Assessing shipping noise as a potential driver of harbour seal (Phoca vitulina) habitat selection

Skye Wynn-Simmonds; Gaëtan Richard; Cécile  Vincent

doi:10.7557/3.8031

Authors

Skye Wynn-Simmonds PELAGIS (UAR 3462) CNRS - La Rochelle Université, 5 allée de l’Océan, 17000 La Rochelle, France & Société d’Observation Multi-Modale de l’Environnement, 300 Rue Pierre Rivoalon, 29200 Brest, France https://orcid.org/0009-0006-8711-0086
Gaëtan Richard Société d’Observation Multi-Modale de l’Environnement, 300 Rue Pierre Rivoalon, 29200 Brest, France
Cécile Vincent PELAGIS (UAR 3462) CNRS - La Rochelle Université, 5 allée de l’Océan, 17000 La Rochelle, France

DOI:

https://doi.org/10.7557/3.8031

Keywords:

Anthropogenic impact, Marine mammals, Noise pollution, Shipping noise, Phoca vitulina, Co-occurence, Habitat selection, Spatial modelling, Acoustic modelling

Abstract

Over the past decade, anthropogenic noise from activities such as shipping has significantly increased in the ocean, raising questions on their potential impact on coastal species such as harbour seals. In this study, we assessed the spatial overlap between ships (equipped with AIS transmitters) and harbour seals (tracked using telemetry) in the English Channel, one of the densest shipping areas in the world. We then studied how their habitat selection varied according to environmental parameters taking into account shipping noise as a potential driver. A total of 28 harbour seals were captured and equipped with GPS-GSM tags. AIS data (ships > 15 m length) was used to estimate shipping traffic density and model the associated shipping noise. We then used generalised additive mixed models to assess harbour seals’ habitat selection using distance to haulout, distance to shore, bathymetry, tidal current, sediment type, and shipping noise as explanatory variables. The model selected had an explained deviance of 71.8%. Our findings indicate that distance to haulout sites was the primary driver of habitat selection (~91.5% deviance), while other environmental factors such as bathymetry (~4.4%), distance to shore (~3.1%), tidal current (~0.3%), sediment type (~0.6%), and shipping noise (~0.1%) had only minor influences on their selection. Despite a high spatial overlap between shipping activity and tracked seals (73% of overlap), the weak contribution of shipping noise suggests that either seals may be habituated to chronic noise exposure or that noise levels rarely exceed tolerance threshold levels. To the best of our knowledge, this is the first article integrating shipping noise into harbour seals’ habitat selection models. These findings provide an understanding of harbour seal habitat selection in anthropogenic environments.

References

Akaike, H. (1973). Information Theory and an Extension of the Maximum Likelihood Principle. In B. N. Petrov, & F. Csaki (Eds.), Proceedings of the 2nd International Symposium on Information Theory (pp. 267–281). Budapest: Akademiai Kiado.

Avila, I. C., Kaschner, K., & Dormann, C. F. (2018). Current global risks to marine mammals: Taking stock of the threats. Biological Conservation, 221, 44–58. https://doi.org/10.1016/j.biocon.2018.02.021

Bailey, H., Hammond, P. S., & Thompson, P. M. (2014). Modelling harbour seal habitat by combining data from multiple tracking systems. Journal of Experimental Marine Biology and Ecology, 450, 30–39. https://doi.org/10.1016/j.jembe.2013.10.011

Bhagarathi, L. K., DaSilva, P. N. B., Maharaj, G., Balkarran, R., & Baksh, A. (2024). The impact of anthropogenic sound on marine mammals: A review. International Journal of Life Science Research Archive, 7(2), 009–033. https://doi.org/10.53771/ijlsra.2024.7.2.0070

Bivand, R., & Rundel, C. (2023). rgeos: Interface to Geometry Engine - Open Source ('GEOS'). R package version 0.5-9. https://CRAN.R-project.org/package=rgeos

