Summary,Conclusions and Recommendations

7.0Summary, Conclusions and Recommendations

The RMT’s M&E program is scheduled and funded to run through at least 2015. However, the RMT elected to produce this Interim Report both as a ‘report card’ on implementation of the Yuba Accord forregulators, stakeholders and the broader scientific community, and to help inform the relicensing process before the Federal Energy Regulatory Commission (FERC) currently underway for YCWA facilities in the Yuba River Watershed (the Yuba River Development Project, FERC Project No. 2246). By contrast to many FERC relicensings, which are confronted with scant current resource data and 30-50 year old flow regimes, the RMT has obtained a wealth of information on fisheries and aquatic resources of the lower Yuba River to evaluate the instream flow requirements of the Yuba Accord, which were recently approved by the SWRCB in 2008. The issuance of this Interim Report does not conclude RMT activities. Rather, the RMT intends to continue to conduct monitoring activities associated with the suite of studies referenced in Chapter 2 of this Interim Report. The RMT also will seek input and comment from the scientific community in order to refine the work planned for the next few years.

In the following sections, the monitoring and evaluation requirements specified in the Yuba Accord Fisheries Agreement and objectives for the development of the Yuba Accord flow schedules are summarized, followed by conclusions and recommendations of this Interim Report.

7.1M&E Program Requirements

As previously described, the RMT developed the M&E Program framework based on the scientific application of the regulatory constructs of ‘good condition’ and ‘viable salmonid populations’. It is useful, however, to also consider the original objectives for the development of the Yuba Accord flow schedules, and the specific assignments included in the Yuba Accord Fisheries Agreement.

7.1.1Objectives for Development of Accord Flow Schedules

The predecessor to the RMT was referred to as the Lower Yuba River Accord Technical Team (TT), some members of which currently remain as members of the RMT. The TT was responsible for development of the Yuba Accord flow regime. The development of that flow regime was undertaken with the goal of achieving several objectives, including the following.

  • Maximize the occurrence of “optimal” flows and minimize the occurrence of sub-optimal flows, within the bounds of hydrologic variationand available storage.
  • Maximize the occurrence of appropriate flows for Chinook salmon and steelhead immigration, spawning, rearing, and emigration.
  • Provide month-to-month flow sequencing in consideration of Chinook salmon and steelhead life history periodicities.
  • Provide appropriate water temperatures for Chinook salmon and steelhead immigration and holding, spawning, embryo incubation, rearing and emigration.
  • Promote a dynamic, resilient, and diverse fish assemblage.
  • Minimize potential stressors to fish species and life stages.
  • Develop flow regimes that consider all freshwater life stages of salmonids and allocate flows accordingly.

7.1.2Fisheries Agreement

The implementation of the Yuba Accord flow regimes was initially ensured by a binding legal contract - the Lower Yuba River Fisheries Agreement. The Fisheries Agreement, executed in 2007, specifies certain monitoring activities for the RMT, including the following.

  • Monitoring and evaluating the effectiveness of the implementation of the Yuba Accord in achieving its physical and contractual objectives, including flow schedules, Conference Year flows and the Water Purchase Agreement.
  • Evaluating the condition of fish resources in the lower Yuba River.
  • Evaluating the viability of lower Yuba River fall-run Chinook salmon and any subpopulations of the Central Valley steelhead DPS and spring-run Chinook salmon ESU that may exist in the lower Yuba River.
Good Condition & Viable Salmonid Populations

In order to fulfill the assignments of the Fisheries Agreement, the RMT developed the M&E Program framework based on two regulatory constructs: (1) California Fish & Game Code § 5937 which uses the term “good condition” as a benchmark to evaluate the success of flow prescriptions; and (2) the “Viable Salmonid Population” (VSP) concept initially developed by NMFS to facilitate establishment of ESU-level delisting goals and to assist in recovery planning by identifying key parameters related to population viability. In keeping with these constructs, the RMT’s M&E Program framework was designed to address two overarching goals:

  • Evaluate whether implementation of the Yuba Accord maintains fish in “good condition” and promotes “viable salmonid populations” in the lower Yuba River.
  • Identify and evaluate relationships between flows and water temperatures resulting from implementation of the Yuba Accord, and fish population and aquatic habitat attributes.

