4.0 NEW DEVELOPMENTS IN ANADROMOUS SALMONID LIFE HISTORY CHARACTERIZATIONS

Transcription

1 4.0 NEW DEVELOPMENTS IN ANADROMOUS SALMONID LIFE HISTORY CHARACTERIZATIONS This section provides information on lifestage-specific biological characteristics, temporal and spatial distributions, and flow and water temperature relationships for spring-run and fall-run Chinook salmon and steelhead in the lower Yuba River. It specifically emphasizes recently collected data by the RMT that demonstrate new understanding of the lifestage periodicities and flow and temperature relationships, by contrast to previously reported information. 4.1 CHINOOK SALMON Four principal life history variants of Chinook salmon are recognized in the Central Valley and are named for the timing of their spawning runs: fall-run; late fall-run; winter-run; and springrun. Spring-, fall-, and late fall-runs of Chinook salmon have been reported to occur in the lower Yuba River (Massa and McKibbin 2005). Of these runs, Central Valley spring-run Chinook salmon were listed as threatened under the ESA during 1999, and NMFS reaffirmed the threatened status of this ESU during The Central Valley fall-/late fall-run Chinook salmon ESU (a combination of the fall- and late fall-runs as characterized by NMFS) was included on the Species of Concern List under the ESA in 2004 due to concerns about population size and hatchery influence (NMFS 2009). The lower Yuba River is utilized by two principal phenotypic Chinook salmon runs (i.e., springrun and fall-run). Although late fall-run Chinook salmon populations occur primarily in the Sacramento River (CDFG Website 2007 as cited in RMT 2010b), incidental observations of phenotypic late fall-run Chinook salmon have been reported to occur in the lower Yuba River (D. Massa, CDFG, pers. comm. 2009; M. Tucker, NMFS, pers. comm. 2009). Examination of the 8 years of the available VAKI Riverwatcher data confirms relatively low numbers of Chinook salmon passing upstream of Daguerre Point Dam during January and February (see Chapter 5). However, available information suggests that at least some of these fish, potentially characterized as late fall-run Chinook salmon, may represent strays from the Coleman National Fish Hatchery on Battle Creek 1. For example, six Chinook salmon adults were recovered during the late-winter and early-spring portion of the 2008 escapement surveys with coded-wire tags demonstrating that all six of these fish were late fall-run Chinook salmon from the Coleman National Fish Hatchery (YCWA 2009). Consequently, this Interim Report focuses on spring-run and fall-run Chinook salmon in the lower Yuba River. 4.2 SPRING-RUN CHINOOK SALMON The primary characteristic reported to distinguish spring-run Chinook salmon from the other runs of Chinook salmon is that adult spring-run Chinook salmon enter their natal streams during the spring, and hold in areas downstream of spawning grounds for up to several months prior to 1 The mouth of Battle Creek is located at Sacramento RM 270, while the mouth of the Feather River confluence is located at Sacramento RM 80. Yuba Accord M&E Program 4-1 April 2013

2 spawning (Rutter 1904; Reynolds et al. 1993; both as cited in Yoshiyama et al. 1996). For this Interim Report, the RMT developed representative temporal distributions for specific spring-run Chinook salmon lifestages through review of previously conducted studies, as well as recent and currently ongoing data collection activities of the M&E Program (e.g., Vaki Riverwatcher monitoring, carcass surveys, redd surveys, rotary screw trapping, etc.). The resultant lifestage periodicities encompass the majority of activity for a particular lifestage, and are not intended to be inclusive of every individual in the population. These periodicities represent the RMT s synthesis of the best available data regarding utilization of the lower Yuba River by phenotypic spring-run Chinook salmon. The lifestage-specific periodicities for lower Yuba River spring-run Chinook salmon are summarized in Table 4-1, and are discussed below. Table 4-1. Lifestage-specific periodicities for spring-run Chinook salmon in the lower Yuba River. Lifestage Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Spring-run Chinook Salmon Adult Immigration & Holding Spawning Embryo Incubation Fry Rearing Juvenile Rearing Juvenile Downstream Movement Smolt (Yearling+) Emigration ADULT IMMIGRATION AND HOLDING For the lower Yuba River, adult spring-run Chinook salmon immigration and holding has previously been reported to primarily occur from March through October (Vogel and Marine 1991; YCWA et al. 2007), with upstream migration generally peaking during May (SWRI 2002). For purposes of evaluating water temperature suitability, the RMT (2010b) identified the springrun Chinook salmon adult immigration and holding period as extending from April through August and did not include September, because of cooler water temperature indices for spawning during September which represents an overlapping period of holding and spawning. Previously, it has been reported that spring-run Chinook salmon in the lower Yuba River hold over during the summer in the deep pools and cool water downstream of the Narrows 1 and Narrows 2 powerhouses, or further downstream in the Narrows Reach (CDFG 1991a; SWRCB 2003), where water depths can exceed 40 feet (YCWA et al. 2007). Congregations of adult Chinook salmon (approximately 30 to 100 fish) have been observed in the outlet pool at the base of the Narrows 2 Powerhouse, generally during late August or September when the powerhouse is shut down for maintenance. During this time period, the pool becomes clear enough to see the fish (M. Tucker, NMFS, pers. comm. 2003; S. Onken, YCWA, pers. comm. 2004). While it is Yuba Accord M&E Program 4-2 April 2013

3 difficult to visually distinguish spring-run from fall-run Chinook salmon in this situation, the fact that these fish are congregated this far up the river at this time of year indicates that some of them are likely to be spring-run Chinook salmon (NMFS 2007). Past characterizations of spring-run Chinook salmon distributions from available literature on the lower Yuba River have provided some anecdotal references to behavioral run details (such as migration timing and areas of holding and spawning), but the referenced information has not provided or referenced the basis for these descriptions. Spring-run Chinook salmon have been reported to migrate immediately to areas upstream of the Highway 20 Bridge after entering the lower Yuba River from March through October (Vogel and Marine 1991; YCWA et al. 2007), and then over-summer in deep pools located downstream of the Narrows 1 and 2 powerhouses, or further downstream in the Narrows Reach through the reported spawning period of September through November (CDFG 1991a; SWRCB 2003). The RMT s examination of preliminary data obtained since the VAKI Riverwatcher infrared and videographic sampling system has been operated (2003 present) found variable temporal modalities of Chinook salmon ascending the fish ladders at Daguerre Point Dam. The RMT s 3- year acoustic telemetry study of adult spring-run Chinook salmon tagged downstream of Daguerre Point Dam during the phenotypic adult upstream migration period has provided new information to better understand adult spring-run Chinook salmon temporal and spatial distributions in the lower Yuba River. The results from the Vaki Riverwatcher monitoring, and particularly from the acoustic telemetry study found past characterizations of temporal and spatial distributions to be largely unsupported, as phenotypic adult spring-run Chinook salmon were observed to exhibit a much more diverse pattern of movement, and holding locations in the lower Yuba River were more expansive than has been previously reported. Although some of the acoustically-tagged spring-run Chinook salmon were observed to adhere to other previously reported characterizations, observations from the telemetry study also identified that a large longitudinal extent of the lower Yuba River was occupied by the tagged phenotypic adult spring-run Chinook salmon during immigration and holding periods (Figure 4-1). Figure 4-1 displays all individual fish detections obtained during the mobile tracking surveys conducted from May 2009 until November Also, temporal migrations to areas upstream of Daguerre Point Dam occurred over an extended period of time (Figure 4-2). The tagged phenotypic adult spring-run Chinook salmon in the lower Yuba River actually migrated upstream of Daguerre Point Dam from May through September, and utilized a broad expanse of the lower Yuba River during the summer holding period, including areas as far downstream as Simpson Lane Bridge (i.e., ~RM 3.2), and as far upstream as the area just below Englebright Dam. A longitudinal analysis of acoustic tag detection data indicated that distributions were non-random, and that the tagged spring-run Chinook salmon were selecting locations for holding. Yuba Accord M&E Program 4-3 April 2013

4 New Developments in Anadromous Salmonid Life History Characterizations Englebright Dam Daguerre Point Dam Number of Chinook Salmon Figure 4-1. Spatial distribution of all individual acoustically-tagged adult phenotypic spring-run Chinook salmon (SRCS) detections obtained from the mobile tracking surveys conducted during 2009, 2010 and Marysville Hallwood Daguerre Dry Creek Parks Bar Timbuctoo Narrows Englebright Reach Figure 4-2. Spatial and temporal distribution of all individual acoustically-tagged adult phenotypic spring-run Chinook salmon detected from the mobile tracking surveys conducted during 2009, 2010 and 2011 in the lower Yuba River. Yuba Accord M&E Program 4-4 April 2013

5 The area of the river between Daguerre Point Dam and the Highway 20 Bridge was largely used as a migratory corridor by the tagged adult spring-run Chinook salmon during all 3 years of the study (Figure 4-3). Telemetry data in this area demonstrated relatively brief periods of occupation, characterized by sequential upstream detections as individually-tagged fish migrated through this area. By contrast, frequent and sustained detections were observed from the Highway 20 Bridge upstream to Englebright Dam. Examination of individual detection data indicated that tagged phenotypic adult spring-run Chinook salmon that moved upstream of Daguerre Point Dam had generally passed through the Daguerre Point Dam fish ladders by the end of September during all three years. Acoustic tag detection data were used to discern tagged spring-run Chinook salmon residing in holding areas during June, July and August, and shifting to spawning areas during September into early October. This observation was repeated during all three years of the study, and in all occupied reaches. Telemetry data demonstrated that the majority of tagged phenotypic adult spring-run Chinook salmon that ascended the ladders at Daguerre Point Dam also continued to move farther upstream to the Timbuctoo, Narrows, and Englebright Dam reaches during September, coincident with the initiation of spawning activity. Prolonged occupancy in pool habitats was observed during the summer months from Simpson Lane Bridge (i.e., ~RM 1.8) upstream to Englebright Dam (i.e., ~RM 24). The majority of tagged spring-run Chinook salmon were detected in the plunge pool located immediately downstream of Daguerre Point Dam from the onset of tagging in May/June, through the oversummer holding period as late as September (Figure 4-4) 2. Figure 4-4 displays all individual fish detections obtained during the mobile tracking surveys conducted from May 2009 until November 2011 in the Daguerre Point Dam pool. Periods of occupation in the Daguerre Point Dam pool during the study ranged from 0 to 116 days (additional discussion regarding holding below Daguerre Point Dam is provided in Chapter 5). This observation was consistent for all three years of the study (2009, 2010 and 2011). Only the large pool located in the downstream section of the Narrows Reach (i.e., the Narrows Pool) was occupied for a longer temporal period, and no other area of the river was utilized by a higher proportion of the tagged phenotypic adult spring-run Chinook salmon for an extended temporal period than the Daguerre Point Dam pool. Up to one-half of the tagged phenotypic adult springrun Chinook salmon were located in areas downstream of Daguerre Point Dam during the oversummer holding periods during 2009, 2010 and There are no definitive explanations for this observation, but it is possible that Daguerre Point Dam represented a passage impediment, or that these fish over-summered in the Daguerre Point Dam pool due to suitable habitat conditions available below the dam (e.g., favorable water depths, cover, water temperatures and proximity to spawning gravels). 2 An important consideration is that the majority of the tagged spring-run Chinook salmon were captured and released in the Daguerre Point Dam pool, yet these tagged fish were observed to exhibit an extended period of occupation in this downstream area during the immigration/holding periods. Yuba Accord M&E Program 4-5 April 2013

6 New Developments in Anadromous Salmonid Life History Characterizations N State Route 20 Bridge Daguerre Point Dam (DPD) Miles Figure 4-3. The area (red line) between Daguerre Point Dam and the Highway 20 Bridge in the lower Yuba River was primarily used as a migration corridor by phenotypic adult spring-run Chinook salmon. Figure 4-4. Spatial distribution of all individual acoustically-tagged phenotypic adult spring-run Chinook salmon (SRCS) detections in the Daguerre Point Dam pool obtained from the mobile tracking surveys conducted during 2009, 2010 and Yuba Accord M&E Program 4-6 April 2013

7 NMFS (2007) stated that when high flow conditions occur during winter and spring, adult spring-run Chinook salmon and steelhead can experience difficulty in finding the entrances to the ladders because of the relatively low amount of attraction flows exiting the fish ladders, compared to the magnitude of the sheet-flow spilling over the top of Daguerre Point Dam. In addition, NMFS (2007) stated that the angles of the fish ladder entrance orifices and their proximities to the plunge pool also increase the difficulty for fish to find the entrances to the ladders. It had been previously hypothesized by the RMT that perhaps upstream passage could be associated with either an ascending or descending hydrograph, or that the fish ladders may impede or prohibit passage at high or low flow levels. The RMT examined passage and flow data to evaluate these hypotheses. The daily number of adult Chinook salmon passing upstream of Daguerre Point Dam obtained by the Vaki Riverwatcher system from 2004 through 2011, and mean daily flows at the Marysville Gage 3, are presented for each year in Figures 4-5 and 4-6. Examination of these figures does not reveal any consistent trend or relationship between adult Chinook salmon passage upstream of Daguerre Point Dam and flow rate. Chinook salmon passage was observed over a variety of flow conditions, including ascending or descending flows, as well as during extended periods of stable flows. To further evaluate whether adult Chinook salmon upstream passage through the ladders at Daguerre Point Dam is associated with specific flow levels, daily counts of Chinook salmon and mean daily flows at the Marysville Gage were examined for the 8 survey years combined (Figure 4-7). Overall, adult Chinook salmon were observed passing through the fish ladders at Daguerre Point Dam over a relatively wide range of flows. Although not depicted in Figure 4-7, Chinook salmon passage, although not numerous, was observed at mean daily flows exceeding 10,000 cfs during 2005, 2006, 2010 and 2011, years which can be characterized by relatively high flows during spring into summer. These years also experienced fish passage occurring at flows ranging from about 5,000 to 10,000 cfs (Figure 4-7). Examination of individual years (Figures 4-8 and 4-9) further illustrates that Chinook salmon upstream passage through the ladders at Daguerre Point Dam not only occurs over a wide range of flows but that, at least to some degree, passage occurs during the upstream migration period irrespective of flow rates (over the range of flows examined). In other words, passage occurs at higher flows during wetter years characterized by high flows from spring into summer, and at lower flows during drier years characterized by low flows from spring into summer. Flow thresholds prohibiting passage of Chinook salmon through the ladders at Daguerre Point Dam were not apparent in the data. 3 Flows at the Marysville Gage were used for these analyses because they represent flows passing Daguerre Point Dam, taking into account diversions occurring at or upstream of Daguerre Point Dam. Yuba Accord M&E Program 4-7 April 2013

8 600 10, Chinook salmon = 5,927 fish 2004 Chinook Salmon Passing Daguerre Point Dam Flow 9,000 8,000 No. of Fish ,000 6,000 5,000 4,000 3,000 Marysville Flow (cfs) 100 2,000 1, /1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 3/1 Date ,000 No. of Fish Chinook salmon = 11,374 fish 2005 Chinook Salmon Passing Daguerre Point Dam Flow 9,000 8,000 7,000 6,000 5,000 4,000 3,000 2,000 Marysville Flow (cfs) 50 1,000 No. of Fish /1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 3/1 Chinook salmon = 5,203 fish 2006 Chinook Salmon Passing Daguerre Point Dam Flow 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 Marysville Flow (cfs) 50 2,000 No. of Fish 0 0 3/1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 3/1 Date 10, Chinook Salmon Passing Daguerre Point Dam 9,000 Chinook salmon = 1,394 fish 50 Flow 8,000 7, ,000 6,000 5,000 4,000 3,000 Marysville Flow (cfs) /1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 Date 2,000 1,000 0 Figure 4-5. Daily number of adult Chinook salmon passing upstream of Daguerre Point Dam and mean daily flow (cfs) at the Marysville Gage during 2004 through Yuba Accord M&E Program 4-8 April 2013

9 Chinook salmon = 2,533 fish 2008 Chinook Salmon Passing Daguerre Point Dam 10,000 9,000 8,000 No. of Fish Flow 7,000 6,000 5,000 4,000 3,000 2,000 Marysville Flow (cfs) 20 1,000 No. of Fish No. of Fish /1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 3/ Chinook salmon = 5,378 fish Date 0 0 3/1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 3/1 Chinook salmon = 6,469 fish 2010 Chinook Salmon Passing Daguerre Point Dam Flow 2009 Chinook Salmon Passing Daguerre Point Dam Flow 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 2,000 1,000 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 Marysville Flow (cfs) Marysville Flow (cfs) 100 2,000 1,000 No. of Fish 0 0 3/1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 3/ Chinook salmon = 7,785 fish Date 2011 Chinook Salmon Passing Daguerre Point Dam Flow 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 2,000 1,000 Marysville Flow (cfs) 0 3/1 4/1 5/1 6/1 7/1 8/1 9/1 10/1 11/1 12/1 1/1 2/1 Date 0 Figure 4-6. Daily number of adult Chinook salmon passing upstream of Daguerre Point Dam and mean daily flow (cfs) at the Marysville Gage during 2008 through Yuba Accord M&E Program 4-9 April 2013

10 Chinook Salmon Daily Passage (No. of Fish) ,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 Marysville Mean Daily Flow (cfs) Figure 4-7. Adult Chinook salmon daily passage at Daguerre Point Dam and mean daily flow at the Marysville Gage during 2004 through In addition to documentation that adult Chinook salmon passage through the fish ladders at Daguerre Point Dam occurred over a relatively wide range of flows, on an annual basis most Chinook salmon spawning occurs upstream of Daguerre Point Dam. Chinook salmon carcass observations upstream of Daguerre Point Dam can represent up to 93 percent of the annual escapement (Massa et al. 2009), and redd survey data from 2009 and 2010 indicated that up to 81 percent of Chinook salmon spawning occurs upstream of Daguerre Point Dam (Campos and Massa 2011; 2012). These additional data suggest that adult Chinook salmon immigration at Daguerre Point Dam is not prohibited during upstream migration periods. Yuba Accord M&E Program 4-10 April 2013

