Genetics_SOW_2015_03_16.docx

STATEMENT OF WORK

Environmental Consulting Service: 541620 Genetic Testing, Sturgeon 3/16/2015 PR Number: 0040199407 (base period)

1. General:

1.1 Lodi FWO (850 S. Guild Ave, Suite 105, Lodi, CA 95240-3170) staff will provide Genetic Testing for wild-collected White Sturgeon egg samples to contractor for genetic analyses which they will perform at 3300 Industrial Way, Suite 100, West Sacramento, CA 95691-5036.

1.2 Understanding the annual spawning population size of White Sturgeon in the San Joaquin River is needed to assess habitat restoration needs and project effectiveness. This project is the continuation of incremental efforts to demonstrate that relatedness of fertilized eggs can be accurately assessed and used to identify the number of parents involved in spawning activities. We intend for this project to tell us how many spawners were involved with wild egg collections during 2012.

1.3 Contractor Qualifications: must have demonstrated ability to complete this type of work using known spawning matrices of captive White Sturgeon and correctly identify family groups.

2. Place of Performance and Period of Performance Base Period : April 15, 2015 – April 14, 2015 Option periods that MAY be conducted during each of those years (if we collect eggs that need to be analyzed) would include everything in the Scope, except for the publication costs Option Period 1: April 15, 2016 – April 14, 2017 Option Period 2: April 15, 2017 – April 14, 2018 Option Period 3: April 15, 2018 – April 14, 2019 Option Period 4: April 15, 2019 – April 14, 2020

Base Year: Lodi FWO staff completed egg collections in May of 2012 and have been storing the samples since, while waiting for successful demonstration of a group’s ability to conduct needed analyses. Analyses and reporting will be conducted at 3300 Industrial Way, Suite 100, West Sacremento, CA 95691-5036 during April-December 2015. Following completion of a brief technical report, Contractor staff will begin preparation of a manuscript for publication at the same location. The manuscript should be submitted for publication by June 1, 2016 and should describe and discuss all phases of White Sturgeon egg genetics investigations funded by Lodi FWO.

2.2 Annotate the Performance start and end date. Performance shall begin within 30 days of contract acceptance, a brief technical report shall be submitted by December 15, 2015, and the manuscript shall be submitted to a relevant peer-reviewed journal by June 1, 2016. Given the unpredictable nature of the publishing process, no deadline will be imposed for when the manuscript shall be published. However, all reasonable efforts shall be made to ensure publishing by December 15, 2016.

3. Scope Each egg shall be subjected to an egg-specific DNA extraction protocol. Contractor shall perform polymerase chain reaction (PCR) amplification on egg samples using the twelve fluorescently end-labeled microsatellite marker loci to generate multi-locus genotypes. All PCR products shall be visualized by electrophoresis on an ABI 3730 automated capillary sequencer. Fragment size analysis shall be completed using Geneious (R8) software. Individual genotypes shall be coded (presence or absence of alleles). Genetic data shall be analyzed following published methods. Family groups shall be estimated via relatedness using maximum likelihood algorithms and/or analysis of Principle Components specific for genetic data. The number of contributing adults shall be estimated from either inferred family groups or cluster analysis. Contractor shall present findings regarding collections and analysis results in a technical memo and include all raw data as supplementary material. Contractor shall meet at least once with the technical coordinator (information below) to discuss preliminary results. Upon successful completion of Task 3, Contractor shall compile results from Phases I, II, and III in a detailed manuscript for publication in a peer reviewed journal.

4. Deliverables and/or Delivery Schedule:

Findings regarding collections and analyses shall be provided in a technical memorandum. The technical memorandum shall be provided by December 15, 2015. The manuscript shall be submitted for publication to a peer-reviewed journal by June 1, 2016. The submitted manuscript and associated project raw data shall be provided to the technical coordinator by June 1, 2016.

Electronic versions of all technical memoranda, presentations, manuscripts, and associated raw data shall be provided to the technical coordinator.

5. Data Management Plan (DMP) N/A

6. Government-Furnished Equipment (GFE) / Government-Furnished Information (GFI) N/A

7. Evaluation and Acceptance Government acceptance is contingent upon being able to demonstrate that the agreed upon tests are completed and results interpreted and provided as described. No other evaluation will be necessary.

8. Quality Control/Quality Assurance:

Where appropriate, QC will be maintained according to industry standards and made available to the agency with the contractor’s proposal.

9. Technical Coordinator:

Zachary Jackson, Supervisory Fisheries Biologist, 850 S. Guild Ave, Suite 105, Lodi, CA 95240-3170, 209-334-2968 extension 408, Zachary_Jackson@fws.gov.