SOURCES SOUGHT
A -- Genetic Analysis of Archived Tissue Samples Collected from Alaskan Harbor Porpoise (Phocoena phocoena) - FIGURE 1
- Notice Date
- 6/18/2014
- Notice Type
- Sources Sought
- NAICS
- 541712
— Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
- Contracting Office
- Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), Western Acquisition Division-Boulder, 325 Broadway - MC3, Boulder, Colorado, 80305-3328, United States
- ZIP Code
- 80305-3328
- Solicitation Number
- NFFS7300-14-02365DR
- Archive Date
- 6/27/2014
- Point of Contact
- DianaRomero, Phone: 303-497-3761
- E-Mail Address
-
diana.romero@noaa.gov
(diana.romero@noaa.gov)
- Small Business Set-Aside
- N/A
- Description
- FIGURE 1 THIS IS A REQUEST FOR INFORMATION (RFI) ONLY - The Government is currently conducting market research to gather information and identify potential sources for the requirement identified below. A solicitation is not available at this time, and requests for a solicitation will not receive a response. This notice does not constitute a commitment by the United States Government. NOAA's Acquisition & Grants Office, Western Acquisition Division-Boulder, in support of the National Marine Mammal Lab (NMML) seeks potential vendors to provide development of genetic markers and to conduct genetic analyses of samples of Alaskan harbor porpoise, for the purpose of clarifying population structure, see the Statement of Work. Please provide the following information as requested: 1) A statement that you believe that your firm has the capability to meet these requirements and perform these services. The name of manufacturer, make or model number specifications, physical, functional, or performance characteristic. 2) Your firm's DUNS number & CAGE code; 3) Your firm's SBA certified small business concern status. Specifically identify if your firm is a small business, HUBZone-certified, Service Disabled Veteran Owned, Woman Owned or SBA 8(a) program certified; All information received in response to this notice shall be treated as Business Sensitive or confidential to the responder, exempt from public release under the Freedom of Information Act. All information submitted in response to this announcement is voluntary; the United States Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the United States Government. Proprietary information submitted should be marked appropriately. All submitted information shall remain with the U.S. Government and will not be returned. The response date for this sources sought is June 25, 2014. No collect calls will be accepted. All responses may be submitted via e-mail to Diana Romero, Purchasing Agent, at diana.romero@noaa.gov. The phone number for the Purchasing Agent is (303) 497-3761. STATEMENT OF WORK: Genetic Analysis of Archived Tissue Samples Collected from Alaskan Harbor Porpoise (Phocoena phocoena) SCOPE The scope of this contract is to provide development of genetic markers and to conduct genetic analyses of samples of Alaskan harbor porpoise, for the purpose of clarifying population structure. BACKGROUND INFORMATION The National Marine Mammal Laboratory (NMML) requires a comprehensive study of the genetics of Alaskan harbor porpoise which involves analyzing archived tissue samples. This research is required to determine the population structure of this species. NMFS is required (under the Marine Mammal Protection Act) to determine stocks for all marine mammals, evaluate the effect of human-caused mortality on each stock, and document this evaluation through a published Stock Assessment Report (see Allen and Angliss 2010). The harbor porpoise's (Phocoena phocoena) preference for shallower waters makes this species highly vulnerable to being caught incidental to net-fishing operations; thus defining appropriate harbor porpoise stocks and monitoring their abundance on a regular basis is warranted to ensure that bycatch does not exceed the Potential Biological Removal in these groups. Although harbor porpoise are found throughout the coastal waters of Alaska, little is known about their population structure. An understanding of population structure is essential to accurately assess the status of this species and interpret trends in abundance. Three management stocks of harbor porpoise are currently recognized in Alaska: 1) the Southeast Alaska stock, 2) the Gulf of Alaska stock, and 3) the Bering Sea stock. The boundaries of these three stocks were identified primarily based upon geography and perceived areas of low density. Outside Alaska (e.g., California, Oregon, and Washington) numerous discrete populations have been identified using a combination of genetic data and gaps in distribution. Given their wide distribution in Alaskan waters and the population genetic structure observed elsewhere, it is highly likely that the currently recognized stocks are actually composed of several smaller populations. Results from dedicated harbor porpoise vessel surveys conducted by the National Marine Mammal Laboratory from 1991 to 2010 within the inland waters of Southeast Alaska found that overall abundance varied considerably by year. Abundance