PWS (Draft)_Juvnile_O.Mykiss BORBDO0034-J_1.docx

BORBDO0033-J

BORBDO0033-J

Performance Work Statement

O. mykiss Population and Life-History Composition Census

December 2019

1.0 Background

A limited knowledge of California Central Valley Steelhead (Oncorhynchus mykiss) hinders our ability to evaluate the status and trends of this Distinct Population Segment (DPS) and quantify the effects of potential stressors such as CVP operations. For example, annual juvenile production from the California Central Valley Steelhead DPS is unknown and therefore take limits at the state and federal pumping facilities are set by expert judgement rather than O. mykiss population dynamics. It is essential that we improve our fundamental understanding of Central Valley O. mykiss biology and ecology in order to better manage and conserve the species.

California Central Valley O. mykiss are distributed throughout most watersheds but often in low abundance, particularly in San Joaquin tributaries (Williams et al. 2016). The species can adopt a broad range of life-history strategies ranging from anadromous (steelhead) to freshwater residents (Rainbow trout). While there is a genetic basis for life-history expression (Pearse et al. 2014), resident O. mykiss can produce offspring that adopt an anadromous life-history and anadromous steelhead can produce freshwater residents (Zimmerman et al. 2009). Current regulatory framework is focused on the anadromous portion of the Central Valley O. mykiss population. However, evidence suggests many O. mykiss in Central Valley are non-anadromous, likely not isolated from the anadromous component of the population.

There are a variety of genetic and environmental factors that influence population dynamics and life-history variation in O. mykiss (Kendall et al. 2014). Past research has emphasized that growth and survival in freshwater, survival during migration and at sea, asymptotic sizes achievable in freshwater, and genetic makeup are likely key factors in determining life-history expression and adaptation (Satterthwaite et al. 2009, 2010, Pearse et al. 2014). This project’s studies will build on past research focusing on evaluating how CVP operations impact the expression and evolution of O. mykiss life histories.

This project is designed to address the requirements outlined in Chapter 4 section 4.10.5.12.3 of the Proposed Action and coordinated long-term operations of the CVP and SWP by aiding the San Joaquin Basin Steelhead Collaborative and providing a Steelhead Life-Cycle Monitoring Program foundation. This project will be funded under CVPIA authority Provision 3046 (g)(4), which states “The primary purpose of this effort shall be to support the Secretary's efforts in fulfilling the requirements of this title through improved scientific understanding concerning, but not limited to measures needed to restore anadromous fisheries to optimum and sustainable levels in accordance with the restored carrying capacities of Central Valley rivers, streams, and riparian habitats.”

Reclamation anticipates this project and associated studies will span five years. However, the project has a modular design that will result in severable deliverables produced on an annual basis. Each modular component will fill critical knowledge gaps and therefore improve our understanding of O. mykiss biology and ecology. Reclamation aims to use the collective components of this project to test hypotheses related to O. mykiss life-history variation and CVP operations and enhance our ability to conserve and manage this species.

2.0 Purpose and Scope of Work

The scope of the project includes a series of complementary, stand-alone studies that will enable Reclamation to accomplish the following objectives.

1. Define methods and objectives for long-term monitoring of O. mykiss in the San Joaquin drainage.

2. Enumerate the population size of O. mykiss in the Stanislaus River

3. Estimate key population demographics (e.g., age structure, sex ratio).

4. Quantify the survival and transition probabilities of key life stages (e.g., egg-to-fry, instream rearing).

Conceptual and quantitative work described in this scope will be encompass multiple O. mykiss life-stages, while implemented field studies will focus on evaluating juvenile life stages. Collectively these efforts aim to generate data for analyses that can inform ongoing steelhead life-cycle and decision-support models. Additional details regarding the efforts are provided in 9.0 Tasks below.

The need for this project is to improve our baseline knowledge of O. mykiss biology and ecology in the San Joaquin drainage. Doing so will enable Reclamation to minimize potential impacts of CVP operations on O. mykiss population dynamics and the expression of anadromy in this species. In collaboration with Reclamation, the Contractor shall:

1. develop a San Joaquin drainage steelhead monitoring plan

2. produce annual estimates of the Stanislaus O. mykiss population size

3. produce annual estimates of population demographics including age structure and annual growth rates

4. quantify rates of egg-to-fry, instream rearing, and outmigration survival, and

5. quantify the abundance outmigrating juvenile O. mykiss that have elected an anadromous life history.