11 Chinook Salmon Daily Passage (No. of Fish) Chinook Salmon Daily Passage (No. of Fish) Chinook Salmon Daily Passage (No. of Fish) 0 0 1,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10, ,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10, Chinook Salmon Daily Passage (No. of Fish) ,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 Marysville Mean Daily Flow (cfs) 0 0 1,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 Marysville Mean Daily Flow (cfs) Figure 4-8. Adult Chinook salmon daily passage at Daguerre Point Dam and mean daily flow at the Marysville Gage during 2004, 2005, 2006 and Acoustically-tagged phenotypic adult spring-run Chinook salmon may have over-summered in the Daguerre Point Dam pool due to suitable habitat conditions. Daguerre Point Dam creates a large, deep pool downstream of the dam that provides several habitat attributes reportedly utilized by holding spring-run Chinook salmon. It has been reported that pools selected by spring-run Chinook salmon for summer holding are usually greater than 6 feet in depth and are near available spawning gravels (Moyle 2002). Sato and Moyle (1987) found that the average maximum pool depth for spring-run Chinook salmon holding in Mill Creek was 8.3 feet, and Grimes (1983) found that the average holding pool depth in Deer Creek was 12 feet. Water depths in the Daguerre Point Dam pool estimated from the SRH2D model ranged from 5.9 feet to 15.5 feet during the summer months in , based on modeled flow rasters of 2,000 cfs to 5,000 cfs 4. Average depths varied by modeled year and ranged from an average depth of 10.5 feet in 2009 to 12.6 feet in 2011 (Figure 4-10). All modeled depths were well within the range reportedly utilized by spring-run Chinook salmon during the over-summer holding period for other California streams. 4 The modeled flows were representative of actual flows in the lower Yuba River during the summers of 2009, 2010 and Yuba Accord M&E Program 4-11 April 2013

12 Chinook Salmon Daily Passage (No. of Fish) Chinook Salmon Daily Passage (No. of Fish) Chinook Salmon Daily Passage (No. of Fish) 0 0 1,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10, ,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10, Chinook Salmon Daily Passage (No. of Fish) ,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 Marysville Mean Daily Flow (cfs) 0 0 1,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 Marysville Mean Daily Flow (cfs) Figure 4-9. Adult Chinook salmon daily passage at Daguerre Point Dam and mean daily flow at the Marysville Gage during 2008, 2009, 2010 and Daguerre Point Dam also provides cover in the form of a bubble curtain that extends along the dam s entire 575-foot span (Figure 4-11), and suitable spawning gravels are in direct proximity of the Daguerre Point Dam pool where Chinook salmon have been observed spawning (Campos and Massa 2011). Moyle (2002) reported that adult spring-run Chinook salmon will hold under ledges or bubble curtains created by water plunging into pools, and DesLaurier (1991) found that spring-run Chinook salmon in the Salmon River, California primarily used cover provided by bubble curtains and bedrock ledges. In addition, water temperatures at the Daguerre Point Dam pool ranged from 51 F to 60 F from May through September during 2009, 2010 and 2011 when tagged spring-run Chinook salmon were observed in this area. These temperatures were within the reported suitable range for the spring-run Chinook salmon immigration/holding lifestage (see Chapter 5 for additional discussion). Yuba Accord M&E Program 4-12 April 2013

13 Figure Modeled 2D raster of water depths in the pool located immediately downstream of Daguerre Point Dam on the lower Yuba River. Figure Bubble curtain at the Daguerre Point Dam plunge pool on the lower Yuba River. Yuba Accord M&E Program 4-13 April 2013

14 4.2.2 ADULT SPAWNING For the lower Yuba River, the spring-run Chinook salmon spawning period has been reported to extend from September through November (CDFG 1991a; YCWA et al. 2007). Limited reconnaissance-level redd surveys conducted by CDFG since 2000 during late August and September have detected Chinook salmon redd construction generally beginning during the first or second week of September. Neither CDFG or later surveys conducted by the RMT have detected a bimodal distribution of spawning activities (i.e., a distinct spring-run spawning period followed by a distinct fall-run Chinook salmon spawning period), and instead have detected a slow build-up of redd construction generally starting in early September and continuing into the main fall-run spawning period of October and November. Information regarding spring-run Chinook salmon spawning activity can be inferred from observations of acoustically-tagged fish during 2009, 2010 and Examination of the acoustically-tagged spring-run Chinook salmon data revealed a consistent pattern in fish movement. In general, acoustically-tagged spring-run Chinook salmon exhibited an extended holding period, followed by a rapid movement into upstream areas (upper Timbuctoo Reach, Narrows Reach, and Englebright Reach) during September. Then, a period encompassing approximately one week was observed when fish held at one specific location, followed by rapid downstream movement. The approximate one-week period appeared to be indicative of spawning events, which ended by the first week in October. These observations, combined with early redd detections and initial carcasses appearing in the carcass surveys (see below), suggest that the spring-run Chinook salmon spawning period in the lower Yuba River may be of shorter duration than previously reported, extending from September 1 through mid-october. The earliest spawning, presumed to be spring-run Chinook salmon, has been reported to generally occur in the upper alluvial reaches (i.e., below the Narrows pool) and progressively moving downstream throughout the fall-run Chinook salmon spawning season (NMFS 2007). Spring-run Chinook salmon spawning in the lower Yuba River is believed to occur upstream of Daguerre Point Dam. USFWS (2007) collected data from 168 Chinook salmon redds in the lower Yuba River on September 16-17, 2002 and September 23-26, 2002, considered to be spring-run Chinook salmon redds. The redds were all located above Daguerre Point Dam. During the RMT s pilot redd survey conducted from the fall of 2008 through spring of 2009, the vast majority (i.e., 96%) of fresh Chinook salmon redds constructed by the first week of October 2008, potentially representing spring-run Chinook salmon, were observed upstream of Daguerre Point Dam. Similar distributions were observed during the other two years of redd surveys, when weekly redd surveys were conducted. About 97 and 96% of the fresh Chinook salmon redds constructed by the first week of October were observed upstream of Daguerre Point Dam during 2009 and 2010, respectively. Yuba Accord M&E Program 4-14 April 2013

15 CHINOOK SALMON REDD DISTRIBUTIONS Other than the presumption, supported by acoustically-tagged fish observations, that the earliest (i.e., September to mid-october) spawning fish are spring-run Chinook salmon, there is no definitive manner in which to distinguish between spring-run and fall-run Chinook salmon redds. Therefore, the following discussion addresses Chinook salmon redds, not differentiated by run. Chinook salmon redd surveys were conducted by the RMT during the 2009, 2010 and 2011 spawning seasons. During 2009 and 2010, Chinook salmon redd surveys were conducted approximately weekly on a near-census basis throughout most of the lower Yuba River. Approximately 20.9 mi of the 24 mi of the total length of the lower Yuba River was surveyed during the redd surveys. About 0.7 mi of the lower Yuba River located immediately below the first set of riffles downstream of Deer Creek to the top of Narrows Pool was not surveyed due to rugged and dangerous conditions in the steep canyon known as the Narrows. No surveys were conducted in the 0.4 mi section of river directly upstream of Daguerre Point Dam due to safety concerns of working in close proximity to the dam. Additionally, an approximate 2 mi section of the lower Yuba River from Simpson Lane Bridge to the confluence with the Feather River was not regularly surveyed because redds have not been observed in this area during past surveys. However, this section of the river was surveyed once during peak Chinook salmon spawning to ascertain that this section was not being utilized for spawning. Also, it is important to note that during the 2011 Chinook salmon spawning season, a random sampling method at monthly sampling intervals was implemented, by contrast to near-census weekly sampling during 2009 and 2010 (Refer to RMT M&E Program Protocols and Procedures at CHINOOK SALMON REDD SPATIAL DISTRIBUTIONS During the 2009 and 2010 survey years, over 6,500 redds were counted in the extensive redd surveys of the lower Yuba River. Chinook salmon utilized much of the entire ~21 miles surveyed of the lower Yuba River for spawning, with the exception of the lowermost 3 miles of the river where no spawning was observed. Chinook salmon redd distributions, summarized by month, for the 2009 and 2010 monitoring years are shown in Figures 4-12 and For each month, the central location of all newly constructed redds was identified and depicted in the figures. During both survey years, the highest concentrations of newly constructed redds were initially observed above the Highway 20 Bridge. Chinook salmon redds were found predominantly in the Timbuctoo and Parks Bar reaches during all three years of annual redd surveys (2009, 2010, 2011). Together, these two reaches represented about 67, 74 and 66% of all redds observed each survey year, respectively. Chi square analysis was utilized to determine if the percentage of redds in all reaches were similar among years. The percentage of redds by reach was similar among the first two years of annual redd surveys (2009, 2010) (X 2 = 1.15, P = 0.992, X 2 = 1.15, P = 0.992) and significantly different during the 2011 survey year (X 2 = 28.66, P <0.0001) when different survey methods were used. Yuba Accord M&E Program 4-15 April 2013

16 Figure Monthly Chinook salmon newly-constructed redd distributions in the lower Yuba River from September through December during the 2009 redd survey. The green marker indicates an approximation of the most centrally-located redd of all newly constructed redds (i.e., the redd associated with the smallest accumulated distance to all other redds). Figure Monthly Chinook salmon newly constructed redd distributions in the lower Yuba River from September through December during the 2010 redd survey. Yuba Accord M&E Program 4-16 April 2013

17 The 2009 and 2010 redd surveys were near-census surveys and conducted with the same methodology, and therefore, are directly comparable. Because the 2011 redd survey was not a near-census survey, the results of the 2011 redd survey are not directly comparable to the 2009 and 2010 surveys, with the exception of general spatial distribution of redds. Specifically, Chinook salmon redd locations preferentially occur 3.5 to 4.5 times more often than random chance would predict in Timbuctoo Bend, which is the farthest upstream alluvial geomorphic reach (Pasternack et al. 2013). Redds also occur statistically significantly more often than by random chance in the Parks Bar geomorphic reach, which is located between Highway 20 Bridge and the confluence with Dry Creek (Pasternack et al. 2013). Chinook salmon redds within the Timbuctoo and Parks Bar reaches are highly clustered, with large unoccupied areas in between high density redd locations (Pasternack et al. 2013). Figures 4-14 and 4-15 display abundances of Chinook salmon redds in the entire lower Yuba River and in the Timbuctoo Bend and Parks Bar reaches, respectively, for the 2009 and 2010 redd surveys. Each circle represents the abundance of redds that were observed within 100 linear feet of each other. As demonstrated in the figures, the locations with the highest densities of redd construction in the 2009 survey were generally the same locations with the highest densities of redd construction in the 2010 survey. Chinook salmon redds were found predominantly in the riffle, riffle transition, and run morphological units during all three years of annual redd surveys (2009, 2010, 2011). Together, these three morphological units contained about 79, 73 and 85% of all Chinook salmon redds observed each survey year, respectively. Chi square analysis also was utilized to determine if the percentage of redds in all morphological units were similar among years. The percentage of redds by morphological unit was similar among the first two years of annual redd surveys (2009, 2010) (X 2 = 1.71, P = 0.999, X2 = 1.71, P = 0.999) and significantly different during the 2011 survey year (X 2 = 33.85, P =<0.001) which may represent a sampling artifact. At typical fall flows provided under the Yuba Accord, Chinook salmon spawners avoided lateral bars, point bars, and medial bars (i.e., the edges of islands) (Pasternack et al. 2013). Chinook salmon redd locations for the 2009 and 2010 surveys were analyzed to determine if the observed spawning locations were randomly distributed along the longitudinal profile of the lower Yuba River utilizing protocols developed by Wyrick and Pasternack (2011). Because an equal chance exists of a random point occurring anywhere along the length of the river, a plot of the longitudinal frequency distribution for a random dataset should be approximately uniform. If the observational data exhibits a non-uniform frequency distribution, then an ordered, nonrandom plot demonstrating preferential selection should result (factors influencing Chinook salmon spawning site selection are discussed below under Chinook Salmon Spawning Habitat Suitability and Availability). Yuba Accord M&E Program 4-17 April 2013

18 Figure Chinook salmon redd abundance in the lower Yuba River during the 2009 and 2010 redd surveys. Figure Chinook salmon redd abundance in the Timbuctoo Bend and Parks Bar reaches during the 2009 and 2010 redd surveys. Yuba Accord M&E Program 4-18 April 2013

19 Spatial analysis of Chinook salmon redds during the 2009 and 2010 redd surveys indicated nonrandom distributions within the longitudinal length of lower Yuba River. As demonstrated in Figure 4-16, very similar cumulative longitudinal distributions of Chinook salmon redds were observed during the 2009 and 2010 surveys. The cumulative longitudinal distribution plots exhibit non-uniform distributions, suggesting that selective preference is influencing the locations of Chinook salmon redd construction in the lower Yuba River. In other words, Chinook salmon appear to preferentially select specific sites for redd construction throughout the length of the lower Yuba River. Moreover, these sites appear to have been preferentially selected during both of the survey years. In addition, Figure 4-16 visually suggests a preference by Chinook salmon for spawning in upstream locations until the top of the alluvial valley is reached (Pasternack et al. 2013). Figure Cumulative longitudinal distribution of Chinook salmon redd locations in the lower Yuba River during the 2009 and 2010 redd surveys. CHINOOK SALMON REDD TEMPORAL DISTRIBUTIONS When the cumulative temporal distributions of all Chinook salmon redds for all three survey years are plotted together, similar patterns emerge (Figure 4-17). The temporal distributions of Chinook salmon redds during the 2009 and 2010 survey years are nearly indistinguishable. Despite the use of a different sampling methodology in 2011, a similar cumulative temporal distribution of redds was observed, although shifted about a week later into the season. During all three survey years, 50% of all Chinook salmon spawning activity had been completed by mid- October, and 90% had been completed by mid-november (Figure 4-17). Yuba Accord M&E Program 4-19 April 2013

20 Figures 4-18 through 4-20 show the temporal variation in fresh redds constructed among three general sections of the lower Yuba River. During all three survey years, the proportion of Chinook salmon redds began with the highest concentrations upstream of the Highway 20 Bridge, while the proportion of redds increased in a downstream direction, until the end of November in 2009, and through mid-december in 2010 and Figure Fitted cumulative distribution curves for the number of observed Chinook salmon redds from September through December in the lower Yuba River during the 2009, 2010 and 2011 spawning periods. Figure Stacked histograms of the weekly proportion of Chinook salmon redds in three sections of the lower Yuba River from September through December during the 2009 redd survey. Yuba Accord M&E Program 4-20 April 2013

21 Figure Stacked histograms of the weekly proportion of Chinook salmon redds in three sections of the lower Yuba River from September through December during the 2010 redd survey. Figure Stacked histograms of the weekly proportion of Chinook salmon redds in three sections of the lower Yuba River during the 2011 redd survey 5. 5 Sampling was conducted in randomly selected morphological units at a monthly sampling interval. Yuba Accord M&E Program 4-21 April 2013

22 CHINOOK SALMON SPAWNING HABITAT SUITABILITY AND AVAILABILITY The RMT evaluated Chinook salmon spawning habitat suitability and availability in the lower Yuba River with the use of microhabitat suitability prediction modeling, development of associated reach-specific Chinook salmon spawning WUA-discharge relationships, and a rough estimation of potential carrying capacity for Chinook salmon spawners in the lower Yuba River. Additional potential relationships between Chinook salmon spawning site selection and various physical and biological variables also were investigated to potentially aid in the identification and prediction of suitable Chinook salmon spawning habitat in the lower Yuba River. MICROHABITAT SUITABILITY PREDICTION To evaluate microhabitat suitability prediction for Chinook salmon spawning in the lower Yuba River, it was first necessary to develop the best possible bio-verified microhabitat prediction model for predicting observed Chinook salmon spawning locations with the highest accuracy. Given multiple sets of habitat suitability criteria previously developed for Chinook salmon spawning in the lower Yuba River (i.e., Beak and USFWS) and similar rivers (i.e., the lower Tuolumne River), several bio-verification tests were used to quantitatively compare the alternative sets of criteria. These bio-verification performance tests consisted of: (1) comparing the difference of the mean combined habitat suitability index (CHSI) value for utilized versus available habitat; (2) comparing the Z-values of Mann Whitney U tests of CHSI rankings for utilized versus available habitat among the different habitat suitability criteria (HSC) sources; and (3) comparing the Forage Ratio performance of hydraulic habitat suitability indices (HHSIs) and CHSIs with respect to the ability of each alternate HSC set to best predict utilization and avoidance relative to random chance. Among these, the Mann-Whitney U test and the Forage Ratio test both included quantifying performance beyond 95% confidence. The best performing microhabitat prediction model combined Beak, Inc. (1989) depth and velocity HSCs, a new substrate HSC (S5c) developed by the RMT, and the lower Yuba River 2D modeling suite. Specifically, this model (CHSI S5c) never performed the worst relative to the other HSCs for any bio-verification test, and performed the best at the Forage Ratio tests, which are the most rigorous of the bio-verification tests that were applied. This combination correctly identified 76.5% of Chinook salmon redds observed in the survey as having been constructed in preferred habitat. The CHSI S5c model correctly identified 69.3% of the redds observed in the survey as having been constructed in preferred habitat. For additional discussion, refer to Pasternack et al. (2013). For the 23-31% of the Chinook salmon redds that were not correctly predicted by the CHSI S5c model, one-third of them were within 3 ft (~1 m) of the edge of the preferred habitat, and half of them were within 5 ft of the edge of the preferred habitat for both survey years ( , ). However, given the accuracy of the GPS unit used (~1-m), it is possible that some of these redds actually were in preferred habitat according to the model. It is also possible that conditions changed some since the river was mapped (Timbuctoo Bend in 2006 and most of the rest of the alluvial river in 2008). Yuba Accord M&E Program 4-22 April 2013

