The O’Donnell Lab

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Sustainable Fisheries

The O’Donnell Lab, led by Research Scientist Tim O’Donnell, conducts applied genomics research that directly informs fisheries management, regulation, and conservation. We use genomic tools to address critical data gaps in fisheries science, monitoring, and decision-making, with the goal of improving long-term sustainability. Our research priorities are shaped through close collaboration with commercial and recreational fishing communities, conservation organizations, and state and federal agencies, ensuring that our work targets the most pressing needs. Although our primary focus is on New England fisheries, we are expanding our efforts to support sustainable fisheries management at national and global scales.

Research Focus

The research projects that the O’Donnell Lab conducts generally fall into three broad categories: population genetics, environmental DNA, and innovative tool development.

Population Genetics

Accurate fisheries stock assessments depend on defining stock boundaries that reflect true biological structure. When assessment units are spatially mismatched with biological reality, results can be biased, increasing the risk of overexploiting distinct spawning components and incorrectly estimating stock productivity. These errors can reduce biodiversity, destabilize population dynamics, and lead to inefficient resource use. Robust stock delineation is best achieved through a multidisciplinary approach that integrates traditional fisheries data with modern genomic tools such as low-coverage whole-genome sequencing. This approach generates genome-wide data across millions of loci, enabling the detection of fine-scale population structure as well as signals of natural selection and local adaptation to environmental conditions. Incorporating high-resolution genomic information into stock assessments strengthens management decisions and supports more effective, sustainable fisheries regulation.

Featured Projects:

Genomic population structure of Atlantic herring in US waters to inform fishery management

Atlantic herring in the U.S. are managed as a single stock, with area-based catch limits allocated using outdated 1990s-era estimates and a limited understanding of population structure and movement, despite recognition that these dynamics have likely changed. This project partners with state fisheries biologists and commercial fishing captains to sample herring from known spawning grounds and use low-coverage whole-genome sequencing to resolve population structure and develop SNP markers that distinguish spawning components. The application of this tool will enable managers to set biologically informed, area-specific quotas that better protect individual spawning groups and enhance the resilience of the herring fishery.

Environmental DNA

Environmental DNA (eDNA) is genetic material naturally shed by organisms into their surroundings (e.g., mucus, scales, feces). Its collection and analysis have rapidly emerged as powerful tools for species monitoring. When applied within a consistent spatial and temporal framework, eDNA—using either single-species assays or metabarcoding—can effectively characterize species distributions, habitat use, and community composition, especially in environments where conventional sampling is logistically challenging or limited. The O’Donnell Lab conducts eDNA research across freshwater, estuarine, and offshore systems, with the goal of generating high-resolution spatiotemporal distribution data for aquatic organisms that directly inform fisheries monitoring and management decisions.

Featured Projects:

Evaluating the effects of offshore wind development on fisheries using eDNA

As offshore wind development accelerates off the southern coast of Massachusetts, coordinated monitoring is urgently needed to understand and manage its impact on fisheries and the broader marine ecosystem that supports the state’s blue economy. This project established a coordinated eDNA-based monitoring program to assess how offshore wind construction and operation affect marine biodiversity and fisheries off Massachusetts. The resulting biodiversity data will inform fisheries and energy managers about species distribution changes, fishing displacement risks, and whether wind turbines function as fish aggregation devices.

Tracking winter flounder presence across Cape Cod estuaries using eDNA

Winter flounder is an economically important Northwest Atlantic flatfish that has declined in abundance and spawns in estuaries during winter and early spring, where its demersal eggs are vulnerable to disturbance from dredging and other coastal construction. Current data on winter flounder spawning activity are lacking for most New England estuaries, leading to conservative restrictions on construction activities. We used eDNA and qPCR to survey six Massachusetts estuaries over 12 months, revealing consistent bimodal patterns in winter flounder DNA that align with expected peaks in adult spawning and juvenile presence. These results show that eDNA is an effective tool for tracking winter flounder occupancy and timing, providing managers with actionable information to better balance construction activities and species protection.