Blair, H. B., Merchant, N. D., Friedlaender, A. S., Wiley, D. N., & Parks, S. E. (2016). Evidence for ship noise impacts on humpback whale foraging behaviour. Biology Letters, 12(8), 20160005. https://doi.org/10.1098/rsbl.2016.0005

Blanchet, M.-A., Vincent, C., Womble, J. N., Steingass, S. M., & Desportes, G. (2021). Harbour Seals: Population Structure, Status, and Threats in a Rapidly Changing Environment. Oceans, 2(1), 41–63. https://doi.org/10.3390/oceans2010003

Boehlert, G., & Gill, A. (2010). Environmental and Ecological Effects of Ocean Renewable Energy Development – A Current Synthesis. Oceanography, 23(2), 68–81. https://doi.org/10.5670/oceanog.2010.46

Boyi, J. O., Heße, E., Rohner, S., Säurich, J., Siebert, U., Gilles, A., & Lehnert, K. (2022). Deciphering Eurasian otter (Lutra lutra L.) and seal (Phoca vitulina L.; Halichoerus grypus F.) diet: Metabarcoding tailored for fresh and saltwater fish species. Molecular Ecology, 31(19), 5089–5106. https://doi.org/10.1111/mec.16635

Bretschneider, H., Bosschers, J., Choi, G. H., Ciappi, E., Farabee, T., Kawakita, C., & Tang, D. (2014, 31 August–5 September). Specialist Committee on hydrodynamic noise: Final report and recommendations to the 27th ITTC. Proceedings of the 27th International Towing Tank Conference, Volume 2, Copenhagen. https://www.ittc.info/media/6091/sc-noise.pdf

Brunbjerg, A. K., Hale, J. D., Bates, A. J., Fowler, R. E., Rosenfeld, E. J., & Sadler, J. P. (2018). Can patterns of urban biodiversity be predicted using simple measures of green infrastructure? Urban Forestry & Urban Greening, 32, 143–153. https://doi.org/10.1016/j.ufug.2018.03.015

Dauvin, J.-C. (2019). The English Channel: La Manche. In World Seas: An Environmental Evaluation (pp. 153–188). Elsevier. https://doi.org/10.1016/B978-0-12-805068-2.00008-5

Duarte, C. M., Chapuis, L., Collin, S. P., Costa, D. P., Devassy, R. P., Eguiluz, V. M., Erbe, C., Gordon, T. A. C., Halpern, B. S., Harding, H. R., Havlik, M. N., Meekan, M., Merchant, N. D., Miksis-Olds, J. L., Parsons, M., Predragovic, M., Radford, A. N., Radford, C. A., Simpson, S. D., … Juanes, F. (2021). The soundscape of the Anthropocene ocean. Science, 371(6529), eaba4658. https://doi.org/10.1126/science.aba4658

Erbe, C., Dunlop, R., & Dolman, S. (2018). Effects of Noise on Marine Mammals. In H. Slabbekoorn, R. J. Dooling, A. N. Popper, & R. R. Fay (Eds.), Effects of Anthropogenic Noise on Animals (Vol. 66, pp. 277–309). Springer New York. https://doi.org/10.1007/978-1-4939-8574-6_10

Erbe, C., Marley, S. A., Schoeman, R. P., Smith, J. N., Trigg, L. E., & Embling, C. B. (2019). The Effects of Ship Noise on Marine Mammals—A Review. Frontiers in Marine Science, 6, 606. https://doi.org/10.3389/fmars.2019.00606

Erbe, C., McCauley, R., & Gavrilov, A. (2016). Characterizing marine soundscapes. In A. N. Popper & A. Hawkins (Eds.), The Effects of Noise on Aquatic Life II (Vol. 875, pp. 265–271). Springer New York. https://doi.org/10.1007/978-1-4939-2981-8_31

Erbe, C., Reichmuth, C., Cunningham, K., Lucke, K., & Dooling, R. (2016). Communication masking in marine mammals: A review and research strategy. Marine Pollution Bulletin, 103(1–2), 15–38. https://doi.org/10.1016/j.marpolbul.2015.12.007