The geographic scope of the work is split between the Stanislaus and Lower San Joaquin River, California.

3.0 Type of Contract: The Government anticipates award of a Firm-Fixed Priced contract.

4.0 Period of Performance: The anticipated period of performance of the contract is August 1, 2020 through July 31, 2021, with 4 Option Years (2021-2025).

5.0 Administrative Information:

5.1 Recognized Holidays:

The Government recognized Holidays are as follows:

5.2 Place of Performance

The work to be performed under this contract shall be performed at the Contractor’s facility and other places appropriate for meetings.

Access to private property may be necessary to complete this PWS. Reclamation will work with private landowners to facilitate access. Under no circumstances should the Contractor access private property without prior approval from the landowner. Additionally, under no circumstances shall the Contractor release the results of the field surveys except to the respective landowner without prior authorization by Reclamation.

All field surveys shall be conducted by qualified professionals. Specific qualifications for professionals conducting these surveys shall be developed in coordination with Reclamation and may include prior professional experience, professional registrations, professional licenses, and permits or certifications issued by the National Marine Fisheries Service (NMFS), the United States Fish and Wildlife Service (USFWS), and/or the California Department of Fish and Wildlife (CDFW).

5.3 Security:

The contractor shall be responsible for safeguarding all government equipment, information and property provided for Contractor use.

The Contractor shall be responsible for obtaining any rights-of entry and/or permission from Reclamation, State or Local entities and/or private landowners regarding assess to any properties that may be subject to any field visits.

5.4 Contractor Key Personnel:

Contractor shall name a project manager and identify other key personnel prior to the commencement of work.

5.5 Contractor Travel:

Any travel performed by the contractor shall be in accordance with the Federal Travel Regulation, 41 CFR 300-304 and Clause WBR 1452.231-80, Contract Reimbursable Travel Costs – Bureau of Reclamation. The Clause can be found under the information of this requirement.

5.6 Deliverables:

The Contractor shall develop an initial project and deliverables schedule no later than one (1) month after contract award. The project schedule will include development of a San Joaquin basin steelhead monitoring plan and associated juvenile O. mykiss monitoring and research activities in accordance with Table 5.6.

· All deliverables (other than invoices) shall be delivered to the Contracting Officer’s Representative (COR) at Reclamation’s Bay-Delta Office on the specified due dates listed below.

· All electronic deliverables to be posted externally shall be compliant with Section 508 Amendment to the Rehabilitation Act of 1973 (https://section508.gov/content/learn/laws-and-policies).

· All electronic deliverables to be posted and all materials made available to the general public shall meet Reclamation’s Visual Identity Standards (https://www.usbr.gov/vip/IV-p-reports.html).

· All data shall be delivered in a format that is discoverable and useable by end users inside and outside the government, and consistent with Memorandum M-13-13 Open Data Policy – Managing Information as an Asset (https://project-open-data.cio.gov/policy-memo/).

· All draft electronic deliverables shall be developed and submitted using Microsoft (MS) Office programs as applicable (e.g., Word, Excel, PowerPoint, Project, etc.) and all spatial data will be submitted using ESRI ArcGIS.

· All data management, summaries, and statistical analyses will be developed and submitted using program R (https://www.r-project.org/).

Table 5.6 Schedule of Major Deliverables (see Tasks for more detail)

6.0 Government-Furnished Property

No Government-Furnished Property will be provided for this contract. Government will not furnish any property, services, utilities, etc.

7.0 Applicable Publications: (Current Editions)

There are no applicable publications at this time. Relevant standards are described in the tasks below as applicable.

8.0 Objectives:

· Develop a comprehensive monitoring plan that encompasses the O. mykiss life cycle and potential life-history pathways.

· Obtain annual estimates of O. mykiss population size in the Stanislaus River.

· Characterize O. mykiss population demographics (e.g., age structure, annual growth rates).

· Estimate survival at several life stages and stage transitions (e.g., egg-to-fry, instream rearing, juvenile outmigration).

· Quantify the abundance of juvenile anadromous O. mykiss outmigrants.

