Modesto irrigation district don pedro project

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Don Pedro Project Oncorhynchus mykiss Population Study Plan




FERC NO. 2299
Oncorhynchus mykiss Population Study Plan
August July 2011
Related Study Requests: SWRCB-05, 06
1.0 Project Nexus
The continued operation and maintenance (O&M) of the Don Pedro Project (Project) may contribute to cumulative effects on habitat availability and production of in-river life stages of Oncorhynchus mykiss (O. mykiss).
2.0 Resource Agency Management Goals
The Districts believe that four agencies have resource management goals related to salmonid species and/or their habitat, including Central Valley steelhead: (1) U.S. Department of Interior, Fish and Wildlife Service (USFWS); (2) U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service (NMFS); (3) California Department of Fish and Game (CDFG); and (4) State Water Resources Control Board, Division of Water Rights (SWRCB).
A goal of the USFWS (2001) Anadromous Fish Restoration Program (AFRP), as stated in Section 3406(b)(1) of the Central Valley Project Improvement Act, is to double the long-term production of anadromous fish in California’s Central Valley rivers and streams. Objectives in meeting this long-term goal include: (1) improve habitat for all life stages of anadromous fish through provision of flows of suitable quality, quantity, and timing, and improved physical habitat; (2) improve survival rates by reducing or eliminating entrainment of juveniles at diversions; (3) improve the opportunity for adult fish to reach spawning habitats in a timely manner; (4) collect fish population, health, and habitat data to facilitate evaluation of restoration actions; (5) integrate habitat restoration efforts with harvest and hatchery management; and (6) involve partners in the implementation and evaluation of restoration actions.
NMFS has developed Resource Management Goals and Objectives for species listed under the Magnuson-Stevens Fishery Conservation and Management Act (16 U.S.C. §1801 et seq.) and the Endangered Species Act (ESA) (16 U.S.C. §1531 et seq.), as well as anadromous species that are not currently listed but may require listing in the future. NMFS’ (2009) Public Draft Recovery Plan for Sacramento River Winter-run Chinook salmon, Central Valley Spring-run Chinook salmon, and Central Valley steelhead (Draft Recovery Plan) outlines the framework for the recovery of ESA-listed species and populations in California’s Central Valley. For Central Valley steelhead, the relevant recovery actions identified for the Tuolumne River are to: (1) conduct habitat evaluations, and (2) manage cold water pools behind La Grange and Don Pedro dams to provide suitable water temperatures for all downstream life stages.
CDFG’s mission is to manage California's diverse fish, wildlife, and plant resources, and the habitats upon which they depend, for their ecological values and for their use and enjoyment by the public. CDFG’s resource management goals, as summarized in restoration planning documents such as “Restoring Central Valley Streams: A Plan for Action” (Reynolds et al. 1993), are to restore and protect California's aquatic ecosystems that support fish and wildlife, and to protect threatened and endangered species under California Fish and Game Code (Sections 6920–6924).
SWRCB has responsibility under the federal Clean Water Act (33 U.S.C. §11251–1357) to preserve and maintain the chemical, physical and biological integrity of the State’s waters and to protect water quality and the beneficial uses of stream reaches consistent with Section 401 of the federal Clean Water Act, the Regional Water Quality Control Board Basin Plans, State Water Board regulations, the California Environmental Quality Act, and any other applicable state law.
3.0 Study Goals
