Author Archives: gfay

Applying tree analysis to assess combinations of Ecosystem-Based Fisheries Management actions in Management Strategy Evaluation: a summary

Lucy McGinnis, 11 February 2021

[Editors note, we’re starting a new series where lab members write posts about eachothers’ research. Thanks Lucy for taking the reins on this first one!]

headshot of Amanda Hart, PhD candidate & first author of the publication.

Amanda Hart, PhD candidate

There is no one miracle cure for commercial fisheries. But last year, lab PhD candidate Amanda Hart published her first first author paper with PI Gavin Fay in Fisheries Research that considered how combinations of management actions that could make progress towards developing sustainable practices.

It starts with an ecosystem-scale perspective. In the past, fishery management strategies were built around individual species. However, as our understanding of the environmental, societal, and economic pressures that govern fisheries has grown, efforts have shifted toward Ecosystem-Based Fisheries Management (EBFM). EBFM takes into account the effects of inter-species interactions and abiotic pressures such as climate change and habitat availability, as well as fleet and gear interactions and the socio-economic drivers on the other end of the fishing line.

As fisheries around the world shift toward this approach, there is need to evaluate the performance of such strategies.Picture of the masthead for the publication in Fisheries Research

Amanda used Management Strategy Evaluation (MSE) to model scenarios and compare the efficacy of various management strategies on a ten species fishery characteristic of Georges Bank, USA, one of New England’s fishing hotspots. MSE simulates environmental management scenarios and identifies management procedures that have the greatest effects towards desired outcomes. MSE also can show how uncertainty associated with the fishery and management system influences outcomes.

Starting with historic biomass and catch information, they defined a management procedure to simulate that included three components: target fishing mortality, indicator-based harvest control rules, and catch ceilings. They conducted one thousand model simulations for each scenario (for a total of 29,000 simulations) over a thirty-year projection. The projections were then evaluated based on twelve performance metrics: frequency of species overfished, frequency of aggregate group collapse, piscivore catch, benthivore catch, planktivore catch, elasmobranch catch, frequency of system collapse, system biomass, system catch, biomass diversity, catch diversity, and catch revenue. This let them assess the effect of various management strategies on biological, catch, diversity, and economic objectives. Regression trees were used as a novel method of understanding how the different management actions drove the variability seen in the performance metrics obtained from the simulations.

Catch ceilings were consistently identified as the main drivers of variability in the results. By placing a limit on the total removals from the ecosystem (summed over all ten species), they achieved higher diversity, biomass, revenue, and lower frequencies of collapse. Optimal management performance corresponded with catch ceilings of 125-150 kt. Increasing the catch ceiling above this level did not substantially increase the system catch or revenue.

In fact, procedures that imposed high catch ceilings, or no catch ceiling at all, performed poorly, resulting in the highest frequency of aggregate collapse due to overfishing. Overfishing damages the structure of the ecosystem, resulting in negative long-term effects on its recovery and stability. That’s the trade-off between catch and biomass: the more fish you catch, the less you leave, which makes it difficult for stocks to replenish.

Without an optimal catch ceiling, there were still ways to improve management outcomes in the simulation results. Implementing ecosystem indicator-based harvest control rules and reduced target fishing mortality rates, even when there were fewer restrictions on overall catch, resulted in systems that performed better, which highlights the important role of these combined strategies in managing fisheries.

Amanda is a current NMFS-Sea Grant Population and Ecosystem Dynamics Fellow. We’re looking forward to learning more about the applications of MSE Amanda is conducting in her PhD research. Stay tuned!

Hart, A.R. and Fay, G., 2020. Applying tree analysis to assess combinations of Ecosystem-Based Fisheries Management actions in Management Strategy Evaluation. Fisheries Research, 225, p.105466.

Postdoctoral researcher positions. Apply!

Jobs jobs jobs!

Pleased to announce three postdoctoral research associate positions at UMass Dartmouth & NOAA Fisheries Northeast Fisheries Science Center, including one position working with our group (position #3):

1) The use of fine-scale fishery dependent data to evaluate potential impacts to fishery operations due to offshore wind energy development.
2) The development of oceanographic indicators from satellite data that are relevant for the management and assessment of the Northern shortfin squid, Illex illecebrosus, on the Northeast U.S. continental shelf.
3) The development and evaluation of multispecies stock assessment models for tactical use in providing fisheries management advice.

