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John Farrell

John M. Farrell

Professor and Director, Thousand Island Bio Station

250 Illick Hall
1 Forestry Dr.
Syracuse, New York 13210

Phone: (315) 470-6990

Email: jmfarrell@esf.edu

PhD SUNY College of Environmental Science and Forestry, 1998. Fisheries Science and Management, Aquatic Ecology, Wetlands Restoration, Invasive Species.


  • EFB 496 Senior Synthesis in Aquatic and Fisheries Science - A senior level capstone course focuses on professionalism and communications where we will discuss and experience job opportunities in this field and anticipate what is expected by potential employers.  We will cover job interviews, skill development, leadership and other important qualities in the workplace.  The second part of the course addresses science and management through modules that dissect issues in the aquatic and fisheries realm relevant to the broader society and environmental sustainability. 
  • EFB 681 Aquatic Ecosystem Restoration and Enhancement - The guiding principles for ecological restoration of freshwater aquatic ecosystems focusing on effects of nutrient loading, sedimentation, flow alteration, and habitat loss. Factors leading to loss of aquatic resources and the effectiveness of techniques to restore habitat and fauna are analyzed. Student presentation of a case study and field excursions to perturbed areas and recent restoration projects are required.
  • EFB 388 Ecology of Adirondack Fishes -  An introduction to field-based fish ecology and management of the Adirondack and St. Lawrence River regions. Extensive field based experience with various sampling procedures and fisheries investigation techniques. Classroom and laboratory experience on introduction to theory, concepts leading to individual projects regarding aspects of local/regional questions. Taught at the Cranberry Lake Biological Station www.esf.edu/clbs with field excursions to the Thousand Islands Biological Station www.esf.edu/tibs.

Current Graduate Advisees

Current Graduate Advisees

Ericka AugustynEricka Augustyn

  • Degree Sought: MS
  • Graduate Advisor(s): Farrell
  • Area of Study: Fish & Wildlife Biology & Management

Stacy FurgalStacy Furgal

  • Degree Sought: MS
  • Graduate Advisor(s): Farrell and Paterson
  • Area of Study: Fish & Wildlife Biology & Management

Jessica GoretzkeJessica Goretzke

  • Degree Sought: MS
  • Graduate Advisor(s): Farrell
  • Area of Study: Fish & Wildlife Biology & Management

LinkedIn: https://www.linkedin.com/in/jessicagoretzke/

Graduate Research Topic
Fish and plant community response to habitat restoration in the Thousand Islands Region of the St. Lawrence River and the development of restoration techniques for the establishment of beneficial species of submersed aquatic vegetation

Research Interests

My interests revolve around the broad topic of aquatic ecology and management of aquatic resources. I am interested in developing biological understanding to improve management and stewardship. Much of my research is focused on fish ecology, coastal wetland ecology and their application toward addressing environmental problems facing freshwater ecosystems.