23 CHINOOK SALMON SPAWNING HABITAT-DISCHARGE RELATIONSHIPS The best microhabitat prediction model (CHSI S5c) was used to compute weighted usable area (WUA) as a function of discharge (also known as the WUA-discharge relationship) at three spatial scales: (1) the entire lower Yuba River; (2) above Daguerre Point Dam and below Daguerre Point Dam; and (3) by geomorphic reach. The Chinook salmon spawning WUAdischarge relationships calculated with this model showed that a discharge of ~600 cfs yields the highest amount of Chinook salmon spawning habitat (WUA) at all spatial scales. Flows less than 400 cfs or greater than ~880 cfs would noticeably decrease Chinook salmon spawning habitat availability in the lower Yuba River. Riffles are the most used morphological unit for spawning on the lower Yuba River, because they are the channel features that have the best combination of depth, velocity, and substrate as well as the preferred patch size of that combination (see Pasternack et al. 2013). Microhabitat modeling found that as flows increase above ~700 cfs, the velocity on riffles becomes too swift for spawning, resulting in a decrease in habitat quality. While other morphological units (e.g., medial bars, slow glides, and point bars) may transition into the preferred hydraulic range at flows greater than 700 cfs, these units are too small to offset the loss of preferred habitat due to higher velocities in the riffles. Maintaining the landforms preferred for Chinook salmon spawning (riffles, riffle transitions, and runs) during the spawning season (i.e., with flows at ~600 cfs) yields the most high quality spawning habitat throughout the lower Yuba River. From the analyses at both the river segment scale and for above and below Daguerre Point Dam (Figure 4-21), the peak WUA value occurred at 600 cfs. The top of the WUA curve occurs over a relatively narrow range of discharge (~ cfs) compared to the total range of in-channel discharges (0-5,000 cfs). Preferred physical habitat is abundant at 600 cfs and greatly diminished by 3,000 cfs, even though the latter is still within bankfull flow. Figure Chinook salmon spawning WUA-discharge relationships for the entire lower Yuba River (left) and for above and below Daguerre Point Dam (right). Yuba Accord M&E Program 4-23 April 2013

24 A Chinook salmon spawning WUA-discharge relationship also was calculated for each geomorphic reach 6 (Figure 4-22). It should be noted that the reaches have different total wetted areas, which influences the relative magnitude of WUA in each reach. For discharges greater than 1,000 cfs, the Parks Bar and Hallwood reaches have the highest WUA values, while the Marysville Reach has the lowest. The WUA-discharge relationships for the Timbuctoo Bend and Marysville reaches exhibit a strong decline in WUA when flows exceed 1,000 cfs. The WUA-discharge relationships for the Parks Bar, Hallwood, and Daguerre Point Dam reaches show a rapid decline in WUA after flow exceeds 1,000 cfs, but then level off at roughly half of their peak WUA value at flows ranging from about 3,000 to 5,000 cfs. The Dry Creek Reach exhibits the most unusual behavior in WUA-discharge relationship, with a peak in spawning WUA at 600 cfs, a gently declining WUA as flows increase to 3,000 cfs, and then an increase in WUA towards the peak WUA value as flows increase to 5,000 cfs. At 600 cfs, preferred Chinook salmon spawning habitat is on the in-channel bed where there are riffles, runs, and riffle transitions. At 3,000 cfs all of the preferred habitat present at 600 cfs is no longer present, with preferred habitat primarily located on a medial bar, in a secondary channel, and on a small point bar. At 5,000 cfs (i.e., near-bankfull flow on the river) the medial bar is entirely inundated and the flat top of the bar theoretically is providing high quality spawning habitat. The secondary channel has expanded to yield more preferred habitat, but the center of that channel has shifted to represent avoided habitat. Other small bar areas along the periphery are relatively flat and are yielding preferred habitat. Notably, at 5,000 cfs, habitat quality does not exhibit a wide range. Instead, it is either non-habitat (CHSI=0) or highest quality habitat (CHSI>0.8). The Dry Creek Reach gains its uniqueness from its landscape position just upstream of Daguerre Point Dam. Although the dam is relatively small and commonly passes sediment-laden floodwaters, it does have a backwater zone and the fluvial geomorphology is characterized by a dynamic mosaic of bars and channels governed by backwater hydraulics. Geomorphic metrics highlight the uniqueness of the Dry Creek Reach with regard to the availability of suitable hydraulics at near-bankfull flows. This reach has the greatest mean baseflow and bankfull widths at the reach scale in the lower Yuba River (Wyrick and Pasternack 2012). It also has the highest width/depth ratio and the second lowest slope. The weighted mean substrate size is 88 mm. There is nothing unique about the Dry Creek Reach in terms of morphological units. The availability of these conditions is typical upstream of run-of-the-river dams whose sediment storage capacity is filled in. 6 A Chinook salmon spawning WUA-discharge relationship was not developed for the Englebright Dam Reach, because with the exception of the spawning gravels injected by the Corps in 2007 and 2010, the RMT substrate map does not reveal any suitable gravel/cobble in this reach. This is consistent with Chinook salmon redd observations in this reach where all of the redds were located on injected substrate (Campos and Massa 2011b, 2012). Yuba Accord M&E Program 4-24 April 2013

25 Figure Chinook salmon spawning WUA-discharge relationships for the geomorphic reaches of the lower Yuba River. CHINOOK SALMON SPAWNING CARRYING CAPACITY Carrying capacity of a river can be estimated using estimates of suitable habitat area and area of habitat being utilized. At a flow of 600 cfs, the total area of the lower Yuba River with CHSI greater than 0.4 is about 6.6 million ft 2 (~600,000 m 2 ). This area of potentially suitable Chinook salmon spawning habitat is larger than the Chinook salmon spawning WUA index because it is based on the assumption that any given area with a CHSI > 0.4 represents suitable spawning habitat, with no weighting based on the CHSI value. The use of a CHSI > 0.4 as a threshold to distinguish potentially suitable spawning habitat is based upon the extensive bio-verification analyses conducted for the RMT predictive spawning model. While the precise area that an individual Chinook salmon redd requires is not known, the RMT s intensive redd pilot study in 2008 found that the mean Chinook salmon redd size was 59.7 ft 2, which is consistent with the range of values from other published studies. In addition, a nearly equal amount of occupied and unoccupied area within a cluster of observed redds was typically observed (i.e., one redd every Yuba Accord M&E Program 4-25 April 2013

26 119.5 ft 2 ). If one redd was assumed to require an area of ft 2, the lower Yuba River would be able to support up to a maximum of approximately 55,000 redds. The mean Chinook salmon redd size during the RMT s 2009 and 2010 Chinook salmon redd surveys was approximately 67 and 73 ft 2, respectively. Calculating the estimated carrying capacity using twice the largest mean redd size of 73 ft 2 results in an estimation of about 45,000 Chinook salmon redds. ADDITIONAL VARIABLES INFLUENCING CHINOOK SALMON REDD SITE SELECTION In addition to velocity, depth, and substrate characteristics that were used in modeling predicted Chinook salmon spawning habitat as previously discussed, several additional types of physical and biological variables were explored to identify potential relationships with Chinook salmon spawning site selection in the lower Yuba River at various spatial scales. These variables included spawning site persistency and site length, hydraulics, geomorphology, morphological unit size, microhabitat patch size, topographic change, distance from wetted edge, hydraulic convergence, and water temperature. SEGMENT-SCALE SPAWNING SITE PERSISTENCY To determine whether spawning site selection at the segment scale occurs at persistent locations from year-to-year and how long those persistent sites are, the river was divided into equal intervals of a set length and the relation between abundance of redds in each interval was evaluated for the 2009/2010 and 2010/2011 survey years. The persistence analyses revealed that there are persistent sites and there is a characteristic site length. A sensitivity analysis revealed that the correlation in redd counts from year-to-year increased as interval size increased up to a size of 420 (~2 times baseflow width). Thus, 420 is the characteristic site length. Second, there was a strong correlation between the spatial distribution of 2010/2011 redds and the spatial distribution of 2009/2010 redds (r 2 = 0.80) at the characteristic site length of 420. In other words, Chinook salmon spawners return to similar locations in the lower Yuba River from yearto-year. In particular, nine redd clusters each accounted for more than 3% of the total redds in both years. HYDRAULICS AND GEOMORPHOLOGY Hydraulic and geomorphologic variables were analyzed in relation to Chinook salmon spawning site selection, at the reach-scale, and at the morphological unit scale, as discussed below. Reach-Scale Spatial analysis of redd occurrence within the geomorphic reaches revealed significant differences depending on landscape position. During both survey years (2009/2010 and 2010/2011), the highest frequency of Chinook salmon redds occurred in the Timbuctoo and Parks Bar reaches. The abundance of redds in other reaches relative to the area of each reach indicates avoidance at the reach scale. Two factors explain the strong preference for Chinook salmon spawning in the Timbuctoo Bend Reach. First, an individual spawner s instinct to migrate farthest upstream would result in the fish spawning in Timbuctoo Bend, the uppermost alluvial reach in the lower Yuba River. Second, of all alluvial reaches, the Timbuctoo Bend Yuba Accord M&E Program 4-26 April 2013

27 Reach has the lowest water temperature during the peak (early October) of Chinook salmon spawning activity. Additional potential relationships between biological and physical variables were quantitatively explored. Biological variables, including number of redds and Forage Ratio, were correlated with physical variables, which included mean water depth and velocity, bed slope, width:depth ratio, weighted mean substrate size, and bankfull wetted width. Neither biological variable showed a statistically significant, valid correlation with any physical variable. Therefore, at the reach scale, it appears that the strongest factor driving Chinook salmon spawning distribution is simply the instinct to migrate upstream to the uppermost alluvial reach. Morphological Unit-Scale To quantitatively explore geomorphic-biologic relationships at the morphological unit scale, key hydraulic and geomorphic variables (i.e., mean water depth and velocity, or mean substrate size) were extracted at the morphological unit scale and correlated against morphological unit-scale Forage Ratio. However, there were no statistically significant correlations between biological and physical variables at this spatial scale, suggesting that Chinook salmon spawners are selecting some other attribute of the landform related to its topography, or they are going to the preferred morphological units and then selecting more localized physical attributes that are not characteristic of the morphological unit s mean physical state. MORPHOLOGICAL UNIT SIZE In addition, morphological unit size preference by spawning Chinook salmon was evaluated to determine if spawners prefer or avoid any particular size of a morphological unit. Regardless of morphological unit type or survey year, the highest Forage Ratio for all three morphological unit types was the 1, ft 2 size range. Other size ranges appeared to be preferred, but for no obvious reason. The results of this analysis were insufficient to use in better predicting Chinook salmon redd occurrence. MICROHABITAT PATCH SIZE To evaluate the potential relationship between habitat patch size and Chinook salmon spawning preference, the Forage Ratio test was used with different size classes of habitat patches for two different habitat types: (1) highest quality habitat (i.e., CHSI S5c > 0.8); and (2) preferred habitat (i.e., CHSI S5c > 0.4). The results indicate that Chinook salmon spawners preferred smaller patches of highest-quality habitat in proportion to their availability, whereas they preferred larger patches of preferred habitat relative to their availability. The median size of patches that Chinook salmon spawners used was consistently large for preferred habitat (~70,000 ft 2 ) and generally smaller for highest-quality habitat (~16,000 ft 2 ). Overall, habitat patches in the 1,000 to 10,000 ft 2 size range were consistently highly utilized relative to their available area. Other sizes appear to be preferred up to a size limit, 40,000 ft 2 for highest-quality habitat (CHSI S5c > 0.8), and 80,000 ft 2 for preferred habitat (CHSI S5c > 0.4). However, the results of this analysis are insufficient to use in better predicting Chinook salmon redd occurrence in the model. Yuba Accord M&E Program 4-27 April 2013

28 TOPOGRAPHIC CHANGE It has been hypothesized that Chinook salmon spawners have evolved to avoid spawning in areas that erode during floods, especially if the erosion is deeper than redd burial depth, even though spawners are selecting redd sites during non-erosive flows. Therefore, an evaluation was conducted to determine whether the Chinook salmon redd locations during 2009/2010 and 2010/2011 were in areas that have undergone net scour or fill (or experienced no change) over the previous decade. The results of this analysis indicate that Chinook salmon spawners strongly prefer areas that have undergone downcutting. Spawners preferred areas of downcutting five times more than would be expected to occur with random chance, and they preferred areas of non-cohesive bank migration four times more than would be expected with random chance. For both survey years, % of the redds consistently occurred in these types of scour areas. In addition, spawners preferred in-channel fill, which was the only type of fill preferred. Chinook salmon spawners may be attracted to areas that experience scour or fill, possibly because such locations have rejuvenated substrates and suitable hydraulics. In addition, there was a statistically significant Chinook salmon spawning preference for channel scour between 1 and 2 ft of cut (which is within the range of egg burial depths), and a tolerance for a wide range of moderate cut and fill. DISTANCE FROM WETTED EDGE The potential relationship between Chinook adult salmon spawning and proximity to channel bank demonstrated that Chinook salmon spawners do not preferentially choose redd location based on physical proximity to the wetted edge. During the Chinook salmon spawning season, favorable hydraulic conditions are present throughout the wetted channel of the lower Yuba River. HYDRAULIC CONVERGENCE One possible process that could influence spawning site selection is the presence/absence and/or degree of lateral velocity convergence. Because no quantitative methodology of analysis of velocity vectors is currently available, a visual inspection of the nine most heavily used sites by Chinook salmon spawners was conducted. Chinook salmon redds were visually found to be located in all types of lateral flow patterns (i.e., laterally converging, uniform, and diverging) with no apparent preference for a single type. Redds appeared to be equally occurring upstream of, on and downstream of peak velocity locations as well. Therefore, redd occurrence was deemed to not have a systemic selection of a particular pattern of lateral velocity convergence. In other words, if the magnitude of depth and velocity are in the range preferred by Chinook salmon spawners, then they appear to use it regardless of the hydraulic convergence pattern. This result is consistent with the results of Elkins et al. (2007) and other unpublished findings on the lower Mokelumne River. Yuba Accord M&E Program 4-28 April 2013

29 WATER TEMPERATURE As shown in Figures 4-12 and 4-13, as the Chinook salmon spawning season progressed during both the 2009 and 2010 spawning seasons, the number of fresh redds constructed increased in a downstream direction. The RMT hypothesized that the observed trend of initial Chinook salmon redd construction occurring in upstream areas, then moving downstream as the spawning season progressed, may be related to water temperature. To examine this hypothesis, the spatial distribution of newly constructed redds was plotted for each half-month period for 2009 and 2010, combined with the average water temperatures for the days the redd surveys were conducted within the half-month periods, interpolated by river mile from water temperature monitoring recorder data 7. These relationships are demonstrated in Figures 4-23 and As demonstrated in Figures 4-23 and 4-24, Chinook salmon spawning activity appeared to be associated with water temperature. In general, fresh Chinook salmon redds were constructed in areas characterized by relatively cool water temperatures (about 56 F or lower), and these thermally suitable areas extended farther downstream as the spawning season progressed. The relationship between spawning activity (i.e., redd construction) and water temperature was further examined by plotting the number of Chinook salmon redds constructed at one degree F intervals for all Chinook salmon redds observed from September through December of 2009 and 2010 (Figures 4-25 and 4-26). For each date that a fresh Chinook salmon redd was observed, its river mile location (obtained through GPS coordinates taken at the time of redd observation) was used to estimate water temperatures at that location on that date through linear interpolation, as previously described. As demonstrated in Figures 4-25 and 4-26, newly constructed Chinook salmon redds were not observed at temperatures less than 46 F nor were they observed at temperatures higher than 62 F. For the two years of extensive area Chinook salmon redd surveys, approximately 83% of all newly constructed redds were observed at or below the Chinook salmon spawning upper optimal water temperature value of 56 F, and about 97% of all newly constructed redds were observed at or below the upper tolerable water temperature value of 58 F (see Chapter 5 for additional discussion). 7 Water temperature monitoring data were obtained from YCWA. Water temperatures estimated to the nearest 0.1 river mile were calculated via interpolation from 10 monitoring locations distributed throughout the lower Yuba River. Graphic representations include redd observations during surveys that were initiated in one biweekly period, but extended into the next half-month period (e.g., the survey conducted from September 28 through October 1 of 2009). Yuba Accord M&E Program 4-29 April 2013

30 Figure Semi-monthly Chinook salmon redd distributions in the lower Yuba River from September through December during the 2009 redd survey. Water temperatures throughout the lower Yuba River during the time of the redd surveys are depicted. Yuba Accord M&E Program 4-30 April 2013

31 Figure Semi-monthly Chinook salmon redd distributions in the lower Yuba River from September through December during the 2010 redd survey. Water temperatures throughout the lower Yuba River during the time of the redd surveys are depicted. Yuba Accord M&E Program 4-31 April 2013

32 1,200 1, Redd Survey 1, Number of Redds ,200 1, Water Temperature (ºF) 2010 Redd Survey 1, Number of Redds Water Temperature (ºF) Figure The number of newly constructed Chinook salmon redds in the lower Yuba River from September through December during both the 2009 and 2010 redd surveys, and water temperatures at the time and location of the redd observations. 40% 35% 2009 Redd Survey 30% Percentage of Total Redds 25% 20% 15% 10% 5% 0% 40% 35% Water Temperature (ºF) 2010 Redd Survey Percentage of Total Redds 30% 25% 20% 15% 10% 5% 0% Water Temperature (ºF) Figure The percentage of newly constructed Chinook salmon redds at each water temperature value in the lower Yuba River from September through December during both the 2009 and 2010 redd surveys. Yuba Accord M&E Program 4-32 April 2013