Info for all 3 positions and how to apply.

Info for the position with our group. (also pasted below)

Post-doctoral Researcher
Multispecies fisheries assessment modeling
NOAA Fisheries Northeast Fisheries Science Center, Woods Hole, MA, and University of Massachusetts Dartmouth

Accounting for species interactions in both stock assessment modeling and fisheries management is of increasing interest. Most current scientific advice for fisheries management is based on results from single species population dynamics models but if fisheries management is to become ecosystem-based, models that consider multispecies interactions are required. Multispecies models have wide use in research, but not yet in tactical management and require simulation testing to ensure the level of performance expected of tactical fishery assessment models.  Multispecies models “of intermediate complexity” between single population and full ecosystem models potentially combine the best aspects of current single species assessment models with key ecological linkages between species. The Northeast Fisheries Science Center (NEFSC) is currently applying a suite of these models to a simulated system coarsely modeled after the Georges Bank fish community.

The post-doctoral researcher (PR) will develop and evaluate multispecies models for tactical use in providing fisheries management advice. This innovative research is facilitated by substantial long-term ecological datasets within the region, and built on a foundation of existing models, such that the PR will take the models to the next level where they can be used in a management arena. The PR will collaborate with Dr. Sarah Gaichas in the NEFSC Ecosystem Dynamics and Assessment Branch, Dr. Kiersten Curti in the NEFSC Population Dynamics Branch, and Dr. Gavin Fay in the Fisheries Oceanography department of UMASS Dartmouth, on a project to evaluate the performance of both length- and age-based multispecies approaches for providing management advice. The primary objective of this work is to assess the impact of structural uncertainty in length- and age-based multi- and single-species population dynamic models on the estimation of underlying population parameters. This comparison is particularly important for multispecies models, which incorporate an added source of mortality through size-dependent predation.

A general multispecies statistical catch-at-age model has already been developed in AD Model Builder (ADMB). The length-based multispecies model (Hydra) has also been developed in ADMB but is currently being used as an operating model for multispecies simulation testing. To evaluate Hydra’s performance as an estimation model, the PR will first convert it from a simulation to estimation model.  Both multispecies models, as well as existing age- and length-based single species models, will then be fit to simulated data to evaluate model performance and examine the consequences of ignoring species interactions in assessment models. Finally, both multispecies models will be fit to actual observations from Georges Bank to evaluate operational potential within in a particular region.

Required Qualifications

  • A completed (or nearly-completed) PhD degree in a relevant discipline, such as fisheries science, statistics, oceanography, ecology, quantitative ecology, or other related field that demonstrates a strong quantitative background.
  • Demonstrated experience of fluency in statistical/modeling programming languages (e.g. AD Model Builder, C++, R).
  • Strong written and oral communication skills, as evidenced preferably through publications in the peer-reviewed scientific literature and reporting and presentations to a variety of audiences.

Preferred Qualifications

  • Experience fitting population dynamics models to data for fisheries stock assessment.
  • Experience and interest in using open data science tools for collaboration, project management, and reproducible research.
  • Knowledge of fisheries management, and understanding of the management process in the U.S.

Location, duration, and salary

The position will be primarily located at NOAA Fisheries in Woods Hole, MA with some expectation for travel to scientific meetings. The PR will also engage with students and staff in Dr. Gavin Fay’s lab at UMass Dartmouth SMAST (New Bedford), with flexibility for some work at that location. It is anticipated that work for this position will be conducted remotely. Further information on the NEFSC can be found via the institution’s website ( Further information about the UMass Dartmouth School for Marine Science and Technology and the Fay lab’s research can be found at ( and

This position is full-time for 1.5 years and has an annual salary of $55-60K with benefits and funding for travel to scientific meetings, with the second year contingent on funding availability and satisfactory progress during the first year. Start date is flexible, and the successful candidate could begin as soon as possible.


