Draft_PWS_1.pdf

PERFORMANCE WORK STATEMENT (PWS)

For

REAL-TIME GENETIC MONITORING FOR THE CENTRAL VALLEY PROJECT

1.0 SCOPE

1.1 OBJECTIVE - The objective of this contract is to acquire contractor services to genetically identify the run of Chinook Salmon collected from the Central Valley Project (CVP) salvage facility and other relevant monitoring locations.

1.2 BACKGROUND -

Reclamation operates the Central Valley Project (CVP) in coordination with the State Water Project (SWP) which is operated by the California Department of Water Resources (DWR). Operations of the CVP and SWP impact water quality and quantity, fish distribution and survival, and available aquatic tidal habitats in the San Francisco Bay-Delta. The National Marine Fisheries Service (NMFS) evaluated these stressors in their Biological Opinion on the Long-term Coordinated Operation of the CVP and SWP (LTO BiOp) and concluded they are likely to jeopardize the continued existence of endangered Sacramento River winter run Chinook salmon, threatened Central Valley spring run Chinook salmon, threatened Central Valley steelhead, and threatened southern Distinct Population Segment of North American green sturgeon.

Central Valley Chinook salmon stocks differ in their Endangered Species Act listing status. Yet, it is often difficult to distinguish individuals from the different Evolutionarily Significant Units (ESUs).

Consequently many of the salmon monitoring and evaluation efforts in the Central Valley and Bay- Delta are hampered by uncertainty about stock identification and proportional effects of management actions. Studies have identified that the current length-at-date (LAD) methods for stock identification of juvenile Chinook salmon captured at Delta and river monitoring sites often have poor accuracy. The inaccuracy of the LAD method is likely due to differences in fish distribution during early rearing, habitat-specific growth rates, and inter-annual variability in temperatures and food availability that lead to overlap in the stock’s range of sizes.

The upcoming Proposed Action for Reclamation’s Central Valley Project (CVP) identified a requirement for stock identification of juvenile Chinook salmon being salvaged at the CVP and SWP salvage facilities in the Sacramento-San Joaquin Delta (Delta). These data serve as one of the most heavily relied upon data sets used to estimate the effect of project operations (e.g., entrainment loss) on fish species. The frequency and density of particular runs of Chinook salmon are important factors that influence Delta export operations between December and June. This is especially important because LAD methods cannot identify salmon runs with high accuracy. Determining the genetic identity of the fish could avoid or minimize the duration of export reductions triggered by the loss of fish falling within the older juvenile Chinook salmon size range that were not genetically winter-run or spring-run Chinook salmon (i.e., listed salmon runs). As such, rapid genetic processing for certain Chinook salmon class-size at the salvage facilities is required to provide information in near real-time for Delta water operations.

In addition to genetic information for Chinook salmon collected at the salvage facilities in the Delta, there may also be other genetic information needs for CVP operations. The annual threshold and incidental take limit of winter-run Chinook salmon at the Delta salvage facilities are determined based on the estimated number of juvenile winter-run Chinook salmon expected to enter the Delta. Referred to as juvenile production estimate (JPE), this estimate is calculated using catch numbers in the upper Sacramento River. Run identification of Chinook salmon collected in the upper Sacramento River may be necessary to ensure accurate JPE from year to year.

Overall, the goal of this project is to continue the Coordinated Genetic Monitoring Program, which began in 2015 (though genetic results exist for earlier years, as early as 1996). The objective of the genetic monitoring program is to improve accuracy of Central Valley fish monitoring programs by providing genetic stock identification information for tissues that may be collected from Red Bluff, Knights Landing, Delta Juvenile Fish Monitoring Program, salvage facilities, Sacramento River Fish stranding studies, and Mossdale monitoring stations. Samples will be collected from all four runs of Chinook salmon based on length-at-date (i.e., samples will be collected from Chinook of various sizes throughout the sampling period). Sample analyses may also include other difficult to identify species (e.g., larval Delta smelt or green sturgeon) or ambiguous samples (i.e., poor condition). The Rapid Genetic Protocol effort is one component of this Central Valley-Wide Genetic Monitoring Program (described below).

Genetic Analysis at Delta Fish Salvage Facilities

Rapid Genetic Procedures: Some of the action triggers in Reclamation’s Proposed Action and National Marine Fisheries Service (NMFS) Biological Opinion are based on loss of genetically confirmed juvenile winter-run Chinook salmon. The objective of the protocol was to process genetic samples collected from larger-sized juvenile salmon (i.e., winter-run LAD and larger fish) as soon as feasible after exceeding a loss density trigger, because true winter-run Chinook salmon are almost always in this size category. Due to interest from state agencies, there is also a desire to apply rapid genetic procedures to spring-run sized (LAD) salmon as well at the salvage facilities. As such, Reclamation will work with the Contractor to accommodate rapid genetic ID for spring-run LAD fish as much as possible.