However, through development of this M&E Interim Report and discussions within the RMT, it became apparent that the two original goals of the M&E Program, presented in the overview framework in 2010,needed to be updated in consideration ofinformation obtained since the drafting of the goals and the M&E Program framework. Compelling information includes, in particular, recognition that the anadromous salmonid populations in the lower Yuba River are not independent populations, and that population responses to in-river conditions are obfuscated by out-of-basin factors and regional interactions. Hence, if the goals of the M&E Program were to be re-drafted today, then they would be expressed as follows.

  • Evaluate the condition and viability of fish populations in the lower Yuba River associated with implementation of the Yuba Accord.
  • Identify and evaluate relationships between fish population and aquatic habitat attributes, and flows and water temperatures associated with implementation of the Yuba Accord.
  • Determine whether the Yuba Accord flow schedules provide conditions that are protective of the fishery resources of the lower Yuba River (within the constraints of hydrologic variability).
Applicability of VSP and Extinction Risk Criteria

The M&E Program Framework developed by the RMT (2010) utilized VSP performance indicators that were identified based on the precept that the lower Yuba River anadromous salmonid populations represented independent populations. However, the RMT has identified a substantial amount of reproductive interaction between lower Yuba River and lower Feather River anadromous salmonid stocks. As described in Chapter 5 of this Interim Report, phenotypic spring-run Chinook salmon in the lower Yuba River likely represents hybridization between spring- and fall-run Chinook salmon in the lower Yuba River, hybridization with Feather River fall- and spring-run Chinook salmon stocks, and hybridization with the Feather River Fish Hatchery spring-run Chinook salmon stock, which itself represents hybridization between Feather River fall- and spring-run Chinook salmon populations. Additionally, it is likely that anadromous O. mykiss stocks are similarly hybridized, with fluid intermixing of lower Feather River and lower Yuba River fish.

The recognition of the extent of hybridization and lack of reproductive isolation of lower Yuba River and lower Feather River anadromous salmonid stocks logically constrains the manner in which the VSP concept can be applied to the lower Yuba River, because many of the VSP metrics are designed to evaluate the viability of discrete, independent populations. Even the simplified approach suggested by Lindley et al. (2007) to evaluate ‘extinction risk’ is of limited applicability in the evaluation of highly introgressed populations whose evaluation metrics are directly influenced by other stocks, and out-of-basin factors. Locally, Feather River Fish Hatchery management practices and Feather River flows and water temperatures, which influence straying rates into the lower Yuba River,also influence resultant lower Yuba River anadromous salmonid population parameters.

Only some of the VSP performance indicators identified in the RMT (2010) M&E Program framework would be appropriate for application specifically to lower Yuba River anadromous salmonids. For example, there are several performance indicators (and associated analytics) that either were included in the M&E Program framework, or evolved over the course of study development and initial data collection activities, that are appropriate for evaluation of habitat conditions in the lower Yuba River. These performance indicators and analyticsinclude spatial organization of morphological units (e.g., lateral variability/diversity, adjacency, randomness, and abundance), persistence of morphological units through time, floodplain connectivity, entrenchment, channel sinuosity, substrate size, changes in topographic depth, scour and fill processes, bankfull and flood flow recurrence interval, maintenance of watershed processes to maintain suitable habitat for anadromous salmonid lifestages, and the quality, number, size and distribution of morphological units available for spawning Chinook salmon.