Interested applicants that meet the requirements should review the SMAST Code of Conduct and Diversity Statement, then submit an application consisting of cover letter, CV, and contact information for at least two professional references to the following job posting:

Questions about the position can be directed by email to Dr. Gavin Fay (, Dr. Sarah Gaichas (, or Dr. Kiersten Curti (

UMass Dartmouth values excellence, diversity, transparency, student-centeredness, accountability, innovation, engagement, collaboration, collegiality and safety. UMass Dartmouth employees and applicants for employment are protected by federal laws, Presidential Executive Orders, and state and local laws designed to protect employees and job applicants from discrimination on the basis of race, religion, color, sex (including pregnancy, gender identity, and sexual orientation), national origin, age, disability, family medical history or genetic information, military service, veteran status or other non-merit based factors. For more information about benefits and working at UMass Dartmouth, view the Human Resources website

Welcome Lucy McGinnis!

This month we welcomed new MS student Lucy McGinnis to the lab! Lucy will be working on a NEFSC-funded project to evaluate use of fishery dependent data in stock assessments. You can read more about Lucy on the lab People page.

Master's student Lucy McGinnis

Successful whale tagging expedition with Stellwagen Bank National Marine Sanctuary

Dr. Tammy Silva


Lab postdoc Dr. Tammy Silva has been hard at work in the field this summer conducting sand lance surveys, tagging and tracking shearwaters, and more! Here, Tammy shares her experiences with last month’s whale tagging expedition.


(Tammy Silva, July 10, 2019)

Two weeks ago, the research team from Stellwagen Bank National Marine Sanctuary (SBNMS) assembled on Cape Cod with some of the best whale researchers in the world to complete our 17th whale tagging expedition. SBNMS has been tagging whales since 2004, making this one of the longest and near continuous whale tagging projects in the world. The main goal of this project is to collect fine-scale movement data to help us understand the underwater behavior of whales including how they use the water column. This information is crucial for developing strategies to reduce risk of entanglement and ship-strike, the 2 leading causes of death for large whales.

DTAG (left) and CATS (right)

To collect these data, we used 2 types sound and movement tags: DTAGs ( and CATS (


DTAGs are equipped with hydrophones to record sounds produced by and heard by the tagged whale, as well as high-resolution motion sensors to measure depth, pitch, roll and heading of the tagged animal. CATS have most of the sensors above, plus high-quality video cameras. These state-of-the-art tags give us a glimpse of what these animals are doing underwater when we can’t see them. In addition to water column use, these tags enable us to study acoustic communication, social interactions, physiology, energetics, dive behavior, and foraging behavior of baleen whales. This work is a huge group effort! We collaborate with scientists from the Center for Coastal Studies (Provincetown), Moss Landing Marine Laboratories, National Marine Fisheries Service, Ocean Alliance, University of California Santa Cruz, University of Michigan, Stanford University, Syracuse University, and Woods Hole Oceanographic Institution.

A CATS fine-scale movement and video recording tag being placed on the humpback whale “Mystery” (Photo by J. Tackaberry; NMFS permit # 18059).

This year we were working out of Stage Harbor in Chatham, MA. Each morning we’d get up way before sunrise, transit on the sanctuary’s R/V Auk ~ 1 – 2 hours east of Chatham where we’d find 50 – 100 humpback whales feasting on sand lance. Absolutely amazing to see! And makes 3 am wake-up calls so worth it!


Once we found whales, we’d launch 2 RHIBS: the tagging vessel, Balena, and the focal follow vessel, LuNa. The Balena would approach and tag whales (all work conducted under NMFS permit #18059). Once a tag was on, the LuNa would stick with the tagged animal (also called a focal follow) to conduct behavioral sequencing, or writing down everything the tagged animal does. Having behavioral observations at the surface helps provide some context to what we see on the tag record and combined with the underwater tag data, provides a more complete picture of the whale’s behavior.

The R/V Auk and focal follow vessel LuNa with a group of feeding humpbacks. (Photo by J. Tackaberry; NMFS permit # 18059).

Highlights of this year’s cruise included:

  • 28 humpback whales tagged,
  • Many 24+ hour deployments on humpbacks (great for learning about differences in day/night behavior),
  • 2 fin whales tagged,
  • Longest tag deployment on a fin whale on the east coast of the US (+5 hours).

