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Science Center for Marine Fisheries Science (SCeMFiS)

University of Southern Mississippi

Virginia Institute of Marine Science

Last Reviewed: 02/10/2020

SCeMFiS utilizes academic, recreational, and commercial fisheries resources to address urgent scientific problems limiting sustainable fisheries.

Center Mission and Rationale

The Science Center for Marine Fisheries (SCeMFiS) provides academic research products essential for the sustainable management of shellfish and finfish resources. SCeMFiS seeks to simultaneously achieve the goals of sustainable fish and shellfish stocks and sustainable fish and shellfish fisheries. A multi-decadal evolution in fisheries management in the U.S. has formalized the criteria for sustainability and developed sophisticated modeling tools to achieve this goal; but success is limited by insufficient information on the finfish and shellfish stocks and fisheries and insufficient development of numerical applications to surmount the modeling challenges posed by these sustainability goals. Rapid climate change continues to expose the limitations of present-day data resources and assessment, exacerbating the gap between data resource availability and data resource needs. Increasingly complex management requirements continue to reveal limitations in data resources, data analysis, and model construction, thereby limiting the attainment of maximum sustainable yield.

The attainment of the dual goals of sustainable fish stocks and sustainable fishing industries requires a dual focus on (a) the assessment process that determines the status of the stock and (b) the regulatory process that provides the vehicle by which the fishery is managed to optimize stock status while supporting a robust industry. SCeMFiS supports an academic research program encompassing both components of the management process. SCeMFiS’ capabilities encompass the range of oceanographic, fisheries, and marine biological disciplines essential for addressing the data resource and analytical challenges faced by modern-day fisheries management.

Research program

The Science Agenda

SCeMFiS-mission-pertinent accomplishments: For SCeMFiS, the following examples show accomplishments pertinent to the SCeMFiS mission and to the needs of members. A SCeMFiS Director was appointed to the Mid Atlantic Fisheries Management Council. SCeMFiS placed three individuals on the Atlantic Surfclam Working Group and three on the Ocean Quahog Working Group. Both assessments successfully passed peer review. Present catches of surfclams and ocean quahogs are now well below the OFL (overfishing limit) for both species, demonstrating that these industries have a unique opportunity to expand production. This is highly unusual, as most marine species are fully utilized.

