HatcheryGenetics_PWS_20250909.pdf

PERFORMANCE WORK STATEMENT (PWS)

Genetic Analysis of Salmon and Steelhead Production at the USACE

Hatchery Facilities in the Russian River Part 1

General Information

1. GENERAL: This is a non-personnel services contract to provide genetic data and analysis on fish raised at, returned to, and spawned at the San Francisco District’s facilities, as well as technical expertise regarding their effects on US Endangered Species Act-listed Coho salmon and Steelhead in the Russian

River basin. The Government shall not exercise any supervision or control over the contract service providers performing the services herein. Such contract service providers shall be accountable solely to the

Contractor who, in turn is responsible to the Government.

1.1 Description of Services/Introduction: The contractor shall provide all personnel, equipment, supplies, facilities, transportation, tools, materials, supervision, and other items and non-personal services necessary to provide genetic data and analysis on fish and the technical interpretation thereof except for those items specified as government furnished property and services. The contractor shall perform to the standards in this contract.

1.2 Background The Russian River Coho salmon and Steelhead hatchery programs were founded with local broodstock and therefore constitute native lineages. However, for many years, no natural-origin fish were used as broodstock (i.e., segregated programs), although they have now transitioned to integrated programs where broodstock is composed of hatchery- and natural-origin adult Steelhead. Nevertheless, natural-origin adults returning from sea and entering the hatchery have typically been relatively sparse and have not provided a sufficient number of fish to meet natural-origin broodstock goals. As a consequence, these programs have remained largely “closed”.

Molecular genetic data can be used to understand many elements of hatchery production of Steelhead and other fishes, including extent of inbreeding and its effects on survival, variance in reproductive success and family size, age structure, and rates of iteroparity. In addition, when broodstock is sampled in two such programs, direct estimates of migration rate and directionality between them can be derived

1.3 Objectives: Provide genetic data and analysis on fish raised at the San Francisco District’s facilities to increase genetic diversity and avoid mating of close relatives:

• Genotype data for all fish that are potential broodstock for the spawning season.

• Spawning/breeding matrices derived from the genotype data for all potential Coho salmon broodstock.

• Genotype data and analysis for a limited number of natural area-origin fish for evaluation as potential broodstock.

• Execute genetic analysis to provide allocation lists of Coho broodstock to be retained at the hatchery for spawning, and to be released into multiple watersheds in order to maximize genetic diversity and support regional recovery efforts.

1.4 Scope: Provide genetic data and analysis on fish raised at the San Francisco District’s facilities to increase genetic diversity and avoid mating of close relatives.

1.5 Period of Performance: The period of performance shall be 400 days

1.6 General Information

DRAFT

1.6.1 Quality Control The contractor shall demonstrate an effective quality control program to ensure services are performed in accordance with this PWS. The contractor’s quality control program is the means by which he assures himself that his work complies with the requirement of the contract.

1.6.2 Quality Assurance: The government shall evaluate the contractor’s performance under this contract in accordance with the with the requirements of this PWS.

1.6.5 Place of Performance: The work to be performed under this contract will be performed at the contractor’s facilities.

1.6.6 Type of Contract: The government will award a firm fixed price contract.

1.6.7 Physical Security: The contractor shall be responsible for safeguarding all government equipment, information and property provided for contractor use.

1.6.9 Post Award Conference/Periodic Progress Meetings: The Contractor agrees to attend any post award conference convened by the contracting activity or contract administration office in accordance with

Federal Acquisition Regulation Subpart 42.5. The contracting officer, Contracting Officers Representative

(COR), and other Government personnel, as appropriate, may meet periodically with the contractor to review the contractor's performance. At these meetings the contracting officer will apprise the contractor of how the government views the contractor's performance and the contractor will apprise the Government of problems, if any, being experienced. Appropriate action shall be taken to resolve outstanding issues.

These meetings shall be at no additional cost to the government.

1.6.10 Contracting Officer Representative (COR): The (COR) will be identified by separate letter. The

COR monitors all technical aspects of the contract and assists in contract administration The COR is authorized to perform the following functions: assure that the Contractor performs the technical requirements of the contract: perform inspections necessary in connection with contract performance:

maintain written and oral communications with the Contractor concerning technical aspects of the contract:

issue written interpretations of technical requirements, including Government drawings, designs, specifications: monitor Contractor's performance and notifies both the Contracting Officer and Contractor of any deficiencies; coordinate availability of government furnished property, and provide site entry of

Contractor personnel. A letter of designation issued to the COR, a copy of which is sent to the Contractor, states the responsibilities and limitations of the COR, especially with regard to changes in cost or price, estimates or changes in delivery dates. The COR is not authorized to change any of the terms and conditions of the resulting order.

1.6.11 Key Personnel: The follow personnel are considered key personnel by the government: The contractor shall provide a contract manager who shall be responsible for the performance of the work. The name of this person and an alternate who shall act for the contractor when the manager is absent shall be designated in writing to the contracting officer. The contract manager or alternate shall have full authority to act for the contractor on all contract matters relating to daily operation of this contract. The contract manager or alternate shall be available between 8:00 a.m. to 3:00 p.m., Monday thru Friday except Federal holidays.

PART 2

DEFINITIONS & ACRONYMS

2. DEFINITIONS AND ACRONYMS:

2.1. DEFINITIONS:

2.1.1. CONTRACTOR. A supplier or vendor awarded a contract to provide specific supplies or service to the government. The term used in this contract refers to the prime.

2.1.2. CONTRACTING OFFICER. A person with authority to enter into, administer, and or terminate contracts, and make related determinations and findings on behalf of the government. Note: The only individual who can legally bind the government.

2.1.3. CONTRACTING OFFICER'S REPRESENTATIVE (COR). An employee of the U.S. Government appointed by the contracting officer to administer the contract. Such appointment shall be in writing and shall state the scope of authority and limitations. This individual has authority to provide technical direction to the Contractor as long as that direction is within the scope of the contract, does not constitute a change, and has no funding implications. This individual does NOT have authority to change the terms and conditions of the contract.

2.1.4. DEFECTIVE SERVICE. A service output that does not meet the standard of performance associated with the Performance Work Statement.

2.1.5. DELIVERABLE. Anything that can be physically delivered, but may include non-manufactured things such as meeting minutes or reports.

2.1.6. KEY PERSONNEL. Contractor personnel that are evaluated in a source selection process and that may be required to be used in the performance of a contract by the Key Personnel listed in the PWS. When key personnel are used as an evaluation factor in best value procurement, an offer can be rejected if it does not have a firm commitment from the persons that are listed in the proposal.

2.1.7. PHYSICAL SECURITY. Actions that prevent the loss or damage of Government property.

2.1.8. QUALITY ASSURANCE. The government procedures to verify that services being performed by the Contractor are performed according to acceptable standards.

2.1.9. QUALITY ASSURANCE Surveillance Plan (QASP). An organized written document specifying the surveillance methodology to be used for surveillance of contractor performance.

2.1.10. QUALITY CONTROL. All necessary measures taken by the Contractor to assure that the quality of an end product or service shall meet contract requirements.

2.1.11. SUBCONTRACTOR. One that enters into a contract with a prime contractor. The Government does not have privity of contract with the subcontractor.

2.1.12. WORK DAY. The number of hours per day the Contractor provides services in accordance with the contract.

2.1.12. WORK WEEK. Monday through Friday, unless specified otherwise.

2.2. ACRONYMS:

ACOR Alternate Contracting Officer's Representative

AFARS Army Federal Acquisition Regulation Supplement

AR Army Regulation

CCE Contracting Center of Excellence

CFR Code of Federal Regulations

CONUS Continental United States (excludes Alaska and Hawaii)

COR Contracting Officer Representative

COTR Contracting Officer's Technical Representative

COTS Commercial-Off-the-Shelf

DA Department of the Army

DD250 Department of Defense Form 250 (Receiving Report)

DD254 Department of Defense Contract Security Requirement List

DFARS Defense Federal Acquisition Regulation Supplement

DMDC Defense Manpower Data Center

DOD Department of Defense

FAR Federal Acquisition Regulation

HIPAA Health Insurance Portability and Accountability Act of 1996

KO Contracting Officer

OCI Organizational Conflict of Interest

OCONUS Outside Continental United States (includes Alaska and Hawaii)

ODC Other Direct Costs

PIPO Phase In/Phase Out

POC Point of Contact

PRS Performance Requirements Summary

PWS Performance Work Statement

QA Quality Assurance

QAP Quality Assurance Program

QASP Quality Assurance Surveillance Plan

QC Quality Control

QCP Quality Control Program

TE Technical Exhibit

PART 3

GOVERNMENT FURNISHED PROPERTY, EQUIPMENT, AND SERVICES

3. GOVERNMENT FURNISHED ITEMS AND SERVICES:

3.1. Services: The Government will provide no services

3.2 Facilities: The Government will provide no facilities.

3.3 Utilities: The Government will provide no utilities.

3.4 Equipment: The Government will provide no equipment.

3.5 Materials: The Government will provide tissue samples collected from endangered Coho salmon and threatened Steelhead.

PART 4

CONTRACTOR FURNISHED ITEMS AND SERVICES

4. CONTRACTOR FURNISHED ITEMS AND RESPONSIBILITIES:

4.1 General: The Contractor shall furnish all supplies, equipment, facilities and services required to perform work under this contract that are not listed under Section 3 of this PWS.

PART 5

SPECIFIC TASKS

5. Specific Tasks:

5.1. Basic Services. Provide genetic data and analysis on fish raised at, returned to, and spawned at the

San Francisco District’s facilities, as well as technical expertise regarding their effects on US Endangered

Species Act-listed Coho salmon and Steelhead trout in the Russian River basin.

5.2. Task Description.

5.2.1 Endangered Coho Salmon Tasks

This scope of work would provide for the analyses of genetic data and the construction of the breeding matrix needed for Coho salmon to be crossed in the upcoming 2025-26 spawning season. The agreement also provides for limited genetic analysis and identification of natural origin Coho salmon captured. This analysis will include evaluation of specific fish as potential broodstock or as products of the program.

Specifically, this project will use molecular genetic data and statistical analyses to provide:

• Evaluation of Coho salmon production by genetic analysis of broodstock and creation of matrices for potential breeding partners in the 2025-26 breeding season.

• Provision of technical advice and expertise through consultation with staff from the USACE, and other participating agencies, both through participation in workgroup meetings and other ad hoc meetings, as well as in-person, email and telephone consultations.

This work will use tissue samples that will have already been collected and provided by the government.

All Coho salmon will be genotyped with at least 95 single nucleotide polymorphism markers and with a molecular sex identification assay.

Coho Task Deliverables:

• Genotype data for all Coho salmon that are potential broodstock for the 2025-26 spawning season.

• Spawning/breeding matrices derived from the genotype data for all potential broodstock for the

2025-26 spawning season.

• Genotype data and analysis for a limited number of ocean return Coho salmon for evaluation as potential broodstock or for products of the program.

• Provide allocation lists of Coho broodstock to be retained at the hatchery for spawning, and to be released into multiple watersheds in order to maximize genetic diversity and support regional recovery efforts.

5.2.3 Steelhead Tasks

This scope of work would provide for the analyses of such data for broodstock from the Steelhead program in 2025-26 spawning season, and their analysis to provide information about the above-mentioned attributes of these programs. Specifically, this project will use molecular genetic data and statistical analyses to provide the following:

• Evaluation of inbreeding and relatedness in Steelhead broodstock used for production in the 2022 breeding seasons at Warm Springs Hatchery (WSH) and Coyote Valley Fish Facility (CVFF), as well as estimates of any consequent reductions in survival to reproduction of their progeny.

• Evaluation of variance in reproductive success and family size of Steelhead produced at WSH and

CVFF.

• Determination of age structure of broodstock both by spawn year and birth Cohort. Size information will be used to evaluate appropriate size-based criteria for determining age.

• Estimates of rates of iteroparity of fish from WSH and CVFF, as well as direct estimates of directionally specific migration rates between the two programs.

• Estimation of the fraction of broodstock that comes from different sources.

This work will use tissue samples that have already been collected and provided to the principal investigators, as well as data from previous genotyping efforts with Russian River Steelhead broodstock.

All Steelhead will be genotyped with at least 95 single nucleotide polymorphism markers and a genetic sex identification assay

Steelhead Task Deliverables:

• Genotype data for all Steelhead used as broodstock in Russian River production at WSH and

CVFF in the 2026 spawning season.

• Analysis and evaluation of genotype data for all Steelhead spawned 2025 spawning season and a written report describing the analysis and interpretation of the fitness of hatchery produced fish.

• Provision of technical advice and expertise through consultation with staff from the USACE, and other participating agencies, both through participation in workgroup meetings and other ad hoc meetings, as well as in-person, email and telephone consultations.

PART 7

ATTACHMENT/TECHNICAL EXHIBIT LISTING

7. Attachment/Technical Exhibit List:

7.1. Attachment 1/Technical Exhibit 1 – Performance Requirements Summary

7.2. Attachment 2/Technical Exhibit 2 – Deliverables Schedule

TECHNICAL EXHIBIT 1

Performance Requirements Summary

The contractor service requirements are summarized into performance objectives that relate directly to mission essential items. The performance threshold briefly describes the minimum acceptable levels of service required for each requirement. These thresholds are critical to mission success.

Performance Objective

(The Service required—usually a shall statement)

Standard Performance Threshold

(This is the maximum error rate. It could possibly be

“Zero deviation from standard”)

Method of

Surveillance

PRS # 1.

The contractor shall genotype fish for potential spawning in the programs

Part 5.

The contractor provides data and recommendations for spawning.

Zero deviation Review of submittals by

COR/QA.

PRS #2

The contractor shall provide the spawning matrix for Coho salmon

The contractor provides the spawning matrix

Deviations induced by

NOR captured during spawn

Review of submittal and updates by

COR/QA

TECHNICAL EXHIBIT 2

DELIVERABLES SCHEDULE

Deliverable Frequency # of Copies Medium/Format Submit To

Genotype data for all

Coho salmon that are potential broodstock

Once N/A PDF COR

Spawning/breeding matrices derived from the Coho genotype data for all potential broodstock

Once N/A PDF COR

Genotype data and analysis for a limited number of ocean return

Coho salmon for evaluation as potential broodstock

< 100 fish N/A PDF COR

Allocation list for

Coho broodstock to retain, and streams to release to

Once N/A PDF COR

Genotype data for all

Steelhead used as broodstock

Once N/A PDF COR

Genotype data and analysis for a limited number of natural origin Steelhead for evaluation as potential broodstock

< 100 fish N/A PDF COR

Analysis and statistics report for all stealhead data.

Once N/A PDF COR DRAFT