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Seal Ecology and Assessment Research in the Northwest Atlantic

We study the ecology of seals in the Northwest Atlantic to support conservation management and promote public stewardship of a healthy and diverse marine environment.

New England/Mid-Atlantic

On This Page

A larger harbor seal and a smaller gray seal swim at the center of a circular illustration of an ecosystem to portray the vital role that seals play in supporting the food web and enhancing biodiversity. The illustration shows a tour boat with visitors viewing a seal in the distance to represent how seals provide recreational and tourism opportunities. The harbor seal chases a school of sand lances and small hake on the left, to show how seals consume a diverse diet of mostly small fish.

There are two main species of seals that breed and forage in the U.S. Northwest Atlantic: harbor seals and gray seals. We research these seal populations to learn more about how many there are, where they live, and what they eat. This helps us understand their role in the ecosystem, and how they might be affected by factors like changing climate conditions.

As sentinels of the marine environment, seals can provide insight into the state of a changing ecosystem. One site where the Northeast Fisheries Science Center and their partners conduct research is Muskeget Island, where teams survey, capture, and sample animals to collect information on population abundance, individual animal health, diet, and behaviors.

Seal Abundance

Our seal research program focuses on harbor seal and gray seal ecology, primarily throughout the waters of Maine, New Hampshire, Massachusetts, Rhode Island, and New York. We monitor the abundance of both populations primarily using aerial photographic surveys along important haul-out sites such as beaches, sand bars, jetties, ledges, and rock piles that seals use to rest and give birth.

gray seals in the water at Chatham Harbor

We conduct harbor seal abundance surveys along the coast of Maine in late May to early June to coincide with the peak pupping period. These surveys provide an index of the number of pups born and of the total population. We conduct gray seal abundance surveys during the pupping season in January at colonies in Massachusetts and Maine, with the main goal of monitoring the annual number of pups born. We also conduct seasonal surveys at other times of year along coastal waters to monitor both harbor seal and gray seal abundance and habitat use. We use both manned and uncrewed aircraft to monitor the seal populations. Check out our Pinniped Distribution Query Tool to query and download results of these surveys.

ear bones recovered from seal stomach content analysis

Fish ear bones, or otoliths, recovered from a seal stomach help researchers determine prey species.

Trophic Ecology

Using multiple approaches to estimate diet composition improves our understanding of what seals eat and how this varies in space and time. We examine harbor seal and gray seal diets by the following methods: 

  1. Analysis of seal fecal material collected at several haul-out sites on Cape Cod and in Nantucket Sound
  2. Examination of seal stomachs collected from animals accidentally killed in commercial fishing operations
  3. Studying fatty acids in the blubber of live or dead animals

Our staff have recently begun to experiment with using DNA in stomach contents to identify prey, and also work with research partners who study diet via stable isotopes in hair and blood. We will integrate this information into ecosystem models so we can better understand the nutritional relationships among marine species and how much seal predation contributes to natural mortality of commercially important fish stocks.

Map showing the satellite tracks of 4 seal pups.
Satellite tracks of 4 individual gray seal pups tagged in January 2023 off Nantucket, MA. Research conducted under NOAA research permit #26939. Credit: NOAA Fisheries/Kimberly Murray
 

Movements and Distribution

We capture and tag harbor seals and gray seals to improve estimates of abundance and to better understand habitat use at sea and on land. Satellite tags provide information on seasonal movements throughout U.S. and Canadian waters as well as haul-out and diving behavior. In addition, longer-lasting acoustic tags provide information on the presence and survival of individual seals in particular areas. See satellite tracks of gray seal pups tagged in 2024.

Nasal swab sample are collected from a gray seal pup for virology analysis

Researchers swab samples from gray seal pup.

Biological Sampling

We also live-capture and sample harbor and gray seals. We work closely with our academic, government, and non-government research partners to conduct captures and to collect and analyze tissue, serological, and genetic samples. From these samples we gain information on the health of the animals, presence of disease and contaminant loads in the wild population, diet, and stock structure.

a dead young gray seal lies on the deck of a fishing boat entangled in netting

Gray seal caught in fishing gear. Photo: NOAA Fisheries.

Bycatch Analysis

Our staff analyzes annual mortality associated with incidental capture in commercial fishing gear and evaluates the potential impact of other human activities on seal populations. Serious injury and mortality estimates are incorporated into annual stock assessment reports.

A "tinyworld" photo of the seal sampling team at the top of the lighthouse

Researchers participate in winter fieldwork at the Nantucket National Wildlife Refuge. Photo: Milton Levin.

Collaborations

Scientific staff collaborate with regional universities, non-profit research organizations,and multiple government agencies to conduct seal research in the western North Atlantic region. Our staff are also members of international scientific groups that focus on North Atlantic seals.

researcher releasing drone above seals on beach

Researchers use a drone to photograph the Muskeget gray seal pupping colony.