We even received an “official” award from Fay Lab PhD candidate Robert Wildermuth!

Thanks Robert!

This year’s cruise was a huge success and we already can’t wait for next year! Thanks to the Volgenau Foundation, International Fund for Animal Welfare, National Marine Sanctuary Foundation, and SBNMS for continued funding and support.

Robert Wildermuth awarded 2018 NMFS-Sea Grant Fellowship

Huge congratulations to PhD candidate Robert Wildermuth, recipient of a 2018 NMFS-Sea Grant Population & Ecosystem Dynamics Graduate Fellowship!

UMass Dartmouth press release:

NMFS-Sea Grant press release:

Robert joins Fay Lab PhD candidate Megan Winton as current NMFS-Sea Grant Fellows from UMassD SMAST.

Fay Lab attends American Fisheries Society annual meeting in Tampa

Post by Ashley Weston:

A couple of weeks ago Amanda, Gavin, and myself from the Fay lab attended the annual American Fisheries Society (AFS) meeting in Tampa, Florida. While we were there I gave an oral presentation about the first chapter of my master thesis work. Between the feedback, diverse symposia, chances to network, and all around fish-related atmosphere AFS never fails to be a great conference.


AFS was particularly helpful to me at this point in my graduate experience because I have been in the weeds of my analysis and getting results for my first chapter and I had the chance to pick my head up and remember the overall big questions of “why am I doing this work?” and “what does this mean in the grand scheme of things?” through putting together my presentation. In addition, with my hot-off-the-press results, the questions, feedback, and conversations I had at AFS allowed me to better formulate the whole story of my first chapter research and get the most out of my results.

I find it inspiring and helpful to sit in on different symposia at these large conferences. I particularly enjoyed the symposia “Ten Years of Science-Based Management in US Fisheries” and Dr. Michael Sissenwine’s talk about progress in policy with respect to the Magnuson-Stevens Act and the challenges associated with making policy a reality in fisheries. I also enjoyed the “Progress Toward Ecosystem-Based Fisheries Management” symposium because it reiterated a lot of what I had learned in Gavin’s EBFM class but gave perspectives from different parts of the world.  Another noteworthy symposium was the “Management Strategy Evaluation” session which ended a little differently than most with a panel discussion from a variety of stakeholders such as fishermen, scientists, council staff, and non-governmental agency members giving their viewpoints on how to advance the use of MSEs. Again, getting out of my little coding bubble and seeing what other people are doing puts things into perspective and I always learn a lot.

While these conferences are always full of talks, they don’t skimp on the chance for you to “network”. They took us to the Lowry Park Zoo for the student networking event and the Aquarium for the grand networking event! It’s true that the fisheries field is a small world and most everyone is eager to meet new people and talk about fish, so your network grows quickly.

Outside of the formal networking experience Amanda and I got to do a bit of exploring around Tampa as well. We ventured out on what we thought would be a short casual walk to lunch, but it turns out walking two miles in the Tampa heat is much more difficult than anticipated! It is so humid there this time of year. But, in seeing most of Tampa’s scenic river walk we got to see a wild manatee! For me this was a first and definitely made the hike worth it!

Ashley’s talk at the AFS meeting was titled “Performance of Alaskan groundfish harvest control rules under climate change given recruitment-environmental linkages in stock assessments”.

Other Fay lab work presented at the meeting included:
Fay, G., G.N. Tuck, M. Haddon. Evaluating monitoring and management strategies for Macquarie Island Patagonian toothfish (Oral presentation by Gavin), &
Hart, A.R., G. Fay. Evaluating an ecosystem-based fishery management model for Georges Bank using ceilings on system removals (Poster presentation by Amanda).

Postdoctoral position in Management Strategy Evaluation

Postdoctoral Fellow
Quantitative fisheries and ecosystem science
University of Massachusetts Dartmouth, New Bedford, MA

The Department of Fisheries Oceanography at the University of Massachusetts Dartmouth’s School for Marine Science and Technology (SMAST) is looking for an outstanding Postdoctoral Fellow (PF) to work under the supervision of Dr. Gavin Fay, assistant professor of Fisheries Oceanography, to develop and evaluate quantitative tools for assessing and managing fisheries in the Northeast U.S. under climate change.