European Commission (2019). EMODnet Geology – Seabed Substrate Map of European marine areas (1:1,000,000 scale). European Marine Observation and Data Network (EMODnet). Available at: https://www.emodnet.eu/geology

Findlay, C. R., Rojano-Doñate, L., Tougaard, J., Johnson, M. P., & Madsen, P. T. (2023). Small reductions in cargo vessel speed substantially reduce noise impacts to marine mammals. Science Advances, 9(25), eadf2987. https://doi.org/10.1126/sciadv.adf2987

Frisk, G. V. (2012). Noiseonomics: The relationship between ambient noise levels in the sea and global economic trends. Scientific Reports, 2(1), 437. https://doi.org/10.1038/srep00437

Gabriele, C. M., Ponirakis, D. W., Clark, C. W., Womble, J. N., & Vanselow, P. B. S. (2018). Underwater Acoustic Ecology Metrics in an Alaska Marine Protected Area Reveal Marine Mammal Communication Masking and Management Alternatives. Frontiers in Marine Science, 5, 270. https://doi.org/10.3389/fmars.2018.00270

Gomez, C., Lawson, J. W., Wright, A. J., Buren, A. D., Tollit, D., & Lesage, V. (2016). A systematic review on the behavioural responses of wild marine mammals to noise: The disparity between science and policy. Canadian Journal of Zoology, 94(12), 801–819. https://doi.org/10.1139/cjz-2016-0098

Grigg, E. K., Allen, S. G., Craven-Green, D. E., Klimley, A. P., Markowitz, H., & Elliott-Fisk, D. L. (2012). Foraging distribution of Pacific harbor seals (Phoca vitulina richardii) in a highly impacted estuary. Journal of Mammalogy, 93(1), Article 1. https://doi.org/10.1644/11-MAMM-A-128.1

Hastie, G. D., Russell, D. J. F., Benjamins, S., Moss, S., Wilson, B., & Thompson, D. (2016). Dynamic habitat corridors for marine predators; intensive use of a coastal channel by harbour seals is modulated by tidal currents. Behavioral Ecology and Sociobiology, 70(12), Article 12. https://doi.org/10.1007/s00265-016-2219-7

Hildebrand, J. A. (2009). Anthropogenic and natural sources of ambient noise in the ocean. Marine Ecology Progress Series, 395, 5–20. https://doi.org/10.3354/meps08353

Hildebrand, J. A., Frasier, K. E., Baumann-Pickering, S., & Wiggins, S. M. (2021). An empirical model for wind-generated ocean noise. The Journal of the Acoustical Society of America, 149(6), 4516–4533. https://doi.org/10.1121/10.0005430

Huon, M., Jones, E. L., Matthiopoulos, J., McConnell, B., Caurant, F., & Vincent, C. (2015). Habitat selection of gray seals (Halichoerus grypus) in a marine protected area in France: Gray Seal Habitat Selection. The Journal of Wildlife Management, 79(7), Article 7. https://doi.org/10.1002/jwmg.929

Huon, M., Planque, Y., Jessopp, M. J., Cronin, M., Caurant, F., & Vincent, C. (2021). Fine‐scale foraging habitat selection by two diving central place foragers in the Northeast Atlantic. Ecology and Evolution, 11(18), Article 18. https://doi.org/10.1002/ece3.7934

Jacobs, S. R., & Terhune, J. M. (2002). The eﬀectiveness of acoustic harassment devices in the Bay of Fundy, Canada: Seal reactions and a noise exposure model. Aquatic Mammals 28(2), 131–146.

