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Research and Current Projects

Projects Underway

Jensen Project
A Meta-Analysis of the Impact of Forage Fish Abundance on Predator Productivity

Lead PI: Olaf Jensen (Rutgers). Industry Liasion: Eleanor Bochenek. There is increased interest and debate surrounding the management of “forage fish” stocks in the U.S. and abroad. A task force funded by the Lenfest Oceans Program has recommended much stricter controls on harvest of forage fish to protect their predators. This project will evaluate the empirical link between forage fish abundance and predator productivity using a global database of fish stock assessments, trawl survey indices, and abundance time series for select seabird and marine mammal populations.

Infographic and When does fishing forage species affect their predators?

Nesslage Project
Design of a Cooperative Winter Pelagic Survey for Atlantic Menhaden in the Mid-Atlantic

Lead PI: Geneviève Nesslage (UMCES). Industry Liasion: Jeff Kaelin. The goal of this project is to design a cooperative winter pelagic survey for Atlantic menhaden in the Mid-Atlantic region to provide estimates of trends in abundance and structure of the northern portion of the stock inhabiting midshelf waters during winter and early spring. The current menhaden stock assessment is only informed by northern bottom trawl and seine surveys conducted in inshore waters. This project will help address data deficiencies and better inform the menhaden assessment by designing a winter pelagic survey of the northern portion of the stock in months and areas currently unsampled by midwater gear.

Support of the Survey Design Working Group for the NMFS Clam Survey

Lead PI: Eric Powell (USM). The surfclam and ocean quahog stock survey occurs simultaneously using the F/V Pursuit as the survey vessel. Through 2011, the R/V Delaware II was used and the survey took place every 3 years. When that vessel was retired, the protocol changed to one in which one-third of the survey was done each year. Since 2008, the total number of survey stations has declined in the region covering SVA, DMV, NJ, and LI. This decline has accelerated under the R/V Pursuit because of a desire to cover certain regions in one year to simplify assessment modeling. The result may be to increase the likelihood of a biased low or biased high survey index due to reduced sampling density in a patchy population. Work to be completed: a reappraisal of the clam quahog survey sampling design which has not previously been evaluated with respect to the relationship between sample number and stock patchiness. This issue is uniquely important for the entirety of the continental shelf benthic biota, not just the commercial clam species. Additional funding will also support for 2 members of the working group to attend meetings.

- 61st Northeast Regional Stock Assessment Workshop (61st SAW) Assessment Report
(471page .pdf) (NEFSC access to sections)

There is a new issue (CRD 17-10) of the Center Reference Document Series entitled 63rd Northeast Regional Stock Assessment Workshop (63rd SAW) Assessment Report, by the Northeast Fisheries Science Center.

- R-package for survey design analysis - (zip install file)

This package contains all of the functions for stratified random surveys developed for NEFSC by Stephen Smith in 2006 plus functions for post-stratification and domain estimates. Documentation is available using the R help() facility available for all packages once the package is installed.

SCeMFiS was instrumental in the establishment of the NEFSC Survey Design Working Group. This group, supported in part by SCeMFiS, will make recommendations for improving the survey design for the surfclam and ocean quahog survey. This will be the first such redesign in the history of the survey. SCeMFiS funded 3 projects to provide data resources to this working group. An R package was developed to provide statistical support for evaluation of sampling design. The R statistical package provided to the Survey Design Working Group provides software that could be implemented in the evaluation of any survey design, regardless or marine, lacustrine, or terrestrial and regardless of geographic extent on taxon.

Black Sea Bass
Finfish Assessment Team

Lead PI: Steve Cadrin (UMass): Developing a benchmark assessment that will meet the stringent demands of peer review requires a group of scientists of varying expertise, which the NMFS-NEFSC terms Working Groups. SCeMFiS has assembled a team of assessment experts from the academic community to provide such expertise. SCeMFiS academics have participated in benchmark assessments for scup, black sea bass, and Atlantic mackerel. The black sea bass assessment recently peer reviewed as the first successful peer review of this species since 2008, in part due to the efforts of SCeMFiS scientists who participated in model development for this challenging fish. Among the innovations was a model that accounted for the spatial structure of this species. Spawning stock biomass is judged to be well above Bmsy leading to the opportunity for increasing quotas for this fishery.

