John M. Farrell | Environmental 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.

Current Graduate Advisees

Current Graduate Advisees

Katelyn BarhiteKatelyn Barhite

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

Anna ConklynAnna Conklyn

  • Degree Sought: PHD
  • Graduate Advisor(s): Farrell
  • Area of Study: Fish & Wildlife Biology & Management
  • Undergraduate Institution: Cornell University (Biological Sciences)

Graduate Research Topic
I am investigating the intersection of invasive species and disease ecology through the interrelationship of the round goby and viral hemorrhagic septicemia virus in the Thousand Islands region of the St. Lawrence River.

Amanda LemoineAmanda Lemoine

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

Thornton RitzThornton Ritz

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

Andrea SmithAndrea Smith

  • Degree Sought: MPS in Environmental & Forest Biology
  • Graduate Advisor(s): Farrell

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.

Publications (selected since 2014)

Massa E.A., and J. M. Farrell. 2020. Improving habitat connectivity in a Typha dominated wetland shows increased larval northern pike survival. Wetlands 40:273–286.

Gallo, B., J. M. Farrell, and B. Leydet. 2020. Fisheries and the gut microbiome: Using next generation sequencing (NGS) and microbial ecology to better understand fish-microbe interactions.  Fisheries 45:271-282.

Walton-Rabideau, Lédée, E. J. I., J. P. Leblanc, P. Szekeres, J. D. Midwood, A. J. Gallagher, J. M. Farrell, and Steven J. Cooke. 2020. Spatiotemporal ecology of juvenile Muskellunge (Esox masquinongy) and Northern Pike (Esox lucius) in upper St. Lawrence River nursery bays.  Ecology of Freshwater Fish 29:346-363.  

Leblanc, J. P., C. C. Killourhy, J. M. Farrell.  2020. Round goby (Neogobius melanostomus) and native fishes as potential nest predators of centrarchid species in the upper St. Lawrence River. Journal of Great Lakes Research 46:216–224.

Getchell, R. G., First, E. J., Bogdanowicz, S. M., Andrés, J. A., Schulman, A. T., Kramer, J., Eckerlin, G. E., Farrell, J. M., and H. Marquis. 2019.  Investigation of round goby viral hemorrhagic septicemia outbreak in New York. Journal of Fish Diseases 7:1029-1033. 

Walton-Rabideau, S.E., Newell, M., Jeanson, A.L., Lédée, E. J. I., Farrell, J. M., S. J. Cooke. 2019. Evaluation of tag retention, healing, growth and behavior in age-0 muskellunge Esox masquinongy following acoustic transmitter implantation.  North American Journal of Fisheries Management 39:652-663. 

Goretzke, M. Windle, J.M. Farrell.  2019. Range Expansion of the Western Tubenose Goby (Proterorhinus semilunaris Heckel, 1837) in eastern Lake Ontario and the upper St. Lawrence River.  BioInvasion Records 8:694-698.

Neveldine, B., Leblanc, J. P., J. M. Farrell.  2019. Vegetation response and juvenile northern pike (Esox lucius) outmigration following connectivity enhancement of a Typha dominated coastal wetland.  Wetlands 39:921–934. 

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.  

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.

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. 

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 43:1141-1152.

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 74:1158–1172.

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 11:369–380.

Crane, D. P., and J. M. Farrell.  2015.  Muskellunge egg incubation habitat in the upper Niagara River.  Journal of Great Lakes Research 41:448-453.

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 41:387-395. 

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 40:258-267.

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 40:325-335.

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.