Jones, E. L., G. D. Hastie, S. Smout, J. Onoufriou, N. D. Merchant, K. L. Brookes and D. Thompson (2017). Seals and shipping: quantifying population risk and individual exposure to vessel noise. Journal of Applied Ecology 54(6): 1930-1940. https://doi.org/10.1111/1365-2664.12911

Kastelein, R. A., Wensveen, P. J., Hoek, L., Verboom, W. C., & Terhune, J. M. (2009). Underwater detection of tonal signals between 0.125 and 100kHz by harbor seals (Phoca vitulina). The Journal of the Acoustical Society of America, 125(2), Article 2. https://doi.org/10.1121/1.3050283

Kastelein, R. A., Helder-Hoek, L., Gransier, R., Terhune, J. M., Jennings, N., & de Jong, C. A. F. (2015). Hearing thresholds of harbor seals (Phoca vitulina) for playbacks of seal scarer signals, and effects of the signals on behavior. Hydrobiologia, 756(1), Article 1. https://doi.org/10.1007/s10750-014-2152-6

Keating, K. A., & Cherry, S. (2004). Use and interpretation of logistic regression in habitat-selection studies. Journal of Wildlife Management, 68(4), 774–789. https://doi.org/10.2193/0022-541x(2004)068[0774:uaiolr]2.0.co;2

Learmonth, J. A., MacLeod, C. D., Santos Vazquez, M. B., Pierce, G. J., Crick, H. Q. P., & Robinson, R. A. (2006). Potential effects of climate change on marine mammals. Oceanography and Marine Biology: An Annual Review, 44, 431-464. https://doi.org/10.1016/j.envint.2009.10.008

Lecornu, F., & De Roeck, Y.-H. (2009). PREVIMER-Observations & Prévisions Côtières. La Houille Blanche, 95(1), 60–63. https://doi.org/10.1051/lhb:2009006

Lemos, L. S., Haxel, J. H., Olsen, A., Burnett, J. D., Smith, A., Chandler, T. E., Nieukirk, S. L., Larson, S. E., Hunt, K. E., & Torres, L. G. (2022). Effects of vessel traffic and ocean noise on gray whale stress hormones. Scientific Reports, 12(1), 18580. https://doi.org/10.1038/s41598-022-14510-5

MacGillivray, A., & de Jong, C. (2021). A Reference Spectrum Model for Estimating Source Levels of Marine Shipping Based on Automated Identification System Data. Journal of Marine Science and Engineering, 9(4), 369. https://doi.org/10.3390/jmse9040369

MathWorks Inc. (2023). MATLAB version: 23.2.0 (R2023b), Natick, Massachusetts: The MathWorks Inc. https://www.mathworks.com

Maurer, N., Boyi, J. O., Schick, L. A., Nachtsheim, D. A., Schaffeld, T., Gross, S., Teilmann, J., Schnitzler, J., & Siebert, U. (2025). Unsealing behaviour: Variation in harbour seal (Phoca vitulina) responses to anthropogenic sound in relation to individual health. Marine Pollution Bulletin 214: 117777. https://doi.org/10.1016/j.marpolbul.2025.117777

Mikkelsen, L., Johnson, M., Wisniewska, D. M., van Neer, A., Siebert, U., Madsen, P. T., & Teilmann, J. (2019). Long‐term sound and movement recording tags to study natural behavior and reaction to ship noise of seals. Ecology and Evolution, 9(5), 2588–2601. https://doi.org/10.1002/ece3.4923

Nachtsheim, D. A., Johnson, M., Schaffeld, T., Van Neer, A., Madsen, P. T., Findlay, C. R., Rojano-Doñate, L., Teilmann, J., Mikkelsen, L., Baltzer, J., Ruser, A., Siebert, U., & Schnitzler, J. G. (2023). Vessel noise exposures of harbour seals from the Wadden Sea. Scientific Reports, 13(1), 6187. https://doi.org/10.1038/s41598-023-33283-z

Nowacek, D. P., Thorne, L. H., Johnston, D. W., & Tyack, P. L. (2007). Responses of cetaceans to anthropogenic noise. Mammal Review, 37(2), 81-115. https://doi.org/10.1111/j.1365-2907.2007.00104.x

Orians, G. H., & Pearson, N. E. (1979). On the theory of central place foraging. In D. J. Horn, R. D. Mitchell & G. R. Stairs (Eds.) Analysis of Ecological Systems (pp. 154–177). Columbus: Ohio State University Press.

