PWS (Draft)_Adult_O.Mykiss BORBDO0034-A_1.pdf

BORBDO0034-A

Performance Work Statement

Monitoring Adult Anadromous O. mykiss in the Lower San Joaquin and Stanislaus River

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 monitoring and research that will enable Reclamation to accomplish the following objectives.

1. Enumerate the abundance of anadromous adult O. mykiss returning to spawn in the Stanislaus River.

2. Estimate the return timing of anadromous adult O. mykiss and how that relates to variable flow and temperature conditions.

This scope of work focuses on the adult O. mykiss life-stage. The overarching aim of this project is to generate data and analyses that can inform ongoing steelhead life-cycle and decision-support models while working collaboratively with Reclamation. Additional details regarding the efforts are provided in 9.0 Tasks below.

The need for this project is to improve baseline knowledge of O. mykiss abundance 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 monitoring plan (MP) focused on quantifying the abundance and timing of returning anadromous adult O. mykiss in the Stanislaus River, and

2. collect tissue samples (i.e., fin tissue, and scales) from O. mykiss greater than 16 inches for genetic analyses and length-at-age reconstruction.

3. quantify the annual abundance of adult O. mykiss returning to spawn in the Stanislaus River.

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 2 Option Years (2021-2023).

5.0 Administrative Information:

5.1 Recognized Holidays:

The Government recognized Holidays are as follows:

New Year’s Day Labor Day Martin Luther King Jr.’s Birthday Columbus Day President’s Day Veteran’s Day Memorial Day Thanksgiving Day Independence Day Christmas Day

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 that includes monitoring 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)

Deliverable Description Due Date

Anadromous adult O. mykiss Monitoring Plan December 2020

Technical memorandum including annual estimates of anadromous O. mykiss escapement

Annually in June 2021 and 2022

Technical memorandum including a synthesis of monitoring data and analysis of run timing.

June 2023

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 monitoring plan focused on evaluating the abundance and timing of returning anadromous adult O. mykiss.

• Integration of the adult O. mykiss monitoring plan with broader life-cycle monitoring plans under development.

• Obtain annual estimates of adult O. mykiss escapement.

• Collect biological samples (e.g., scales, otoliths, and fin tissue) from anadromous adult

O. mykiss

• Estimate the relationship between CVP-related environmental variables and the timing and success of migrating anadromous adult O. mykiss in the Stanislaus River.

9.0 Tasks

Description of Work:

This Contractor shall complete a Stanislaus River monitoring plan focused on quantifying the abundance and timing of returning anadromous adult O. mykiss. The Contractor shall include detailed information on survey and analytical methodology in addition to the spatiotemporal scope of monitoring. This contract shall cover monitoring activities including the installation and operation of two wire fyke traps on the lower San Joaquin River and operation of a resistance-board weir and VAKI Riverwatcher on the Stanislaus River during the spawning migration period of O. mykiss. The Contractor shall collect biological samples (e.g., scales, otoliths, and fin tissue) from anadromous adult O. mykiss when possible. In addition, the Contractor shall analyze the relationship between CVP-related environmental variables (e.g., flow and temperature) on the timing of anadromous adult O. mykiss migration. Task-specific details and deliverables are described below.

Task 1: Anadromous Adult O. mykiss Monitoring Plan

The Contractor shall develop a monitoring plan (MP) focused on quantifying the abundance and timing of returning anadromous adult O. mykiss in the Stanislaus River. The MP will include detailed information on the survey and analytical methodology, efficiency tests of fish traps and monitoring infrastructure, and quality assurance/quality control plan. In addition, the Contractor will develop testable hypotheses focused on the abundance and timing of returning O. mykiss in relation to CVP-related environmental variables (e.g., flow and temperature). 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 MP with input from Reclamation and other project partners. A Draft MP shall be submitted to Reclamation for review and comment. The Contractor shall incorporate comments on the Draft MP into a Final MP.

Task 1 Deliverables:

1) Electronic Draft and Final MP and schedule. Draft due October 31, 2020. Final due December 31, 2020 or within four weeks after Reclamation’s comments are provided.

