John M. Farrell | Environmental and Forest Biology | SUNY-ESF
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John M. FarrellProfessor and Director, Thousand Island Bio Station

John Farrell

250 Illick Hall
1 Forestry Drive
Syracuse, NY 13210


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


EFB 492 Senior Synthesis in Aquatic and Fisheries Science.  Students will develop a synthesis by defining a scientific hypothesis on an aquatic topic of interest, gathering/analyzing data from the literature or elsewhere, interpreting findings, and presenting their work both orally and in a written technical report. That synthesis will relate to prior coursework and current issues in aquatic sciences. Spring. Prerequisite: Senior standing in the Aquatic and Fisheries Science major. Spring.

EFB 681 Aquatic Ecosystem Restoration and Enhancement, 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 effectiveness of techniques to restore habitat and fauna are analyzed. Student presentation of a relevant topic and field excursions to perturbed areas and recent restoration projects are required. Fall.

Research Interests

My interests revolve around the broad topic of aquatic ecology and management of aquatic resources. I use longitudinal studies and targetted research to examine ecological change and guide management and conservation initiatives. Much of my research is focused on fish ecology, coastal wetland ecology and addressing environmental problems facing freshwater ecosystems.



  • Massa, E. A., J. M. Farrell.  2019.  Prey selection by larval northern pike (Esox lucius) exposed to different zooplankton assemblages representing seasonally flooded wetland and nearshore bay habitats.  Limnol. Oceanogr. 64, 1200-1213.  doi: 10.1002/lno.11107 
  • Miano, A. J., Leblanc, J. P., J. M. Farrell.  2019. Laboratory evaluation of spawning substrate type on potential egg predation by round goby (Neogobius melanostomus).  Journal of Great Lakes Research 45:390-393.
  • Rougemont, Q., Carrier, A., Leluyer, J., Ferchaud,  A-L., Farrell, J.M., Hatin, D., Brodeur, P.,  Bernatchez, L., 2019.  Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin. Evolutionary Applications;1–21.doi: 10.1111/eva.12765
  • Foubert, A., C. Le Pichon, M. Mingelbier, J. M. Farrell, J. Morin, F. Lecomte.  2019.  Modeling the effective spawning and nursery habitats of northern pike within a large spatiotemporally variable river landscape (St. Lawrence River, Canada).  Limnol. Oceanogr. 64, 803-819.  doi: 10.1002/lno.11075
  • Miller, L. M., J. M. Farrell, K. L. Kapuscinski, K. Scribner, B.  L. Sloss, K. Turnquist, C. C. Wilson. 2017. A Review of Muskellunge Population genetics: implications for management and future research needs. American Fisheries Society Symposium 85:385-414.
  • Farrell, J. M., R. G. Getchell, K. L. Kapuscinski, and S. R. LaPan. 2017. Long-term trends of St. Lawrence River muskellunge: effects of viral hemorrhagic septicemia and round goby proliferation creates uncertainty for population sustainability.  American Fisheries Society Symposium 85:275-301.
  • Leblanc, J. P., B. L. Brown, J. M. Farrell.  2017.  Increased walleye Sander vitreus egg-to-larvae survival following spawning habitat enhancement in a tributary of Eastern Lake Ontario.  North American Journal of Fisheries Management 37:999–1009.
  • Turnquist; K. N., Wesley L., J. M Farrell, P. A. Hanchin,  K. L.Kapuscinski; L. M. Miller; K.T Scribner; C. C. Wilson, and B. L. Sloss.  2017.  Genetic structure of muskellunge in the Great Lakes region and the effects of supplementation on genetic integrity of wild populations.  Journal of Great Lakes Research 43(6):1141-1152.
  • Getchell, R. G., E. R. Cornwell, S. Bogdanowicz, J. Andrés, W. N. Batts, G. Kurath, R. Breta, J. G. Choil, J. M. Farrell, P. R. Bowser.  2017.  Complete sequences of four viral hemorrhagic septicemia virus (VHSV) IVb isolates and their virulence in northern pike fry.  Diseases of Aquatic Organisms 126:211-227.
  • Crane, D. P., and J. M. Farrell.  2017. Trends in body condition of smallmouth bass and northern pike (1982-2013) following multiple ecological perturbations in the St. Lawrence River. Canadian Journal of Fisheries and Aquatic Sciences. 10.1139/cjfas-2016-0160.
  • Gunderson, M. D., K. L. Kapuscinski, D. P. Crane, and J. M. Farrell.  2016. Rapid colonization of the Niagara River by non-native flowering rush Butomus umbellatus (Linnaeus, 1753).  Aquatic Invasions Volume 11, Issue 4: 369–380.
  • Crane, D. P., and J. M. Farrell.  2015.  Muskellunge egg incubation habitat in the upper Niagara River.  Journal of Great Lakes Research 41(2):448-453.
  • Kapuscinski, K. L., J. M. Farrell, M. A. Wilkinson.  2015.  Abundance, biomass, and macrophyte consumption by rudd in Buffalo Harbor and the Niagara River, and potential herbivory by grass carp.  Journal of Great Lakes Research 41(2)387-395. 
  • Crane, D P., L. M. Miller, J. S. Diana, J. M. Casselman, J. M. Farrell, K. L. Kapuscinski,  J. K. Nohner. 2015.  Muskellunge and Northern Pike Ecology and Management: Important Issues and Research Needs.  Fisheries 40:6, 258-267.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Rippke, M. B., M. T. Distler, and J. M. Farrell. 2010. 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.
  • Toner, J. , 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.