Non-rapid Genetic Procedures:

Many juvenile Chinook salmon will be salvaged but not require the rapid genetic procedure since they are not winter-run sized nor trigger an export operation. In these cases, Reclamation will have all tissue samples collected at the CVP genetically identified. Reclamation estimates it may accumulate a backlog of ~1,000 samples each year. Our goal is to have the current water year samples that do not trigger an operational action to be genetically identified within 2 weeks during January through April (8 biweekly periods). We plan to have fish tissues that are collected after April 30th analyzed with more cost-effective methods that consequently have a slower turnaround time.

2.0 REFERENCES - Not applicable

3.0 TASKS - The contractor shall perform the following tasks:

Task 1. Identify population of origin from juvenile salmonid tissue samples from the Tracy Fish Collection Facility and other monitoring programs using approved genetic methods. This task will require contractor to be “on call” (including holidays and weekends) to receive and immediately analyze (within 24 hours) high-priority samples (e.g., those samples that trigger a reduction to CVP/SWP exports). Also, this task will support the biweekly and annual genetic data collections from juvenile salmonid tissues.

Task 2. Project Management

A. Secure and manage all staff; ensure staff have the technical training and expertise to accomplish the tasks and associated activities to meet scientific standards.

B. Prepare and submit monthly invoices to Reclamation as instructed and notify Reclamation project managers with any major changes to anticipated expenses.

C. Develop annual study plans. Study plan should include a data management plan that includes: protocol for data entry and quality assurance and control (QAQC); metadata documentation; and data back-up procedures.

D. Provide email updates and technical assistance to COR related to genetics.

E. Meet with Reclamation at least monthly to review timelines, provide updates, and discuss ongoing data analyses, reporting, and other deliverables.

F. Presentations, technical memoranda, publications, EDI data archive project page, and public outreach documents will acknowledge Reclamation funding and the contract/agreement number.

Task 3. Data Management and Sharing

A. Annual publication of QAQC’d data and metadata files to the EDI Data Portal or a similar repository.

B. Summarize data as needed for Reclamation reporting and information needs.

C. Share data with partner agencies or stakeholders upon request.

D. Enter a short summary of this project along with the project title, period of performance, milestones, budget, and list of deliverables and due dates into the Delta Science tracker with input from the COR. Recipient will enter pertinent updates annually. The Delta Science Tracker is an online platform to inventory and summarize science activities in the Delta with the intent of improving communication among the Delta science community, promoting opportunities for collaboration, and tracking funding opportunities and expenditures. The Tracker serves as a mechanism for sharing information about scientific activities, highlights opportunities for collaboration, and provides access to related publications and outputs.

E. Annual report summarizing genetic identification results by August 31st each year. This report would include comparison of LAD and genetic assignments for the year and interannual data comparison when applicable.

4.0 PERFORMANCE REQUIREMENTS SUMMARY

Task No.

Task Description

Performance

Indicator

Performance

Standard

Minimum Acceptable Quality

Level Task 1 Identify population of origin from juvenile salmonid tissue samples using approved genetic methods.

Differences between agreed upon and actual delivery of sample results.

Data results delivered on time

Data should be delivered on-time no less than 98% of the time.

Task 2 Project Management. Prepare for and meet A-E requirements as scheduled.

Complete A and C prior to the start of each season (i.e., December- January).

Complete other requirements at the

Review invoices and study plans

Attendance/discussions at scheduled meetings scheduled frequency.

Task 3 Data Management and Sharing

Data undergo routine QAQC; metadata are created and updated at least annually;

data are shared on a regular basis; fully QAQC’d data are uploaded to the EDI Data Portal at least annually.

Data shared with Reclamation or partners by agreed upon deadlines

QAQC process is documented and implemented

Data posted by agreed upon deadlines

Review data and metadata

Tasks 1, 2

Genetic identification, Project Management, and Data Management & Sharing

Quality Work is conducted in a manner consistent with its description in annual study plans. Solutions to failed sample analyses are pursued immediately.

Reporting standards are met more than 75% of the time.

5.0 DATA AND REPORTS - The contractor shall provide the following data and reports as follows:

Item No.