Recent Publications

  • Crane, D. C., J. M. Farrell, D. Einhouse, and J. Lantry.  2015.  Trends in body conditions of native piscivores following round goby invasion in Lakes Erie and Ontario.  Freshwater Biology 60:111-124.
  • Kapuscinski, K. L., J. M. Farrell, M. A. Wilkinson, L. C. Skinner, W. Richter, A. J. Gudlewski, and G. Paterson. 2014.  Low Concentrations of Contaminants in an Invasive, Omnivorous Cyprinid, the Rudd, in a Great Lakes Area of Concern.  Bulletin of Environmental Contamination & Toxicology 93:567-573.
  • Kapuscinski, K.L., J. M. Farrell, S. Stehman, T. Tschaplinski, D. D. Fernando, and M. A. Teece. 2014. Selective herbivory by an invasive cyprinid, the Rudd (Scardinius erythrophthalmus).  Freshwater Biology 59:2315-2327.
  • Roseman, E.F., P. Thompson, J. M. Farrell, N. Mandrak, and C. A. Stepien.  2014. Conservation and management of fisheries and aquatic communities in Great Lakes connecting channels.  Journal of Great Lakes Research 40, Supplement 2:1-6. http://www.sciencedirect.com/science/article/pii/S0380133014000598
  • Henning, B. F., K.L. Kapuscinski, and J. M. Farrell.  2014.  Nearshore fish assemblage structure and habitat relationships in protected and open habitats in the upper St. Lawrence River.  Journal of Great Lakes Research 40, Supplement 2:154-163. http://dx.doi.org/10.1016/j.jglr.2013.11.003
  • Farrell, J. M., H. Brian Underwood, and K.L. Kapuscinski.  2014.  Fine scale habitat use by age-1 stocked muskellunge and wild northern pike in an upper St. Lawrence River bay.  Journal of Great Lakes Research 40, Supplement 2:148-153. http://www.sciencedirect.com/science/article/pii/S0380133013001706
  • Kapuscinski, K. L, J. M. Farrell, and M. A. Wilkinson.  2014.  Trends in the muskellunge (Esox masquinongy) population and fishery of the Buffalo Harbor (Lake Erie) and upper Niagara River.  Great Lakes Research 40, Supplement 2:125-134. http://dx.doi.org/10.1016/j.jglr.2012.11.006
  • Kapuscinski, K. L, and J. M. Farrell.  2014.  Habitat factors influencing fish assemblages at muskellunge nursery sites.  Great Lakes Research 40, Supplement 2:135-147. http://dx.doi.org/10.1016/j.jglr.2012.11.007.
  • Crane, D.C., J. M. Farrell, and K.L. Kapuscinski.  2014.  Identifying important micro-habitat characteristics of muskellunge spawning locations in the upper Niagara River.  Journal of Great Lakes Research 40(2) 325-335.
  • Murry, B. A., and J. M. Farrell.  2014.  Resistance of the size structure of the fish community to ecological perturbations in a large river ecosystem.  Freshwater Biology 59:155-167.
  • Kapuscinski, K.L., Sloss, B.L., and J. M. Farrell. 2013.  Genetic population structure of muskellunge in the Great Lakes.  Transactions of the American Fisheries Society 142:1075-1089
  • Crane, D.C., and J. M. Farrell. 2013. Spawning substrate size, shape, and siltation influence walleye egg retention.  North American Journal of Fisheries Management 33:329–337.
  • Kapuscinski, K. L., J. M. Farrell, and M. A. Wilkinson. 2012.  First Report of Abundant Rudd Populations in North America.  North American Journal of Fisheries Management 32(1):82-86.
  • Kapuscinski, K. L., Farrell, J. M., and M. A. Wilkinson. 2012.  Feeding patterns and population structure of an invasive cyprinid, the rudd Scardinius erythrophthalmus (Cypriniformes, Cyprinidae), in Buffalo Harbor (Lake Erie) and the upper Niagara River.  Hydrobiologia 693:169-181.
  • Kapuscinski, K. L., J. M. Farrell, and B. A. Murry. 2012.  Feeding strategies and diets of young-of-the-year muskellunge from two large river ecosystems.  North American Journal of Fisheries Management 32:635-647.