Climate-mediated changes in the Northeast U.S. Shelf Large Marine Ecosystem are unprecedented, and the impacts of these changes on marine fisheries resources are increasing. Once abundant and supporting a profitable fishing industry, some groundfish stocks in the Northeast U.S. have declined to record-low biomass in recent years, whereas others have increased. Shifts in productivity of Northeast U.S. groundfish may reflect individual species responses to recent warming and associated oceanographic changes. It is crucial to understand how fisheries management procedures could consider climate-driven changes and evaluate whether these procedures would result in more adaptive, successful management of groundfish species given forecasted climate change. Management Strategy Evaluation (MSE) is a powerful simulation-based framework for structured decision-making that can compare the performance and robustness of management options given uncertainty and quantify tradeoffs among multiple, possibly competing ecological, economic, and societal objectives.

The PF will collaborate with scientists at the University of Massachusetts Dartmouth, Gulf of Maine Research Institute, and the NOAA Fisheries Northeast Fisheries Science Center on a 3-year research project to develop and apply a MSE for Northeast US groundfish fisheries that tests the performance of stock assessment methods and harvest control rules under climate change. The PF will develop alternative climate-responsive fisheries management procedures for key species and write code to implement these within an MSE framework, linking modeling efforts with results and activities of other project researchers. The PF will undertake MSE analyses that include technical interactions as part of a mixed fishery analysis, and quantify the expected ecological and economic performance of the alternative management procedures. The PF will interact closely with another postdoc based at GMRI to coordinate application of the project’s modeling framework. The computer programs developed by the PF will provide a general framework that can apply to other species and/or large marine ecosystems. The PF will take a lead role in the writing and publication of reports, peer-reviewed papers, and presentations at scientific meetings on the results of this research.


  • An earned PhD degree in a relevant discipline, such as Fisheries Science, Statistics, Ecology, or other related field, that demonstrates a strong quantitative background. [candidates with nearly-completed PhDs will also be considered]
  • Experience fitting statistical models to data, including demonstrated fluency in statistical/modeling programming languages (e.g. R, AD Model Builder, Template Model Builder).
  • Strong written and oral communication skills, as evidenced through publications in the peer-reviewed scientific literature and presentations to a variety of audiences.

Additional knowledge, skills and abilities:

  • Experience fitting population dynamics models to data for fisheries stock assessment and application of simulation testing frameworks like Management Strategy Evaluation is preferred.
  • Knowledge of fisheries management, and understanding of the management process in the U.S.
  • Ability to work independently and as part of a team to successfully complete project goals.
  • Strong pedagogical skills.

The position has an annual salary of $55K plus benefits. The position is full-time for three years, with the second and third years of funding conditional on the PF making satisfactory progress during the first year. Start date is flexible; the successful candidate could begin as early as October 2017.

The position will be located at the University of Massachusetts Dartmouth SMAST’s new marine science building in New Bedford, MA with expectation for travel to scientific meetings and for meetings with regional project partners. The PF will join a dynamic group of graduate students and postdoctoral researchers in a growing lab focused on quantitative approaches for fisheries assessment and ecosystem-based management. Opportunities exist for teaching, student mentoring, academic training, and participation in regional scientific advisory working groups dependent on PF interests and career goals. The PF will be encouraged to collaborate with students and staff at all collaborating institutions. In addition to Dr. Fay, project PIs include Dr. Lisa Kerr & Dr. Andrew Pershing (GMRI), Dr. Sarah Gaichas (NOAA NEFSC), and Dr. Steve Cadrin (UMass Dartmouth). Further information on UMass Dartmouth SMAST, GMRI, and the NOAA NEFSC can be found via the institutions’ websites (;; For information on the Fay lab see

Qualified applicants should submit a cover letter, CV, writing samples (e.g. copies of relevant publications), and contact information for three professional references by clicking here. Questions about the position should be directed via email to Dr. Gavin Fay at Review of applications will begin October 1, 2017 and continue until the position is filled.