33 CHINOOK SALMON SPAWNING TIMING AND CARCASS DISTRIBUTIONS Annual adult Chinook salmon escapement surveys have been conducted on the lower Yuba River since 1953, but without a consistent methodology. Inconsistencies included differing survey reach demarcations, survey durations, and sampling areas. Moreover, models used for escapement estimation (i.e., Peterson, Jolly-Seber, Schaefer) were not consistent among years. Additionally, the lower Yuba River from the Narrows Pool downstream to the Highway 20 Bridge (also referred to as the Blue Point Mine Reach and the Rose Bar Reach) was not surveyed until 1994, and was consistently surveyed only since Recent surveys (1994, ) have been more consistent in both survey duration and area, resulting in more comparable escapement estimates, particularly prior to 2011 when the carcass survey methodology was modified. In an effort to include a more equitable number of years employing consistent data survey techniques, and for the purpose of developing consistent comparisons of Chinook salmon carcass temporal distribution data to time and flow metrics, the following analyses used to represent pre-accord flow conditions, whereas the years 2006, 2008, 2009 and 2010 were used to represent Accord flow conditions. The 2007 adult Chinook salmon escapement was not used in the present analysis because fresh carcasses were not reported by reach that year. Currently, only three Chinook salmon redd surveys (2009, 2010 and 2011) have been conducted in the lower Yuba River. This number of available redd surveys precludes any rigorous study of multi-year trends in the timing of Chinook salmon spawning and their relationships with annual expressions of flows. Therefore, the following sections evaluate potential relationships between annual expressions of lower Yuba River flows and the temporal distribution of fresh carcasses, to infer information regarding the influence of flows on the timing of Chinook salmon spawning from 1999 through For a complete description of analytic methods used in the Chinook salmon carcass analyses see Attachment 4-A. The annual fresh carcass cumulative temporal distributions for the reaches upstream and downstream of Daguerre Point Dam are displayed in Figure 4-27 and Figure 4-28, respectively. Although both figures represent the annual temporal distributions of adult Chinook salmon fresh carcasses first appearing in the carcass surveys, in the subsequent analysis they were used to infer information regarding the temporal distributions of spawning timing. Inspection of Figures 4-27 and 4-28 suggests a time delay of up to approximately two weeks between the timing of fresh carcasses appearing in the surveys in the downstream reach, relative to upstream of Daguerre Point Dam. In general, the annual temporal carcass distributions upstream of Daguerre Point Dam demonstrate that approximately 10% occurred after September 25, and 50% occurred after October 5, while downstream of Daguerre Point Dam approximately 10% of the annual carcass cumulative temporal distribution occurred after October 5, and 50% occurred after October 20. Additionally, the figures indicate that during 2009 and 2010, fresh carcasses appeared in the surveys upstream of Daguerre Point Dam earlier than those occurring during the other years, which suggests that (at least upstream of Daguerre Point Dam) spawning also occurred earlier during 2009 and 2010 than in previous years. Yuba Accord M&E Program 4-33 April 2013

34 Fresh Carcasses Relative Cumulative Proportion Lower Yuba River Chinook Salmon Upstream DPD /1 9/16 10/1 10/16 10/31 11/15 11/30 12/15 12/30 Date Figure Fitted cumulative relative distributions for Chinook salmon fresh carcasses observed upstream of Daguerre Point Dam during 1999 through Fresh Carcasses Relative Cumulative Proportion Lower Yuba River Chinook Salmon Downstream DPD /1 9/16 10/1 10/16 10/31 11/15 11/30 12/15 12/30 Date Figure Fitted cumulative relative distributions for Chinook salmon fresh carcasses observed downstream of Daguerre Point Dam during 1999 through Yuba Accord M&E Program 4-34 April 2013

35 TEMPORAL DISTRIBUTIONS OF CHINOOK SALMON CARCASSES DURING PRE-ACCORD AND ACCORD YEARS The annual cumulative temporal distributions of Chinook salmon fresh carcasses during the pre- Accord years and Accord years (displayed in Figures 4-27 and 4-28, above) were utilized to develop the average fitted distribution for pre-accord years and Accord years, both upstream (Figure 4-29) and downstream (Figure 4-30) of Daguerre Point Dam. Table 4-2 provides the 25 and 50 percentile dates for those average fitted cumulative temporal distributions. Upstream of Daguerre Point Dam, the date when 25% of the cumulative distribution of carcasses occurred is approximately 7 days earlier during the Accord period relative to the pre-accord period. The date when 50% of the cumulative distribution occurred is approximately 11 days earlier during the Accord period relative to the pre-accord period. Downstream of Daguerre Point Dam, the date when 25% of the cumulative distribution of carcasses occurred is approximately 3 days earlier during the Accord period relative to the pre-accord period. The date when 50% of the cumulative distribution occurred is approximately 2 days later during the Accord period relative to the pre-accord period. Overall, Chinook salmon spawning timing in the lower Yuba River, as demonstrated by fresh carcass data, has occurred somewhat earlier (about 1 week) upstream of Daguerre Point Dam during the Accord years relative to the pre-accord years. In addition, downstream of Daguerre Point Dam, the spawning season has expanded by starting slightly earlier and ending slightly later during the Accord years relative to the pre-accord years. CHINOOK SALMON CARCASS TEMPORAL DISTRIBUTION RELATIONSHIPS WITH FLOW In the following section, the series of annual D 25% and D 50% values (i.e., when 25% and 50% of the cumulative temporal distribution of fresh carcasses occur) for fresh Chinook salmon carcass appearance for the reaches upstream and downstream of Daguerre Point Dam were used as dependent variables to assess potential trends in spawning as a function of time and flow. A simple linear regression approach was used to assess potential trends between the series of annual D 25% and D 50% values and time and flow variables. Four sets of regression analyses were conducted, one for each combination of timing metric (i.e., D 25% or D 50% ) and reach (i.e., upstream or downstream of Daguerre Point Dam). Ten explanatory flow variables were used in the regression analyses (see Attachment 4-A). Yuba Accord M&E Program 4-35 April 2013

36 1 Chinook Salmon Carcass Temporal Distribution Upstream of DPD Fresh Carcasses Relative Cumulative Proportion Pre-Accord ( ) Accord (2006, 2008, 2009, 2010) 0 9/1 9/16 10/1 10/16 10/31 11/15 11/30 12/15 12/30 Date Figure Average fitted cumulative temporal distributions of Chinook salmon fresh carcasses observed upstream of Daguerre Point Dam during the pre-accord and Accord years. 1 Chinook Salmon Carcass Temporal Distribution Downstream of DPD Fresh Carcasses Relative Cumulative Proportion Pre-Accord ( ) 0.1 Accord (2006, 2008, 2009, 2010) 0 9/1 9/16 10/1 10/16 10/31 11/15 11/30 12/15 12/30 Date Figure Average fitted cumulative temporal distributions of Chinook salmon fresh carcasses observed downstream of Daguerre Point Dam during the pre-accord and Accord years. Yuba Accord M&E Program 4-36 April 2013

37 Table 4-2. Comparison of the 25 and 50 percentile dates of the Chinook salmon carcass temporal distributions for pre-accord and Accord time periods, both upstream and downstream of Daguerre Point Dam. Period Upstream of Daguerre Point Dam Downstream of Daguerre Point Dam Day 25% Month/Day Day 50% Month/Day Day 25% Month/Day Day 50% Month/Day Pre-Accord 44 10/ / / /8 Accord 37 10/ / / /9 Flow variables did not show any statistically significant correlation with D 25% and D 50% upstream of Daguerre Point Dam. However, downstream of Daguerre Point Dam, three flow variables (AQ D25%, AQ D50% and WQ D25%-14 ) 8 showed statistically significant (P(F) 0.05) linear relationships with the timing response variables D 25% and D 50%. The three statistically significant relationships demonstrate a negative correlation between the flow variable and the timing variable, suggesting that higher flows tend to be associated with earlier occurrences of spawning, as inferred through the appearance of fresh carcasses. Figure 4-31 displays the data and predicted line for the relationship between D 25% and AQ D25%, downstream of Daguerre Point Dam, while Figure 4-32 displays the data and predicted line for the relationship between D 50% and AQ D50%. The predicted linear relationship between D 25% and AQ D25% that explains about 51% of the variability in the data appears to be stronger than the predicted linear relationship between D 50% and AQ D50% that only explains about 39% of its data variability. In both regressions, the data points associated with the year 1999 appeared to drive the statistical significance of the resulting regression lines. The predicted regression lines resulting from fitting the data without the 1999 data points were not statistically significant (P(F) = ) for the relationship between D 25% and AQ D25%, or for the relationship between D 50% and AQ D50% (P(F) = ). However, while the resulting correlations were not statistically significant, they still remained negative. In general, Figures 4-31 and 4-32 suggest that downstream of Daguerre Point Dam, there may be a moderate inverse relationship between the timing of the appearance of fresh carcasses in the survey (and potentially spawning timing) and the average flow conditions during the early to mid-portion of the spawning season. In other words, higher flows tend to be associated with earlier occurrences of spawning, as inferred through the appearance of fresh carcasses. 8 The flow variable expressed as AQ D25% represents the average of daily flows (cfs) measured at the Maryville or Smartsville gages for the period extending from September 1 through the date corresponding to D 25%. The flow variable expressed as AQ D50% represents the average of daily flows (cfs) measured at the Maryville or Smartsville gages for the period extending from September 1 through the date corresponding to D 50%. The flow variable expressed as WQ D25%-14 represents the average of daily flows (cfs) measured at the Maryville or Smartsville gages for the week ending 14 days before the date corresponding to D 25%. Yuba Accord M&E Program 4-37 April 2013

38 /4 11/24 D 25% r 2 = P(F) = /14 11/ / / / ,000 1,200 AQ D25% (cfs) Figure Relationship between the D 25% of the cumulative distribution of fresh Chinook salmon carcasses in the lower Yuba River downstream of Daguerre Point Dam and the corresponding average of mean daily flows (cfs) measured at the Maryville Gage (i.e., AQ D25% ) /4 11/ /14 D 50% 65 11/ r 2 = P(F) = /25 10/ / ,000 1,200 AQ D50% (cfs) Figure Relationship between the D 50% of the cumulative distribution of fresh Chinook salmon carcasses in the lower Yuba River downstream of Daguerre Point Dam and the corresponding average of mean daily flows (cfs) measured at the Maryville gage (i.e., AQ D50% ). Figure 4-33 displays the data and predicted line for the relationship between D 25% and the variable representing the weekly average daily flow (cfs) measured at the Maryville Gage for the week ending 14 days before the date corresponding to D 25% (WQ D25%-14 ), downstream of Daguerre Point Dam. The relationship was statistically significant (P(F) = 0.024) and moderately strong (r 2 = 0.45), explaining approximately 45% of the variability present in the data. The relationship predicts an earlier D 25% with higher average flows for the week ending 14 days before the date corresponding to D 25%. As with the relationships discussed above, the data point associated with the year 1999 drives the statistical significance of the resulting regression line. The exclusion of the 1999 data point resulted in a statistically non-significant regression (P(F) = Yuba Accord M&E Program 4-38 April 2013

39 0.176). Although this regression is not statistically significant, it still predicts an inverse relationship (i.e., a negative correlation) /4 11/24 D 25% r 2 = P(F) = /14 11/ / / / ,000 1,200 WQ D25%-14 (cfs) Figure Relationship between the D 25% of the cumulative distribution of fresh Chinook salmon carcasses in the lower Yuba River downstream of Daguerre Point Dam and corresponding weekly average of mean daily flows (cfs) measured at the Maryville Gage during the week ending 14 days before D 25% (i.e., WQ D25% -14 ). CHINOOK SALMON REDD SUPERIMPOSITION AND FLOW RELATIONSHIPS As a performance indicator of the M&E Program, the RMT identified the need to measure the potential impact of Chinook salmon redd superimposition in the lower Yuba River. Redd superimposition has been reported to occur in salmonids when spawning habitats become limited (Weeber et al. 2010), whether by habitat limitations or high spawner abundance. Redd superimposition can occur when gravel and other substrate particles within a pre-existing redd are excavated and disturbed by the spawning activities of subsequent females (Weeber et al. 2010). Superimposition has been inferred as a major cause of density-dependent embryo mortality through egg displacement (Prenskiy 1990; Chebanov 1991; Fukushima et al. 1998). However, redd superimposition does not necessarily result in egg mortality in the original egg pocket because most superimposing redds are not constructed directly above the pre-existing egg pocket of the original redd (SJRRP 2008). Redd superimposition also has been reported to be the result of beneficial social interactions amongst interbreeding groups (Greene and Guilbault 2008). As an alternative to the negative consequences of pervasive competition for spawning areas, Allee (1938) proposed potential beneficial outcomes for breeding groups that reproduce in low to medium densities. Higher spawning densities may increase the likelihood of finding a mate, lower the risk of predation, and improve the fitness of offspring (Liermann and Hilborn 2001; Reynolds and Gross 1992). Bed mobilization and increased bed roughness as a result of aggregate spawning activity has been demonstrated to reduce algal accumulations and silt deposition on gravel surfaces, thus improving the permeability of the spawning beds and resulting in increased hyporheic flows Yuba Accord M&E Program 4-39 April 2013

40 within individual redds (Peterson and Foote 2000; Moore et al. 2004; Moore 2006). Aggregate or mass spawning may actually improve habitat quality by redistributing, sorting and cleaning spawning gravels (McNeil and Ahnell 1964; Montgomery et al. 1996; Moore et al. 2004; Schuett-Hames 2000). Female brook char and brown trout spawners have actually been found to prefer spawning on existing redd sites disturbed by previous spawning activity (Essington et al. 1998). Mass aggregate spawning in Chinook salmon has been reported to occur in Central Valley rivers (SJRRP 2008). To better understand the potential effects of this observation, Chinook salmon redd spatial data on the lower Yuba River were analyzed for the 2009 and 2010 surveys to determine whether redd superimposition had any potentially measureable disturbance on the egg pocket of previously constructed redds. A stratified sub-sample of Chinook salmon redds for each survey season was more closely investigated to obtain specific measures of pot and tail spill dimensions. These specific redd measurements were used to calculate mean pot and tail spill dimensions for application to the yearly survey data to obtain indicators of superimposition impact 9. Existing literature on redd morphology describes both quantitative and qualitative measures for redd physical attributes such as size of the excavated pot, tail spill deposits and more specifically, the depth at which the egg pocket occurs within a Chinook salmon redd. Evenson (2001) reported the location of the egg pocket to exist at a depth between 22.5 and 26.5 cm (0.74 and 0.87 ft) within the upstream fraction of the tail spill (Figure 4-34). However, quantitative measures of the egg pocket location relative to the external dimensions of a Chinook salmon redd have not been definitively reported. Qualitative information does exist which can help to identify the relative location of the egg pocket and can provide a foundational basis by which to conduct a superimposition analysis using lower Yuba River data. Several studies on salmonid redd characteristics consistently report the egg pocket to occur within the tail spill of salmonid redds (Burner 1951; SWRCB 2007; Weeber et al. 2010). As a female salmonid excavates gravel substrates during spawning, a pit (i.e. redd pot) is created where eggs are laid and subsequently covered by additional gravel excavations. This general location of the egg pocket is illustrated in Figure 4-34, and Figures 4-35 and For more information on the methods used to characterize redd physical measurements, please refer to the specific Protocols and Procedures for Annual Redd Surveys available at Yuba Accord M&E Program 4-40 April 2013

41 Figure Diagrammatic side view of a Chinook salmon redd showing the relative location and mean depth of egg pockets on the Trinity River, CA, as reported in Evenson (2001). Figure Illustrative side view of a salmonid redd showing the location of the egg pocket (pit), as presented in SWRCB (2007). Yuba Accord M&E Program 4-41 April 2013

42 Figure Side-view diagram of the stream substrate at a bull trout redd showing the relative locations of the egg pockets, as reported in Weeber et al. (2010). Burner (1951) provides the most quantitative and useable indication of egg pocket location for several salmonid species including Chinook, silver, chum and sockeye salmon redds on the Columbia River and its tributaries. The author measured the daily progression of redd construction for fall-run Chinook salmon including redd depth (i.e. pot depth) and the longitudinal upstream construction of an individual redd over a period of 18 days, noting both the behavior and presence of male and female salmon during the study. The relative location of the pot and tail spill was observed to change during the course of redd construction. The author found that the completed redd dimensions were quite different than during the original days of construction, as the final location of the mounded tail spill was often situated where the pot had been originally constructed several days to weeks prior. Of note, Burner (1951) did not consider the long tapering downstream slope of the tail spill to be an essential part of the collected redd measurements as, live eggs were rarely found there. Additionally, he found that encroachment along the elongated slope of the tail spill by neighboring redds did not endanger the eggs laid in the original redd. These key points serve to further clarify the actual location of the egg pocket. Burner (1951) provided the following scaled diagrammatic view of a representative redd observed during the study (Figure 4-37). Yuba Accord M&E Program 4-42 April 2013