The O. mykiss Population Study will examine the relative influences of various factors on the production of in-river life stages of O. mykiss in the Tuolumne River, identify critical life-stages that may represent a life-history “bottleneck”, and compare relative changes in the population between alternative resource management scenarios.
4.0 Existing Information and Need for Additional Information
Information regarding the status, abundance, and habitat use of O. mykiss populations in the Tuolumne River is summarized in the Pre-Application Document (PAD), as well as in annual O. mykiss monitoring reports most recently filed with the FERC on January 15, 2011. Based upon both routine surveys conducted by the Districts, as well as more recent intensive snorkel surveys carried out as part of the April 3, 2008 FERC Order (123 FERC ¶ 62,012), the following information regarding in-river rearing population sizes and habitat use of O. mykiss is available.
Observations of O. mykiss have been recorded in the Tuolumne River since 1981 in various river monitoring programs, including snorkeling, seining, rotary screw trapping, as well as targeted monitoring efforts most recently documented in Stillwater Sciences (2011). These O. mykiss monitoring efforts have found juvenile and adult size classes most frequently along 5–10 river miles of the Tuolumne River downstream of La Grange Dam (River Mile 42–52), with very low numbers of individuals found at locations farther downstream. Water temperatures in this reach are generally suitable for O. mykiss, typically ranging from 11.8°C (53.2°F) to 23.1°C (70.3°F) in summer (Stillwater Sciences 2009), and from 10.2°C (50.4°F) to 14.4°C (58°F) in winter (Stillwater Sciences 2010). Although specific spawning locations have not been documented to date, routine O. mykiss observations in this portion of the river suggest suitable habitat conditions, with decreasing suitability moving downstream as a result of several factors (e.g., water temperature, predator habitat, etc.). A tracking study of adult O. mykiss was initiated in spring 2010 and will be completed in 2011. Although low numbers of O. mykiss carcasses have been identified during fall spawning surveys conducted since 1997, only one adult O. mykiss (276 millimeters Fork Length) has been identified at the counting weir and very little active spawning by O. mykiss has been documented to date by CDFG or other parties.
Despite a growing body of monitoring data, very little information is available regarding steelhead life-history and habitat use specific to the Tuolumne River. For this reason, there have been only limited attempts made to assess the relative importance of factors influencing the anadromous or resident forms of O. mykiss in the Tuolumne River. This study plan develops conceptual models that, depending upon data availability, may extend to quantitative modeling of the Tuolumne River O. mykiss population to assess the effects of habitat availability during summer and assess potential “bottlenecks” to in-river O. mykiss production.
5.0 Study Methods
The O. mykiss Population Study will rely upon existing literature and information, including previously conducted Tuolumne River studies, as well as interrelated relicensing studies in the development of both conceptual and possibly quantitative population models to examine the relative importance of factors affecting O. mykiss production and population levels.
5.1 Study Area
The study area includes potential spawning and rearing habitat in the Tuolumne River from the La Grange Dam (River Mile 52) downstream to Roberts Ferry Bridge (River Mile 39.5). The downstream extent of the study reach corresponds to the majority of O. mykiss observations documented in routine winter and summer O. mykiss surveys (Stillwater Sciences 2011).
5.2 General Concepts
The following general concepts apply to the study:

  • The model focuses on variables that are influenced by Project and non-Project factors.

  • Project-specific and resource-specific data will be used to calibrate and validate the model whenever possible.

  • Model outputs consist of representation of the modeled response variable under an existing baseline or initial condition, as well as predictions under one or more scenarios.

  • Although model uncertainties will be identified as part of this study, modeling predictions may show statistically significant differences from baseline conditions that are not ecologically or biologically significant. Should this occur, the criteria and rationale for biological significance will be documented along with the results.

5.3 Study Methods
Step 1 – Develop Conceptual Model from Previously Conducted Studies. Information from previously conducted studies, as well as the concurrent Salmonid Populations Information Integration and Synthesis Study (Study Plan W&AR-5), will be summarized. Using this information, conceptual models will be developed as narrative and graphical descriptions of the potential density-dependent and density-independent factors affecting each in-river life-stage of O. mykiss in the Tuolumne River.
Step 2 – Develop Quantitative Population Model. Using conceptual models developed in Step 1, a quantitative population model will be developed to provide a framework to examine the relative influences of in-river factors in controlling the equilibrium population sizes determined in recent reach-specific surveys (Stillwater Sciences 2008, 2009, 2010). Although habitat-specific density estimates from existing data may be developed as a function of water temperature, the study approach will use these estimates and other sources to develop a multi-stage stock production model (Baker 2009) in which starting numbers of a particular life-stage (stock) are mathematically modeled to predict how the numbers change as the cohort goes through subsequent life-stages.
Since very little information exists supporting the development of a full life-cycle model of anadromous O. mykiss that includes outmigration through the Delta as well as ocean residency, it is anticipated that the completed model will only consider in-river life-stages from spawning, to incubation, juvenile rearing, to adult in-river residency, with the potential to consider additional life stages such as modeling small number of out-of-basin immigrants or smolt emigrants from this population. Individual life-stage to life-stage steps will be modeled using independent sub-models, which can be implemented with methodologies ranging from common stock production forms (e.g., Beverton-Holt). This approach allows model structure to be initially developed without detailed consideration of the underlying mechanisms, but also allows the introduction of one or more mechanisms affecting life-stage to life-stage survival. A redd superimposition model may be used for the step from female spawners to deposited eggs if spawning gravel suitability or actual redd superimposition observations suggest this is occurring. A linear model may be used to reflect density-independent mortality (e.g., the step from eggs to emergent fry, in which mortality is not affected by density). Lastly, the Beverton-Holt (1957) and “hockey stick” models (Barrowman and Myers 2000) are typically used for density-dependent1 interactions (e.g., the life-step from fry to juvenile in circumstances when available habitat limits the population). More elaborate compartment or individual-based models may be introduced as sub-models to reflect variations in habitat conditions due to seasonal shifts in river flow or water temperature, predation or other factors.
The modeled life-stage structure, the factors selected and default values for parameters and stock production forms will be determined from Tuolumne River data and previously conducted studies, literature values, and agency consultation. For example, a carrying capacity (K) is generally specified for all density-dependent stock-production relationships. Information from prior habitat use assessments (Stillwater Sciences 2008, 2009, 2010) will be used to provide current estimates of rearing densities by habitat type (e.g., riffle, pool head, run, etc.) and literature review will be used to establish maximum densities. To determine carrying capacity (K), maximum densities within particular habitat types will be combined with up-to-date estimates of habitat availability from the ongoing Tuolumne River Instream Flow Study2 as well as the following interrelated studies being conducted as part of relicensing:

  • Spawning Gravel Study (Study Plan W&AR-4)

  • Salmonid Redd Mapping Study (Study Plan W&AR-8)

  • Predation Study (Study Plan W&AR-7)

  • Oncorhynchus mykiss Habitat Assessment Study (Study Plan W&AR-12) and

  • Temperature Criteria Assessment Study (Study Plan W&AR-14)

In order to parameterize the model, estimates of life-stage specific survival (r) will also be made from literature searches (e.g., incubation success due to gravel quality or temperature) as well as professional judgment. Understanding that very little O. mykiss life-history information exists specific to the Tuolumne River, parameter selection will rely more heavily on literature sources and prior modeling experience. Validation of the completed model will be carried out by modeling of summer-rearing population sizes in comparisons to recent population estimates (2008–2011) developed through intensive snorkel surveys (e.g., Stillwater Sciences 2008, 2009, 2010).

Step 3 – Evaluation of Factors Affecting O. mykiss Populations. To determine the life-stages and model parameters that most affect O. mykiss production, a sensitivity analysis will be conducted of the parameters and values in the model. The sensitivity analysis will evaluate the equilibrium juvenile and adult population sizes using initial parameter values established in Step 2, followed by varying the initial parameter values by:

  • Decreasing initial value by 50%

  • Decreasing initial value by 25%

  • Increasing initial value by 33%

  • Increasing initial value by 100%

For each change in value, the model will be used to calculate the equilibrium population size, holding all other values constant For sensitive parameters, additional scrutiny will be focused on the source of data, and the potential for the Project to influence those parameters. It should be noted, however, that sensitivity analyses of this type cannot explore the potential interactions of multiple input values that are simultaneously increased or decreased.

Step 4 – Evaluation O. mykiss Population Sizes under Current Project Operations. An evaluation of the population size of O. mykiss under the current FERC flow schedules will be compared with observed population estimates during spring and summer (Stillwater Sciences 2008, 2009, 2010).
Step 5 – Prepare Report. The Districts will prepare a report that includes the following sections: (1) Study Goals, (2) Methods and Analysis, (3) Results, (4) Discussion, and (5) Conclusions.
6.0 Schedule
The Districts anticipate the schedule to complete the study proposal as follows assuming FERC issues its Study Plan Determination by December 31, 2011 and the study is not disputed by a mandatory conditioning agency:

  • Conceptual Model Development (Step 1) January 2012–March 2012

  • Population Model Development (Step 1) March 2012–September 2012

  • Modeling Workshop (Step 2) May 2012

  • Modeling Sensitivity and Evaluation (Steps 2, 3, and 4) June 2012–September 2012

