op Jersy Mokelumne River FWS PARK 850 F 17-Nov Fall 2001 Mokelumne R Fish Ins Jersey Pt,san Joaq.r Mokelumne River EBMD