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NEFSC Protected Species Branch Staff

Sean Hayes

Sean Hayes

Current Activities

Sean Hayes became Chief of the Protected Species Branch in 2016. As Branch Chief, Sean works with branch and center staff to support sound science geared at quantifying the relative impacts of various limiting factors preventing the recovery of endangered species, as well continued ecological research, population assessment and study of anthropogenic impacts such ocean noise and bycatch on protected marine species. Sean believes the principal goal of the Protected Species Branch science is to further our understanding of our animals and their ecological needs/challenges in order to remove the ambiguity around areas of stake holder concern. Whether clarifying the relative impact of shipping, fishing or climate change on endangered species, or understanding the impacts of recovering pinnipeds on a food web that includes human consumers, the purpose of the Protected Species Branch is to enable managers and stakeholders to make scientifically informed decisions towards sustainable human uses of marine resources in the North Atlantic.

A theme that has been running through Sean's research efforts both as a scientist and now program manager is developing creative 'out of the box' techniques to address previously 'unanswerable' questions for the purposes of understanding the constantly shifting balance in ecosystems resulting from anthropogenic impacts of things like habitat alteration, introduced species and increased resource consumption. As society grapples with balancing the social expectations for things to be 'the way they were', while being regularly confronted with the unintended consequences of human population growth and technological advancement, Sean is fascinated by the challenge of using science to help society advance while moving down a path of sustainability.


Sean considers the duties of civil service to be the most rewarding career possible and is thankful for the opportunity to work on the very challenging science and conservation issues surrounding protected species in both in Northeast US waters as well as national and international waters. He recognizes this can only be done through strong partnerships with federal, state, academic, industry, and non-governmental organization partners. The work is never dull and the results of our work are always important.

After growing up on a sheep farm in upstate NY, Sean received undergraduate degrees from SUNY Cobleskill and Cornell and his PhD from UC Santa Cruz where he studied marine mammal communication, physiology and reproductive behavior in large cetaceans and pinnipeds. Sean began working for the Pacific Islands Fisheries Science Center (then Southwest Fisheries Science Center) on Hawaiian monk seals in 2001, and then transitioned to salmon and the Southwest Fisheries Science Center Santa Cruz lab from 2002-2016, where he developed and led several research programs working on the life history and ecology Pacific salmon species across a range of environments from small coastal streams to large inland rivers, through estuaries and in the marine environment. Sean participated in NOAA's Leadership Competencies Development Program between 2014-2016, where he gained both a greater understanding of civic duty and an appreciation for the massive size of NOAA's seemingly impossible mission. In an agency of many talented scientists, Sean decided to explore whether he could make a greater contribution to the agency by blending his years of science experience with newly trained leadership skills by working in more of a management capacity. In May 2016, Sean became the Protected Species Branch Chief at NOAA's Northeast Fisheries Science Center in Woods Hole Massachusetts where he is supervising the teams managing the center's Endangered Species Act and Marine Mammal Protection Act based research portfolio including salmon, marine mammal and sea-turtle research programs and is currently enjoying a 'sweet spot' where he remains engaged with the science but working to focus scientific effort on where our greatest needs are and will be. He also is enjoying being much closer to his family and farm in NY, and exploring life in his new home on beautiful Cape Cod with his pups and partner.

Selected Publications:

Hayes SA, Ammann AJ, Harding JA, Hassrick JL, deWitt L, and Morgan CA. 2016. Observations of steelhead in the California Current lead to a marine-based hypothesis for the "half-pounder" life history, with climate change implications for anadromy. N. Pac. Anadr. Fish Comm. Bull. 6: 97-105. doi:10.23849/npafcb6/97.105.

Hassrick JL, Henderson MJ, Huff DD, Sydeman W, Sabal M, Harding J, Amman A, Crandall E, Bjorkstedt EP, Garza JC, and Hayes SA. 2016. Early ocean distribution of juvenile Chinook salmon in an upwelling ecosystem. Fisheries Oceanography. 25(2): 133-146.

Demetras NJ, Huff DD, Michel CJ, Smith JM, Hayes SA, and Lindley ST. 2016. Development of underwater recorders to quantify predation of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river environment. Fishery Bulletin. 114(2): 179-185.

Sabal M, Hayes SA, Merz JE, and Setka JD. 2016. Habitat alterations and a non-native predator, Striped Bass, increase native salmon mortality in the California Central Valley, USA. N. Am. J. Fish. Manage.

Osterback AMK, Frechette DM, Hayes SA, Shaffer SA, and Moore, JW 2015. Long-term shifts in anthropogenic subsidies to gulls and implications for an imperiled fish. Biological Conservation. 191: 606-613.

Frechette D, Osterback AMK, Hayes SA, Moore JW, Shaffer SA, Pavelka M, Winchell C, and Harvey JT. 2015. Assessing the Relationship between Gulls Larus spp. and Pacific Salmon in Central California Using Radiotelemetry. North American Journal of Fisheries Management. 35(4): 775-788.