43 Figure Diagrammatic view of a fall-run Chinook salmon redd measured daily, from Burner (1951) as reproduced by Gallagher et al. (2007). Analysis of the scaled dimensions provided in Figure 4-37 indicates the egg pocket to be contained within the downstream portion of the pot. Specifically, the egg pocket begins at roughly ½ the total excavated pot length and continues downstream for approximately six feet. Field measurements collected on the lower Yuba River in 2009 and 2010 measured only the visible pot length; this is an important difference in measurement convention, with implications on how redd superimposition was measured utilizing data from the 2009 and 2010 surveys. Lower Yuba River Chinook salmon redd measurement conventions were overlaid with Burner s (1951) diagram to better understand how potential redd superimposition impact can be evaluated (Figure 4-38). Redd measurements collected on the lower Yuba River were collected using the visible pot and tail spill dimensions during weekly surveys. Of particular note is that the visible pot length measured during the 2009 and 2010 redd surveys represents roughly half of the total pot excavations present in Burner s (1951) diagram. This difference in measurement convention was reflected in lower Yuba River redd dimensional data which indicated that pot length measurements collected during the 2009 and 2010 surveys were approximately one-half the distance reported in Burner (1951). The mean pot length recorded in 2010 was 1.8 meters, or 5.9 feet. This distance closely approximates ½ the total excavated pot length of 12 feet as reported in Burner (1951) and provides additional justification to utilize the appropriately scaled pot lengths measured on the lower Yuba River to better approximate the location of the egg pocket using data from the 2009 and 2010 surveys. Yuba Accord M&E Program 4-43 April 2013

44 Pot Length Tail Spill Length Figure Diagrammatic view of a fall-run Chinook salmon redd measured daily, demonstrating the representative pot and tail spill polygons (in red) using actual lower Yuba River redd measurement conventions. Note that lower Yuba River redd measurements were taken of only the visible pot length resulting in a measureable truncation of total pot dimensions. To develop a relative indicator of Chinook salmon redd superimposition impact, the following methods were applied to lower Yuba River redd data. In order to better represent the actual pot excavations of spawning female Chinook salmon from the 2009 and 2010 surveys, the mean recorded pot lengths were increased by a factor of two and used with the original mean pot width measurements to construct an ellipse that was representative of the total pot dimensions for each redd observed (Figure 4-39). A tail spill ellipse was then drawn using the mean length and width measurements recorded during the two-year study. Tail spill ellipses were drawn directly downstream of the recorded redd location at a downstream distance equaling the original pot measurements. This provided a measureable overlap in pot and tail spill ellipses using known redd dimensional elements from Burner (1951) which were found to closely approximate lower Yuba River redd physical measurements. Both pot and tail spill ellipses were oriented according to flow vectors calculated at base flow using the RMT s SRH-2D flow model. The location of the egg pocket was then defined as the area of overlap between the pot and tail spill ellipses (Figure 4-40). Yuba Accord M&E Program 4-44 April 2013

45 Mean Pot Length Mean Pot Length 2 Figure Diagrammatic view of the total calculated pot ellipse. Flow Vector Tail Spill Ellipse Recorded Redd Position Tail Spill Ellipse Drawn at Original Pot Length Measurement Egg Pocket Pot Ellipse Figure Conceptual view of the pot and tail spill ellipses used to indicate the relative location of the egg pocket. Using known redd physical attribute data from Burner (1951), we can demonstrate that this conceptual model identifies the location of the egg pocket reasonably well. The resulting pot and tail spill ellipses overlap to create a representative egg pocket area that closely approximates the reported location of Chinook salmon ova (Figure 4-41). Yuba Accord M&E Program 4-45 April 2013

46 Recorded Redd Position Egg Pocket Figure Conceptual view of the pot and tail spill ellipses, demonstrating the relative ability of the conceptual model to identify the location of the egg pocket as identified from Burner (1951). In order to estimate Chinook salmon redd superimposition, a relative indicator of impact was developed using the model results. Because the tail spill superimposition on existing redds has not been reported to result in any noticeable impact to egg development (Burner 1951), focus was placed on the relative superimposition of the redd pot over modeled egg pocket locations. Thus, the overlap of a neighboring redd s tail spill on existing egg pockets was not used as a relative indicator of Chinook salmon redd superimposition impact. Rather, superimposition impact was measured only for those areas where the pot ellipse from a neighboring redd overlapped the modeled egg pocket polygon of a pre-existing redd (Figure 4-42). Additionally, areas of pot excavation resulting in the overlap of a pre-existing redd pot and/or tail spill ellipses outside of the egg pocket were not identified as having an impact to incubating eggs. As an indicator of redd superimposition impact, the area of overlap of adjacent redd pot ellipses on modeled egg pocket locations were measured in ArcGIS for each strata and an index was developed to better understand the actual potential for egg pocket disturbance relative to the number of Chinook salmon redds observed for each survey year. Using this method, we can infer that index values ranging from 0-1 can represent varying degrees of increasing potential for redd superimposition impact, with values approximating zero representing a low potential for redd superimposition impact. Yuba Accord M&E Program 4-46 April 2013

47 Pot Ellipse No Impact Egg Pocket Indicator of Superimposition Impact Tail Spill Ellipse No Impact Adjacent Pot Ellipse Figure Conceptual view of the pot and tail spill ellipses, demonstrating how Chinook salmon redd superimposition impact indicators were defined. The index of potential superimposition impact was calculated as:, where is the total number of redds demonstrating a measurable degree of superimposition. is the total number of redds observed during the survey season. is the average measure of overlap for redds exhibiting superimposition. This analytical approach identified that cumulative superimposition impact indices were quite low, with indices ranging from zero to a maximum of 0.13 (Table 4-3). This result was not surprising, given that a relatively small fraction (29.6%) of the 6,344 combined total redds observed during the 2009 and 2010 surveys demonstrated a measureable level of superimposition, and that for these redds the actual calculated overlap by adjacent pot ellipses on identified egg pocket polygons ranged widely between 0.002% and 100%, with a mean overlap of 41.4% ± 2.1% (95% CI). These relatively small overlapping areas contributed to the low index values calculated from the 2009 and 2010 surveys on the lower Yuba River, and suggest that redd superimposition appears to have a low potential for impact to incubating eggs via encroachment to the egg pocket by adjacent redd pots. Yuba Accord M&E Program 4-47 April 2013

48 Table 4-3. Weekly observed Chinook salmon redds, number of redds with measureable egg pocket ellipse overlap, average egg pocket ellipse overlap, and index of redd superimposition impact in the surveyed reaches of the lower Yuba River during 2009 and Shaded areas represent surveys that were incomplete or suspended due to high flows and/or turbidity. Survey Week Total Redds Observed Redds w ith Egg Pocket Overlap Average Egg Pocket Overlap Index of Supe rim position Im p act 9/7/ /14/ /21/ /28/ /5/ /12/ /19/ /26/ /2/ /9/ /16/ /23/ /30/ /7/ /14/ /21/ /28/ /13/ /20/ /27/ /4/ /11/ /18/ /25/ /1/ /8/ /15/ /22/ /29/ /6/ /13/ /20/ /27/ Chinook salmon redd superimposition on the lower Yuba River appears to have a small relative potential effect on the total number of observed redds for any given spawning season. The lower Yuba River exhibits non-random redd distributions, characterized by dense spawning aggregations generally congregated within the uppermost alluvial reaches of the river. The potential for beneficial effects associated with aggregate spawning (e.g. lower risk of predation for emerging alevins, reduced algae and silt accumulation on spawning beds, higher hyporheic flows associated with increased bed permeability) as described in Greene and Guilbault (2008) may help to understand why lower Yuba River Chinook salmon engage in aggregate spawning to some degree. Some salmonid species have been found to preferentially spawn near existing redds, and that factors other than fish density and habitat availability determine redd location selection (Essington et al. 1998). Although this study cannot directly demonstrate beneficial effects associated with aggregate Chinook salmon spawning in the lower Yuba River, it is clear that potential adverse impacts to Chinook salmon redds incurred by superimposition appear to be minimal. Yuba Accord M&E Program 4-48 April 2013

49 4.2.3 EMBRYO INCUBATION The spring-run Chinook salmon embryo incubation period encompasses the time period from egg deposition through hatching, as well as the additional time while alevins remain in the gravel while absorbing their yolk sacs prior to emergence. The length of time for spring-run Chinook salmon embryos to develop depends largely on water temperatures. In well-oxygenated intragravel environs where water temperatures range from about 41 to 55.4 F embryos hatch in 40 to 60 days and remain in the gravel as alevins for another 4 to 6 weeks, usually after the yolk sac is fully absorbed (NMFS 2009b). In Butte and Big Chico creeks, emergence occurs from November through January, and in the colder waters of Mill and Deer creeks, emergence typically occurs from January through as late as May (Moyle 2002). In the lower Yuba River, the RMT (2010b) initially concluded that the phenotypic spring-run Chinook salmon embryo incubation period generally extends from September through February. However, based upon recent evaluation of acoustically-tagged phenotypic spring-run Chinook salmon adults and the indicated reduced duration of the spawning period (September to mid- October), the RMT further examined the periodicity of embryo incubation. The RMT estimated the duration of spring-run Chinook salmon embryo incubation based on water temperatures monitored in the lower Yuba River, expressed as accumulated thermal units (ATUs). An ATU is a unit of measurement used to describe the cumulative effect of water temperature over time. One ATU is defined as degrees Fahrenheit above freezing, accumulated during a 24-hour period (Piper et al as cited in Armour 1991). ATUs have been used to measure and track the development of incubating salmonid eggs in laboratory and field studies throughout the Pacific Northwest. CDFG (1998) states in A status review of spring-run Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento River drainage (1998) that the required number of ATUs from the time of egg fertilization to fry emergence is 1550 F ATU (Armour 1991). As stated in Armour (1991), development from fertilization to hatching requires 850 ATUs, and an additional 700 units are required from hatching to beginning of fry emergence. Thus, to evaluate the duration of embryo incubation to fry emergence in the lower Yuba River, it was assumed that 1,550 Fahrenheit ATUs (CDFG 1998) were required from egg fertilization to fry emergence. Accumulated thermal units were calculated using mean daily temperatures as reported at the USGS Smartsville Gage for available years and appropriate months of data (2002 through 2011). Applied to the end of the spring-run Chinook salmon spawning period (early to mid-october), spring-run Chinook salmon embryo incubation can be generally characterized as extending through December. Thus, the estimated embryo incubation period for phenotypic spring-run Chinook salmon generally extends from September through December in the lower Yuba River. Review of the available water temperature monitoring data at the Smartsville Gage during the phenotypic spring-run Chinook salmon spawning and potential embryo incubation periods demonstrated that four years of data ( ) were available to represent pre-accord conditions, and five years of data (2006, 2007, ) were available to represent Accord Yuba Accord M&E Program 4-49 April 2013

50 conditions. Application of the requirement of 1,550 ATUs from egg fertilization to fry emergence at the end of the spring-run Chinook salmon spawning period (early to mid-october) results in the spring-run Chinook salmon embryo incubation period extending approximately one week later under the Accord, relative to pre-accord conditions. In other words, the accumulation of 1,550 ATUs during the estimated phenotypic spring-run Chinook embryo incubation period takes approximately one week longer under the Accord years, relative to pre-accord years CHINOOK SALMON JUVENILE REARING Past studies on the lower Yuba River have provided baseline biological data and important insights into suitable methods for characterizing juvenile salmonid habitat occurrence. Beak Consultants, under contract with CDFW, conducted juvenile salmonid habitat utilization surveys during (Beak 1989), Kozlowski (2004) reports information on snorkel surveys conducted during 2000, and SWRI et al. (2000) reported on juvenile salmonid habitat utilization surveys conducted from 1992 through More recently, Gard (2008) reported results of snorkel surveys conducted during in the lower Yuba River, although the objective of those surveys was to obtain microhabitat utilization criteria. However, considerable amounts of time have passed since the previous surveys were conducted, each of these studies utilized differing reach delineations and specific habitat unit characterizations, and information available from previously conducted studies does not coincide with the time period since implementation of the Yuba Accord. Fish diversity and habitat occurrence have been related to channel form, but previous aquatic ecology research has not thoroughly described channel types, nor used consistent objective methods for delineating them. Methods for classifying channel areas based on morphologic and hydraulic metrics have developed rapidly in recent years (e.g. Emery et al. 2003; Clifford et al. 2005; Moir and Pasternack 2008; Pasternack 2008). Recent research suggests that juvenile fish diversity and habitat occurrence are weakly related to longitudinally distributed features (i.e. riffles, runs, glides, pools, etc.), and strongly related to laterally distributed features (i.e., backwaters, vegetated margins, boulder-strewn margins, lateral alluvial bars, mid-channel chutes, etc.). If the suggested relationship of juvenile fish diversity to laterally distributed features is correct, then the conventional use of longitudinally distributed features as the foundation for stratifying the sampling of mesohabitats for snorkel surveys may be inappropriate. The significance of longitudinally distributed and laterally distributed mesohabitats on habitat use by juvenile salmonids was investigated by Beechie et al. (2005) on a large river in the North Cascades of Washington. They found that the highest densities of juvenile Chinook and coho salmon were in bank and backwater units in winter. Steelhead densities were highest in bank units in winter. Thus, juvenile salmonids were found to select particular mesohabitats among the diversity of those which were laterally distributed. Further, Beechie et al. (2005) expressed doubt that juveniles would make use of longitudinally distributed mesohabitats, such as glides, riffles, runs, and pools. In the lower Yuba River, Gard (2008) found that out of the 468 locations where young-of-the-year (YOY) Chinook salmon (and steelhead/rainbow trout) were observed, Yuba Accord M&E Program 4-50 April 2013

51 all but 8 (i.e., 98.3%) occurred near the banks of the river. This finding further suggests that sampling of juvenile salmonids in the lower Yuba River should be stratified according to laterally distributed habitats, rather than longitudinally stratified habitats. JUVENILE CHINOOK SALMON HABITAT USE Rotary screw trap (RST) data suggest that the lower Yuba River possesses a rich juvenile fish fauna comprised of both native and non-native taxa and which is dominated by juvenile Chinook salmon. In addition, RST data suggest that juvenile Chinook salmon primarily emigrate from the lower Yuba River at sizes <50mm fork length (as described in the following section of this chapter). Anecdotal reports from multiple stakeholders on the lower Yuba River suggest that juvenile fishes are present in the river throughout the year. However, few data were available pertaining to juvenile habitat use on the lower Yuba River. To better understand juvenile habitat use in the lower Yuba River, a series of habitat use surveys employing snorkel methods were conducted to assess juvenile fish communities, the timing of juvenile fish presence in the river, and the areas used by juvenile fishes. Snorkel surveys were performed in seven reaches along the lower Yuba River (Figure 4-43) during January, February, March, June, and September of Figure RMT juvenile snorkeling survey site locations on the lower Yuba River. The RMT s juvenile fish snorkel survey observed a total of eight fish species among all of the survey periods throughout the surveyed reaches. General flows and water temperatures for each snorkel period are provided in Table 4-4. Chinook salmon were the most frequently observed positively identified species, followed by Sacramento pikeminnow, and Sacramento sucker. Juvenile fishes occupied a number of different morphological units throughout the survey. Although the majority of observations occurred in morphological units that are typically wet at Yuba Accord M&E Program 4-51 April 2013

52 baseflow, a number of observations did occur in morphological units that were inundated at higher flows (e.g., lateral bars). Juvenile Chinook salmon occurred primarily in lateral bar, slackwater, slow glide, and riffle transition morphological units. Additional anlyses and discussion of the fish community and other species observed besides Chinook salmon are provided in Chapter 5. Table 4-4. Ranges of mean daily flows and water temperatures during each survey period from the Smartsville Gage (flow and temperature) and the Marysville Gage (flow). Temperature Mean Daily Flow Mean Daily Flow Survey Period 0 F Above DPD (CFS) Below DPD (CFS) January February March June September SPATIAL AND TEMPORAL DISTRIBUTIONS To assess major trends in spatial patterns of juvenile Chinook salmon abundances in the lower Yuba River, the average density observed was calculated for each surveyed reach. A series of sub-sample polygons was created by clipping the 880/530 cfs (i.e., baseflow) flow polygon by the boundaries of each reach, and dividing each reach polygon into five sub-sample polygons. ArcGIS was used to assign each fish observation to a sub-sample polygon based on either presence in the polygon or proximity to the polygon, if the observation occurred on the outside edge of the polygon. Densities of juvenile Chinook salmon were calculated by dividing the total number of individuals in each sub-plot by the area of the sub-plot. ANOVA was used to compare densities among reaches, with sub-plots as replicates. To assess major trends in temporal patterns of juvenile Chinook salmon abundances, monthly densities per reach were calculated using ArcGIS to assign each observation to a major reach, and dividing the total number of observations per reach per month by the area of the reach. ANOVA was used to compare among sample periods, with reaches as replicates. The density of juvenile Chinook salmon was highly variable throughout the lower Yuba River. Observations indicated that, with the exception of the upstream-most survey reach (i.e., Englebright Dam Reach) the density of juvenile Chinook salmon generally was higher in the survey reaches located upstream rather than downstream of Daguerre Point Dam. However, there was no statistically significant difference in the mean density of observed juvenile Chinook salmon among reaches (ANOVA, F 6,25 = 1.09, P = 0.398, Figure 4-44). Lower densities were observed in the Englebright Dam and Daguerre Point Dam reaches, and higher densities were observed in the Timbuctoo Bend and Dry Creek reaches. Yuba Accord M&E Program 4-52 April 2013

53 Figure Observed densities of juvenile Chinook salmon across all survey reaches. The densities of Chinook salmon observations by survey month are shown in Figure 4-45, with significantly higher density during March than during January, June, and September (ANOVA, F 4,30 = 7.87, P < 0.001). A peak in juvenile Chinook salmon abundance was observed during March (of 2012). This observation is supported in part from RST surveys in the lower Yuba River from , which identified peak emigration timing for juvenile Chinook salmon to occur from January through March (see Juvenile Emigration, below). Fewer juvenile Chinook salmon were observed during January and February, with the lowest densities recorded during the June and September surveys. Emigration from the lower Yuba River may account for the decline in observed abundance of juvenile Chinook salmon as the survey months progressed. Figure Observed densities of juvenile Chinook salmon during each survey month. Months sharing the same letter(s) indicate that densities were not significantly different. Yuba Accord M&E Program 4-53 April 2013

