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

315-470-6990
jmfarrell@esf.edu

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

Teaching

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

Anna ConklynAnna Conklyn
alconkly@syr.edu

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

Stacy FurgalStacy Furgal
slfurgal@syr.edu

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

Benjamin GalloBenjamin Gallo
bdgallo@syr.edu

  • Degree Sought: MS
  • Graduate Advisor(s): Farrell and Leydet
  • Area of Study: Fish & Wildlife Biology & Management
  • Undergraduate Institution: University of New Hampshire Durham

LinkedIn
Web Link

Graduate Research Topic
My Research focuses on the fish gut microbiome and how it is shaped by the fishes environment. I will principally examine the gut microbiomes of Age-0 Northern Pike (E. lucius) from different spawning locations to determine the effect spawning site has on the inoculation and subsequent composition of the fishes gut microbiota.


Jessica GoretzkeJessica Goretzke
jagoretz@syr.edu

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

Links
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


ZI XUN KUAZI XUN KUA
zkua01@syr.edu

  • Degree Sought: MS
  • Graduate Advisor(s): Farrell and Stella
  • Area of Study: Ecology
  • Undergraduate Institution: Ohio State University of Columbus (Evolution and Ecolog)

Graduate Research Topic
For my Masters research, I am studying the effects of water regulation changes on aquatic wetland community of the St. Lawrence River at the Thousand Islands Biological Station (TIBS) following the implementation of Plan 2014. The main objectives of the study will focus on the hydrologic fluctuation effects on muskrat occupancy and the subsequent interactive effects of muskrat disturbances on the aquatic community.


Iman PakzadIman Pakzad
ipakzad@syr.edu

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

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.

Publications (since 2008)

 

  • 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. 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.
  • 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.

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.
  • Stewart LaPan, MS (graduated, co-advised with Dr. James Gibbs), 9/12-5/14, Avifauna and herpetofauna response to coastal wetland enhancement in the upper St. Lawrence River.
  • Ben Amos, MPS (MPS, graduated), 5/13/5/15, Spatial scale and natal influence on spawning site fidelity in Northern Pike (Esox lucius L.)
  • Andrew Miano, MS (graduated), 5/13-5/15, Influence of invasive round goby egg predation on broadcast spawning fish species in the Great Lakes.
  • Kelly Huffman, MPS (graduated, co-advised with Dr. Chris Whipps), 9/13-5/15, Environmental determinants of gender ratio in Northern Pike (Esox lucius L.)