62nd Northeast Regional Stock Assessment Workshop (62nd SAW), Assessment Summary Report

Briefing Book from SAW Report

MAFMC Summary Report

GIS Layers for Nantucket & Georges Bank

Area Closures for Bottom Tending Gear Within Georges Bank
Photo: Eric Powell

Generation of GIS layers for Nantucket and Georges Bank closed areas

Lead PIs: Eric Powell (USM) & Roger Mann (VIMS): Fishing has been restricted in two areas by the creation of Habitat Management Areas (HMAs), one off Nantucket Shoals (NS) and one on Georges Bank (GB). The surfclam fishery is seeking an exemption because the bottom type occupied by surfclams is primarily sand and so is not the type of bottom identified as important habitat for protection under the closure. Information on bottom type, however, is spotty relative to the scale of the closed areas and the locations potentially fishable using hydraulic dredges. The SCeMFiS team will analyze NMFS survey data and data from the fishing fleet operating in the NS/GB region to provide improved differentiation between habitat of concern and high-energy sands supporting surfclam production. These analyses will provide information on subregions in the HMAs supporting live market-size surfclams and regions of complex habitat as evidenced by the presence of untowable bottom, location of reported dredge damage (by inference bottom with boulders or other obstructions), and locations where the survey dredge caught cobbles, rocks, and boulders.

The death assemblage as a marker for habitat and an indicator of climate change: Georges Bank, surfclams and ocean quahogs

Analysis of ancillary survey data and surfclam fishery tow data for the Georges Shoals Habitat Management Area on Georges Bank and the Great South Channel Habitat Management Area

GIS Data (zip), Layers (zip) and Files (.docx)


Bottlenose Dolphin
Photo: Willy Volk

Marine Mammal Poster


Whale Breaching
Photo: Whit Wells, Wikimedia Commons


Independent advisory team for marine mammal assessments - Phase IV

Lead PI: Paula Moreno (USM). The Marine Mammal Protection Act sets two goals for recovery of marine mammal stocks that are related to incidental mortality (M/SI) in fisheries: 1) reducing M/SI below the Potential Biological Removal (PBR) level within six months after implementation of a take reduction plan (TRP) and 2) reducing M/SI to insignificant levels within five years of the implementation of the TRP. M/SI rates are used to classify fisheries into categories: frequent, occasional, and remote. The ability to classify fisheries depends on the quality of the observer program and of setting PBR accurately. The analyses that developed the PBR formula did not consider the implications to the stock of classifying fisheries and imposing the above-mentioned goals. As a result, the risk to the stock under the current management system has not been fully evaluated. The existing MSE will be extended by including multiple fisheries, each with a different M/SI rate and a different level of observer coverage. The processes of assessing whether a stock is strategic, selecting which fisheries to focus conservation efforts on, and the consequences of those efforts in terms of reductions in M/SI will be included in the MSE. The outcomes of the MSE will be compared among schemes for allocating observer effort and classifying fisheries. The PBR (Potential Biological Removal) Tier System project developed by the SCeMFiS marine mammal team and funded by the Western Pacific Management Council involved a management strategy evaluation (MSE) of alternative approaches for calculating PBR. The computer code for the MSE is open-source.

clam survey dredge bar spacing

Subtle difference in bar spacing between a lined dredge vs the Dameron-Kubiak dredge
Photo: VIMS Molluscan Ecology

Juvenile survey for surfclams and ocean quahogs

Lead PI: Roger Mann (VIMS). The movement of the federal survey to an industry vessel has increased the efficiency of capture of market-size clams, but reduced the selectivity for juveniles. This project developed and fabricated a dredge liner to support a targeted juvenile survey in the new surfclam and ocean quahog industry-vessel based survey carried out by the NMFS-NEFSC.