7.2Performance Corresponding to the Yuba Accord Agreement Structure

The Yuba Accord includes a suite of binding legal agreements, as well as regulatory orders, that combine to ensure flows, revenues and water supplies for Yuba River resources and stakeholders. To date, all of the obligations in the Fisheries, Water Purchase and Conjunctive Use agreements of the Yuba Accord have been fulfilled by the responsible parties, and implementation of the Yuba Accord continues to proceed successfully. In particular, signatories to the Fisheries Agreement have achieved the following results.

  • Flows in the lower Yuba River have adhered to the required Yuba Accord flow schedules for all years. During the CEQA process for the Yuba Accord, flows pursuant to the Yuba Accord Fisheries Agreement were released as a pilot program during 2006 and 2007. For each of the years during which the Yuba Accord flow schedules have been implemented, thewater year and corresponding North Yuba River Index (NYI) (upon which the Accord flow schedules are based) and the Yuba River Index ((YRI) as established in D-1644, and which is closely associated with the broader Sacramento Valley Index) are listed in Table 7-1. The Accord flow schedule and YRI may change monthly, based on SWRCB Bulletin 120 reports, beginning in February of each year through May or later if any subsequent Bulletin 120 reports are issued in any particular year. The classification is then fixed until at least the following February.
  • As discussed in Chapter 1 and specified in Table 1-1 of this Interim Report, during 2003 theSWRCBissued Revised Decision (RD)-1644, which specified new instream flow requirements for the lower Yuba River. For comparative purposes, these flow requirements and the Yuba Accord flow requirements are presented in Figure 7-1, along with mean daily flows measured at the Marysville Gage, since the Yuba Accord has been implemented.
  • Water transfers pursuant to the Water Purchase agreement have been fulfilled. Supplemental groundwater transfers were successfully implemented in 2008, 2009 and 2010 in accordance with the provisions of the Fisheries and Water Purchase agreements.
  • The RMT has met regularly for over six years and has conducted the assignments embodied in the Fisheries Agreement, including scheduling of flows as needed, implementing the M&E Program, and disbursing funds from the RMF as necessary and appropriate.
  • The RMT typically meets twice per month, and has focused most of its efforts on development and conduct of the M&E Program. The RMT oversees a staff of up to 11 Full-Time Equivalents (FTEs), operates office, shop and storage facilities, disburses up to $1 million or more in annual budgets, and implements up to 12 separate study efforts per year. In addition, the RMT has applied for and received various grants, and entered into cooperative or research agreements with various resources agencies and academic collaborators. The scope and spectrum of the scientific study program conducted by the RMT are unique in the Central Valley.
  • The RMT typically has, and continues to operate on a consensus basis. It has not been necessary to utilize the dispute resolution provisions in the Fisheries Agreement.
  • The RMT has successfully conducted the comprehensive M&E Program, comprised of a broad suite of studies focused on anadromous species in the lower Yuba River. To date, the RMT has expended approximately $4.5 million of the original $5.5 million RMF budget.
  • The RMT has hosted four annual symposia (2009, 2010, 2011 and 2012). These symposia have shared annually updated findings of the M&E Program with the broader scientific community. Attendance at the symposia has increased each year, with attendance at the 2012 symposium approaching upwards of 100 people, including regulators, academicians, stakeholders, NGOs, and students.

Table 7-1. The North Yuba River Index and Yuba River Index for each of the years during which the Yuba Accord flow schedules have been implemented.

Year / NYI (Accord Schedule) / YRI / Notes
2006 / NA (1) / Wet / No year type defined, but would have been an Accord Schedule 1 year.
2007 / 2 / Dry / YRI changed from Wet to Below Normal in February, changed from Below Normal to Dry on April 10 - an Accord Schedule 2.
2008 / 3 / Critical / Accord Schedule changed from 2 to 3. YRI changed from Dry to Critical on May 9.
2009 / 2 / Below Normal / Accord Schedule changed from 3 to 2 on April 8. YRI changed from Critical to Dry on March 10 and from Dry to Below Normal on May 18.
2010 / 2 / Below Normal / Accord Schedule 2. YRI was Dry from March 10 to May 11, then Below Normal.
2011 / 1 / Wet / Accord Schedule 1 as of February 9; YRI changed from Below Normal to Above Normal on February 9 and to Wet on April 9.
2012 / 2 / Below Normal / Accord Schedule changed from 1 to 3 on February 9, changed from 3 to 4 on March 8 and changed from 4 to 2 on April 10. YRI changed from Wet to Dry to Critical to Below Normal on same dates as NYI.