54 Distance from Shore To evaluate the location of observed juvenile Chinook salmon in relation to distance from shore, juvenile Chinook salmon observations were overlaid with the 880/530 cfs baseflow polygon in ArcGIS. The 880/530 cfs baseflow polygon did not encompass all juvenile Chinook salmon observations, potentially due to subtle shifts in the shape of the river since the creation of the polygon, and because observations recorded during June and September were collected at flows exceeding those of the baseflow polygon. Therefore, observations which were located outside of the baseflow polygon were removed from any further analyses. Distances between observations and the shoreline were measured in feet for each observation. The mean distance from shore was calculated by season, site, and by 20 mm size class using ANOVA with individual distances for each observation as replicates. Because the distance data violated the assumptions of normality, a log 10 transformation was applied to all distance data. When compared across sample reaches (Figure 4-46), juvenile Chinook salmon were observed further from shore in the Marysville survey reach than in other reaches (ANOVA F 6,4864 = 70.57, P < 0.001). When compared across sample months (Figure 4-47), juvenile Chinook salmon were generally located further from shore as the year progressed (ANVOA F 4,4866 = 24.39, P < 0.001). Chinook salmon juveniles exhibited a similar pattern of observations farther from shore as they grew in size (Figure 4-48), although individuals in the mm size class were observed closer to shore than smaller or larger size classes (ANOVA F 3,4867 = 60.69, P < 0.001). Figure The mean distance from shore of observations of juvenile Chinook salmon across sample reaches. Shared letters indicate no significant difference from Tukey HSD post-hoc pairwise comparison analysis. Figure The mean distance from shore of observations of juvenile Chinook across sample months. Shared letters indicate no significant difference from Tukey HSD post-hoc pairwise comparison analysis. Yuba Accord M&E Program 4-54 April 2013

55 Figure The mean distance from shore of observations of juvenile Chinook salmon in each 20 mm size class. Shared letters indicate no significant difference from Tukey HSD post-hoc pairwise comparison analysis. Juvenile Chinook salmon appeared to occupy areas in close proximity to the shore during most survey months and in most survey reaches. However, in the Marysville reach, juveniles were distributed considerably further from shore relative to the other reaches. The Marysville reach has an extended shallow sandy bar on the north bank on which large woody debris collects, which may provide refuge to juveniles away from the shoreline. When compared across months, juvenile Chinook salmon remain within 10 feet of shore until June, and stayed relatively close to shore until September. Similarly, smaller juveniles tended to remain closer to shore than larger juvenile Chinook salmon. Both of these findings are consistent with observations of juvenile Chinook salmon occupying areas further from shore as they age (e.g., Allen 2000). However, juveniles in the mm size class actually occupied a mean distance further from shore than individuals in the mm size class. Mesohabitat Characteristics In the context of this analysis, mesohabitat is defined as the interdependent set of the hydraulic variables over a morphological unit, including the actual physical conditions occupied by an organism at the time of observation. This is contrasted with morphological unit, which refers to a static assignment of a piece of physical space to a habitat type based on standardized reference conditions. To evaluate potential relationships between juvenile Chinook salmon observations and mesohabitat characteristics, mean column water velocity at 60% depth (or at an average of the 80% and 20% depth) and the total measured stream depth at each Chinook salmon observation were overlaid with the mesohabitat characterization plot by Pasternack et al. (2012). In addition, potential relationships were evaluated separately between juvenile Chinook salmon observations by 20 mm size class and: (1) measured total stream depth; (2) the vertical position of the fish in the water column relative to total depth (depth of fish/total depth); and (3) the mean water velocity at Chinook salmon observation locations. Yuba Accord M&E Program 4-55 April 2013

56 The general trends in mesohabitat occupation (as contrasted with morphological units) occupied by juvenile Chinook salmon throughout the survey are shown in Figure As shown in the figure, juvenile Chinook salmon occupied primarily slackwater and slow glide mesohabitats, and were rarely encountered in water deeper than 4.5 ft or faster than 2 ft/s. Figure Overlay of the total measured stream depths and mean column water velocities at which juvenile Chinook salmon were encountered with mesohabitat characterizations. The size of the circle indicates the log 10 transformed number of juveniles occurring at the total measured stream depth and mean column water velocity. To investigate potential relationships between different ages (using size) of juvenile Chinook salmon observations and mesohabitat characteristics, juvenile salmon were grouped by size class (Table 4-5). Size classes of mm and 110 mm+ were combined in this analysis due to their small sample sizes. Larger individuals tended to occur in deeper water than the individuals in the smallest size class (ANOVA, F 3,5538 = 28.94, P < 0.001) (Figure 4-50). The proportional depth (i.e., vertical position in the water column) where juvenile salmon were observed indicates a trend of increasingly deeper water utilization as the individuals grow, until a size larger than 90 mm is reached, at which time the larger juveniles were observed again closest to the shore (ANOVA, F 3,5538 = 62.35, P < 0.001; Figure 4-51). Chinook salmon generally occurred in the lower half of the water column, regardless of actual water depth, and occurred in progressively faster water as they grew (ANOVA, F 3,5538 = 99.18, P < 0.001; Figure 4-52). Yuba Accord M&E Program 4-56 April 2013

57 Table 4-5. Observed number of juvenile Chinook salmon within each size class during each survey month of Size Class January February March June September Total Proportion mm mm mm mm mm Figure Mean total water depth of locations where juvenile Chinook salmon were observed by size class. Size classes sharing the same letter(s) were not significantly different. Figure The mean proportional depth (vertical position in the water column) occupied by juvenile Chinook salmon for each size class. A proportional depth of 0 is the stream bottom, while a proportional depth of 1 is the surface. Size classes sharing the same letter(s) are not significantly different. Yuba Accord M&E Program 4-57 April 2013

58 Figure The mean water velocity in which individual juvenile Chinook salmon were observed. Size classes sharing the same letter(s) were not significantly different. In summary, the vast majority of observations of juvenile Chinook salmon in the lower Yuba River occurred in water velocities and depths indicative of slackwater and slow glide mesohabitats. Juvenile Chinook salmon are known to prefer slower water habitats than many other members of Oncorhynchus (Quinn 2005), and have been previously reported to actively seek out slow backwaters, pools, or floodplain habitat for rearing (Sommer et al. 2001; Jeffres et al. 2008). The snorkeling data collected by the RMT during 2012 are generally consistent with other data available for multiple rivers (Bjornn and Reiser 1991). Juvenile Chinook salmon in the mm size class tended to occupy shallower habitats than larger (and presumably older) individuals, which is consistent with other observations of salmonids (e.g., Bjornn and Reiser 1991). Similarly, juvenile Chinook salmon showed a clear preference for faster water (up to an average of about 1.8 ft/s) as they grew, consistent with trends found with salmonids in other rivers (Bjornn and Reiser 1991). Juveniles also preferred a station deeper in the water column as they aged, with the exception of fishes larger than 90 mm FL. Whether this reflects bias from a small sample size of juvenile Chinook salmon greater than 90 mm FL (n = 19), behavioral avoidance of snorkelers, or actual habitat preference is not known. The overall findings from this survey indicate that juvenile Chinook salmon in the lower Yuba River initially prefer slower, shallower habitat, and move into faster and deeper water as they grow CHINOOK SALMON JUVENILE EMIGRATION Based upon review of available information, the RMT (2010b) recently identified the spring-run Chinook salmon fry rearing period as extending from mid-november through March, the juvenile rearing period extending year-round, and the young-of-year (YOY) emigration period extending from November through mid-july. Recent evaluations of available data and information conducted for this Interim Report are generally consistent with these lifestage timings, with the exception of the fry rearing period, and the juvenile (YOY) emigration (i.e., downstream movement) periods. Associated with the previously described shortened duration of spring-run Chinook salmon spawning, the fry rearing period is estimated to extend from mid- Yuba Accord M&E Program 4-58 April 2013

59 November through mid-february. Updated characterization of the juvenile (YOY) emigration (i.e., downstream movement) period extends from mid-november through June. Because it is not possible to reliably differentiate between juvenile spring- and fall-run Chinook salmon in the lower Yuba River, the following discussion pertains to emigrant juvenile Chinook salmon without run differentiation. Annual rotary screw trapping (RST) has been conducted on the lower Yuba River from 1999 to June near Hallwood Boulevard, located approximately 6 RM upstream from the city of Marysville. From 1999 to 2006, CDFW s RST monitoring efforts generally extended from fall (October or November) through winter, and either into spring (June) or through the summer (September) annually (Figure 4-53). Although the duration of each trapping season varied, each annual sampling effort encompassed the temporal period associated with the bulk of juvenile Chinook salmon emigration (Massa 2005; Massa and McKibbin 2005; Massa and Campos 2009). The RMT took over operation of the year-round RST effort in the fall of 2006, and continued operations through August Trap efficiency tests were conducted as part of RST monitoring during the survey periods. Weekly trap efficiency evaluations allowed Chinook salmon abundance estimates to be generated during those survey periods. Forty-three trap efficiency tests were completed during the years when efficiency values ranged from 1.2% to 16.6% (Table 4-6). An estimated 2,919,475 and 1,463,955 juvenile Chinook salmon from the 2007 and 2008 brood years emigrated past the Hallwood Boulevard RST site, respectively (Campos and Massa 2010; Campos and Massa 2011). Catch expansions were not completed during periods where no efficiency evaluation was conducted. Observed catch was used in lieu of abundance estimates when comparing annual data sets. Methods to extrapolate efficiency results were explored, but were found to be inappropriate based on the available data. 50,000 45,000 40,000 35,000 Marysville Flow (CFS) 30,000 25,000 20,000 15,000 10,000 5,000 0 Figure Weekly operational status and flow at the Hallwood Boulevard RST site on the lower Yuba River from October 1, 1999 to September 30, Solid shaded areas indicate periods of operation. 10 No sampling occurred from October 2002 to June Yuba Accord M&E Program 4-59 April 2013

60 Regression analyses were used to explore potential relationships between efficiency values, RST performance variables and environmental river conditions. Environmental conditions and performance variables were found to have weak correlative associations with trap efficiency values. Parameters for the predictive functions (e.g., α, β 0, β 1, β 2 ) were estimated using least squares estimation procedures. Predictive capabilities of the regression models were generally weak and the best fitting model could only explain 32% (R 2 = 0.32, P = 0.01) of the variability in the data (Table 4-7). Therefore, the RMT concluded that it was not appropriate to apply capture efficiency results to periods when capture efficiency tests were not conducted as a further effort to numerically estimate the abundance of emigrating juvenile salmonids. Table 4-6. Summary data for trap efficiency tests conducted at the Hallwood Boulevard RST site on the lower Yuba River from Sam pling Period Released Recovered Efficiency Sam pling Period Released Recovered Efficiency December 24, December 24, 2008 no efficiency tes t December 31, December 31, Ja n u a ry 7, January 7, Ja n u a ry 14, January 14, Ja n u a ry 21, January 21, Ja n u a ry 28, January 28, February 4, February 4, February 11, February 11, February 18, February 18, February 25, February 25, 2009 no efficiency tes t M a r c h 3, M arch 4, M a r c h 10, M arch 11, M a r c h 17, M arch 18, M a r c h 24, M arch 25, M a r c h 31, April 1, April 7, April 8, April 14, April 15, April 21, April 22, April 28, April 29, M a y 5, M ay 6, 2009 M a y 12, M ay 13, 2009 M a y 19, M ay 20, 2009 no efficiency tes t M a y 26, M ay 27, 2009 Ju n e 2, June 3, 2009 Ju n e 9, June 10, Table 4-7. Regression statistics for trap efficiency as a function of Marysville Gage flow (cfs), turbidity (ntu), water velocity (m/sec.), daily cone revolutions and days of normal operation (Efficie ncy) (Efficie ncy) (Efficie ncy) (Efficie ncy) (Efficie ncy) Constant (0.752) (0.380) (0.144) (0.152) (0.132) Log MRY flow (0.357) (0.644) (0.164) (0.165) (0.178) Turbidity (0.019)** (0.050)** (0.054)* (0.010)*** Velocity (0.060)* (0.343) (0.422) Revolutions 1.120E E 06 (0.761) (0.740) Days o f O peration (0.028)** R Squared Adjusted R Squared No. O bservations P values re p o rte d in parentheses. *, **, *** In d icate s sign ifican ce at the 90%, 95% and 99% le ve l, re sp e ctive ly Yuba Accord M&E Program 4-60 April 2013

61 Analysis of the fitted distribution of weekly juvenile Chinook salmon catch at the Hallwood Boulevard RST site from survey year 1999 through 2008 revealed that most emigration occurred from late-december through late-april in each survey year (Figure 4-54). Approximately 95 percent of the observed catch across all years based on the fitted distribution occurred by April 30. Analysis of the cumulative distributions of pre-accord and Accord monitoring years revealed a temporal shift in timing of emigration in the fitted distributions. Emigration of juvenile Chinook salmon generally appeared to occur nearly one month later under the Accord, relative to pre-accord years of sampling Cumulative Distribution of Weekly Observed Catch n c tio F ra e tiv la u m u C All Years Expected Distribution Pre Accord Expected Distribution Accord Expected Distribution Figure Expected temporal distributions from a fitted asymmetrical logistic function of the weekly observed catch of juvenile Chinook salmon at the Hallwood Boulevard RST site on the Yuba River from JUVENILE CHINOOK SALMON PEAK EMIGRATION TIMING An evaluation of peak emigration dates and the median (50% of the cumulative distribution) dates for juvenile Chinook salmon passing the Hallwood Boulevard RST site was conducted. The methods for determining peak emigration and median dates followed the methods proposed by Keefer et al. (2008) using a 10-day moving average as the basis for the peak calculations. Peak emigration date was found to be a statistically significant predictor of the median date and described 77% (r 2 = 0.77, P = ) of the variability in the data (Figure 4-55). This significant relationship between peak and median dates suggests that both metrics are good measures to evaluate emigration timing for any given year. For all survey years, peak emigration Yuba Accord M&E Program 4-61 April 2013

62 dates ranged from December 22 to March 3 and the average date of peak emigration over all years was January 30 (±27 days, 95% CI). The median dates ranged from December 19 to February 26 and the average date of the median date of emigration over all years was January 26 (±22 days, 95% CI). To examine potential differences between pre-accord and Accord data sets, the daily count data of juvenile Chinook salmon were combined and analyzed. Peak and median emigration dates during Accord years were found to occur nearly a month later in the year, relative to pre-accord sampling years. The peak emigration date for pre-accord sampling year was February 3, and the peak emigration date during Accord sampling years was March 3. The median emigration date during pre-accord sampling years was January 25, and the median emigration date during Accord sampling years was February 23 (Table 4-8). Figure Simple linear regression between the peak and median dates of emigrating juvenile Chinook salmon at the Hallwood Boulevard RST site on the lower Yuba River during sampling years Table 4-8. Annual peak and median dates of juvenile Chinook salmon emigration, as determined from RST sampling conducted at the Hallwood Boulevard site for sampling years Sampling Year Pre-Accord Average Accord Average Peak Date 1/26 2/1 1/9 12/22 3/3 12/28 3/3 2/5 2/25 2/3 3/3 Median Date 1/17 2/7 1/11 1/9 2/13 12/19 2/26 2/13 2/2 1/25 2/23 Statistically insignificant (P > 0.05) but positive trends were observed in the peak and median emigration dates among the sampling years. Regression analysis was used to explore potential relationships between the peak and 50% median dates during each sampling season. Parameters for the model (e.g., α, β 0, β 1, β 2 ) were estimated using least squares estimation procedures. Figure 4-56 shows scatter plots with linear regression lines, coefficients and r 2 values. Yuba Accord M&E Program 4-62 April 2013

63 Days from October Peak y = 3.375x 6640 R² = P (F) = % median y = x R² = P(F) = Figure Simple linear regression of the annual peak and 50% median dates of emigrating juvenile Chinook salmon at the Hallwood Boulevard RST site on the lower Yuba River during sampling years JUVENILE CHINOOK SALMON EMIGRATION SIZE AND DEVELOPMENTAL PHASE The sizes of juvenile Chinook salmon emigrants were investigated for each survey year at the Hallwood Boulevard RST site on the lower Yuba River. All years showed the bulk of emigrants occurring in the mm size range (Table 4-9). The highest proportion of Chinook salmon emigrants larger than 49 mm occurred during the 1999 sampling year and nearly reached 30% of the total number of individuals captured that year. By contrast, during the 2005 sampling year just over 5% of the emigrating juvenile Chinook salmon were longer than 49 mm. Very few juvenile Chinook salmon emigrants observed at the Hallwood Boulevard RST site were greater than 90 mm, and the proportion exceeded 1% only once (during the 1999 sampling year). Table 4-9. Annual proportion (October September) of six fork length classes of juvenile Chinook salmon captured at the Hallwood Boulevard RST site on the lower Yuba River from Fork Length Sampling Period <30 mm mm mm mm mm 110+ mm < < < < <0.001 < < < < < < < < < < < <0.001 Yuba Accord M&E Program 4-63 April 2013