News and Outreach

Publications

  • Marine Mammal Stock Assessment Reports
  • Bycatch and Serious Injury and Mortality Reports
  • Heywood, E.I., Murray, K.T., Doughty, L. et al. Postweaning horizontal movements and diving behavior of a recovering grey seal (Halichoerus grypus atlantica) population in the western North Atlantic. Anim Biotelemetry 13, 10 (2025).
  • Wood, S.A., E. Josephson, K. Precoda, and K.T. Murray. 2022. Gray seal (Halichoerus grypus) pupping trends and 2021 population estimates in U.S. waters. Northeast Fisheries Science Center reference document 22-14. DOI: 10.25923/9hjq-gb82
  • Sigourney, D.B., K.T. Murray, J.R. Gilbert, J.M. Ver Hoef, E. Josephson, and R.A. DiGiovanni, Jr. 2021. Application of a Bayesian hierarchical model to estimate trends in Atlantic harbor seal (Phoca vitulina vitulina) abundance in Maine, U.S.A., 1993–2018. Marine Mammal Science. DOI: 10.1111/mms.12873
  • Murray, K.T., J.M. Hatch, R.A. DiGiovanni Jr., and E. Josephson. 2021. Tracking young-of-the- year gray seals Halichoerus grypus to estimate fishery encounter risk. Mar. Ecol. Prog. Ser. 671:235–245. 
  • den Heyer, C.E., W.D. Bowen, J. Dale, J-F. Gosselin, M.O. Hammill, D.W. Johnston, S.L.C. Lang, K.T. Murray, G.B. Stenson and S.A. Wood. 2020. Contrasting trends in gray seal (Halichoerus grypus) pup production throughout the increasing northwest Atlantic metapopulation. Marine Mammal Science. DOI: 10.1111/mms.12773 
  • Wood, S.A., K.T. Murray, E. Josephson and J. Gilbert. 2019. Rates of increase in gray seal (Halichoerus grypus atlantica) pupping at recolonized sites in the United States, 1988-2019. Journal of Mammalogy. 
  • Hernandez, K.M., A.L. Bogomolni, J.H. Moxley, G.T. Waring, R.A. DiGiovanni Jr., M.O. Hammill, D.W. Johnston, L. Sette and M.J. Polito. 2019. Seasonal variability and individual consistency in gray seal (Halichoerus grypus) isotopic niches. Canadian Journal of Zoology 97(11): 1071–1077. DOI: 10.1139/cjz-2019-0032.
  • Pace, R.M.III, E. Josephson, S.A. Wood, K. Murray and G. Waring (retired). 2019. Trends and patterns of seal abundance at haul-out sites in a gray seal recolonization zone. NOAA Tech Memo NMFS-NE 251; 17 p. DOI: 10.25923/qd3s-we77.
  • Martins, M.C.I., L. Sette, E. Josephson, A. Bogomolni, K. Rose, S.M. Sharp, M. Neimeyer and M. Moore. 2019 Unoccupied aerial system assessment of entanglement in Northwest Atlantic gray seals (Halichoerus grypus). Marine Mammal Science 35:1613–1624. DOI: 10.1111/mms.12590
  • Cammen, K.M., T.F. Schultz, W.D. Bowen, M.O. Hammill, W.B. Puryear, J. Runstadler, F.W. Wenzel, S.A. Wood and M. Kinnison. 2018. Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds. Ecology and Evolution. DOI: 10.1002/ece3.4143
  • Johnston, D.W., J. Dale, K.T. Murray, E. Josephson, E. Newton and S. Wood. Comparing occupied and unoccupied aircraft surveys of wildlife populations: assessing the gray seal (Halichoerus grypus) breeding colony on Muskeget Island, USA. 2017. Journal of Unmanned Vehicle Systems 5:178–191. DOI: 10.1139/juvs-2017-0012.
  • Puryear, W.B., M. Keogh, N. Hill, N, J. Moxley, E. Josephson, K.R. Davis, C. Bandoro, D., Lidgard, A. Bogomolni, M. Levin, S. Lang, M. Hammill, D. Bowen, D.W. Johnston, T. Romano, G. Waring and J. Runstadler. 2016. Prevalence of influenza A virus in live-captured North Atlantic gray seals: a possible wild reservoir. Emerging Microbes and Infections 5(8):e81. DOI: 10.1038/emi.2016.77. 
  • Wood, S.A., T.R. Frasier, B.A. McLeod, J.R. Gilbert, B.N. White, W.D. Bowen, M.O. Hammill, G.T. Waring and S. Brault. 2011. The genetics of recolonization: an analysis of the stock structure of grey seals (Halichoerus grypus) in the northwest Atlantic. Canadian Journal of Zoology 89(6): 490–497. DOI: 10.1139/z11-012.

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Last updated by Northeast Fisheries Science Center on 04/04/2025