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Jonathan Shenker

Emeritus Faculty | College of Engineering and Science - Ocean Engineering and Marine Sciences

Personal Overview

Dr. Shenker directs the university's Sportfish Research Institute (SRI), which is dedicated to studies of the recreational fishery species that are tremendously important to Florida. Research focuses on bonefish, tarpon, snook grouper, snapper and other fish species. Dr. Shenker and the SRI are spearheading efforts to assess the response of fish populations to habitat restoration programs in the Indian River Lagoon, and to increase the productivity of managed mosquito control impoundments as a nursery habitat for snook and tarpon,  In addition, his laboratory is collaborating with Harbor Branch Oceanographic Institution, the Bonefish and Tarpon Trust, and the National Fish and Wildlife Foundation to restore the bonefish population in the Florida Keys.  This joint program is studying wild spawning aggregations in the Bahamas and utilizing that work to develop an aquaculture program for bonefish that will provide a wide array of tools that can be employed for population restoration.  He is also expanding his initial research and educational endeavors on fisheries and population connectivity in Cuban ecosystems.

In addition to field and laboratory research, Dr. Shenker and his laboratory staff and students present talks and provide information to local and regional sport fishing organizations and publications. Funded in part by state and local grants, SRI also seeks funding and participation from corporations associated with the fishing industry and from private individuals.

Educational Background

B.S. Cornell University 1975
M.S. University of South Carolina 1977
Ph.D. Oregon State University 1986

Professional Experience

Dr. Shenker has worked on the biology and ecology of fishes from many parts of the world, ranging from Florida and the Caribbean to the North Pacific Ocean and West Africa. He also studies a wide range of habitats, including freshwater, estuarine, and deep ocean systems, artificial and natural reefs, marshes and sea grasses, and anywhere else fish might live. His fisheries biology and aquaculture research has determined how oceanographic and meteorological conditions can control the annual variability of economically important fish populations, and how habitats can be managed to enhance their suitability for fishes. He has published 45+ papers, and had graduated 44 M.S. students and 7 Ph.D. students during his 25 years at Florida Tech. A large number of undergraduate students work as research assistants in his laboratory, and many conduct their own research projects.

Additional Duties

Dive Officer, Florida Tech Dive Control Board

Co-Chair, Indian River Lagoon Research Institute

Member, Institutional Animal Care and Use Committee

Selected Publications

Poulakis, G.R., J.M. Shenker and D. Scott Taylor. 2002. Habitat use by fishes after tidal reconnection of an impounded estuarine wetland in the Indian River Lagoon, Florida (USA). Wetlands Ecology and Management 10:51-69.

Bartels, C., T. Anderson, M. Hixon and J.M. Shenker. 2002. Larval recruitment in Exuma Sound, Bahamas: Comparison of Light Trap and Channel Net Data. U.S. Fishery Bulletin 100:404-413.

Shenker, J.M, R. Crabtree, E. Cowie, H. Patterson, C. Stevens, K. Yakubik. 2002. Recruitment of tarpon (Megalops atlanticus) leptocephali into the Indian River Lagoon, Florida. Contrib. Mar. Sci. 35:55-69.

Dankwa, H.R., J.M. Shenker, J. Lin, P.K. Ofori-Danson, and Y. Ntiamoa-Baidu. 2004.
Fisheries of Two Tropical Lagoons in Ghana, West Africa. Fisheries Management and Ecology 11:379-386.

Blandon, I. R., R. Ward, F. J. Garca De Len, S. J. Robertson, A. M. Landry, A. O. Anyyanwu, J. M. Shenker, M. Figuerola, T. C. Gesteira, A. Zerbi, C. D. Acua Leal, W. Dailey. 2007. Studies in Conservation Genetics of Tarpon (Megalops atlanticus) I. Microsatellite Variation across the Distribution of the Species. Pp. 131-147 In: Ault, J.S. Biology and Management of the World Tarpon and Bonefish Fisheries. CRC Press.