UMass Dartmouth’s School for Marine Science & Technology (SMAST) is a nationally and internationally recognized research institution located in New Bedford, Massachusetts; the nation’s top fishing port. SMAST’s cutting-edge research projects emphasize interdisciplinary basic-to-applied marine sciences and the development of innovative technologies. The SMAST marine science campus, in collaboration with the Massachusetts Division of Marine Fisheries (DMF), creates a major marine science hub in the Northeast US, bringing together more than 150 faculty, students, and staff engaged in education, research and policy related to commercial fishing, coastal preservation, ocean observation, and climate change.

About University of Massachusetts Dartmouth:
The University of Massachusetts Dartmouth distinguishes itself as a vibrant public university actively engaged in personalized teaching and innovative research, and acting as an intellectual catalyst for regional and global economic, social, and cultural development.

The University of Massachusetts Dartmouth values excellence, diversity, transparency, student-centeredness, accountability, innovation, engagement, collaboration, collegiality and safety.
University of Massachusetts Dartmouth employees and applicants for employment are protected by federal laws, Presidential Executive Orders, and state and local laws designed to protect employees and job applicants from discrimination on the bases of race, religion, color, sex (including pregnancy, gender identity, and sexual orientation), national origin, age, disability, family medical history or genetic information, military service, veteran status or other non-merit based factors.

The University of Massachusetts reserves the right to conduct background checks on potential employees.

Lab group biographies added, belated welcomes

We have added bios of lab group members to the People page. Click on the People link to learn about graduate students and their research in the Fay lab.

As part of this update, we welcome (to the internet version of the lab) MS student Amanda Hart and postdoctoral researcher Dr. Vanessa Trijoulet.

Amanda joined us early fall 2016 and, in between a full load of coursework, is working currently on evaluating the performance of ecosystem based management procedures for New England.

Vanessa joined us in November 2016 from the University of Strathclyde, where in her PhD she applied bio-economic models to quantify the effect of seal predation on West of Scotland groundfisheries. Vanessa is working jointly with Dr’s Kiersten Curti & Tim Miller at NOAA’s Northeast Fisheries Science Center in Woods Hole, and holds a visiting scholar appointment in the Fay lab.

Great to have both Amanda and Vanessa as part of the team!

New paper reports on 1st Atlantis ecosystem model summit

A recently published paper in Ecological Modelling (Weijerman et al. 2016) reports on the first Atlantis Ecosystem Model Summit, held in December 2015 in Honolulu, HI.

The Atlantis Summit brought together developers and users of the Atlantis model worldwide, as well as the larger end to end ecosystem modeling community. The aims of the workshop were “to provide a better understanding of the current modeling work, elicit wider interest, and foster collaboration within the Atlantis community“.

Gavin and Robert attended the meeting, moderating a session on the use of Indicators in Atlantis and participating in a pre-meeting workshop on developing a simulation testing toolbox. In the paper (linked below), the Summit Steering Committee (including Gavin) report on the main outcomes of the conference.

Work continues on preparation of manuscripts describing the results of common scenarios run in multiple Atlantis models, and in the development of R tools to use Atlantis for Management Strategy Evaluation and ecosystem assessment model performance testing.
A collection of R packages for interfacing with Atlantis, many developed during the meeting, can be linked to via the r4atlantis organization on github.

Weijerman, M., J.S. Link, E.A. Fulton, E. Olsen, H. Townsend, S. Gaichas, C. Hansen, M. Skern-Mauritzen, I.C. Kaplan, R. Gamble, G. Fay, M. Savina, C. Ainsworth, I. van Putten, R. Gorton, R. Brainard, K. Larsen, T. Hutton. 2016. Atlantis Ecosystem Model Summit: Report from a workshop. Ecological Modelling 335: 35-38.

Postdoc position available: multispecies fisheries modeling

Tim Miller, Kiersten Curti (NOAA Fisheries) and I are looking for a great fisheries modeling postdoc to work on multispecies state-space stock assessment models in the Northeast US.

The position will be based at the NOAA Fisheries Northeast Fisheries Science Center in Woods Hole, Massachusetts. Work space will also be available in my lab at UMass Dartmouth. The position is for 2 years with salary of $55k. This would be a good position for quantitative types who want to apply and develop their ADMB/TMB skills.

A full position description can be found below and at the following link: