Recovery Plan For California's Central Valley Salmon and Steelhead Trout

Introduction

This Recovery Plan serves as a road-map that describes the steps, strategy, and actions that must be taken to return winter-run chinook salmon, spring-run chinook salmon and steelhead to viable status in the Central Valley, California thereby ensuring their long-term (time scales greater than 100 years) persistence and evolutionary potential.

Background

The rivers draining the Great Central Valley of California (‘Central Valley’) and adjacent Sierra Nevada and Cascade Range once were renowned for their production of large numbers of Pacific salmon (Clark 1929; Skinner 1962 in Yoshiyama et al. 1998). The Central Valley system historically has been the source of most of the Pacific salmon produced in California waters (CDFG 1950, 1955; Fry and Hughes 1951; Skinner 1962; CDWR 1984 in Yoshiyama et al. 1998). Chinook salmon (Oncorhynchus tshawytscha) historically were, and remain today, the only abundant salmon species in the Central Valley system (Eigenmann 1890; Rutter 1908 in Yoshiyama et al. 1998), although small numbers of other salmon species also have occurred occasionally in its rivers (Collins 1892; Rutter 1904a, 1908; Hallock and Fry 1967; Moyle et al. 1995 in Yoshiyama et al. 1998). Anadromous steelhead (O. mykiss) apparently were common in Central Valley tributaries (USFC 1876; Clark 1973; Latta 1977; Reynolds et al. 1993 in Yoshiyama et al. 1998) but records for them are few and fragmented, partly because they did not support commercial fisheries (Yoshiyama et al. 1998).

Since European settlement of the Central Valley in the mid-1800s, populations of native chinook salmon and steelhead have declined dramatically. California's salmon resources began to decline in the late 1800s, and continued to decline in the early 1900s, as reflected in the decline of chinook salmon commercial harvest. The total commercial catch of chinook salmon in 1880 was 11 million pounds but by 1922, it had dropped to seven million pounds, and reached a low of less than three million pounds in 1939 (Lufkin 1996).

In addition to commercial harvest of chinook salmon, another major factor affecting anadromous salmonids during this period was hydraulic gold mining, which began in the 1850s. By 1859, an estimated 5,000 miles of mining flumes and canals diverted streams used by salmonids for spawning and nursery habitat. Habitat alteration and destruction also resulted from the use of hydraulic cannons, hydraulic and gravel mining, which leveled hillsides and sluiced an estimated 1.5 billion cubic yards of debris into the streams and rivers of the Central Valley (Lufkin 1996).

Despite the prohibition of hydraulic mining in 1894, habitat degradation continued. Habitat quantity and quality have declined due to: construction of levees and barriers to migration, modification of natural hydrologic regimes by dams and water diversions, elevated water temperatures and water pollution from agriculture and industry (Lufkin 1996).

Although the effects of habitat degradation on fish populations were evident by the 1930s, rates of decline for most anadromous fish species increased following construction of major water project facilities (USFWS 2001), which primarily occurred around the mid- 1900s. Many of these water development projects completely blocked the upstream migration of chinook salmon and steelhead to spawning and rearing habitats, and altered flow and water temperature regimes downstream from terminal dams. As urban and agricultural development of the Central Valley continued, numerous other stressors to anadromous salmonids emerged and continue to affect the viability of these fish today. Four of the more important stressors include: barriers to historic habitat, the continued commercial and recreational harvest of chinook salmon, predation of chinook salmon and steelhead from introduced species such as striped bass and black bass, and the high demand for limited water supply resulting in reduced in-stream flows, increased water temperatures and highly altered hydrology in the Sacramento-San Joaquin Delta.

Recovery Strategy

A broadly focused framework is necessary to serve as a strategic planning guide to integrate the actions contributing to the overarching goal of recovery of the two chinook salmon ESUs and the steelhead DPS. Because of the complexity associated with the multi-faceted considerations for Central Valley recovery efforts, this strategic planning framework incorporates: (1) viability at both the ESU/DPS and population levels; (2) prioritising watersheds currently occupied by at least one of the three listed species into three tiers – core 1, 2, or 3; and (3) prioritising unoccupied watersheds for reintroductions.

