Statement of Work - CKMR_Redacted.pdf

STATEMENT OF WORK

National Oceanic and Atmospheric Administration (NOAA)

NOAA FISHERIES

Southeast Fisheries Science Center-Panama City Laboratory

Development of Close-kin mark-recapture (CKMR) methods to estimate absolute abundance of the oceanic whitetip (Carcharhinus longimanus)

I. Background/Overview:

The oceanic whitetip shark is listed as threatened throughout its range under the Endangered Species Act (ESA), with international trade of its fins being one of the most significant threats to the species (Young & Carlson 2020). Typically, population assessments are used for the estimation of absolute abundance; however, this is one of the most difficult parameters to estimate (Bravington et al. 2014), especially for highly migratory species such as sharks, tunas, and billfish. Genetic mark-recapture methodologies are similar to those of traditional mark recapture but differ in several important ways that make the genetic approach ideal for highly migratory species. A genetic mark is the genotype of an individual across a number of characterized loci; therefore, it is natural, permanent, and can be recovered from a processed carcass, fin clips from live animals, and/or other tissue samples. Genetic marks are transmitted from parent to offspring, and are thus partially shared between relatives. This expands the scope of what may be considered a “recapture” to closely related individuals (kin). Combining information on kin recaptures with models informed by life history to relate the number of kin to the population size, is a recent technique known as close-kin mark-recapture (CKMR, Bravington et al. 2016). Close-kin mark-recapture to estimate population size of oceanic whitetip shark will improve/validate estimates derived from population/stock assessments.

Currently estimates derived through population assessments have a high degree of uncertainty and this level of uncertainty will likely increase in future assessments due to the prohibition on harvest of oceanic whitetip (i.e. catches will no longer be reported, and catches are fundamental in deriving population size through a stock assessment). Thus, an absolute abundance estimate via close-kin mark-recapture has the potential to provide a potentially robust indicator of the species’ status and measure progress towards meeting demographic recovery criteria.

II. Scope of Work The vendor will develop appropriate genomic tools for use in CKMR. Next-generation sequencing techniques will be used to characterize genetic variation within and among samples of oceanic whitetips previously collected from Cuba, Haiti, Bahamas, and the United States from a variety of fishery dependent and independent surveys. Once these genetic tools are developed from archived samples in the Atlantic Ocean this technique can then be applied to samples from the Pacific Ocean with additional samples collected through international engagement at the Regional Fishery Management Organization (RFMO) level.

III. Tasks

a. Focus will be on double digest Restriction Associated DNA (ddRAD) library preparation, sequencing, bioinformatics, data analysis and GT-seq panel design. Deliverables include a final report, GT-seq panels, a database of composite genotypes from samples the

Northwest Atlantic, and preliminary estimates of population size in these regions using

CKMR.

IV. Period of Performance

July 2024 to June 2026.

V. Place of Performance

Mote Marine Laboratory, Sarasota, FL and Texas A&M University

Deliverable Schedule

A progress report will be submitted following the completion of the first year of work (July 2025)

All work and deliverables (Final report) shall be completed and submitted during the timeframe from July 2024 to June 2026 and shall also include GT-seq panels, a database of composite genotypes from samples the Northwest Atlantic, and preliminary estimates of population size in these regions using CKMR.

VI. Special Requirements

The vendor must have access to archived and historical samples of oceanic whitetip shark previously collected from Cuba, Haiti, Bahamas, and the United States.

a. Confidentiality and Data Privacy

This contract may require that services contractors have access to Privacy Information. Services contractors are responsible for maintaining confidentiality of all subjects and materials and may be required to sign and adhere to a Non-disclosure Agreement (NDA).

b. Intellectual Property Rights

All deliverables are the property of the U.S. Government. All documents, analyses, files (digital or other), reports, notes and photos are to be used only by Contractor personnel assigned to this purchase order. Documents, files and other data are to be stored exclusively on Government owned equipment and at no point should be saved or archived on personal drives or devices.

Copies are not to be disseminated to anyone outside of the NMFS or to any other contractor personnel without explicit release from the Government.

c. IT Security

N/A

d. Section 508 Compliance

Pursuant to Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d) as amended by P.L.

105-220 under Title IV (Rehabilitation Act Amendments of 1998), all Electronic and Information Technology (EIT) developed, procured, maintained and/or used under this contract shall be in compliance with the “Electronic and Information Technology Accessibility Standards” set forth by the Architectural and Transportation Barriers Compliance Board (also referred to as the “Access Board”) in 36 CFR Part 1194. The complete text of Section 508 Standards can be accessed at http://www.access-board.gov/ or at http://www.section508.gov.

VII. Required Knowledge and Experience:

Key personnel must have a Ph.D. in Biological Sciences or related field.

The vendor must have an advanced knowledge of population genetics

The vendor must have access to historical samples from multiple locations

The vendor will have participated in recovery workshops for oceanic whitetip shark.

VIII. Project Lead:

Panama City Laboratory,