  • Eckerlin G. E., Farrell J. M., Casey R, Hope K, Bowser P, Casey J, and Groocock G.  2011.  Temporal variation in incidence of viral haemorrhagic septicaemia virus type IVb among smallmouth bass Micropterus dolomieu (Lacepède) in the St. Lawrence River.  Transactions of the American Fisheries Society 140:529–536.
  • M. B. Rippke, M. T. Distler, and J. M. Farrell. Post-glacial vegetation dynamics of an upper St. Lawrence River coastal wetland: Paleoecological evidence for a recent historic increase in cattail (Typha). Wetlands 30(4):805-816.
  • Marty, J.E., M. R. Twiss, J. J. Ridal, Y. de Lafontaine, and J. M. Farrell. 2010. From the Great Lakes flows a Great River: Overview of the St. Lawrence River Ecology supplement. Hydrobiologia 647:1-5.
  • Farrell, J. M., K. T. Holeck, E. L. Mills, C. E. Hoffman, and V. J. Patil. 2010. Recent Ecological Trends in Lower Trophic Levels of the International Section of the St. Lawrence River: A Comparison of the 1970s to the 2000s. Hydrobiologia 647:21–33.
  • Farrell, J. M., B. A. Murry, D. J. Leopold, A. Halpern, M. Rippke, K. S. Godwin, and S. D. Hafner. Water-level regulation and coastal wetland vegetation in the upper St. Lawrence River: inferences from historical aerial imagery, seed banks, and Typha dynamics. Hydrobiologia 647:127–144.
  • J. Toner, J. M. Farrell, and J. V. Mead. 2010. Muskrat abundance responses to water-level regulation within freshwater coastal wetlands. Wetlands 30:211-219.
  • Kelder, B.F. amd J.M. Farrell. 2009. A spatially explicit model to predict walleye spawning in an eastern Lake Ontario tributary. North American Journal of Fisheries management 29: 1686-1697.
  • Farrell, J. M., C. Skov and A. P. Nilsson. 2008. Preface to an International Pike Symposium: Merging Knowledge of Ecology, Biology, and Management for a Circumpolar Species. Hydrobiologia 601:1-3.
  • Murry, B. A., J. M. Farrell, M. K. Schulz, and M. Teece. 2008. The effect of egg size and nutrient content on larval performance: implications to protracted spawning in northern pike (Esox lucius Linnaeus, 1758). Hydrobiologia 601:71-82.
  • Cooper, J.E., J.V. Mead, J. M. Farrell, and R. G. Werner. 2008. Coexistence of pike (Esox lucius) and muskellunge (E.masquinongy) during early life and the implications of habitat change. Hydrobiologia 601:41-53.
  • Nilsson, C. Skov, and J. M. Farrell. 2008. Current and future directions for pike ecology and management: a summary and synthesis. Hydrobiologia 601:137-141.
  • Farrell, J. M., R. M. Klindt, J. M. Casselman, S. R. LaPan, R. G. Werner, and A. Schiavone. 2007. Development, implementation, and evaluation of an international muskellunge management strategy for the upper St. Lawrence River. Environmental Biology of Fishes 79:111-123.
  • Murry, B. A., and J. M. Farrell. 2007. Quantification of native muskellunge nursery: influence of body size, fish community composition, and vegetation structure. Environmental Biology of Fishes 79:37-47.
  • Smith, B. V., J. M. Farrell, H. B. Underwood, and S. Smith. 2007. Year class strength of St. Lawrence River northern pike. North American Journal of Fisheries Management 27:481-491.
  • Farrell, J. M., J. V. Mead, and B. A. Murry. 2006. Protracted spawning of St. Lawrence River northern pike (Esox lucius): simulated effects on survival, growth, and production. Ecology of Freshwater Fish 15:169-179.
  • Bosworth, A., and J. M. Farrell. 2006. Genetic divergence among northern pike from spawning locations in the Upper St. Lawrence River. North American Journal of Fisheries Management 26:676-684.
  • Murry, B. A., J. M. Farrell, P. Smyntek, and M. Teece. 2006. Effect of lipid extraction on the interpretation of fish community trophic relationships determined by stable carbon and nitrogen isotopes. Canadian Journal of Fisheries and Aquatic Sciences 63:2167-2172.