Bridging the gap between the ESU/DPS and population levels are population groups or salmonid eco-regions, which are delineated based on climatological, hydrological, and geological characteristics. The Central Valley Technical Recovery Team’s (TRT) identification of four population groups (hereafter referred to as diversity groups) that chinook salmon historically inhabited in the Central Valley are as follows:

• The basalt and porous lava diversity group composed of the upper Sacramento River and Battle Creek watersheds
  
• The northwestern California diversity group composed of streams that enter the mainstem Sacramento River from the northwest
  
• The northern Sierra Nevada diversity group composed of streams tributary to the Sacramento River from the east, and including the Mokelumne River, and
  
• The southern Sierra Nevada diversity group composed of streams tributary to the San Joaquin River from the east.

Historically, the Sacramento River winter-run chinook salmon ESU was composed of four populations within the basalt and porous lava diversity group and the Central Valley spring-run chinook salmon ESU was represented in all four of the diversity groups, with as many as 18 or 19 total populations. In addition to the four previously mentioned diversity groups, the Central Valley steelhead DPS has two more historic diversity groups: the Suisun Bay region which consists of tributaries to or near Suisun Bay and the Central Western California region, which contains west-side San Joaquin Valley tributaries. It is hypothesised that historically 81 independent populations of steelhead were dispersed throughout the six diversity groups.

Currently, the Sacramento River winter-run chinook salmon ESU is composed of a single population which is dependent on hatchery production and the Central Valley spring-run chinook salmon ESU is composed of three diversity groups with fish exhibiting spring-run chinook salmon life histories occurring in 12 watersheds. Only three of those 12 watersheds contain viable spring-run chinook salmon populations. The current distribution of steelhead is less well understood, but the DPS is composed of at least four diversity groups and at least 26 populations.

Three priority levels have been established to help guide recovery efforts for watersheds that are currently occupied by at least one of the three listed chinook salmon and steelhead species. Of highest priority are Core 1 populations, which have been identified based on a variety of factors, including:

1. the known ability or significant immediate potential to support independent populations
2. the role of the population in meeting the spatial and/or redundancy viability criteria
3. the severity of the threats facing the populations
4. the potential ecological or genetic diversity the watershed and populations could provide to the species, and
5. the capacity of the watershed and population to respond to the critical recovery actions needed to abate those threats.

Core 1 populations form the foundation of the recovery strategy and must meet the population-level biological recovery criteria for low risk of extinction set out in Table 4-1. NMFS believes that this set of Core 1 populations should be the first focus of an overall recovery effort. Core 2 population areas also form part of the recovery strategy by contributing to the highest potential to support geographically diverse populations. Core 2 populations must meet the biological recovery criteria for moderate risk of extinction set out in Table 4-1. These populations are of secondary importance in terms of recommended priority of recovery efforts. Finally, the complete attainment of ESU/DPS-level biological recovery criteria will likely also require the presence of populations listed as Core 3. Core 3 populations are present on an intermittent basis and are characterized as being dependent on other nearby populations for their existence. The presence of these populations provides increased life history diversity to the ESU/DPS and is likely to buffer against local catastrophic occurrences that could affect other nearby populations. Dispersal connectivity between populations and genetic diversity may be enhanced by working to recover smaller Core 3 populations that serve as stepping stones for dispersal.

Addressing the primary threats and risk factors for each of the ESU and DPS’s will require reintroducing populations to historic, and currently unoccupied habitats. Candidate areas for reintroduction have been identified and prioritized as either primary or secondary. Efforts to reintroduce fish to these areas will be challenging, expensive, and will require unparalleled efforts to gain stakeholder support. We prioritized these areas based on watershed-specific information, which is summarized in Chapter 5 (Recovery Scenarios) and described in more detail in Appendix A (Watershed Profiles). Some areas that were historically accessible to anadromous salmonids have been excluded from consideration for reintroductions because they are so critically impaired by hydroelectric development and channel inundation that we felt efforts should be focused on areas with a higher potential for success.

Recovery will be expensive and time-consuming, and will require changes in the management and monitoring of aquatic resources and habitats. Successful implementation of this recovery plan will require the support, efforts and resources of many entities, from Federal and state agencies to individual members of the public. Because of these challenges, the Recovery Plan requires an achievable strategy to select and implement recovery actions.

This Recovery Plan establishes a strategic approach to recovery. Because recovery of the two chinook salmon ESUs and the steelhead DPS will require implementation over an extended period of time, a stepwise strategy has been adopted, based on the threats assessment process and identification of priority threats, which first addresses more urgent near-term needs, upon which to build toward full recovery. As this Recovery Plan is implemented over time, additional information will become available to help determine whether the threats have been abated, to further develop understanding of the linkages between threats and chinook salmon and steelhead population responses, to identify any additional threats, and to evaluate the viability of chinook salmon and steelhead in the Central Valley.