School of alewives
Photo: J. Prezioso, NEFSC

Understanding impacts of fishing forage fish

Lead PIs: Olaf Jensen (Rutgers Univ.) and Robert Leaf (USM): The Lenfest report, “Little Fish, Big Impact,” has had a big impact on the policy arena for fisheries on forage fish, suggesting that harvest policies be much more restrictive, and in many cases, totally prohibit fishing forage fish.  Research has shown that many populations exhibit substantial natural fluctuations that could cause them to meet these criteria or to be classified as “overfished” even in the absence of fishing or while fishing at FMSY.  In general, natural variability is dominant and alternative models provide better description of population dynamics than standard stock assessment models. The objective of this proposal is to address the limitations of the Lenfest forage fish report in collaboration with an international team of researchers assembled by Dr. Ray Hilborn.  The SCeMFiS team will re-analyze the data and models considered by the Lenfest task force while considering natural variation and alternative forage species. 

Hilborn, R., Amoroso, R., Bogazzi, E., Jensen, O.P., Parma, A., Szuwalski, C., and C.J. Walters. In press. When does fishing forage species affect their predators? Fisheries Research.


Chub Mackerel
Photo: NOAA

Biostatistical and fishery-dependent sampling of Atlantic chub mackerel, round herring, and Spanish sardine

Lead PI: Robert Leaf (USM): The increased interest in “forage fish” stocks, their role as critical ecological components of Mid-Atlantic ecosystems, and the perception that increasing demand exists for fishmeal, fish oil, and bait has resulted in a proposal by the Mid-Atlantic Fishery Management Council to protect forage fish stocks from directed harvest until “adequate scientific information is available.” Many forage fishes, which include round herring, Atlantic chub mackerel, and Spanish sardine, are the target of fishing pressure but are not currently assessed by NOAA or the ASMFC. SCeMFiS will partner with cooperating harvesters to perform biostatistical sampling in order to examine the life-history characteristics of round herring, Atlantic chub mackerel, and Spanish sardine. The biostatistical data developed in this project will be incorporated into a suite of data limited stock assessment methods and provide a basis for an initial assessment of the status of the stock.

Flounder photo

Large flounder caught in the
recreational fishery
Photo: Don Lohse
Sex and length of summer flounder discards in the recreational fishery

Lead PI: Daphne Munroe (Rutgers Univ.): A recent stock assessment review of summer flounder identified the need to account for sex-specific fishing mortality in the assessment model. Sex-specific information for the population is collected annually by the National Marine Fisheries Service’s (NMFS-NEFSC) trawl survey. Sex composition of the catch, however, is limited and no information is available on sex composition of discards from the recreational fishery. The absence of information on the sex composition of recreationally discarded summer flounder remains a key need for development of a sex-specific stock assessment model. SCeMFiS will partner with the Save the Summer Flounder Fishery Fund (SSFFF) to support a field program to collect sex-at-length of recreational fishery discards using cooperating for-hire vessels fishing out of New Jersey, New York, and Rhode Island. These data will be incorporated directly into a the assessment model already in development.

Sex and length of summer flounder discards in the recreational fishery - Final Report

AFS Presentation by Ryan Harner (see Students section of People for more information)

Arctica islandica

Small arctica islandica used in aging study. Photo: Roger Mann

Development of an ocean quahog recruitment index

Lead PI: Eric Powell (USM): Ocean quahogs (Arctica islandica) are extremely long lived. Although the NMFS-NEFSC survey time series began in 1980, most of the animals fished were borne prior to that time. Consequently, recruitment dynamics for this stock are very poorly understood. Establishing that the current fishery is sustainable requires information on the recruitment dynamics of ocean quahogs over the last 200 years. This can be reconstructed from the age frequency of the population. This project will develop the first age frequencies for ocean quahogs in the northwest Atlantic, with study sites off New Jersey, Long Island, Nantucket, and on Georges Bank.

Pace, S. M., Powell, E. N., Mann, R, Long, M. C., Klinck, J. M. 2017. Development of an Age-Frequency Distribution for Ocean Quahogs (Arctica islandica) on Georges Bank. J. Shellfish Res. 36: 41-53.