9.0 Tasks

Description of Work:

This Contractor shall complete a San Joaquin basin monitoring plan that includes detailed information on life-stage specific monitoring methodology and spatiotemporal scope. In addition, this contract shall cover monitoring activities including an assessment of the existing population size in the Stanislaus River, annual evaluation of the age classes and somatic growth rates of the target population, annual estimates of population vital rates (e.g., egg-to-fry, instream rearing survival, etc.), and annual estimates of the abundance of juvenile anadromous O. mykiss outmigrants. Task-specific details and deliverables are described below.

Task 1: Steelhead Monitoring Plan

The Contractor shall develop a Steelhead Monitoring Plan (SMP) that includes conceptual model of the O. mykiss life cycle and potential life-history pathways, a study design focused on evaluating key life stages (e.g., methods of data collection and analyses, etc.), and quality assurance/quality control plan. The Contractor will develop testable hypotheses based on the conceptual model described above. The Contractor shall utilize previous studies and products of ongoing activities to identify all existing information and assist with identifying new research and monitoring opportunities for consideration. The Contractor shall develop the SMP with input from Reclamation and other project partners. A Draft SMP shall be submitted to Reclamation for review and comment. The Contractor shall incorporate comments on the Draft SMP into a Final SMP.

Task 1 Deliverables:

1) Electronic versions of Draft and Final SMP and schedule. Draft delivered by October 31, 2020. Final delivered by December 31, 2020 or within four weeks after Reclamation’s comments are provided.

Task 2 – Enumeration of Current O. mykiss Population Size

The Contractor shall implement annual surveys to estimate the current O. mykiss population size. At a minimum the surveys will include:

· A mark-recapture component that will enable identification and monitoring of individual fish.

· Data on the spatial and temporal distribution of fish captured, marked, and released.

· Data on fork length, mass, and other morphometrics of individual O. mykiss captured.

· Tissue collection from captured O. mykiss including scales and fin tissue for future genetic analyses.

· A randomized design (e.g., GRTS)

· An analytical framework that produces mean population size estimates with estimates of uncertainty and error.

Juvenile abundances can be estimated using a variety of sampling and mark-recapture methods. Sampling methods employed by the Contractor may include, but will not necessarily be limited to beach seining, electrofishing, and hook-and-line sampling. Similarly, there are numerous methods that can effectively ‘mark’ individual fish including, but not limited to Passive Integrated Transponder (PIT) tags, elastomer tags, spot patterns and image recognition, and close-kin mark-recapture (CKMR). It is essential that surveys implemented by the Contractor be based on a Generalized Random Tessellation Sampling (GRTS) design, regardless of the specific approach. The Contractor shall work with Reclamation and other project partners to identify the temporal period when sampling will occur based on conditions for effective sampling and on the target life stage (e.g. YOY abundance, over winter abundance, etc.). In addition, the Contractor shall implement an analytical estimation of population size, including estimates of uncertainty, using R (https://www.r-project.org/).

The Contractor will produce annual estimates of the Stanislaus River O. mykiss population size. The methods used by the Contractor to complete this task will generate data on the spatiotemporal distribution of the target species and individual fish. The Contractor shall collect tissue samples (e.g., scales) during population surveys to support the completion of tasks described below. The Contractor will work collaboratively with Reclamation and other project partners to identify the optimal sampling and marking methodology and spatiotemporal scope of monitoring.

Task 2 Deliverables:

1) Raw data collected during field surveys submitted as a Comma Separated Values (CSV) files due annually in June of 2021 – 2024.

a. Multiple data files can be submitted using Microsoft (MS) Office programs such as Excel or Access.

2) Annotated R script used for data management and analysis due annually in June of 2021 – 2024.

3) Technical Memorandum including details on study design, survey schedule, annual O. mykiss population estimates, discussion and caveats, and technical and logistical challenges encountered due annually in June of 2021 – 2024.

Task 3: Analysis of Age and Growth

The Contractor shall analyze hard tissues (e.g., scales or otoliths) collected from Stanislaus River O. mykiss to generate annual estimates of fish age and growth. At a minimum these analyses will include:

· Image analysis of hard tissue microstructure (i.e., scale or otolith circuli).