  1. For ocean quahogs, the status of the stock estimates (NEFSC 2017a) permit an increased quota approximately tripling the present quota. The ex-vessel value of the fishery today, a highly conservative measure of economic value, is about $10.4 million; thus an additional $20.8 million in yearly catch could be sustained by the present assessment. This result directly impacted jobs in New Bedford, MA, Atlantic City, Bivalve, Millville, and Pt. Pleasant, NJ, and Nanticoke and Easton, Md.
  2. For Atlantic surfclam, status of the stock estimates (NEFSC 2017b) permit an increased quota approximately 2.5 times the present quota. The ex-vessel value of the fishery today, a highly conservative measure of economic value, is about $30.7 million; thus an additional $46 million in yearly catch could be sustained by the present assessment. This result directly impacted jobs in New Bedford, MA, Atlantic City, Bivalve, Millville, and Pt. Pleasant, NJ, and Nanticoke and Easton, Md.
  3. For black sea bass, the assessment (NEFSC 2017c) permitted the setting of an OFL for the first time in many years. That, plus an increase in estimated biomass permits an increased quota approximately two times the present quota. The ex-vessel value of the commercial fishery today, a highly conservative measure of economic value, is about $8.8 million; thus an additional $8.8 million in catch yearly  could be sustained by the present assessment. The value of the black sea bass recreational fishery is certainly much greater, but economic numbers are not available. Nonetheless, recreationally and commercially, this result directly impacted jobs at most commercial fishing ports and all ocean-side recreational docks from Virginia to Massachusetts.
  4. In support of the surfclam and ocean quahog assessments, SCeMFiS produced the first population age-frequency distributions for ocean quahogs in the western Atlantic Ocean (Pace et al. 2017a,b). These are the oldest non-colonial animals on earth and represent an important U.S. fishery. The project responded to the most important data constraint on quotas for this industry as adjudged by the MAFMC SSC. Additionally, SCeMFiS provided information on growth rates for ocean quahogs that was incorporated into the NEFSC assessment model. In addition, evaluation of juvenile ocean quahog growth rates show that growth rates have been increasing consistently since 1800 as the Mid-Atlantic warms (Pace et al. 2018). This finding lessons the danger posed from overfishing (which is not now occurring) under a given quota.
  5. SCeMFiS was instrumental in the establishment of the NEFSC Survey Design Working Group. SCeMFiS evaluated bias in the present survey (Powell and Mann 2016; Powell et al. 2017b) and developed an R package to evaluate survey designs that was released to the scientific community. This Working Group, supported in part by SCeMFiS, made recommendations for improving the survey design for the surfclam and ocean quahog survey. These recommendations were approved after review and will be implemented in the summer 2018 survey. This is the first such redesign in the history of the survey.
  6. SCeMFiS completed a series of studies of the relationship between surfclam habitat and complex habitat as part of the evaluation of the Georges Shoals and Great South Channel Habitat Management Areas (HMAs), both of which are managed by the New England Fisheries Management Council (NEFMC). These two proposed HMAs would close these regions to bottom tending gear. First, SCeMFiS provided information to the NEFMC that resulted in a one-year gear exemption for the surfclam fishery in the Great South Channel and Georges Shoals HMAs. This exemption is estimated to be worth $18 million in ex-vessel landings value to the surfclam industry in 2016.  SCeMFiS followed this up with a full report to the NEFSC Plan Development Team (PDT) providing detailed analyses of the distribution of complex habitat relative to surfclam habitat and surfclam fishable habitat (Powell et al. 2017a) and the first survey of the region between Nantucket and the Great South Channel. Results led to the removal of the Georges Shoals region as a possible HMA. For the Nantucket Shoals region, SCeMFiS carried out the first survey of the region between Nantucket and the Great South Channel. Results show that the concerns about bottom tending mobile gear being used in the HMA are not sustained for the surfclam fishery, lending weight to an exemption for this fishery. A second report to the NEFSC PDT covering these findings serves as a basis for requesting a permanent exemption, thus maintaining the economic value of the Great South Channel region for the surfclam industry indefinitely.
  7. SCeMFiS scientists developed the first demographic data for the chub mackerel fishery in the western North Atlantic. This forage fish fishery is sensitive due to the lack of a fisheries management plan and stock assessment, both resulting from the absence of basic demographic data. Under MAFMC rules, this fishery would be closed unless sufficient information can be developed to support a Fishery Management Plan (FMP). As part of this project, SCeMFiS scientists participated in an otolith exchange program to intercalibrate European and American researchers. The program is organized by WebGR, a European project that aims to develop Open Source software to support studies of fish growth and reproduction. In particular it promotes the use of online services to organize calibration workshops. The consortium is constituted by: Laboratório Nacional de Recursos Biológicos – IPIMAR (Portugal) – Consortium leader, The Agri-Food & Biosciences Institute (UK), AZTI Tecnalia Foundation (Spain), Federal Agency for Agriculture and Food (Germany), Johann Heinrich von Thünen Institute (Germany), Hellenic Centre for Marine Research (Greece), Instituto Español de Oceanografia (Spain), Institut Français de Recherche pour l’exploitation de la Mer - IFREMER (France), Institute for Marine Resources & Ecosystem Studies (The Netherlands), Institute of Marine Research (Norway), Swedish Board of Fisheries (Sweden), Italian Society for Marine Biology (Italy). SCeMFiS provided the sole U.S. contingent.
  8. The SCeMFiS marine mammal team obtained funding from the Western Pacific Fisheries Management Council to develop a Potential Biological Removal (PBR) Tier System. The team used a management strategy evaluation (MSE) of alternative approaches for calculating PBR (Brandon et al. 2017). Tiers were defined in terms of data availability, with one tier representing the current approach. The availability and use of multiple estimates of abundance led to an ability to meet conservation management objectives, while also having lower variability in PBR limits through time, relative to the current approach. The computer code for the MSE is open-source, and available via: This year, this MSE is being expanded as a tool for marine mammal research. SCeMFiS presented this option to the Pacific Scientific Research Group which peer-reviews marine mammal assessments for the Pacific region.
  9. The surfclam MSE model was finalized in 2015. An implementation of this model directed at area management objectives for surfclams was put into practice in 2015 and is ongoing (Kuykendall et al. 2017). This is an important development in addressing the challenge of climate change on species range and provides the basis for evaluating potential multi-use conflicts on the continental shelf. This model (SEFES = Spatially Explicit Fishery Economics Simulator) is readily adaptable to any fishery and is unique in describing each fishing vessel independently as it operates within the fleet. No other MSE model has this capability.
  10. In preparation for the 2018 summer flounder benchmark assessment, SCeMFiS funded development of a new sex-specific model for summer flounder that will provide a basis for implementation of this model structure across a wide range of marine fish species. Many species have sex-specific behaviors, population demographics, or gear selectivity’s. A number of species change sex during life. Assessment and management of these cases remains uncertain because assessment software tools are limited. Summer flounder is the most valuable finfish in the Mid-Atlantic region. To support model development, SCeMFiS also funded research to collect sex specific information from the recreational fishery. A total of 2,243 discard-sized fish and 842 legal-sized fish were collected and measured aboard for-hire recreational fishing vessels.  Results indicate a clear relationship between sex ratio and fish length, with males more frequently observed at lengths less than the legal limit, giving way to a predominantly female sex ratio as length increased.  In addition to length, latitudinal and seasonal trends were found to have a significant effect on sex ratio in discard-sized fish in the summer flounder recreational fishery with large females more likely in southern, shallow fishing locations early in the season. These results open up new management opportunities that can increase landings and angler satisfaction without endangering sustainability (Morson et al. 2017).
  11. SCeMFiS scientists developed a simple technique to correct population demographics where individual clams are broken during collection by the federal survey. The size frequency is a critical metric for the federal assessment and these broken clams heretofore could not be measured. The hinge portion of a clamshell is rarely destroyed in collection, even when shells (valves) are badly broken.  Hinge structure is species-specific and highly conserved with respect to form. Thus the quantitative relationships between the substructures of the hinge and total clam length/height are also conserved. Measurements of surviving hinge structure can thus be used to recast the length/height of the clam prior to breakage. This correction technique has been implemented on the 2013-2015 NEFSC clam surveys.
    1. The research program designed to evaluate surfclam habitat on Georges Bank has put into electronic format, for the first time, the ancillary NMFS-NEFSC survey data from 1978-2014 for the entirety of the surveyed region, thus providing the basis for routine inclusion of such data in analyses pertinent to that region. Evidence derived therefrom suggest that range shifts on the U.S. east coast continental shelf are catastrophic in nature, that is, they occur on time scales much shorter than the average species life span, and thus long-term planning for these eventualities are essential parts of long-range planning by member companies.
    2. The surfclam MSE project resulted in the coordinated implementation of its primary recommendation on area closures. This is an important development in addressing the challenge of climate change which is shifting the clam’s range to the detriment of the fishery. Enhancing production in the southern portion of the clam’s range is an essential response to limiting the economic impact of climate change.  The surfclam industry in total agreed to close two areas off New Jersey and Maryland. The expectation is that the closure will improve LPUE, support the surfclam quota, and minimize the risk of federally-imposed area management. The surfclam industry provided $24,507 in 2015 for an initial survey of these sites. The areas are expected to be closed for 3-5 years depending upon yearly survey reports and a summer 2018 re-survey of the region is under development. The expectation is that the closure will improve LPUE, support the surfclam quota, and minimize the risk of federally-imposed area management. If the program is fully implemented, the MSE model projects a potential increase of 145,833 bushels of harvest per year at the same numerical removal rate due to clam growth if the program is fully implemented. At $20/bushel this is valued at about $2.9 million.
    3. SCeMFiS economists highlighted the importance of shellfish fisheries to local New England port economies. Traditional multipliers of 3x ex-vessel values were shown to be gross underestimates, a 7x multiplier being more realistic. Similarly, estimates of harm incurred from multi-use conflicts, wind farms in the case of BOEM (2017), are sorely underestimated. SCeMFiS is currently conducting the same analysis for the U.S. squid (Doryteuthis, formerly Loligo) fishery. National Standard 8 states “Conservation and management measures shall, consistent with the conservation requirements of this Act (including the prevention of overfishing and rebuilding of overfished stocks), take into account the importance of fishery resources to fishing communities by utilizing economic and social data that meet the requirement of paragraph (2) [i.e., National Standard 2], in order to (a) provide for the sustained participation of such communities, and (b) to the extent practicable, minimize adverse economic impacts on such communities.” Results from SCeMFiS economists show that implementation of this standard has routinely underestimated the value of fisheries to the U.S. economy.