in the early 1990s was relatively high, lower in 2006 and 2007, and higher again in 2010 (but still lower than the early 1990s). Analysis of these data suggested the occurrence, with high probability, of a decline in abundance ranging from 2 to 4% per year for the entire study area. However, when data from 2011 and 2012 were added to the analyses, the rate of decline was shown to decrease. The reasons for the significant declines that occurred over a number of years are unknown and could include serious injury or mortality in a fishery, movements based on changes in prey distribution, a decrease in survival, a shift in distribution due to habitat degradation, predation; or a combination of these factors. However, when investigating the decline rate by sub-regions within the main study area, NMML documented that the steepest declines occurred in areas where salmon and herring net fisheries operated. Of utmost concern is that incidental takes within a small region could severely impact undefined localized stocks of harbor porpoise which could easily go undetected unless stock structure is identified. Management efforts would, of course, differ depending on whether this area contained one population or multiple populations. Resolving the population structure issue is critical for identifying biologically relevant management units and considered one of the highest priority tasks within NMML. PROJECT DESCRIPTION AND OBJECTIVES To begin to address this data gap in our understanding of Alaskan harbor porpoise stock structure, we propose to conduct a genetic study using archived tissue specimens currently curated by the Southwest Fisheries Science Center. A total of 85 to 90 samples are available for this analysis, representing the coastal regions from Southeast Alaska, the Gulf of Alaska, Cook Inlet, the Aleutian Islands, the Bering Sea and the Beaufort Sea (Figure 1). This study will examine genetic structuring of Alaskan harbor porpoise across the three currently recognized stocks and will focus on the development of novel nuclear markers enabling rapid analysis of future samples collected in FY15 and beyond. The proposed genetic investigations and the expected results of this study are provided below. Various collaborators will be involved in this project to include staff members from the Northwest Fisheries Science Center, Southwest Fisheries Science Center, and individuals responsible for the collection of the samples. Laboratory costs incurred by both SWFSC and NWFSC during this project will be funded by NMML. The contractor will be responsible for developing nuclear genetic markers for harbor porpoise and coordinating the research efforts among the above-named agencies and individual researchers. The contractor is required to perform the following genetic analysis on all available archived harbor porpoise samples maintained at SWFSC. The National Marine Mammal Laboratory (NMML) requires that the contractor develop a panel of nuclear genetic markers specific to North Pacific harbor porpoise. The contractor must be familiar with a variety of molecular genetic procedures including Sanger sequencing, high-throughput genotyping, library prep, hybrid enrichment protocols and targeted next-generation sequencing (NGS). The contractor will be required to draw upon established collaborations with SWFSC to design a custom DNA library for targeted sequencing of the harbor porpoise nuclear genome. Nuclear genotypes will be used to quantify genetic variability across the sampled regions and characterize patterns of genetic structuring among Alaska harbor porpoise. In addition to nuclear markers, the variable mitochondrial control region is to be sequenced for each sample to look for broad-scale structuring, allow comparison with published North Pacific harbor porpoise sequence data, and examine phylogenetic relationships among putative populations and geographic regions. Molecular genetic sex assays will also be performed for all samples using established cetacean markers and protocols consistent with those currently employed at NWFSC and SWFSC. A researcher whose experience in this field is known by both Agency staff and independent cetacean researchers in Alaska is necessary to expedite this research and ensure the overall success of the project. A better understanding of the structure and definition of harbor porpoise populations in Alaska is key to reliably interpreting existing and future data on by-catch, abundance, and trends in this region. Genetic studies offer the best means of obtaining such information. This work will, by developing appropriate species-specific genetic markers, lay the foundation for further assessments. This contract will require a Ph.D. research scientist with expertise in both cetacean ecology and molecular genetics. The contractor will generate both nuclear and mitochondrial molecular genetic data from the archived samples and characterize patterns of genetic structuring among Alaska harbor porpoise. This contract will involve collaborative research among researchers at NMML, SWFSC, and NWFSC.
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