Pante, E., & Simon-Bouhet, B. (2013). marmap: A package for importing, plotting and analyzing bathymetric and topographic data in R. PLoS ONE, 8(9), e73051. https://doi.org/10.1371/journal.pone.0073051

Pebesma, E. (2023). sf: Simple Features for R. R package version 1.0-14. https://CRAN.R-project.org/package=sf

Pebesma, E. J., & Bivand, R. S. (2005). Classes and methods for spatial data in R. R News, 5(2), 9–13. https://CRAN.R-project.org/doc/Rnews/

Possenti, L., De Nooijer, L., De Jong, C., Lam, F.-P., Beelen, S., Bosschers, J., Van Terwisga, T., Stigter, R., & Reichart, G.-J. (2024). The present and future contribution of ships to the underwater soundscape. Frontiers in Marine Science, 11, 1252901. https://doi.org/10.3389/fmars.2024.1252901

Planque, Y., Spitz, J., Authier, M., Guillou, G., Vincent, C., & Caurant, F. (2021). Trophic niche overlap between sympatric harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) at the southern limit of their European range (Eastern English Channel). Ecology and Evolution, 11(15), Article 15. https://doi.org/10.1002/ece3.7739

Poncet, S., Parent, S., Sicard, M., Le Baron, M., Gaultier, M., Hemon, A., Fremau, M-H., Lecarpentier, T., Gabet, L., Gicquel, C., Monnet-Kassas, S., Rault, C., Mahieux, J., Karpouzopoulos, J., Lefebvre, J., Everard, A., Colomb, F., Diard Combot, M., Provost, P., … Vincent, C. (2024). Recensement des colonies et reposoirs de phoques en France en 2022 et 2023. Rapport collectif du Réseau National Phoques. 63 pp.

Prawirasasra, M., Jüssi, M., Mustonen, M., & Klauson, A. (2022). Underwater noise impact of a ferry route on dive patterns of transiting Baltic ringed seals. Estonian Journal of Earth Sciences, 71(4), 201. https://doi.org/10.3176/earth.2022.14

Robbins, J. R., Bouchet, P. J., Miller, D. L., Evans, P. G. H., Waggitt, J., Ford, A. T., & Marley, S. A. (2022). Shipping in the north-east Atlantic: Identifying spatial and temporal patterns of change. Marine Pollution Bulletin, 179, 113681. https://doi.org/10.1016/j.marpolbul.2022.113681

Rolland, R. M., Parks, S. E., Hunt, K. E., Castellote, M., Corkeron, P. J., Nowacek, D. P., Wasser, S. K., & Kraus, S. D. (2012). Evidence that ship noise increases stress in right whales. Proceedings of the Royal Society B: Biological Sciences, 279(1737), 2363–2368. https://doi.org/10.1098/rspb.2011.2429

Sharples, R., Arrizabalaga, B., & Hammond, P. (2009). Seals, sandeels and salmon: Diet of harbour seals in St. Andrews Bay and the Tay Estuary, southeast Scotland. Marine Ecology Progress Series, 390, 265–276. https://doi.org/10.3354/meps08232

Simmonds, M. P. (2018). Marine mammals and multiple stressors: Implications for conservation and policy. In M. C. Fossi & C. Prati (Eds.) Marine Mammal Ecotoxicology (pp. 459–470). Academic Press. https://doi.org/10.1016/B978-0-12-812144-3.00017-6

Simmonds, M. P., Dolman, S. J., Jasny, M., Parsons, E. C. M., Weilgart, L., Wright, A. J., & Leaper, R. (2014). Marine noise pollution--increasing recognition but need for more practical action. Journal of Ocean Technology, 9(1), 71-90.