Figure 7-1. SWRCB Revised Decision (RD)-1644instream flow requirements,Yuba Accord flow requirements,and mean daily flows measured at the Marysville Gage from 2006 - 2012.

Figure 7-1 (continued).

Figure 7-1 (continued).

Figure 7-1 (continued).

7.3Key Findings of the Yuba Accord M&E Program

In addition to specific quantitative analytics, the monitoring and research undertaken as a part of the M&E Program yielded some significant observations that provide important context for conclusions in this Interim Report.

7.3.1Spring-run Chinook salmon in the Lower Yuba River

Phenotypic spring-run Chinook salmon in the lower Yuba River do not represent a “pure” ancestral genome.Spring-run Chinook salmon reportedly were extirpated from the lower Yuba River in 1959 and, as reported by CDFG (1991), a population of spring-run Chinook salmon became re-established in the 1970s due to improved habitat conditions, fish stocked from the Feather River Fish Hatchery, and fish straying from the Feather River. Relatively high straying rates of Feather River Fish Hatchery Chinook salmon into the lower Yuba River continue to be observed. Data obtained through the course of implementing the M&E Program demonstrate that phenotypically “spring-running” Chinook salmon in the lower Yuba River do not represent an independent population – rather, they represent anintrogressive hybridization of the larger Feather-Yuba river regional population. The introgression and phenotypic interchange between the various runs and stocks has implications throughout the analysis of lower Yuba River fisheries data.

7.3.2New Developments in Anadromous Salmonid Life History Characterization

Data and information obtained through implementation of the M&E Program has provided new insights and developments regarding life history characterization of anadromous salmonids in the lower Yuba River. This Interim Report has documented diverse life history strategies of anadromous salmonids in the lower Yuba River. As described in Chapter 4, Chinook salmon and steelhead exhibit highly diverse spatial and temporal distributions in patterns of adult upstream migration, holding and spawning, which may infer spreading of extinction risk in a variable environment such as the lower Yuba River. A particular new development in life history characterization pertains to the upstream migration and holding behavior of phenotypic spring-run Chinook salmon.

Adult Spring-run Chinook Salmon Upstream Migration and Holding

The RMT’s 3-year acoustic telemetry study of adult Chinook salmon tagged during the phenotypic adult spring-run Chinook salmon upstream migration period has provided new information to better understand adult spring-run Chinook salmon temporal and spatial distributions in the Yuba River. The results from the acoustic telemetry study found past characterizations of temporal and spatial distributions to be largely unsupported, as 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.

Previous reports have suggested that spring-run Chinook salmon enter the lower Yuba River during spring and immediately migrate upstream to the uppermost reaches of the lower Yuba River and hold over the summer in the Narrows Pool prior to spawning from September through mid-November. Observations from the telemetry study identified that a large longitudinal extent of the lower Yuba River was occupied by the tagged spring-run Chinook salmon during immigration and holding periods. Also, temporal migrations to areas upstream of Daguerre Point Dam occurred over an extended period of time. The tagged 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 phenotypic summer holding period, including areas as far downstream as Simpson Lane Bridge (i.e., ~RM 1.8), 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. Flows under the Yuba Accord have provided adult spring-running Chinook salmon migratory access to areas located throughout the lower Yuba River, as well as a broad expanse of longitudinally distributed areas selected for holding.