Past Graduate Students

  • Molly Connerton, MS (graduated), 1/1999-8/2003, Double-crested cormorant predation on Northern Pike in the eastern basin of Lake Ontario and the upper St. Lawrence River.  Employed as a Biologist with the US Army Corps of Engineers, Buffalo District, NY.
  • Jason Toner, MS (graduated) 5/00-5/06; Muskrat house abundance and cattail use in upper St. Lawrence River tributary wetlands: Modeling the effects of water level regulation.  Secondary School Environmental Science Teacher at Solvay High School.
  • Alison Halpern, PhD (current, co-advised with Dr. Donald Leopold) 5/00-present, Aquatic nuisance species: Ecology and control of the invasive plant Hydrocharis Morsus-ranae in eastern Lake Ontario and St. Lawrence River wetlands.  Employed as an Aquatic Nuisance Plant Species Ecologist with the State of Washington.
  • Molly Beland (Rippke), MS (graduated), 5/01- 12/03, Holocene vegetation dynamics of an upper St. Lawrence River coastal wetland and surrounding uplands: effects of climate change and anthropogenic disturbance.  Employed as a Biologist with the Michigan Department of Natural Resources.
  • Emily Cloyd, MPS (graduated), 5/01-5/04, Environmental Studies (co-advised with Dr. Donald J. Leopold).
  • Brent Murry, PhD (graduated), 5/01-12/06, Community ecology of fishes in a large river ecosystem.  US Fish and Wildlife Service, Director of Research Puerto Rico.
  • Aaron Bosworth, MS (graduated), 8/01-8/04, Genetic divergence among Northern Pike from spawning locations in the upper St. Lawrence River. Completed dual MS option with Maxwell School of Citizenship and Public Affairs.  Fisheries Biologist, Washington Department of Fish and Wildlife.
  • Thomas Hughes, MPS (graduated), 5/04-5/06, Environmental Interpretation.    Biologist, New York State Parks and Recreation.
  • Brian Kelder, MS, (graduated) 8/05-5/08, Walleye spawning site selection in a Lake Ontario tributary: a predictive tool to guide management.  Restoration Program Manager at Ipswich River Watershed Association, Massachusetts.
  • Geof Eckerlin, MS (graduated), 5/06-12/08, Viral haemorrhagic septicaemia virus type IVb among Smallmouth Bass Micropterus dolomieu (Lacepède) in the St. Lawrence River: An invasive species mediated pathogen?  PhD Student at SUNY ESF; Biologist, NYS DEC Rome Fish Health Laboratory.
  • Katie Woodside, MS (graduated), 8/06-5/09, Development and application of models predicting young-of-the-year Muskellunge presence and abundance from nursery features.  Freshwater Fisheries Biologist, Florida Fish and Wildlife Conservation Commission.
  • Jarrod Hughes, MPS (graduated), 9/07-5/09.  Regional Operations Leader and Sr. Environmental Specialist at Fenstermaker.
  • Kevin Kapuscinski, PhD (graduated), 8/06-5/11, Comparative Ecology of Muskellunge and nearshore fish assemblages in the Great Lakes. Assistant Professor, Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI.
  • Brian Henning, MS (graduated), 9/10 -8/12, Fish habitat enhancement – role of aquatic excavation in cattail-dominated wetlands on fish movement.  Research Scientist at New Jersey Department of Environmental Protection.
  • Derek Crane, PhD (graduated), 9/09 -5/13, Reproductive ecology of native predatory fishes and body condition responses to invasive Round Goby in the lower Great Lakes and connecting channels.  Research Associate, Lake Superior State University, MI.
  • Katherine DeVilbiss, MS (graduated), 6/10-5/13, Potential mechanisms of relative success of three sympatric esocids in the St. Lawrence River.  Contractor-Fisheries, Tunison Laboratory of Aquatic Sciences.
  • Christina Killourhy, MS (graduated), 8/10-5/12, Effects of Round Goby predation on reproductive success of native species based on spawning strategy.  Seasonal Technician, Fisheries, Lake Superior State University.
  • Scott Schlueter, MPS (graduated), 1/07-12/14, Lake sturgeon restoration in the Oswegatchie River: movement and habitat use following reintroduction.  US Fish and Wildlife Service, Biologist, New York Field Office.
  • Mark Leopold, MPS (graduated), 8/10-12/14, Sex ratios as indicators of northern pike population status in the upper St. Lawrence River.
  • Geof Eckerlin, PhD (current), 1/09-present,Viral haemorrhagic septicaemia virus type IVb: Evaluation of fish hosts as a viral reservoir, a community perspective.
  • Ben Amos, MPS (current), 5/13-present, Spatial scale and natal influence on spawning site fidelity in Northern Pike (Esox lucius L.)
  • Andrew Miano, MS (current), 5/13-present, Influence of invasive round goby egg predation on broadcast spawning fish species in the Great Lakes.
  • Stewart LaPan, MS (current, co-advised with Dr. James Gibbs), 9/12-present, Avifauna and herpetofauna response to coastal wetland enhancement in the upper St. Lawrence River.
  • Kelly Huffman, MS (current, co-advised with Dr. Chris Whipps), 9/13-present, Environmental determinants of gender ratio in Northern Pike (Esox lucius L.)
  • John Bateman, PhD (current), 8/14-present, Restoration of Great Lakes Wetlands.