Southall, B. L., Bowles, A. E., Ellison, W. T., Finneran, J. J., Gentry, R. L., Greene, C. R., Jr., Kastak, D., Ketten, D. R., Miller, J. H., Nachtigall, P. E., Richardson, W. J., Thomas, J. A., & Tyack, P. L. (2007). Marine mammal noise exposure criteria: Initial scientific recommendations. Aquatic Mammals, 33(4), 411–521. https://doi.org/10.1578/AM.33.4.2007.411

Southall, B. L., Finneran, J. J., Reichmuth, C., Nachtigall, P. E., Ketten, D. R., Bowles, A. E., Ellison, W. T., Nowacek, D. P., & Tyack, P. L. (2019). Marine mammal noise exposure criteria: Updated scientific recommendations for residual hearing effects. Aquatic Mammals, 45(2), 125–232. https://doi.org/10.1578/AM.45.2.2019.125

Southall, B. L., Nowacek, D. P., Bowles, A. E., Senigaglia, V., Bejder, L., & Tyack, P. L. (2021). Marine mammal noise exposure criteria: Assessing the severity of marine mammal behavioral responses to human noise. Aquatic Mammals, 47(5), 421–464. https://doi.org/10.1578/AM.47.5.2021.421

Spitz, J., Mariotti, L., Ridoux, V., Caillot, E., & Elder, J. F. (2010). The diet of harbour seals (Phoca vitulina) at the southern limit of its European distribution (Normandy, France). NAMMCO Scientific Publications, 8, 313. https://doi.org/10.7557/3.2696

Sylvand B., 1995. The baie des Veys (French coast of the English Channel, western bay of Seine), 1972-1993: structure and long-term evolution of a sedimentary tidal flat benthic ecosystem under estuarine influence. [Doctoral dissertation, University of Caen]. https://archimer.ifremer.fr/doc/00848/96031/

Trigg, L. E., Chen, F., Shapiro, G. I., Ingram, S. N., Vincent, C., Thompson, D., Russell, D. J. F., Carter, M. I. D., & Embling, C. B. (2020). Predicting the exposure of diving grey seals to shipping noise. The Journal of the Acoustical Society of America, 148(2), Article 2. https://doi.org/10.1121/10.0001727

Van Neer, A., Nachtsheim, D., Siebert, U., & Taupp, T. (2023). Movements and spatial usage of harbour seals in the Elbe estuary in Germany. Scientific Reports, 13(1), 6630. https://doi.org/10.1038/s41598-023-33594-1

Wallace, B. (2012). Imap: Interactive Mapping. R package version 1.32. https://CRAN.R-project.org/package=Imap

Wang, X., Du, D., & Peng, Y. (2023). Assessing the Importance of the Marine Chokepoint: Evidence from Tracking the Global Marine Traffic. Sustainability, 16(1), 384. https://doi.org/10.3390/su16010384

Wołowicz, M., Sokołowski, A., & Lasota, R. (2007). Estuaries—A biological point of view. Oceanological and Hydrobiological Studies, 36(3), 113–130. https://doi.org/10.2478/v10009-007-0025-2

Wilson, L. J., & Hammond, P. S. (2019). The diet of harbour and grey seals around Britain: Examining the role of prey as a potential cause of harbour seal declines. Aquatic Conservation: Marine and Freshwater Ecosystems, 29(S1), 71–85. https://doi.org/10.1002/aqc.3131

Wood, S.N. (2023). mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation. R package version 1.9-0. https://CRAN.R-project.org/package=mgcv

Wynn‐Simmonds, S., Planque, Y., Huon, M., Lovell, P., & Vincent, C. (2024). Foraging behavior and habitat selection of harbor seals (Phoca vitulina vitulina) in the archipelago of Saint‐Pierre‐and‐Miquelon, Northwest Atlantic. Marine Mammal Science, e13134. https://doi.org/10.1111/mms.13134

Wynn-Simmonds, S., Vincent, C., Mathias, D., & Richard, G. (2025). Comparative analysis of underwater acoustic propagation models: Evaluating the trade-off between accuracy and computational demands for coastal noise predictions. Marine Pollution Bulletin, 215, 117905. https://doi.org/10.1016/j.marpolbul.2025.117905

Zamon, J. E. (2001). Seal predation on salmon and forage fish schools as a function of tidal currents in the San Juan Islands, Washington, USA. Fisheries Oceanography, 10: 353–366. https://doi.org/10.1046/j.1365-2419.2001.00180.x