Special Activities

SCeMFiS scientists participate in every level of the federal management process. These include assessment meetings coordinated by the National Marine Fisheries Service and management council meetings coordinated by the regional management councils (e.g., MAFMC, GMFMC, ASMFC).

Facilities and Laboratory

A research dredge for collection of pre recruit (to the fishery) size clams was designed and fabricated by industry partners in March-July 2014, and deployed in the August 2014 surveys aboard an industry vessel under charter by NEFSC. SCeMFiS scientists and students participated in dredge testing. A comparison with prior lined dredges demonstrated comparable performance of the new research dredge in clam retention for both target species but with much lower sediment retention and fouling, and greater ease in operation. The new research dredge will be the gear of choice for future selectivity studies, a critical element in assessment of the entire clam population demographic. In addition, the new research dredge demonstrated remarkable ability to retain pre recruit size clams over significant sampling areas, including all size classes down to 20 mm maximum dimension, and densities of pre-recruit clams up to 55 m-2 – both capabilities that have been lacking in prior survey gear.


University of Southern Mississippi

Gulf Coast Research Laboratory
703 East Beach Drive

Ocean Springs, Mississippi, 39564

United States

Virginia Institute of Marine Science

Virginia Institute of Marine Science
The College of William and Mary

Gloucester Point, Virginia, 23062

United States