Task 2: Adult O. mykiss Escapement Estimation

The Contractor shall implement annual surveys to estimate the abundance and timing of returning anadromous adult O. mykiss. At a minimum the surveys will include:

- Operation of a resistance-board weir and VAKI Riverwatcher on the Stanislaus River.

- Data on the abundance and timing of returning adult O. mykiss.

- Installation and operation of two wire fyke traps between the San Joaquin-Stanislaus

River confluence and Old River-San Joaquin River confluence.

- Tissue collection from captured adult O. mykiss including scales, fin tissue for future genetic analyses, and otoliths if carcasses are opportunistically recovered.

- An analytical framework that produces mean escapement estimates with estimates of uncertainty, error, and trap efficiency.

The primary goal of this task is to quantify the annual abundance of adult O. mykiss returning to spawn in the Stanislaus River. The Contractor shall develop operation protocols in collaboration with Reclamation and other project partners to cover the entire steelhead migratory period. The Contractor shall operate a resistance-board weir and VAKI Riverwatcher to generate data on the abundance and timing of adult O. mykiss returning to spawn in the Stanislaus River. The Contractor shall work with Reclamation and other project partners to identify how the resistance-board weir can be modified to capture adult O. mykiss (e.g., installation of a trap box). Capture of adult O. mykiss will provide opportunities to collect tissues (e.g., scale and fin) and potentially tag fish to monitor movement rates and spawning habitat use.

A secondary objective of this task is to monitor the annual abundance and timing of adult O.

mykiss migrating into the San Joaquin River downstream of the San Joaquin-Stanislaus River confluence. The Contractor shall install and operate two fyke traps between the San Joaquin- Stanislaus River confluence and Old River-San Joaquin River Confluence. The Contractor shall collect biological samples (e.g., scale and fin tissue) and mark adult O. mykiss captured in the fyke traps using a combination of Passive Integrated Transponder (PIT) and visual tags (e.g., Floy). The Contractor shall work collaboratively with Reclamation and other project partners to identify an optimal location for trap installation.

Task 2 Deliverables:

1) Raw data collected during field surveys submitted as a Comma Separated Values (CSV) files due annually in June of 2021 and 2022.

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 and 2022.

3) Technical Memorandum including details on study design, survey schedule, annual O.

mykiss escapement estimates, discussion and caveats, and technical and logistical challenges encountered due annually in June of 2021 and 2022.

Task 3: Analysis & Technical Memorandum

The Contractor shall synthesize information generated in the task 2 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 MP from Task 1 using data and information generated in Task 2.

- Identify ongoing knowledge gaps, and monitoring, and research needs related to anadromous adult O. mykiss.

- Analysis and interpretation of how CVP operations (e.g., temperature and flow) may alter the timing and abundance of O. mykiss returning to spawn in the Stanislaus River.

- Management recommendations that can help guide future CVP operations.

The Contractor shall incorporate Task 3 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 3 Deliverables:

1) Annotated R script used for data management and analysis of data generated in Tasks 2 due June of 2023.

2) Technical Memorandum, including analyses, results, and discussion, formatted for submission to a peer-reviewed scientific journal due in June of 2023.

Task 4: 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.

The Contractor shall manage the project scope, budget, and schedule. This task 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 associated stakeholders,

• 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 assist in facilitation of these meetings, provide meeting agendas when necessary, 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. Meeting materials due in draft 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

(a) 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.

(b) 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.

(c) 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.

(d) 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.

(e) 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)

Performance Requirements Summary

Performance Standard/ Acceptable Quality Level* Method of Surveillance

Documents and Data Address all relevant components that could be included. Includes up to date information that is the best available current science. Meet

Review of the materials submitted

Performance Requirements Summary

Performance Standard/ Acceptable Quality Level* Method of Surveillance requirements of applicable laws, statutes, regulations, standards, and principles and guidelines.

Schedule and participate in meetings

Meetings, as needed, are scheduled, attended and facilitated

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

Observation at meetings

Observation at meetings, input from attendees

Provide meeting summaries Prompt meeting summaries addressing input received and technical issues raised during meetings

Review of meeting summaries

Provide annotated R scripts used in data management and analysis

R-based functions, statistical tests, data figure generation can be re-run allowing the reproduction of study results

R scripts will be run on Reclamation computers.

Confirm results produced match those reported in technical memos

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