Evidence of Multidecadal Recruitment in the Ocean Quahog, Artica Islandica in the Western Atlantic Ocean - Sara Pace, USM Master's Thesis

Large Flounder

A large summer flounder
Photo: John DePersenaire
Recreational Fishing Alliance

Sex specific summer flounder

Lead PI: Pat Sullivan (Cornell Univ.): Summer flounder exhibit a sexual size dimorphism, whereby females grow faster and to larger sizes than males making females more susceptible to fishing at earlier ages, by particular gear types, and under particular management regulations. Stock-assessment models that assume similar behavior among sexes and assume similar patterns of selectivity by sex across years, gear-types, and areas may result in biased estimates of population biomass. This project will develop a sex-specific model that accounts for differences in selectivity by sex and will create, as well, a transitional model that will facilitate bridging data gaps between the current assessment approach and the one proposed.

summer flounder biomass

Summer Flounder Biomass
Photo: ASMFC

Improvements in reference point formulation to reduce uncertainty in stock status of summer flounder

Lead PI: Pat Sullivan (Cornell Univ.): In the first year of this project, the SCeMFiS team created a sex-age specific stock-assessment model for summer flounder. Summer flounder exhibit a sexual size dimorphism, whereby females grow faster and to larger sizes than males making females more susceptible to fishing at earlier ages, by particular gear types, and under particular management regulations. Stock-assessment models that assume similar behavior among sexes and assume similar patterns of selectivity by sex across years, gear-types, and areas will result in biased estimates of population biomass. In the second year of this project, the SCeMFiS team will compare performance of age-structured, age-sex structured, and age-sex-length structured assessment models on existing survey and landings information for summer flounder, including evaluation of reference points. Outcomes will help implement a process for incorporating information from such assessments into the stock assessment review and management processes.

Fishing Boats

Fishing Boats
Photo: NOAA

Economic impacts of reduced uncertainty associated with fishery management actions

Lead PI: Tom Murray (VIMS): This project will establish a SCeMFiS economics team. One of the goals for this team is to develop risk assessment indices for selected fisheries.  The risk assessment will include indices reflecting recognized financial and market risk measures including:  financial (cash flow), market (permit values), earnings (net income) and growth orientation.  The risk indices will be tracked to illustrate changes in the indices associate with public management and SCeMFiS science to management investments. 

Economic Activity Associated with SCeMFiS Supported Fishery Products

Measurement of clams

Measurement of clams during survey
Photo: VIMS Molluscan Ecology

Breakage in surfclams and ocean quahogs during survey

Lead PI: Roger Mann (VIMS). The movement of the federal survey to an industry vessel has increased the number of broken clams in survey hauls. This project will develop morphometric relationships between valve length and umbo thickness or valve height to permit estimates of surfclam and ocean quahog lengths to be obtained from broken clams.

2015 - Clam breakage in survey mode: data correction

Poster from Mid-Atlantic Fisheries Management Council Meeting, December 2013

fishing vessel

Working with a dredge
Photo: VIMS Molluscan Ecology

Development of a reference point study team

Lead PI: Eric Powell (USM). Biological reference points are used to develop overfishing limits for federally managed stocks. Obtaining the best reference point for any particular stock remains a challenge for assessment scientists. SCeMFiS will further develop the concept of a reference point study team for evaluation.

Scup Assessment Report


Surf clams
Photo: VIMS Molluscan Ecology

Development of management options for surfclams

Lead PI: Eric Powell (USM). The recent benchmark assessment for surfclams considered a two-stock option for surfclams that was rejected by the Stock Assessment Review Committee. Nevertheless, the continued influence of Mid-Atlantifc Bight warming on the distribution of the surfclam stock suggests that a range of management options may need to be reviewed. SCeMFiS will examine this issue and recommend options to the IAB.

SCeMFiS scientists identified management options that will increase LPUE and also increase stock productivity and stock abundance in the Mid-Atlantic region, while maintaining landings at present quota levels.

View Report "Management Strategy Evaluation for the Atlantic Surfclam Spisula Solidissima Using a Fisheries Economic Model."