Phillis C, Moore JW, Buoro M, Hayes S, Garza C, Pearse D. 2014. Shifting thresholds: rapid evolution of migratory life histories in steelhead/rainbow trout, Oncorhynchus mykiss. PeerJ PrePrints 2:e361v1 http://dx.doi.org/10.7287/peerj.preprints.361v1 (in review with Journal of Heredity)

Cunningham KA, Hayes SA, Rub MW, Reichmuth C. 2014. Auditory detection of ultrasonic coded transmitters by seals and sea lions. Journal of the Acoustical Society of America. 135(4): 1978-1985 [http://dx.doi.org/10.1121/1.4868371]

Beakes MP, Moore JW, Hayes SA, and Sogard SM. 2014. Wildfire and the effects of shifting stream temperature on salmonids. Ecosphere 5(5): http://dx.doi.org/10.1890/ES1813-00325.00321.

Friedland KD, Ward BR, Welch DW, Hayes SA. 2014. Postsmolt Growth and Thermal Regime Define the Marine Survival of Steelhead from the Keogh River, British Columbia. Marine and Coastal Fisheries. 6(1) 1-11. DOI:10.1080/19425120.2013.860065

Hayes SA, Kocik JF. 2014. Comparative estuarine and marine migration ecology of Atlantic salmon and steelhead - blue highways and open plains. Rev Fish Biol Fish DOI 10.1007/s11160-014-9348-8

Frechette DM, Collins AL, Harvey JT, Hayes SA, Huff DD, Jones AW, Langford AE, Moore JW, Osterback AK, Retford NA, Satterthwaite WH, Shaffer SA. 2013. A bioenergetics approach to assessing potential impacts of avian predation on juvenile steelhead (Oncorhyncus mykiss) during freshwater rearing. N Am J Fish Manage. 33(5):1024-1038.

Hayes SA, Teutschel NM, Michel CJ, Champagne C, Robinson PW, Fowler M, Yack T, Mellinger D, Simmons S, Costa DP, MacFarlane RB. 2013. Mobile Receivers: Releasing the mooring to 'see' where fish go. Environ Biol Fish 96(2):189-201 DOI 10.1007/s10641-011-9940-x

Osterback A-MK, Frechette DM, Shelton AO, Hayes SA, Bond MH, Shaffer SA, Moore JW. 2013. High predation on small populations: avian predation on imperiled salmonids Ecosphere. 4(9):116. http://dx.doi.org/10.1890/ES13-00100.1

Frechette D, et al. 2012. Assessing avian predation of juvenile salmonids using PIT tag recoveries and mark-recapture methods N Am J Fish Manage. 32(6):1237-1250. http://dx.doi.org/10.1080/02755947.2012.728171

Hayes SA, Bond MH, Wells BK, Hanson CV, Jones AW, MacFarlane RB. 2012. Using archival tags to infer habitat use of Central California steelhead and coho salmon. In: Parsons B, et al. (eds) Proceedings of the 2nd International Symposium on Advances in Fish Tagging and Marking Technology. American Fisheries Society. 76:471-492.

Hayes SA, Hanson CV, Bond MH, Pearse D, Garza JC, MacFarlane RB. 2012. Should I stay or should I go? The influence of genetic origin on emigration behavior and physiology by resident and anadromous juvenile Oncorhynchus mykiss. N Am J Fish Manage. 32(4):772-780.

Moore JW, Carlson SM, Twardochleb L, Hwan JL, Fox JM, Hayes SA. 2012. Trophic tangles through time: opposing direct and indirect effects of an invasive omnivore PLoS ONE 7(11):e50687

Satterthwaite WH, Hayes SA, Merz JE, Sogard S, Frechette DM, Mangel M. 2012. State-Dependent Migration Timing and Use of Multiple Habitat Types in Anadromous Salmonids. Trans Am Fish Soc. 141(3):781-794.

Claiborne AM, Fisher JP, Hayes SA, Emmett RL. 2011. Size at Release, Marine Survival, and Age of Maturity for Hatchery Spring Chinook Salmon 2002-2005. Trans Am Fish Soc. 140:1135-1144.

Hayes SA, Bond MH, Hanson CV, Jones A, Amman A, Harding J, Perez J, and MacFarlane RB. 2011. Down, Up, Down and "smolting" twice? Seasonal movement patterns by juvenile steelhead in coastal watersheds with bar closing estuaries. Can. J. Fish. Aquat. Sci. 68:1341-1350.

Moore, JW, Hayes SA, Duffy WG, Gallagher SP, Michel C, and Wright BE. 2011. Nutrient fluxes and the recent collapse of coastal California salmon populations Can. J. Fish. Aquat. Sci. 68:1161-1170.

Costa DP, Tremblay Y, and Hayes SA. 2009. Research on Higher Trophic Levels Ed: D Glickson; Oceanography in 2025: A Workshop; National Research Council pp 124-129.

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