The general near-term strategic approach to recovery includes the following elements:

• Secure all extant populations. Both ESUs and the DPS are far short of being viable, and extant populations, even if not presently viable, will likely be needed for recovery. The Central Valley TRT recommends that every extant population be viewed as necessary for the recovery of the ESU and DPS. Wherever possible, the status of extant populations should be improved.
  
• Begin collecting distribution and abundance data for O. mykiss in habitats accessible to anadromous fish. This is fundamental to designing effective recovery actions and eventual delisting. Of equal importance is assessing the relationship of resident and anadromous forms of O. mykiss, including the role the resident fish play in population maintenance and persistence.
  
• Minimize straying from hatcheries to natural spawning areas. Even low levels of straying from hatchery populations to wild ones works against the goal of maximizing diversity within ESUs and populations. A number of actions could reduce straying from hatcheries to natural areas, including replacing off-site releases with volitional releases from the hatchery, allowing all fish that attempt to return to the hatchery to do so, marking or tagging programs that could be used to separate wild and hatchery stocks, and reducing the amount of fish released (see CDFG and NMFS (2001), for a review of hatchery issues).
  
• Conduct critical research on fish passage above rim dams, reintroductions, and climate change. Current climate change information suggests that the Central Valley will become warmer, a challenging prospect for chinook salmon and steelhead – both of which are coldwater fish at the southern end of their distribution. To recover Central Valley salmon ESUs and the steelhead DPS, some populations will need to be established in cooler, high elevation areas now blocked by dams or insufficient flows. Assuming that most of these dams will remain in place for the foreseeable future, it will be necessary to facilitate the movement of fish around the dams in both directions. The near-term will include assessing habitat suitability and passage logistics.
  
• Listed salmonid ESUs are likely to be conservation-reliant (Scott et al. 2005). It seems highly unlikely that enough habitat can be restored in the foreseeable future such that Central Valley salmonid ESUs (and DPS) could be expected to persist without continued conservation management. Rather, it may be possible to restore enough habitat such that ESUs (and DPS) can persist with appropriate management, which should focus on maintaining ecological processes at the landscape level.

The long-term approach to recovery includes the following elements:

• Ensure that every extant diversity group has a high probability of persistence.
  
• Until all ESU viability criteria have been achieved, no population should be allowed to deteriorate in its probability of persistence.
  
• High levels of recovery should be attempted in more populations than identified in the diversity group viability criteria because not all attempts will be successful.
  
• Individual populations within a diversity group should have persistence probabilities consistent with a high probability of diversity group persistence.
  
• Within a diversity group, the populations restored/maintained at viable status should be selected to:
  • Allow for normative meta-population processes, including the viability of core populations, which are defined as the most productive populations
    
  • Allow for normative evolutionary processes, including the retention of the genetic diversity, as well as an increase in genetic diversity through the addition of viable populations in historic habitats
    
  • Minimise susceptibility to catastrophic events.

In addition to the general near- and long-term strategies, applying the viable salmonid population guidelines and recovery criteria presented in this recovery plan results in specific recovery needs for each species. In summary, a program that ultimately results in re-establishing at least two viable populations within each diversity group will be needed to recover winter-run, spring-run, and steelhead. Some flexibility around this criteria is warranted as is explained in the Recovery Scenario chapter, which gives top-down, conceptual descriptions of what a recovered ESU/DPS would look like for each of the three species.

Recovery Goals, Objectives and Criteria

The overarching goal of this Recovery Plan is the removal of the Sacramento River winter-run chinook salmon ESU, Central Valley spring-run chinook salmon ESU, and Central Valley steelhead DPS in the Central Valley Domain from the Federal List of Endangered and Threatened Wildlife (50 C.F.R. 17.11). The objectives and criteria to accomplish this goal builds upon the technical input and guidance provided by the Central Valley TRT, and much of the following discussion is taken directly from information developed by the TRT (Lindley et al. 2004; 2006; 2007).