· Redundant evaluation on microstructure from a subset of scale or otoliths reads (using independent readers) to assess error rate in age assignments and/or annual growth estimates.

· Individual IDs for scales or otoliths that can be linked to the individual source fish.

· An analytical framework that produces mean age structure and mean annual growth rates with estimates of uncertainty and error.

Age structure and annual growth rates are key parameters needed to model population dynamics (e.g., age and size at maturity and/or outmigration, etc). These factors impact population productivity, life-history expression, and size thresholds for electing disparate life-history pathways. Analyzing the microstructure of scales and otoliths is useful for estimating age and growth of O. mykiss however, tradeoffs exist between the use of each structure. Otoliths can be used to estimate daily growth rates in young-of-the-year individuals as well as age and annual growth rates. Otoliths are generally more accurate than scales because they are not subject to reabsorption but require lethal sampling whereas scales do not. The Contractor shall work with Reclamation and other project partners to identify to best tissue type and analytical approach needed to complete this task.

The Contractor shall collect data on the microstructure of scales and otoliths collected from juvenile and adult O. mykiss in the Stanislaus River. Microstructure data will be collected using ImageJ (https://imagej.nih.gov/ij/) or comparable image processing software. The Contractor will collect duplicate data on the microstructure of scales and otoliths from a randomly selected subset of scales and otoliths. This subset of samples will be evaluated by independent technicians. The Contractor will analyze these microstructure data to estimate age and growth of O. mykiss.

Task 3 Deliverables:

1) Raw images and microstructure data collected from individual fish due annually in June of 2021 – 2024.

a. Microstructure data will be submitted as a Comma Separated Values (CSV) files

b. Multiple data files can be submitted using Microsoft (MS) Office programs such as Excel or Access.

2) Annotated R script used for data management and analysis due annually in June of 2021 – 2024.

3) Technical Memorandum including details on sample design, tissue type, age structure, annual growth rates, discussion and caveats, and technical and logistical challenges encountered due annually in June of 2021 – 2024.

Task 4 – Egg-to-Fry Survival Study

The Contractor shall implement a field study designed to estimate rates of egg-to-fry survival. The study and corresponding analysis will include at a minimum:

· Sufficient replication and statistical power to estimate egg-to-fry survival as a function of water temperature, flow, and water quality (e.g., dissolved oxygen).

· A randomized design within the target study location.

· An analytical framework that produces mean survival estimates with estimates of uncertainty and error.

Survival of juvenile salmonids from egg to fry life stages can significantly impact population dynamics. There is relatively little known about how flow and water temperature impact egg-to-fry survival in Central Valley O. mykiss populations. However, it has been hypothesized that the impacts of flow and temperature on O. mykiss are similar to what has been observed in Chinook Salmon (Oncorhynchus tshawytscha; NMFS Biological Opinion 2019; Martin et al. 2017).

Under this task the Contractor shall design and implement a field study focused on estimating the functional relationship between egg-to-fry survival and potential environmental drivers associated with CVP operations (e.g., flow and water temperature). The Contractor will deliver data and results from this study in a format that can be readily incorporated in existing Decision Support Models (DSM) that are used to identify Central Valley Project Improvement Act (CVPIA) funding priorities. The Contractor shall work with Reclamation and other project partners to finalize the study design and analytical framework used to complete this task.

Task 4 Deliverables:

1) Raw data submitted as a Comma Separated Values (CSV) files due annually in June of 2022 and 2023.

a. Multiple data files can be submitted using Microsoft (MS) Office programs such as Excel or Access.

2) Annotated R script used for data management and analysis due annually in June of 2022 and 2023.

3) Technical Memorandum including details on study design, egg-to-fry survival rates, analysis of the functional relationship between environmental covariates (e.g., temperature and flow) and survival, discussion and caveats, and technical and logistical challenges encountered due annually in June of 2022 and 2023.

Task 5: Monitoring Instream & Outmigration Survival, and Outmigration Rate

The Contractor shall implement annual surveys to estimate the instream and outmigration survival and outmigration rate of O. mykiss. At a minimum these surveys and corresponding analyses will include:

· Installation and operation of a PIT-tag antenna array at a downstream reach of the Stanislaus River.

· The Contractor will identify the location of the antenna array during the initial phases of project planning in collaboration with Reclamation and other project partners.