  • Report Preparation September 2012–December 2012

  • Report Issuance January 2013

7.0 Consistency of Methodology with Generally Accepted Scientific Practices
Population modeling is supported by a large body of literature spanning several decades (e.g., Paulik 1973, Moussalli and Hilborn 1986, Sharma et al. 2005). Population models are commonly employed in FERC relicensing projects to predict relative changes in population levels and salmonid production in response to changing variables.
8.0 Deliverables
In addition to the completed model, the Districts will prepare a report, which will document the methodology and results of the study.
9.0 Level of Effort and Cost
Study Plan implementation cost will be provided in the Revised Study Plan.
10.0 References
Baker, P. 2009. Generalizing the multi-stage stock-production paradigm: a flexible architecture for population modeling. In Knudsen EE, Michael H (Eds.). Pacific salmon environmental and life history models: advancing science for sustainable salmon in the future. American Fisheries Society Symposium 71. Bethesda, Maryland.
Barrowman N.J. and R.A. Myers. 2000. Still more spawner-recruitment curves: The hockey stick and its generalizations. Canadian Journal of Fisheries and Aquatic Sciences 57: 665-676.
Beverton, R.J.H., and S.J. Holt. 1957. On the dynamics of exploited fish populations. Ministry Agriculture, Fisheries and Food, Fisheries Investigation Series 2, No. 19. London, England.
Moussalli, E. and R. Hilborn. 1986. Optimal stock size and harvest rate in multistage life history models. Canadian Journal of Fisheries and Aquatic Sciences. 43: 135-141.
Paulik, G.J. 1973. Studies of the possible form of the stock-recruitment curve. Rapports et Proces-Verbaux des Reunions, Conseil International pour L'Exploration de la Mer 164: 302-315.
Reynolds, F.L., T.J. Mills, R. Benthin, and A. Low. 1993. Restoring Central Valley streams: a plan for action. Inland Fisheries Div., Calif. Dept. of Fish and Game. Sacramento CA. 184 p.

Sharma, R., A.B. Cooper, and R. Hilborn. 2005. A quantitative framework for the analysis of habitat and hatchery practices on Pacific salmon. Ecological Modeling 183: 231-250.

Stillwater Sciences. 2008. July 2008 population size estimate of Oncorhynchus mykiss in the lower Tuolumne River. Study plan. Prepared by Stillwater Sciences, Berkeley, California for Turlock Irrigation District and Modesto Irrigation District.
Stillwater Sciences. 2009. March and July 2009 population size estimates of Oncorhynchus mykiss in the lower Tuolumne River. Prepared by Stillwater Sciences, Berkeley, California for Turlock Irrigation District and Modesto Irrigation District.
Stillwater Sciences. 2010. March and August 2010 population size estimates of Oncorhynchus mykiss in the Lower Tuolumne River. Prepared for the Turlock Irrigation District and the Modesto Irrigation District by Stillwater Sciences, Berkeley, CA. November.
Stillwater Sciences. 2011. Tuolumne River 2010 Oncorhynchus mykiss Monitoring Summary Report. Prepared for the Turlock Irrigation District and Modesto Irrigation District by Stillwater Sciences, Berkeley, California. January.
U.S. Department of Commerce, National Marine Fisheries Service (NMFS). 2009. Public Draft Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-Run Chinook salmon and Central Valley Spring-Run Chinook Salmon and the Distinct Population Segment of Central Valley Steelhead. Available online at: <>.
U.S. Department of Interior, Fish and Wildlife Service (USFWS). 2001. Final restoration plan for the Anadromous Fish Restoration Program. A Plan to increase Natural Production of Anadromous Fish in the Central Valley of California. Report of the Anadromous Fish Restoration Program Core Group, Central Valley Project Improvement Act to the Secretary of the Interior. Stockton, CA.

1 Density-dependence in stock-production relationships occurs whenever food or space limitations cause the life-stage specific survival or growth to be related to the numbers of individuals present.

2 The Tuolumne River Instream Flow Study is currently being conducted in accordance with the May 12, 2010 FERC Order Modifying and Approving Instream Flow and Water Temperature Model Study Plans for the Don Pedro Project (Project No. 2299-072), as modified by Ordering Paragraph (A) of the July 21, 2010 FERC Order.

DRAFT - 8/29/11 Revised Study Plan W&AR-10 - Page FERC Project No. 2299

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