In order for the chinook salmon ESUs and the steelhead DPS to achieve recovery, each Diversity Group must be represented, and population redundancy within the groups must be met to achieve Diversity Group recovery. Therefore, Diversity Group criteria include:

• Three viable populations of winter-run chinook salmon within the winter-run chinook salmon Diversity Group at low risk of extinction
  
• A minimum of two viable populations of spring-run chinook salmon within each of the four spring-run chinook salmon Diversity Groups, with the exception of the Northwestern California Diversity Group which historically did not contain independent spring-run chinook salmon populations. For the Northwestern California Diversity Group, observed occupancy will suffice rather than viability, as defined, and
  
• A minimum of two viable populations of steelhead within each of the four extant steelhead Diversity Groups, i.e. the Basalt and Porous Lava Diversity Group, the Northwestern California Diversity Group, the Northern Sierra Nevada Diversity Group and the Southern Sierra Nevada Diversity Group.

Recovery criteria at the population level were established by the Central Valley TRT and are included in this recovery plan (and apply to all three species), as described in Lindley et al. (2007). The TRT incorporated the four viable salmonid population parameters (McElhany et al. 2000) into assessments of population viability, and two sets of population viability criteria were developed, expressed in terms of extinction risk. The first set of criteria deal with direct estimates of extinction risk from population viability models. If data are available and such analyses exist and are deemed reasonable for individual populations, such assessments may be efficient for assessing extinction risk. In addition, the Central Valley TRT also provided simpler criteria. The simpler criteria include population size (and effective population size), population decline, catastrophic rate and effect, and hatchery influence. For a population to be considered at low risk of extinction, i.e. less than five per cent chance of extinction within 100 years, the population viability assessment must demonstrate that risk level or all of the following criteria must be met:

• The effective population size must be more than 500 or the population size must be more than 2,500
• The population growth rate must show that a decline is not apparent or probable
• There must be no apparent or minimal risk of a catastrophic disturbance occurring
• Hatchery influence must be low, as determined by levels corresponding to different amounts, durations and sources of hatchery strays

Additionally, qualitative threat abatement criteria must be met demonstrating that specific threats have been addressed and alleviated. These threat abatement criteria are established to address threats to, or resulting from, spawning grounds, habitat quality and quantity, over-utilisation, disease or predation, inadequate regulatory mechanisms, artificial propagation, climate change, water diversions, and non-indigenous aquatic nuisance species.

Recovery Scenarios

Conceptual recovery scenarios for each species, i.e. winter-run, spring-run and steelhead, are presented in Chapter 5 of this Recovery Plan to provide initial descriptions of what a recovered ESU/DPS would look like. These ESU/DPS-level recovery scenarios have been developed based on ESU/DPS, population, and ecological considerations to identify a combination of populations and population and habitat status levels that meet biological and threat abatement recovery criteria. The scenarios represent some of the many possible combinations of populations, restoration actions, risk minimization and threat abatement.

Considerations for ESU/DPS viability depends on the number of populations within the ESU/DPS, their individual status, their spatial arrangement with respect to each other and sources of catastrophic disturbance, and diversity of the populations and their habitats. In the most general terms, ESU/DPS viability increases with the number of populations, the viability of these populations, the diversity of the populations, and the diversity of habitats that they occupy (Lindley et al 2007).

The Central Valley TRT described the historical populations of Sacramento River winter-run chinook salmon and Central Valley spring-run chinook salmon ESUs in the Central Valley (Lindley et al. 2004). They considered geography, migration rates, genetic attributes, life history diversity, population dynamics, and environmental characteristics in grouping the populations into independent populations and dependent populations. For the Central Valley steelhead DPS, Lindley et al. (2006) identified historical independent populations based on a model that identifies discrete habitat and interconnected habitat patches isolated from one another by downstream regions of thermally unsuitable habitat.

In addition to ESU/DPS and population viability, structure and distribution considerations, the conceptual recovery scenarios incorporate ecological or habitat objectives for each Diversity Group:

• The recovery scenario must address the entire natural ecosystem
  
• The recovery scenario should reflect that viable ESUs/DPSs and populations require a network of complex and interconnected habitats, which are created, altered, and maintained by natural physical process
  
• The spatial distribution and productive capacity of freshwater and estuarine habitats should be sufficient to maintain viable populations identified for recovery
  
• The diversity of habitats for recovered populations generally should resemble historic conditions given expected natural disturbance regimes (wildfire, flood, volcanic eruptions, etc.). Historic conditions represent a reasonable template for a viable population – the closer the habitat resembles the historic diversity, the greater the confidence in its ability to support viable populations
  
• At a large scale, habitats should be protected and restored, with a trend toward an appropriate range of attributes for salmonid viability

The conceptual recovery scenarios were developed with consideration of the biological significance and recovery feasibility of each population. Biological significance was based on current status, potential for improvement, historical significance, proximity to other selected populations with reference to catastrophic risks, and spatial distribution between independent and dependent populations. Feasibility of recovery was based on expected progress as a result of existing programs, absence of apparent impediments toward recovery, and other management considerations, e.g. fish passage potential.