· Estimation of instream and outmigration survival using a multi-state model (or comparable statistical model) that can account for detection probability while estimating the survival and/or recapture probability of individually marked fish.

· Produce estimates of downstream outmigrants that accounts for detection probability.

· An analytical framework that produces mean survival estimates with estimates of uncertainty and error.

The Contractor shall work collaboratively with Reclamation and project partners to design and implement surveys and analyses focused on estimating annual instream-rearing and outmigration survival. The Contractor will incorporate existing infrastructure and parallel Reclamation-funded O. mykiss survival studies where possible. The Contractor shall leverage the study design and data generated in Task 2 Enumeration of Current O. mykiss Population Size described above.

The Contractor will produce annual estimates of outmigrant abundance by using data derive from existing screw trap operations and data generated in Task 2 Enumeration of Current O. mykiss Population Size described above. The Contractor will work collaboratively with Reclamation and other project partners to identify potential locations for new migrant trapping locations and techniques. The Contractor will work with Reclamation to ensure the implemented juvenile migrant monitoring design has a sampling frequency sufficient to produce an unbiased estimate of outmigration abundance. The Contractor will provide recommendations on methods to evaluate migrant trap and antenna efficiency and conduct efficiency trials where and when necessary. The Contractor shall ensure the efficiency of traps and antenna arrays are regularly evaluated under the physical and biological conditions that inference is needed for (e.g. steelhead of a specific size range, range of specific flow conditions, etc.).

Task 5 Deliverables:

1) Raw data collected during field surveys submitted as a Comma Separated Values (CSV) files due annually in June of 2021 – 2024.

a. Multiple data files can be submitted using Microsoft (MS) Office programs such as Excel or Access.

2) Annotated R script used for data management and analysis of instream and outmigration survival, and enumeration of outmigrants due annually in June of 2021 – 2024.

3) Technical Memorandum including details on study design, survey schedule, annual O. mykiss instream-rearing and outmigration survival, annual O. mykiss outmigrant estimates, discussion and caveats, and technical and logistical challenges encountered due annually in June of 2021 – 2024.

Task 6: Synthesis of O. mykiss Research and Monitoring

The Contractor shall synthesize information generated in the task above as well as the information from previous applicable field surveys and modelling efforts. At a minimum this synthesis effort will include:

· A quantitative and qualitative analysis of the hypotheses described in the SMP from Task 1 using data and information generated in Tasks 2-5.

· Analysis of how study results can be scaled and transferred to other CVP watersheds.

· Identification of ongoing knowledge gaps along with monitoring and research needs.

· Analysis and interpretation of how CVP operations (i.e., temperature and flow releases) may alter O. mykiss population dynamics and life-history expression.

· Management recommendations that can help guide future CVP operations.

The Contractor shall incorporate the Task 6 elements described above in a technical memorandum. The Contractor shall produce a document that includes analyses, results, and discussion formatted for submission to a peer-reviewed scientific journal.

Task 6 Deliverables:

1) Annotated R script used for data management and analysis of data generated in Tasks 2-5 due in June of 2025.

2) Technical Memorandum, including analyses, results, and discussion, formatted for submission to a peer-reviewed scientific journal due June of 2025.

Task 7: Project Management

The Contractor shall develop a Project Management Plan (PMP), risk assessment process, quality assessment/quality control plan, Gantt chart and schedule for completing all tasks above. The PMP project schedule shall address each task and include start/finish dates, total duration in days, and key milestone dates. The PMP will be considered as a living document in which the Contractor shall be expected to periodically update over the full performance period of this project. Changes to the PMP are expected to be primarily focused on schedule and Gantt chart updates.

The Contractor shall provide general project management/administration activities in support of this project including but not limited to the following:

· Coordination of seasonal Project activities by the Contractor’s staff, document review, and quality assurance/quality control of work prepared for this Project.

· Scheduling, planning, and conducting meetings and presentations.

· Preparation and reproduction of meeting notes, handouts, and deliverables.

· Coordination and communication with the collaborating partners.

· Preparation of Monthly Progress Report outlining activities of the previous month by sub-task, activities anticipated for the current month by sub-task, issues or topics of concern, and a monthly invoice.