64 Ontogenetic lifestage classifications (e.g., fry, parr and silvery parr) were initially used to identify life history stages through a visual categorization of emigrating juvenile salmonids based on external morphological characteristics. Unfortunately, inconsistencies between the intended characterizations and recorded observations were evident during the 2007 and 2008 survey periods, specifically for fry, parr and silvery parr classifications. For example, a large fraction of juvenile Chinook salmon (and steelhead) were identified as parr, although observations from the Feather River and other Central Valley streams suggest that the majority of juvenile salmonids emigrate from natal streams as fry (DWR 1999; DWR 2003; DWR 2007; Gaines and Martin 2002; Bilski and Kindopp 2009; Snider et al. 1998). The misclassification was also evidenced by the large range of observed fork lengths measured within the parr lifestage on the lower Yuba River. During the survey period, juvenile Chinook salmon visually classified as parr ranged from 28 mm to 98 mm, and steelhead parr ranged from 23 mm to 126 mm (Campos and Massa 2010b). Intuitively, the upper and lower bounds of these observed ranges should have been more appropriately characterized as fry and silvery parr, respectively. Lower Yuba River RST protocols define the fry lifestage as having evident parr marks with a completely absorbed yolk sac, but with the yolk sac insertion being still visible. Watry et.al (2008) described fry as being recently emerged with an absorbed yolk sac and undeveloped pigmentation. Additionally, many authors report salmonids measuring < 50 mm in fork length to be classified as fry (Roper and Scarnecchia 2000; Martin et. al 2001; Kindopp et. al 2009). The USFWS draft rotary screw trap protocol (USFWS 2008), which is intended to serve as a model for all projects implementing RST sampling in the California Central Valley, provides a classification system that includes the fry, parr, smolt and yearling lifestages, but excludes yolk-sac fry and silvery parr classes. Adding uncertainty to lifestage classification, the USFWS protocols note that field staff may elect to classify emigrating salmon as silvery parr if desired, but no mention of fry misclassification was reported. Allen and Hassler (1986) excluded the silvery parr lifestage altogether from their species profile of Chinook salmon, and Watry et. al (2008) also excluded the silvery parr lifestage when assigning lifestages to emigrating Chinook salmon on the Stanislaus River. Given the inconsistencies in field classification, and the variability in published categorization, the RMT discontinued the use of these ontogenetic characterizations, and rely upon the 20 mm fork length bins presented in Table 4-9 to infer potential lifestage distributions during the RST monitoring at the Hallwood Boulevard RST site. See Chapter 5 for additional information on emigrant juvenile Chinook salmon size, growth, condition factor, and their relationships with flow and water temperature. Yuba Accord M&E Program 4-64 April 2013

65 JUVENILE CHINOOK SALMON EMIGRATION RELATIONSHIPS WITH FLOW AND WATER TEMPERATURE The annually estimated temporal distributions of emigrating juvenile Chinook salmon from outmigrant monitoring data demonstrated low correlation with measures of flow and water temperature. Regression analysis was used to explore potential relationships between the estimated distributions of juvenile Chinook salmon and environmental river conditions. Parameters for the model (e.g., α, β 0, β 1, β 2 ) were estimated using least squares estimation procedures. Figure 4-57 shows scatter plots with linear regression lines, coefficients and r 2 values. Flow and water temperature were minimally useful at predicting the percentile expressions of the distributions, and linear regressions using these single variables were able to explain only 21% and 18% of the variability in the data (r 2 ), respectively. Several models using flow and water temperature metrics were considered in an attempt to better predict the estimated percentile expressions of cumulative outmigrant distributions. A multivariate linear regression using water temperature and log transformed flow was best at predicting the percentile expressions (R 2 = 0.57, P = <0.001 ). The equation for the model was: Estimated Percentile Expression = x log(flow) x Temperature. The observed emigration magnitude of juvenile Chinook salmon from all available years of RST data also demonstrated low correlation with measures of flow and water temperature. The observed daily and weekly catch of juvenile Chinook salmon and measures of flow and water temperature were examined to determine whether the emigration of juvenile Chinook salmon could be expressed as a function of measures of Yuba River flows and water temperatures (Figures 4-58 and 4-59). 16,000 Marysville Flow Marysville Temperature , , Marysville Flow (CFS) 10,000 8,000 6,000 y = x R² = Marysville Temperature ( C) 4,000 y = x R² = , Figure Mean weekly flow and water temperature at the Marysville Gage through the corresponding percentile expressions 1%, 10%, 25%, 50%, 75%, 90% and 99% from the fitted cumulative distributions of emigrating juvenile Chinook salmon at the Hallwood Boulevard RST site on the lower Yuba River for sampling years 1999 to Yuba Accord M&E Program 4-65 April 2013

66 Figure Mean weekly flow (blue shading) at the Marysville Gage and Chinook salmon catch (gray bars) for each annual survey at the Hallwood Boulevard RST site on the lower Yuba River from October 1, 1999 to August 31, Yuba Accord M&E Program 4-66 April 2013

67 Figure Mean weekly temperature ( C) at the Marysville Gage and observed Chinook salmon catch at the Hallwood Boulevard RST site on the lower Yuba River from October 1, 1999 to August 31, Yuba Accord M&E Program 4-67 April 2013

68 Regression analysis was used to explore the potential relationships between the observed catch of juvenile Chinook salmon and environmental river conditions. Measures of flow and water temperature were used as predictor variables due to reported correlations between flow and temperature and juvenile salmonid outmigration characteristics. Parameters for the model (e.g., α, β 0, β 1, β 2 ) were estimated using least squares estimation procedures. The best fitting predictive model used the week of observation (beginning on or near October 1 of each sampling year), mean flow at the Marysville Gage, and mean weekly temperature squared as measured at the Marysville Gage to predict the log transformed weekly observed catch (R 2 = 0.47, P = <0.001). The equation for the model was: log(weekly Catch) = x Week x Mean Flow x Mean Temperature 2. Partial results for several regression models are presented in Table Table Results of regression analyses comparing juvenile Chinook salmon catch with flow and temperature metrics on the lower Yuba River for sampling years Daily Chinook Catch: R 2 P Value Day, Flow, Temp <0.001 Day, log(flow), Temp <0.001 Temp <0.001 Day, Flow, Temp <0.001 Flow, Temp <0.001 log(daily Chinook Catch): Day, Flow, Temp <0.001 Day, log(flow), Temp <0.001 Flow, Temp <0.001 Flow Temp <0.001 log(temp) <0.001 Day, Flow, log(temp) <0.001 Flow, log(temp) <0.001 Temp <0.001 Day, Flow, Temp <0.001 Flow, Temp <0.001 Weekly Chinook Catch: Week, Flow, Temp <0.001 Flow, Temp <0.001 log(weekly Chinook Catch): Week, Flow, Temp <0.001 Flow, Temp <0.001 Week, log(flow), Temp <0.001 Week, Flow, Temp <0.001 Week, Temp <0.001 Yuba Accord M&E Program 4-68 April 2013

69 CHINOOK SALMON PEAK EMIGRATION TIMING IN RELATION TO FLOW AND WATER TEMPERATURE The peak and median dates of emigration of juvenile Chinook salmon during all available years of RST data demonstrated statistically non-significant correlation with water temperature (P > 0.05) and significant correlation with flow. The peak and median dates of juvenile Chinook salmon emigration and measures of flow and temperature were examined to determine whether the emigration timing of juvenile Chinook salmon could be expressed as a function of measures of lower Yuba River flows and water temperatures. Several multivariate models using combinations of water temperature and flow variables were considered. Parameters for the best fitting model (e.g., α, β0, β1, β2 ) were estimated using least squares estimation procedures. The best fitting predictive model used the average January March flows at the Marysville Gage to predict the median date of emigration (r 2 = 0.64, P = ) (Figure 4-60). In other words, the higher the flows that occur at the Marysville Gage from January through March, the earlier the median date of juvenile Chinook salmon emigration. This phenomenon could be resulting from an association between a combination of volitional and non-volitional accelerated downstream movement and higher flows and water velocities Days from October 1st y = x R² = P (F) = ,000 4,000 6,000 8,000 10,000 Marysville Gage Flow (cfs) Figure Simple linear regression of the annual median dates of juvenile Chinook salmon emigration at the Hallwood Boulevard RST site and average January March flow at the Marysville Gage on the lower Yuba River from SMOLT OUTMIGRATION Overall, most (about 84 percent) of the juvenile Chinook salmon were captured at the Hallwood Boulevard RSTs soon after emergence from November through February, with relatively small numbers continuing to be captured through June. Although not numerous, captures of (oversummer) holdover juvenile Chinook salmon ranging from about 70 to 140 mm FL primarily occurred from October through January with a few individuals captured into March (Massa 2005; Massa and McKibbin 2005). These fish likely reared in the river over the previous summer, representing an extended juvenile rearing strategy characteristic of spring-run Chinook Yuba Accord M&E Program 4-69 April 2013

70 salmon. Juvenile Chinook salmon captured during the fall and early winter (October-January) larger than 70 mm are likely exhibiting an extended rearing strategy in the Yuba River (Campos and Massa 2010a). Juvenile Chinook salmon that exhibit extended rearing in the Yuba River are assumed to undergo the smoltification process and volitionally emigrate from the river as yearling+ (one year or older) individuals. Based upon review of available information, the RMT (2010b) recently identified the spring-run Chinook salmon yearling+ (smolt) outmigration period as extending from November through mid-may. Review of all available information for this Interim Report results in a slight modification of the smolt outmigration life history periodicity, with the phenotypic spring-run Chinook salmon smolt outmigration period extending from October through mid-may. Multivariate linear regressions accounting for annual mean flow and annual mean temperature (see Chapter 5) were statistically significant at predicting the proportions of emigrants in the 110+ mm size class, representing smolt-sized juvenile Chinook salmon (R 2 = 0.72, P = 0.023). However, smolt-sized Chinook salmon constitute a very small (0.1 percent or less) percentage of the annual emigrant populations. 4.3 FALL-RUN CHINOOK SALMON For this Interim Report, the RMT developed representative temporal distributions for specific fall-run Chinook salmon lifestages through review of previously conducted studies, as well as recent and currently ongoing data collection activities of the M&E Program. As stated for springrun Chinook salmon, the resultant lifestage periodicities encompass the majority of activity for a particular lifestage, and are not intended to be inclusive of every individual in the population. The lifestage-specific periodicities for fall-run Chinook salmon in the lower Yuba River are summarized in Table 4-11, and are discussed below. Table Lifestage-specific periodicities for fall-run Chinook salmon in the lower Yuba River (shaded boxes indicate temporal utilization of the lower Yuba River). Lifestage Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Fall-run Chinook Salmon Adult Immigration & Staging Spawning Embryo Incubation Fry Rearing Juvenile Rearing Juvenile Downstream Movement Yuba Accord M&E Program 4-70 April 2013

71 It is not possible to differentiate between the spring- and fall-runs of Chinook salmon in the lower Yuba River for various lifestage and flow and water temperature considerations. However, for completeness, the following section on fall-run Chinook salmon in the lower Yuba River includes additional information specific to fall-run Chinook salmon that was not previously presented for spring-run Chinook salmon FALL-RUN CHINOOK SALMON ADULT IMMIGRATION AND STAGING Adult fall-run Chinook salmon have been reported to enter the Sacramento and San Joaquin rivers from July through December, and spawn from October through December (Reclamation 2008). Unlike spring-run Chinook salmon, adult fall-run Chinook salmon do not exhibit an extended over-summer holding period in the lower Yuba River (RMT 2010b). Rather, it is believed that they stage for a relatively short period of time prior to spawning. This conventional belief is supported by the recent evaluation by the RMT of the acoustic telemetry monitoring data and the Vaki Riverwatcher data (see Chapter 5). Adult fall-run Chinook salmon immigration and staging has been reported to generally occur in the lower Yuba River from August through November (CALFED and YCWA 2005), and immigration generally peaks in November, with typically greater than 90% of the run having entered the river by the end of November (CDFG 1992; CDFG 1995 in RMT 2010b). The RMT s review of available data indicates that fall-run Chinook salmon immigration generally extends from July through December. As indicated by the eight years of available data of fish passing through the Vaki Riverwatcher systems located in both ladders at Daguerre Point Dam, the average date associated with the median of adult fall-run Chinook salmon passing Daguerre Point Dam was October 14, and the average date that 90% of the annual runs passed the dam was November 17. Additional discussion regarding Vaki Riverwatcher data is provided in Chapter 5. In general, a minimal amount of effort was expended by the RMT to differentiate between falland spring-run Chinook when acoustically-tagging adult immigrating Chinook salmon. A total of eight individuals were acoustically-tagged below Daguerre Point Dam during October By contrast to phenotypic adult spring-run Chinook salmon which exhibited extended periods of holding downstream of Daguerre Point Dam, the acoustically-tagged fall-run adult Chinook salmon held for an average of only about 3 days downstream of Daguerre Point Dam prior to passing upstream through the fish ladders. These data tend to generally confirm the understanding that adult fall-run Chinook salmon spend a relatively short period of time staging prior to migrating to spawning areas and commencing spawning activities SPAWNING The lower Yuba River fall-run Chinook salmon spawning period has been reported to extend from October through December (CALFED and YCWA 2005). Preliminary data from the recently conducted redd surveys, and back-calculations from previous and recent carcass surveys generally confirm this temporal distribution. Yuba Accord M&E Program 4-71 April 2013

72 According to RMT (2010b), fall-run Chinook salmon are primarily observed spawning during October in the upper reaches upstream of Daguerre Point Dam in the lower Yuba River. Spawning fall-run Chinook salmon begin expanding their spatial distribution further downstream in later fall months as suitable temperatures become available near or downstream of Daguerre Point Dam (RMT 2010b). Recent analyses of available redd distribution and water temperature data confirm these previous characterizations. Examination of Figures 4-12 and 4-13 for the periods restricted from October through December (the fall-run Chinook salmon spawning period) show that the measure of central tendency of redd distribution continues to move downstream as the spawning season progresses from October through December. Also, as demonstrated in Figures 4-23 and 4-24, redds were distributed farther downstream as water temperatures became cooler in late October, compared to early October. Fall-run Chinook salmon spawning activity appeared to be associated with water temperature. For all Chinook salmon redds newly-constructed during October through December of 2009 and 2010, approximately 84% were observed at or below the Chinook salmon spawning upper optimal water temperature value of 56 F, and about 97% were observed at or below the upper tolerable water temperature value of 58 F (see Chapter 5 for additional discussion) EMBRYO INCUBATION The fall-run Chinook salmon embryo incubation period has been reported to extend from October through March (YCWA et al. 2007). Based upon consideration of accumulated thermal units from the time of egg deposition through hatching and alevin incubation, the RMT (2010b) therefore also considered the fall-run Chinook salmon embryo incubation period to extend from October through March. This time period is consistent with observed trends in Chinook salmon fry captures in the RSTs, as previously described. Review of recently available data and information, including updated fall-run Chinook salmon spawning spatial and temporal distribution, and recent water temperature monitoring information, confirms the general characterization of the fall-run Chinook salmon embryo incubation period extending from October through March in the lower Yuba River JUVENILE REARING AND OUTMIGRATION Fall-run Chinook salmon juvenile rearing in the lower Yuba River has been reported to primarily occur from December through June (CALFED and YCWA 2005). In the lower Yuba River, most fall-run Chinook salmon reportedly exhibit downstream movement as fry shortly after emergence from gravels, although some individuals rear in the river for a period up to several months and move downstream as juveniles (RMT 2010b). According to RMT (2010b), in past years CDFG employed the run identification methodology to identify fall-run Chinook salmon juveniles captured in the RSTs. Based on CDFG s examination of run-specific determinations, in the lower Yuba River the majority (81.1%) of fall-run Chinook salmon move past the Hallwood Boulevard RST from December through March, with decreasing numbers captured during April (8.9%), May (6.6%), June (3.2%), and July (0.2%) (RMT 2010b). Most of the fish Yuba Accord M&E Program 4-72 April 2013

73 captured from December through March were post-emergent fry (< 50 mm FL), while nearly all juvenile fall-run Chinook salmon captured from May through July were larger ( 50 mm FL) (YCWA et al. 2007). Thus, previous reports suggest that the fry rearing lifestage was considered to extend from December through April, and the juvenile rearing lifestage from March through June. The RMT has reviewed recently available data to further refine juvenile fall-run Chinook salmon lifestage periodicities. Based upon estimation of initial emergence in consideration of the ATUs required for embryo incubation to hatching, and upon size-at-time of juvenile Chinook salmon in the RSTs as previously discussed, the phenotypic fall-run Chinook salmon fry rearing period generally extends from mid-december through April, and the juvenile rearing lifestage extends from mid-january through June. Juvenile downstream movement, which includes both fry and larger juveniles as indicated by captures in the Hallwood Boulevard RSTs, generally occurs from mid-december through June. 4.4 STEELHEAD Steelhead exhibit perhaps the most complex suite of life history traits of any species of Pacific salmonid. Members of this species can be anadromous or freshwater residents and, under some circumstances, members of one form can apparently yield offspring of another form (YCWA 2010). Steelhead is the name commonly applied to the anadromous form of the biological species O. mykiss. The physical appearance of O. mykiss adults and the presence of seasonal runs and yearround residents indicate that both anadromous (steelhead) and resident rainbow trout exist in the lower Yuba River downstream of Englebright Dam. Zimmerman et al. (2009) analyzed otolith strontium:calcium (Sr:Ca) ratios in 964 otolith samples comprised of young-of-year, age-1, age- 2, age-3, and age-4+ fish to determine maternal origin and migratory history (anadromous vs. non-anadromous) of O. mykiss collected in Central Valley rivers between 2001 and 2007, including the lower Yuba River. The proportion of steelhead progeny in the lower Yuba River (about 13%) was intermediate to the other rivers examined (Sacramento, Deer Creek, Calaveras, Stanislaus, Tuolumne, and Merced), which ranged from about 4% in the Merced River to 74% in Deer Creek (Zimmerman et al. 2009). Results from Mitchell (2010) indicate O. mykiss in the lower Yuba River may be exhibiting a predominately residential life history pattern. He suggested that 14 percent of scale samples gathered from 71 O. mykiss moving upstream and trapped in the fish ladder at Daguerre Point Dam from November 1, 2000, through March 28, 2001, exhibited an anadromous life history. Thus, it is recognized that both anadromous and resident life history strategies of O. mykiss have been and continue to be present in the lower Yuba River. However, because it is difficult to distinguish the two life history strategies, the following discussions pertain to O. mykiss in general, unless otherwise specified. Yuba Accord M&E Program 4-73 April 2013