As this Recovery Plan is implemented over time, additional information will become available to help determine whether the threats have been abated, to further develop understanding of the linkages between threats and chinook salmon and steelhead population responses, identify any additional threats, and to evaluate the viability of chinook salmon and steelhead in the Central Valley. Monitoring and adaptive management in the course of implementation of this Recovery Plan will provide more information on the feasibility of recovering the winter- and spring-run chinook salmon ESUs and the steelhead DPS in the Central Valley Domain. Such information is expected to lead to adjustments in recovery expectations and restoration actions and, thus, recovery scenarios.

Recovery Actions

Many complex and inter-related biological, economical, social, and technological issues must be addressed in order to recover anadromous salmonids in the Central Valley. Policy changes at the Federal, State and local levels will be necessary to implement many of the recovery actions identified in this Recovery Plan.

For example, without substantial strides in habitat restoration, fish passage, and changes in water use, recovery will be difficult if not impossible. In many cases, such as the Sacramento-San Joaquin Delta, an improved governance structure is needed to consolidate, streamline and focus the many, often conflicting, regulatory and land use mandates that influence water and habitat management, and species status and recovery. Most importantly, achieving a recovered species status is not likely without a focused effort to secure core populations, reintroduce fish to priority watersheds (where the majority of historic spawning habitat is located), and to restore the ecological function of the interconnected habitats upon which the species depend for their survival.

Implementation and Cost Estimates

It is a challenging undertaking to facilitate a change in practice and policy that reverses the path towards extinction of a species to one of recovery. This change can only be accomplished with effective outreach and education, strong partnerships, focused recovery strategies and solution-oriented thinking that can shift agency and societal attitudes, practices and understanding. Implementation of the recovery plan by NMFS will take many forms and is described in the NMFS Protected Resources Division Strategic Plan 2006 (NMFS 2006a). The Recovery Planning Guidance (NMFS 2006b) also outlines how NMFS shall cooperate with other agencies regarding plan implementation. These documents, in addition to the ESA, shall be used by NMFS to set the framework and environment for plan implementation. The PRD Strategic Plan asserts that species conservation (in implementing recovery plans) by NMFS will be more strategic and proactive, rather than reactive. To maximize existing resources with workload issues and limited budgets, the PRD Strategic Plan champions organizational changes and shifts in workload priorities to focus efforts towards those activities or areas that have biologically significant beneficial or adverse impacts on species and ecosystem recovery (NMFS 2006a). The resultant shift will reduce NMFS engagement on those activities or projects not significant to species and ecosystem recovery.

NMFS actions to promote and implement recovery planning shall include:

• Formalising recovery planning goals on a program-wide basis to prioritise work load allocation and decision-making (to include developing the mechanisms to make implementation, e.g. restoration, possible)
  
• Conducting an aggressive outreach and education programme
  
• Facilitating a consistent framework for research, monitoring and adaptive management that can directly inform recovery objectives and goals, and
  
• Establishing an implementation tracking system that is adaptive, web-based (internet), and pertinent to support the annual reporting for the Government Performance and Results Act, Biennial Recovery Reports to Congress and the Five-Year Status Reviews.

NMFS efforts must be as far-reaching (beyond those under the direct regulatory jurisdiction of NMFS) as the issues adversely affecting the species. Thus, to achieve recovery, NMFS will need to promote the recovery plan and provide needed technical information and assistance to other entities that implement actions that may impact the species’ recovery. For example, NMFS will work with key partners on high priorities such as facilitating passage assessment and working with Counties to ensure protective measures consistent with recovery objectives are included in their General Plans.

An implementation schedule describing time frames and costs associated with individual recovery actions has been developed and is included in this Recovery Plan. Cost estimates for near-term and longer-term recovery actions have been provided wherever possible. Cost estimates have not been identified for all actions due to uncertainties associated with new types of actions that have not been implemented before. Total cost to recovery is challenging to reliably estimate because the biological response of recovery actions is uncertain, achieving recovery will be a long-term effort likely requiring at least a few decades, and new stressors may emerge over time. However, it is estimated that the cost for implementing recovery actions will range from $1.04 to 1.26 billion over the next five years, and over $10 billion over the next 50 years.

Further Reading

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