· Attendance and participation in Progress Meetings with Reclamation and other collaborating agency staff as scheduled to report on Project progress, contract/Project issues and concerns, and other matters related to the administration and execution of this contract.

For each meeting, the Contractor shall provide meeting notes that summarize action items and decision points. Draft meeting notes shall be delivered within five (5) days of the meeting. Final notes, incorporating comments and suggested changes, shall be provided within two (2) days of receipt of all comments.

The Contractor shall manage the project scope, budget, and schedule. This subtask addresses general project management efforts, including, but not limited to:

· Invoicing and monthly progress reports,

· Oversight of day to-day project activities and preparation of deliverables,

· Correspondence with Reclamation and project partners

· Consultant project team management,

· 508 compliance: ensuring all electronically posted documents are compliant with Section 508 Amendment to the Rehabilitation Act of 1973 and in accordance to Reclamation Standards,

· Reclamation Visual Identity standards: ensure all electronically posted and final documents meet Reclamation’s Visual Identity standards

The Contractor shall meet with Reclamation and project partners every other month through the duration of the project to report on project progress and review task milestones. The Contractor shall facilitate these meetings, provide meeting agendas, develop presentation materials describing project progress, and prepare meeting summary notes. The Contractor shall assume monthly conference calls with Reclamation between meetings.

Task 7 Deliverables:

1) Electronic Draft and Final PMP and schedule Draft due 2 weeks after contract award. Final due 2 weeks after Reclamation’s comments are provided.

2) Monthly invoices/progress reports: one hard copy to Reclamation’s Contracting Officer, one electronic copy to Reclamation's COR.

3) Electronic meeting agendas materials and notes. Draft version of meeting materials due 5 days before a meeting. Final meeting materials due 2 days before the meeting. Meeting notes due 5 days after the meeting.

10.0 Performance Assessment

1. Monitoring Performance. During the course of the evaluation period, the COR will track Contractor performance. Interim (mid-term) evaluations may be provided to identify strengths and weaknesses in the Contractor's performance during the period being evaluated. At the end of the period, the COR will assess the Contractor's performance in accordance with the Quality Assurance Surveillance Plan (QASP) and report to the Contracting Officer.

1. Contractor Self-Assessment. Following each evaluation period, the Contractor may provide a written self-assessment of its performance to the COR to be considered in its report to the Contracting Officer. The self-assessment shall be submitted not later than 5 working days after the end of each evaluation period. The self-evaluation shall not exceed 1 page per PRS element. The self-assessment shall address both the strengths and weaknesses of the Contractor's performance during the evaluation period. Where deficiencies in performance are noted, the Contractor shall describe the actions planned or taken to correct such deficiencies and avoid their recurrence. The self-assessment itself will NOT be the basis for the Disincentives determination.

1. COR Recommendation. The COR will consider all evaluations and any other pertinent information, including Contractor self-assessment, and will prepare a report to the Contracting Officer with findings and recommendations. The Contractor will be provided a copy of the draft findings and recommendations of the COR and will be afforded the opportunity to identify factual errors. The COR's draft recommendation is not subject to negotiation and the COR will not engage in discussions with the Contractor. Any errors identified by the Contractor will be addressed by the COR in its final report. The Contractor will be provided a copy of the final COR report at the same time the report is submitted to the Contracting Officer.

1. Payment Determination. The Contracting Officer may meet with the COR to discuss the COR's report. The Contracting Officer will make a final determination in writing as to the percentage of work successfully completed, and the resulting payment to be made. A copy of the determination will be provided to the Contractor no later than 45 calendar days after the end of the period being evaluated. All Contracting Officer decisions regarding Disincentives are unilateral decisions made solely at the discretion of the Government.

1. The Quality Assurance Surveillance Plan is one evaluation method the government uses to surveillance performance to determine whether the Contractor meets the standards of performance as defined in the Performance Work Statement.

QUALITY ASSURANCE SURVEILLANCE PLAN (QASP)/

PERFORMANCE REQUIREMENTS SUMMARY (PRS)

Adequate technical material and facilitation is provided to support the intended purpose of each meeting Observation at meetings

Observation at meetings, input from attendees

*Note - Timeliness is Required for All Tasks Within their Required Timeframes 100% of the Time