Dahlgren, C, J.S. Shenker and R. Mojica. 2007. Ecology of bonefish during the transition from late larvae to early juveniles. Pp. 155-179 In: Ault, J.S. Biology and Management of the World Tarpon and Bonefish Fisheries. CRC Press

Reyier, E. and J.M. Shenker. 2007. Ichthyoplankton community structure in a shallow subtropical estuary of the Florida Atlantic coast. Bull. Mar. Sci. 80:267-293.

Reyier, E.A., J.M. Shenker and D. Christian. 2008. Role of an estuarine fisheries reserve in the production and export of ichthyoplankton. Mar. Ecol. Prog. Ser. 359:249-260.

Adema, R. and J.M. Shenker. 2008. Lethal and sublethal effects of methylmercury on developing embryos of mahi mahi (Coryphaena hippurus). Env. Contam. Toxicol.27:2131–2135. 

Steward, C.A., K.D.  DeMaria and J.M. Shenker. 2009.  Using otolith morphometrics to quickly and inexpensively predict age in the gray angelfish (Pomacanthus arcuatus).  Fisheries Research 99:123–129.

 Jud, Z., C.A. Layman and J.M. Shenker.  2011. Diet of age-0 tarpon (Megalops atlanticus) in anthropogenically-modified and natural nursery habitats along the Indian River Lagoon, Florida.  Environmental Biology of Fishes.  90:222-233.

Adams, A., A.Z Horodysky, R.S. McBride, K. Guindon, J. Shenker, T.C. MacDonald, H.D. Harwell, R. Ward, K. Carpenter.  2013.   Global conservation status and research needs for tarpons (Megalopidae), ladyfishes (Elopidae) and bonefishes (Albulidae).  Fish and Fisheries 15: 280-311.

Stein, W., J. Shenker and M. O'Connell.  2016.  A contribution to the life history of tarpon (Megalops atlanticus) in the northern Gulf of Mexico.  15:496-512.


Major current projects in Dr. Shenker's laboratory focus on processes affecting the recruitment and survival of larval and juvenile fishes. A primary program is the Bonefish Restoration and Conservation Program, where Dr. Shenker works with a team of collaborators to study bonefish prespawning aggregations in the Bahamas.  In addition to tracking fish on their spawning migrations, the team examines behavior and biology of fish at prespawning aggregation sites and tracks their final movements to spawning sites.  Dr. Shenker leads the efforts to collect and hold fish from the prespawning aggregation to induce spawning in captivity and study the embryonic development and the feeding biology of the leptocephalus larvae.  The results of this work are being incorporated into an aquaculture project at Harbor Branch Oceanographic Institution that seeks to develop population restoration tools for the Florida Keys bonefish populations.  In addition to the bonefish work, Dr. Shenker's students have helped identify spawning sites of tarpon off the southeastern Florida coast and in the Gulf of Mexico.  Continuing with the bonefish theme, his graduate students are working on age and growth of adult bonefish populations in Cuba, and on the sensory biology of larval bonefish.

Another major project in Dr. Shenker's laboratory is the analysis of how juvenile tarpon and snook utilize their nursery habitats within managed mosquito control impoundments.  Early results of this study have identified simple and inexpensive modifications of the Rotational Impoundment Management Strategy that can dramatically increase the supply of snook and tarpon from the impoundments to the Indian River Lagoon populations.   

A major component of Indian River Lagoon restoration is the removal of deep deposits of muck from many areas of the lagoon.  A team of Dr. Shenker's students and assistants are assessing the abundance and distribution of juvenile fishes in and around muck removal areas, and determining if muck dredging has any impact on fish populations.

Research & Project Interests

Dr. Shenker’s research focuses on a very diverse range of fish and fisheries issues. The ultimate goals are to characterize and analyze the biological and ecological factors affecting fish populations, and to assist in the development of fish and habitat management strategies. Many projects focus processes affecting reproduction, larval growth, survival and the ultimate recruitment of early life history stages into adult populations. Other research examines the basic biology and physiology of fishes, and the biological and commercial aspects of finfish aquaculture. All of this work involves intensive fieldwork, often developing and using novel sampling gear to answer specific questions. The research also includes extensive laboratory studies, spanning a range of topics that include larval development and taxonomy, molecular population genetics, and sensory biology.

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