Innovative Tool Development

Innovative genomic tools have the potential to transform fisheries science by addressing critical data gaps that have historically constrained effective monitoring and management. The O’Donnell Lab develops tools that build on our core expertise, including SNP panels for rapid population assignment based on low-coverage whole-genome sequencing data, species-specific eDNA assays for highly sensitive detection of target species, and epigenetic methods for aging fish to improve stock assessment accuracy. By complementing traditional approaches, these genomic tools enhance management decision-making, enabling more timely and informed responses to environmental changes and emerging conservation challenges.

Featured Projects:

Generating epigenetic aging clock models for sustainable fisheries management 

Emma Strand, Ph.D.’s, research takes advantage of already predictable epigenetic pattern changes, like those that occur with the passage of time. Using DNA methylation change as biomarker of aging, Dr. Strand generates epigenetic aging clock models that predict age values of individual organisms like fish and squid. Fisheries management depends heavily on accurate age information to sustainably manage populations that will be resilient to future environmental conditions. 

Read more about the Haddock epigenetic aging clock here: Building an ‘epigenetic clock’: Utilizing whole genome DNA methylation patterns to predict age in haddock, Melanogrammus aeglefinus | bioRxiv 

Collaborators: Northeast Fisheries Science Center | NOAA Fisheries, Northwest Fisheries Science Center | NOAA Fisheries, Narragansett Laboratory | NOAA Fisheries 

Meet the Team

Lab Alumni

Carly McCall: Research Associate at GMGI, went to North Carolina State University

Ashley Hoguet: Intern at GMGI, went to Tulane University

Brooke Nye: Intern at GMGI, went to Harvard University

Timia Buckley: Gloucester Biotechnology Academy intern at GMGI

Featured Collaborators 

John Logan, Ph.D., Massachusetts Division of Marine Fisheries

Micah Dean, Ph.D., Massachusetts Division of Marine Fisheries

Rich McBride, Ph.D., NOAA Northeast Fisheries Science Center

Heather Haas, Ph.D., NOAA Northeast Fisheries Science Center

Jeff Kneebone, Ph.D., New England Aquarium

Michael Metzger, Ph.D., Pacific Northwest Research Institute

Heather Glon, Ph.D., Maine Department of Marine Resources

Remy Gatins, Ph.D., Northeastern University

Featured Publications

See Tim O’Donnell’s full list of publications here. 

Strand, E.L., McBride, R.S., Robillard, E., Bodnar, A.G. and O’Donnell, T.P. Building an ‘epigenetic clock’: Utilizing DNA methylation to predict age in Haddock. In Review at Scientific Reports.

Polinski, J.M., Strand, E.L., O’Donnell, T.P., Silva, T.L., Wiley, D.N. and Harke, M.J. (2025), Environmental DNA Documents Ecosystem-Wide Biodiversity Within the Marine Protected Area Stellwagen Bank National Marine Sanctuary. Environmental DNA, 7:e70138.  https://doi.org/10.1002/edn3.70138

Polinski, J.M., O’Donnell, T.P., Bodnar, A.G. (2024) Chromosome-level reference genome for the Jonah crab, Cancer borealis. G3 Genes|Genomes|Genetics https://doi.org/10.1093/g3journal/jkae254

O’Donnell, T.P., & T.J. Sullivan. 2021.Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758). Ecology and Evolution 11: 10659-10671. doi:10.1002/ece3.7878

Funding Sources

Commonwealth of Massachusetts

National Oceanic and Atmospheric Administration

National Science Foundation

Massachusetts Technology Collaborative

Mass Clean Energy Center (MassCEC)

Massachusetts Life Sciences Center

Responsible Offshore Science Alliance (ROSA)

Remmer Family Foundation

Rhode Island Department of Environmental Management

The Sarah K. de Coizart Article TENTH Perpetual Charitable Trust

O’Donnell Lab Gallery