Description

Content

Format

Medium

Delivery

1 Data sharing See Task 1 & 3 descriptions Electronic Spreadsheet

MS

Excel or website

Emailed to COR and partner agencies as described in annual work plan.

2 Annual Study Plan

Describes status/inventory of samples collected during previous years. Describes sample turnaround times.

Electronic document

MS

Word or

PDF

Emailed to COR annually

2 Updates Provides frequent updates Email, Phone, In- Person

Any At least monthly

3 Data posting Metadata and QAQCd data package updated to EDI Data Portal or a similar repository

Per EDI Data Portal specificatio ns Publish Data (edireposito ry.org)

Per EDI Data Portal specifica tions Publish Data (edirepo sitory.or g)

Send url hyperlink to revised EDI data package via email to Reclamation

COR

6.0 DELIVERABLES - The contractor shall submit the following reports in accordance with paragraph 5.0, “DATA AND REPORTS”:

Task 1. Identify population of origin from juvenile salmonid tissue samples from the Tracy Fish Collection Facility, other CVP/SWP facilities, and other monitoring programs using approved genetic methods.

For each individual fish provide:

(a) sample ID, date, time, fish length, length-at-date species identification (for Chinook), and collection location of sample;

(b) identified race (for Chinook salmon); and

(c) probability of identification for each reporting group.

(d) failed samples

Any samples that cannot be analyzed will be identified and a rationale provided. A method for evaluation of accuracy should be identified in the study plan and approved by Reclamation biologists.

This task will require contractor to be “on call” (including holidays and weekends) to receive and immediately analyze (within 48 hours) high-priority samples (e.g., those samples that trigger a reduction to CVP/SWP exports; typically January-March).

Estimated Dates: November through June annually.

Task 1 Deliverables: (1) an MS Excel spreadsheet or webpage containing all genotyped data collected to date and their population assignment submitted as described in annual study plan (see task 2); final data summary submitted by August 31st of each year; and (2) evaluation of accuracy of the genetic baseline.

• Estimated number of hours needed for rapid turnaround of samples: 16 hours x 4 weekends/month x 6 months per year = 384 hours (rounded up to ~400 hours)

• Estimated number of samples (standard flowcell, 470 sample batch): approximately 6000 per year

• Estimated number of samples (micro flowcell, 75 sample batch): approximately 1000 per year

• Estimated number of samples (nano flowcell, 12 sample batch): approximately 200 per year

Task 2. Project Management https://edirepository.org/data/publish-data https://edirepository.org/data/publish-data https://edirepository.org/data/publish-data https://edirepository.org/data/publish-data https://edirepository.org/data/publish-data https://edirepository.org/data/publish-data https://edirepository.org/data/publish-data

1) Prior to initiation of annual sampling and analysis, an annual study plan that includes data management plan and QAQC process will be drafted, shared with Reclamation for comment, and revised as necessary prior to completion of a final annual study plan.

2) The Contractor shall provide the COR with updates on tasks. The updates may describe the work accomplished since the previous update, work currently underway and work anticipated. The update shall state whether the current work is on schedule, and if not, what actions are anticipated in order to get back on schedule. The update shall be provided through email.

3) The Contractor shall perform laboratory QA/QC. The Contractor shall review methods for accuracy and consistency and, where necessary, implement corrective actions. Contractor may provide guidance regarding sample collection, preservation, archive, and inventory.

4) The Contractor shall attend meetings with Reclamation COR regarding the project.

5) The Contractor shall acknowledge Reclamation funding and the contract/agreement number on presentations, technical memoranda, publications, EDI data archive project page, and public outreach documents.

Task 2 Deliverables: (1) Updates on tasks, (2) presentation to Reclamation on annual results, (3) acknowledgment of Reclamation funding, and (4) annual study plans.

Task 3. Data Management and Sharing

1) The Contractor shall publish QAQC’d data and metadata files to the EDI Data Portal or a similar data repository on an annual basis.

2) The Contractor shall summarize data as needed for Reclamation reporting and information needs and share data with partner agencies or stakeholders upon request.

3) The Contractor shall enter a short summary of the project to the Delta Science Tracker with the COR input and update information on an annual basis.

3) The Contractor shall provide an annual report summarizing genetic identification results for the year by August 31st each year. This report would include comparison of LAD and genetic assignments for the year and interannual data comparison when applicable.

Task 3 Deliverables: (1) Publication of QAQC’d data on an online data repository, (2) data summaries,

(3) entry and updates on Delta Science Tracker, and (4) annual reports.