Identifying the Historical Footprint of the Surfclam Spisula solidissima and Habitat Relationships
from a Long-Term Dataset of Death Assemblages and Sedimentology

Captains' response to a declining stock as anticipated in the surfclam (Spisula solidissima) fishery on the U.S. Mid-Atlantic coast by model evaluation




Bottlenose Dolphin
Photo: Willy Volk

Stock Assessment Team Appointments

SCeMFiS is proud to announce the following researchers have been appointed to various stock assessment teams:

Finfish Stock Assessment Team: Jean-Jacques Maguire, Dr. Steve Cadrin, Dr. Robert Leaf, and Dr. Olaf Jensen. The SCeMFiS scup assessment team identified priority issues for the advancement of the scup assessment, reviewed draft working papers, provided data analyses, submitted working papers, participated in the Southern Demersal Working Group, reviewed the working group report, and participated in the Stock Assessment Review Committee (SARC) - Scup Stock Assessment Team Report

Shellfish Stock Assessment Team: Dr. Eric Powell, Dr. Roger Mann, and Dr. Daphne Munroe. The SCeMFiS Shellfish Stock Assessment Team will participate in ocean quahog and surfclam benchmark assessments of the NEFSC.

Marine Mammal Assessment Team: Dr. Paula Moreno, Dr. Andre Punt, Dr. Randall Reeves, Dr. John Brandon. Duties of the team are to 1) review MM Stock Assessment and other technical reports, scientific publications, and administrative or regulatory documents pertaining to MM assessment and management; and 2) attend meetings of the Atlantic Scientific Review Group (SRG) that reviews stock assessments and Take Reduction (TR) Teams that develop and monitor TR Plans/Strategies, and participate in other relevant scientific meetings where MM stock assessment information is presented and discussed. - Phase II Report

Projects Completed

Whale Breaching

Whale Breaching
Photo: Whit Wells, Wikimedia Commons

Independent advisory team for marine mammal assessments - Phase I

Lead PI: Paula Moreno (USM). Marine mammal regulations affect many East Coast fisheries and some of the most important fisheries in the Gulf. SCeMFiS supports a marine mammal assessment team, which provide the basis for further research on marine mammals by SCeMFiS designed to reduce uncertainty of estimates in these assessments such as marine mammal stock abundance or bycatch estimates. Recommendations from this team lead to additional research to be considered in subsequent funding years.

2015 Independent Advisory Team for Marine Mammal Assessment - Final Report – Phase I

Poster from Mid-Atlantic Fisheries Management Council Meeting, December 2013

Sara Beam

Sara Beam, Chesapeake Bay Governor's School teacher, assists in collection during a summer cruise for Arctic islandica
Photo: Sara Beam

Supplementary Funding Project: Participation of a high school teacher in the SCeMFiS project entitled “Ocean quahogs (Arctica islandica) recruitment and life history dynamics.”

Lead PI: Roger Mann (VIMS).The objectives of the teacher participation are as follows:

  • Provide a research field experience for a teacher focusing on teaching marine science to gifted high school students. Through this field experience the teacher will, in turn:

  • Introduce students to coastal oceanography as an extension of their curriculum focus on the Chesapeake Bay, the largest estuary in the continental United States.

  • Introduce students to simple quantitative data collection, analysis and decision tools in support of natural resource management.

  • Provide students with an introduction to long-lived marine species as indicators of climate change.

Read more

Update: Sara Chaves Beam and Bethany Smith have won the Governor’s Conservation Classroom Challenge issued by Virginia Governor Terry McAuliff

Part I & II Photo Gallery of the Dameron-Kubiak Dredge
(click the
i for more information on each slide -
slides will advance automatically unless the user pushes the stop button)


The science agenda of SCeMFiS includes:
  • development of essential biological data on fish stocks, including fecundity, age structure, and sources of mortality;

  • improved models of sampling design, population dynamics, habitat, and fishery performance;

  • evaluation of geographic and depth variations in stock structure and how these relate to the genetics, physiology and sexual dimorphism of species;

  • improved approaches to fishing to limit discard reduction through gear innovation and modifications in fleet deployment consistent with oceanographic processes;

  • improved assessment model formulations to better integrate available data; and

  • refined approaches to establishing biological reference points.


hard clams

All data are shared with federal agencies, fishery management councils, and regional commissions.