74 For this Interim Report, the RMT developed representative temporal distributions for specific steelhead lifestages through review of previously conducted studies, as well as recent and currently ongoing data collection activities of the M&E Program. As with spring-run and fall-run Chinook salmon, the resultant lifestage periodicities are intended to encompass the majority of activity for a particular lifestage, and are not intended to be inclusive of every individual in the population. The lifestage-specific periodicities for steelhead in the lower Yuba River are summarized in Table 4-12, and are discussed below. Table Lifestage-specific periodicities for steelhead in the lower Yuba River. Lifestage Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Steelhead Adult Immigration & Holding Spawning Embryo Incubation Fry Rearing Juvenile Rearing Juvenile Downstream Movement Smolt (Yearling+) Emigration STEELHEAD ADULT IMMIGRATION AND HOLDING The RMT (2010b) examined preliminary data and identified variable annual timing of steelhead ascending the fish ladders at Daguerre Point Dam since the VAKI Riverwatcher infrared and videographic sampling system began operations in For example, Massa et al. (2010) state that peak passage of steelhead at Daguerre Point Dam occurred from April through June during They also suggest that the apparent disparity between the preliminary data and other reports of steelhead adult immigration periodicity may be explained by the previously reported (Zimmerman et al. 2009; Mitchell 2010) relatively high proportion of resident (vs. anadromous) O. mykiss occurring in the Yuba River, because the VAKI Riverwatcher system did document larger (>40.6 cm) O. mykiss ascending the fish ladders at Daguerre Point Dam during the winter months (December through February). The observed timing of larger O. mykiss ascending the fish ladders at Daguerre Point Dam more closely corresponds with previously reported adult steelhead immigration periodicities. The RMT (2010b) identified the period extending from August through March as encompassing the majority of the upstream migration and holding of adult steelhead in the Yuba River. Review of recently collected and analyzed Vaki Riverwatcher information generally confirms this lifestage periodicity (see Chapter 5 for additional discussion). Yuba Accord M&E Program 4-74 April 2013

75 4.4.2 STEELHEAD SPAWNING Steelhead spawning has been reported to generally extend from January through April in the lower Yuba River (CALFED and YCWA 2005; CDFG 1991b; YCWA et al. 2007). This temporal period normally corresponds with winter storms and surface run off which can lead to extended periods when surveys cannot be completed due to high flows, suspended sediments and high turbidity levels in the water. The RMT conducted a pilot redd survey from September 2008 through April 2009 (RMT 2010b). Surveys were not conducted during March, which is a known time for steelhead spawning in other Central Valley rivers, due to high flows and turbidity. An extensive area redd survey was conducted by surveyors kayaking from the downstream end of the Narrows pool to the Simpson Lane Bridge. During the extensive area redd survey, redds that were categorized as steelhead based on previously reported (USFWS 2010) redd size criteria were observed from October through April, with peaks in spawning activity occurring during fall (October) and spring (February and April). However, some of those redds categorized as steelhead, particularly during October, may actually have been small Chinook salmon redds because the size criteria used to identify steelhead redds was found to be 53% accurate for identifying steelhead redds in the lower American River (USFWS 2010). Additional analyses of steelhead redd characteristics presently are continuing to be conducted. Campos and Massa (2010b and 2011) synthesized results of near-census redd surveys conducted on the lower Yuba River during the 2009 and 2010 survey periods. During both annual survey efforts, a substantial proportion of the weekly strata in the January through April time periods were not sampled due to elevated flows and associated turbidity levels. The results from the Accord RMT annual redd surveys provide a temporally disjunct understanding of steelhead spawning in the lower Yuba River. During the 2009 survey period, five weeks (January 18 February 14, and March 1 7, 2010) of the steelhead spawning period were not surveyed due to storm flows and poor visibility. During the 2010 survey period, ten weeks (January 3 January 16 and February 21 April 10, 2011) were also not surveyed due to inclement river conditions and visibility. The resultant cumulative distribution curves are influenced by the aforementioned missing weekly counts occurring at different periods in the steelhead spawning periods. Nonetheless, the 2009 redd distribution appears to be shifted later in the season compared to the 2010 redd distribution (Figures 4-61 and 4-62). Steelhead spawning has been reported to primarily occur in the lower Yuba River upstream of Daguerre Point Dam (SWRI et al. 2000; YCWA et al. 2007). Kozlowski (2004) states that field observations during winter and spring 2000 (YCWA unpublished data) indicated that the majority of steelhead spawning in the lower Yuba River occurred from Long Bar upstream to the Narrows, with the highest concentration of redds observed upstream of the Highway 20 Bridge. USFWS (2007) data were collected on O. mykiss redds in the lower Yuba River during 2002, 2003, and 2004, with approximately 98% of the redds located upstream of Daguerre Point Dam. During the pilot redd survey conducted from the fall of 2008 through spring of 2009, the RMT (2010b) report that most (65%) of the steelhead redds were observed upstream of Daguerre Point Dam. Yuba Accord M&E Program 4-75 April 2013

76 Figure Cumulative temporal distributions of the observed and expected steelhead redd abundance in the surveyed reaches of the lower Yuba River from January 1, 2010 to April 8, Figure Cumulative temporal distributions of the observed and expected steelhead redd abundance in the surveyed reaches of the lower Yuba River from January 1, 2010 to April 13, Based on steelhead redd surveys conducted during the and spawning seasons, steelhead redds show a distinctive pattern spatially throughout the lower Yuba River. Table 4-13 shows the number of redds found in each of the reaches during 2010 and Figure 4-63 displays the proportion of redds in the survey reaches. During both years, the majority of redds occurred in the Timbuctoo Bend and Parks Bar reaches of the lower Yuba River. Although the numbers of redds counted each year were drastically different, the proportions of redds in each of the survey reaches was quite similar. Yuba Accord M&E Program 4-76 April 2013

77 Table Number of observed steelhead redds stratified by morphological unit in each of the reach delineations of the lower Yuba River during 2010 and Morphological Unit Chute 0 n/a % Fast Glide 0 n/a % Hillside 0 n/a % Lateral Bar 0 n/a % Medial Bar 0 n/a % Point Bar 0 n/a % Pool 0 n/a % Riffle 0 n/a % Riffle Transition 0 n/a % Run 0 n/a % Slackwater 0 n/a % Slow Glide 0 n/a % Swale 0 n/a % No MU ID % TOTALS % Percent 0.0% 1.8% 63.4% 27.3% 1.8% 3.5% 2.2% 0.0% 100.0% Morphological Unit Englebright Dam Reach Englebright Dam Reach Narrows Reach 1 Narrows Reach 1 Timbuctoo Bend Reach Timbuctoo Bend Reach January April 2010 Parks Bar Reach Dry Creek Reach January April 2011 Parks Bar Reach Dry Creek Reach Daguerre Dam Reach Daguerre Dam Reach Hallwood Reach Hallwood Reach Marysville Reach Marysville Reach Chute 0 n/a % Fast Glide 0 n/a % Hillside 0 n/a % Lateral Bar 0 n/a % Medial Bar 0 n/a % Point Bar 0 n/a % Pool 0 n/a % Riffle 0 n/a % Riffle Transition 0 n/a % Run 0 n/a % Slackwater 0 n/a % Slow Glide 0 n/a % Swale 0 n/a % No MU ID 0 n/a % TOTALS % Percent 0.0% 0.0% 60.5% 28.9% 0.0% 7.9% 2.6% 0.0% 100.0% 1 No MU delineation yet exists for the Narrows Reach. TOTALS TOTALS Percent Percent Steelhead did not spawn in morphological units at random, nor did they utilize the same morphological units in the same proportions each survey year. In , steelhead appear to have selected the morphological units of fast glide, riffle, riffle transition, and slow glide. In , steelhead shifted to building redds in different habitats (e.g., lateral bar, point bar, riffle transition, and slow glide), most of which are indicative of normally shallow or dewatered areas that are inundated at higher flows, and are usually located near-bank during low flows. Examination of the hydrograph during the survey year indicated that flows during the spawning period were in excess of 2,000 cfs after mid-december of 2010 (and surveys were conducted in flows of up to and including 6,700 cfs) which apparently resulted in the associated shift in habitat utilization by spawning steelhead. Yuba Accord M&E Program 4-77 April 2013

78 Fraction Fraction Figure Reach and morphological unit delineations for steelhead redds observed in the lower Yuba River during 2010 and *Represents morphological units outside of the base flow channel STEELHEAD EMBRYO INCUBATION Previous studies report that steelhead eggs incubate in redds for 3 to 14 weeks prior to hatching, depending on water temperatures (Shapovalov and Taft 1954; Barnhart 1991). After hatching, alevins remain in the gravel for an additional 2 to 5 weeks while absorbing their yolk sacs prior to emergence (Barnhart 1991). The entire embryo incubation lifestage encompasses the time adult steelhead select a spawning site through the time when emergent fry exit the gravel (CALFED and YCWA 2005). In the lower Yuba River, steelhead embryo incubation has been reported to generally occur from January through May (CALFED and YCWA 2005; SWRI 2002). This general time period is consistent with observations of O. mykiss fry captured in the RSTs located at Hallwood Boulevard (see additional discussion, below in Section 4.4.5). Review of recently available data, including updated steelhead spawning spatial and temporal distribution, and recent water temperature monitoring information, confirms the general characterization of the steelhead embryo incubation period extending from January through May in the lower Yuba River. Yuba Accord M&E Program 4-78 April 2013

79 4.4.4 STEELHEAD JUVENILE REARING As previously discussed for juvenile Chinook salmon rearing, past studies on the lower Yuba River have provided baseline biological data and important insights into suitable methods for characterizing juvenile salmonid habitat occurrence, including juvenile O. mykiss. The previously described snorkel survey conducted by the RMT during 2012 resulted in few confirmed observations of O. mykiss (refer to Chapter 5), precluding an evaluation of juvenile O. mykiss spatial and temporal distributions and potential relationships with mesohabitat characteristics and distance to shore, as was presented for juvenile Chinook salmon, above STEELHEAD JUVENILE OUTMIGRATION In the lower Yuba River, juvenile steelhead exhibit variable durations of rearing. Some juvenile O. mykiss may rear in the lower Yuba River for short periods (up to a few months) and others may spend from one to three years rearing in the river prior to emigration. The RMT (2010b) did not distinguish between sub-components of the steelhead juvenile rearing lifestage, but reported an encompassing juvenile rearing and outmigration lifestage, which extended yearround. Recent evaluations of available data and information conducted for this report identified distinct steelhead fry and juvenile rearing periods, as well as yearling+ emigration lifestage periodicities. These periodicities were distinguished through evaluation of bi-weekly length-frequency distributions of O. mykiss captured in rotary screw traps in the lower Yuba River, and other studies that report length-frequency estimates (Mitchell 2010; CDFG 1984). Updated life history periodicities include juvenile steelhead fry rearing extending from April through July, the juvenile rearing period extending year-round, juvenile (YOY) downstream movement extending from April through September, and the smolt yearling+ emigration period extending from October through mid-april. No abundance estimates for juvenile O. mykiss were developed by the M&E Program due to low capture rates at the Hallwood Boulevard RST site, precluding the development and application of capture efficiency extrapolation. Observed catch was used in lieu of abundance estimates when comparing annual data sets. Monitoring efforts at Hallwood Boulevard occurred year-round during four years ( , , and ) of the overall monitoring period. Figure 4-64 shows the fitted cumulative temporal distributions of O. mykiss juvenile captures during the four year-round monitoring efforts. It is readily apparent from examination of Figure 4-64 that the timing of juvenile O. mykiss outmigration can be highly variable among years. During 2006, a very wet year, in general the O. mykiss outmigration period occurred much earlier than the other years, with the median 50% of the cumulative temporal distribution occurring up to about 2 months earlier than during the other years. Overall, analysis of the cumulative temporal distribution of O. mykiss observed catch at the Hallwood Boulevard RST site revealed that most emigration generally occurred from March through July. Approximately 95 percent of the observed catch generally occurred by early August. Yuba Accord M&E Program 4-79 April 2013

80 1.00 Cumulative Distribution of Weekly Observed Catch Cumulative Fraction Figure Expected temporal distributions from fitted asymmetrical logistic functions of the weekly observed catch of juvenile O. mykiss at the Hallwood Boulevard RST site on the lower Yuba River for monitoring years 2000 and In an effort to infer information regarding implementation of the Yuba Accord, Figure 4-65 shows the pre-accord and Accord fitted distributions from combining the and data sets. Analysis of the cumulative distributions of pre-accord and Yuba Accord monitoring years (1999 to 2005 and 2006 to 2009, respectively) did not reveal a consistent temporal shift in the timing of emigration. Excluding survey year 2006 from the Accord cumulative distribution did not result in a more consistent shift in emigration timing relative to pre-accord years. JUVENILE STEELHEAD (O. MYKISS) OUTMIGRATION RELATIONSHIPS WITH FLOW AND WATER TEMPERATURE Flow and water temperature had some correlation with the annually estimated cumulative temporal distributions of emigrating juvenile O. mykiss (Table 4-14). Four survey periods where year-round monitoring occurred ( , , and ) were used in the analysis. Regression analysis was used to explore the potential relationships between the fitted distributions of juvenile O. mykiss and environmental river conditions. Parameters for the model were estimated using least squares procedures. Figure 4-66 shows scatter plots with linear regression lines, coefficients and R 2 values. Flow and temperature were minimally useful at predicting the distributions and linear regressions using these variables were able to explain <0.01% and 15% of the variability in the data (R 2 <0.01, P = 0.764, R 2 = 0.15, P = 0.046). Yuba Accord M&E Program 4-80 April 2013

81 1.00 Cumulative Distribution of Weekly Observed Catch Cumulative Fraction All Years Expected Distribution Pre Accord Expected Distribution Accord Expected Distribution Figure Expected temporal distributions from fitted asymmetrical logistic functions of the weekly observed catch of juvenile O. mykiss at the Hallwood Boulevard RST site on the lower Yuba River for monitoring years Several multivariate regression models using temperature and flow metrics were considered in attempt to better predict the observed percentile expressions. A multivariate linear regression using temperature and log transformed flow was best at predicting the percentile expressions and was able to describe 23% of the variability in the data (R 2 = 0.23, P = 0.037). The equation for the model was: Estimated Percentile Expression = x Mean log(flow) x Mean Temperature. Flow and water temperature had some correlation with the observed emigration magnitude of juvenile O. mykiss over all available years of RST data. The observed daily and weekly catch of juvenile O. mykiss and measures of flow and temperature were examined to determine whether the emigration timing of juvenile O. mykiss could be expressed as a function of weekly measures of lower Yuba River flows and water temperatures (Figures 4-67 and 4-68). Regression analysis was used to explore the potential relationships between the observed catch of juvenile O. mykiss and environmental river conditions. Parameters for the model (e.g., α, β 0, β 1, β 2 ) were estimated using least squares estimation procedures. The best fitting predictive model used the week of observation (beginning on or near October 1 of each sampling year), mean flow at the Marysville Gage, and mean weekly temperature as measured at the Marysville Gage to predict the log-transformed weekly observed catch. This model explained 19% of the variability in the observations (R 2 = 0.19, P <0.001). The equation for the model was: Yuba Accord M&E Program 4-81 April 2013

82 log(weekly Catch) = x Week x Mean Flow x Mean Temperature. Table Fitted temporal distributions of the weekly observed catch of juvenile O. mykiss at the Hallwood Boulevard RST site on the lower Yuba River for monitoring years Shaded areas indicate survey periods when year-round sampling occurred. Pre Lower Yuba River Accord ( ) Yuba River Accord ( ) Cumulative Cumulative ALL YEARS 10/ / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / Yuba Accord M&E Program 4-82 April 2013

83 4,500 Marysville Flow Marysville Temperature 20 4,000 y = 2.586x R² = , Marysville Flow (CFS) 3,000 2,500 2, Marysville Temperature ( C) 1,500 1,000 y = x R² = Figure Mean weekly flow and temperature at the Marysville Gage through the corresponding percentile expressions 1%, 10%, 25%, 50%, 75%, 90% and 99% from the estimated cumulative temporal distributions of emigrating juvenile O. mykiss at the Hallwood Boulevard RST site on the lower Yuba River for monitoring years SMOLT EMIGRATION During their downstream migration, juvenile steelhead undergo a process referred to as smoltification, which is a physiologic transformation and osmoregulatory pre-adaptation to residence in saline environs. Physiologic expressions of smoltification include increased gill ATPase and thyroxin levels, and a more slender body form which is silvery in appearance. In the lower Yuba River, the steelhead smolt emigration period has been reported to extend from October through May (CALFED and YCWA 2005; SWRI 2002; YCWA et al. 2007). The RMT (2010b) indicated that yearling+ steelhead smolt emigration may extend from October through mid-april. Additional review of recently available data confirms this characterization of the temporal distribution of yearling+ steelhead smolt emigration. Although not numerous, captures of (over-summer) holdover juvenile O. mykiss generally ranging from about 60 to 140 mm FL were observed in the RST captures primarily from October through mid-april. These fish likely reared in the river over the previous summer, representing an extended juvenile rearing strategy characteristic of holdover juvenile O. mykiss. Juvenile O. mykiss that exhibit extended rearing in the lower Yuba River are assumed to undergo the smoltification process and volitionally emigrate from the river, and are referred to as yearling+ smolts. Yuba Accord M&E Program 4-83 April 2013

84 Figure Mean weekly flow at the Marysville Gage and O. mykiss catch at the Hallwood Boulevard RST site on the lower Yuba River from October 1, 1999 to August 31, Yuba Accord M&E Program 4-84 April 2013