ANNUAL REPORT

ENVIRONMENTAL AND FOREST BIOLOGY

SUNYCollege of Environmental Science and Forestry

(June 1, 2008 - May 31, 2009; Summer 2008, AY 2008-2009)

NAME: Dr. John M. Farrell

I. INSTRUCTIONAL ACTIVITIES

1. Regular Course Offerings

Course Credit No. No. of Lab.

No. Title Hrs. Students Sections

FALL: EFB 797 Aquatic Ecology Seminar 6 6

2. Non-Scheduled Course Offerings (e.g., 496, 899, 999)

Course No.Credit

No. Title Students Hrs.

SUMMER: EFB 899Masters Research 1 1

FALL: EFB 498 Research Problems 1 3

EFB 798Research Problems 1 8

EFB 899Master’s Research 3 7

EFB 999 Doctoral Research 1 9

SPRING:

EFB 798Research Problems 1 1

EFB 899 Master’s Research 2 10

EFB 999 Doctoral Research 3 19

  1. Continuing Education and Extension (Short courses, workshops, etc.)

4. Guest Lecture Activities

Course No. Title No. of Lectures

II. STUDENT ADVISING AND COUNSELING

A. Number of undergraduates for whom you are the student’s official advisor. _0__

B. Graduate Students - (Name, degree sought, starting date, month & year; if a degree was completed, please give

date and full citation for thethesis or dissertation).

MAJOR PROFESSOR

  1. Geof Eckerlin, MS (graduated Dec 2008), 5/06-12-08, Viral haemorrhagic septicaemia virustype VIb among Smallmouth Bass Micropterus dolomieu (Lacepède) in the St. Lawrence River: An invasive Species mediated pathogen? Master’s Thesis, SUNY College of Environmental Science and Forestry.
  1. Geof Eckerlin, PhD (began Jan 2009), Viral haemorrhagic Septicaemia Virus Type: Evaluation of fish hosts as a viral reservoir, a community perspective.
  1. Katie Woodside, MS (graduated May 2009), 8/06, Development and application of models predicting

young-of-the-year muskellunge presence and abundance from nursery features.Master’s Thesis, SUNY College of Environmental Science and Forestry.

  1. Kevin Kapusinski, PhD (current), 8/06, Ecology of Great Lakes Muskellunge stock identification and contributions of individual spawners to young of year production as inferred from genetic analyses.
  1. Jarrod Hughes, MS (current), 1/07, Walleye habitat restoration – role of substrate particle size and flow in egg redistribution: an indicator of habitat quality?
  1. Scott Schlueter, MS (current, EBT), 1/07, Lake sturgeon restorationin the OswegatchieRiver: movement and habitat use following reintroduction.

CO-MAJOR PROFESSOR

  1. Alison Halpern, PhD (EBT, Co-advised with Dr. Donald Leopold) 5/00, Aquatic nuisance species: ecology and control of the invasive plant Hydrocharis Morsus-ranae in Eastern Lake Ontario and St. Lawrence River wetlands.

MEMBER, STEERING COMMITTEE (other than those listed above)

  1. James Costello, EFB, MS
  2. Juliette Smith, EFB, Ecology, PhD (graduated Fall 2008)
  3. Emily Waldt, EFB, MPS (graduated May 2009)
  4. Jessica Schneider, ES, MS

CHAIRMAN OR READER ON THESIS EXAMS, ETC.

III. RESEARCH COMPLETED OR UNDERWAY

A. Departmental Research (unsupported, boot-legged; title - % time spent)

B. 1. Grant-supported Research (source, subject, amount - total award and current year, award period starting

and ending dates; list graduate research assistants supported by each grant)

Farrell, J. M. 6/2007-6/2009. Development of the Fish Habitat Conservation Strategy: An Evaluation of Toolkit Implementation, Fish Enhancement, Research and Mitigation Fund, National Fish and Wildlife Foundation, Two Years, $563,836 (funded – begins June 2009).

Farrell, J. M. and K. Kapuscinski. 5/2009-4/2011. Muskellunge Esox masquinongy Genetic Structure, Reproductive Ecology, and Interaction with the Fish Community: Acquiring Information Needed for Successful Management. Niagara Greenway Commission, Ecological Greenway Fund, $148,000 (funded – began 5/1/09).

Kevin Kapuscinski

Farrell, J. M.(and 7 co-investigators) Great Lakes Aquatic Community Pathogens Task Group. Great Lakes Research Consortium Small Grants Program $1,000 (funded)

Farrell, J. M. 4/2005-6/2010. Development and Management of St. Lawrence River Fisheries. Federal Aid in Sportfish Restoration, NYS Department of Environmental Conservation. $958,184(current year $215,000).

Kevin Kapuscinski

Geof Eckerlin

Katie Woodside

Farrell, J. M. 6/2007-6/2009. A Conservation Strategy for Enhancement of St. Lawrence River Native Fish Populations, Fish Enhancement, Research and Mitigation Fund, National Fish and Wildlife Foundation, Two Years, $298,341 (current year $148,535).

Jarrod Hughes

K. Schulz, M. A. Teece, J. M. Farrell, and Karin Limburg 2003-2006 (received no-cost extension to 1/2009). Can Fatty Acids Improve Our Ability to Trace Food Web Processes? National Science Foundation, $639,688.

Jacob Gillette

P. Bowser, J. Casey, R. Getchell, and J. M. Farrell2006-2008 (completed May 2009). Viral Hemorrhagic Septicemia Infection in Round Goby and Muskellunge in New York State, NY SeaGrant, $131,662, via Cornell University, subcontract to ESF $3,400.

J. Farrell, J. H. Johnson, T. David, and D. Dittman. 12/2007-12/2008 (no cost-extension granted - completed May 2009). Lake Sturgeon Population Enhancement as a Strategy for Improvement of Ecosystem Function and Controlling Invasive Species Fish Enhancement, Research and Mitigation Fund, National Fish and Wildlife Foundation, (current year $30,000).

J. Farrell, C. Whipps, M. A. Teece, P. Bowser, and J. Casey. Round goby invasion of coastal littoral habitats and risks posed to native fish communities: spill-over of overabundance or a niche shift? NYSeaGrant Annual Call, Pre-proposal accepted, full proposal due June 2008, $148,073 (rejected).

B. Murry, D. Uzardski, J. Farrell, M. Teece, J. Lantry, R. McCullough (Feb 2008) Density-dependent impacts of round goby on GreatLake coastal food webs: developmentof round goby management goals. National SeaGrant Aquatic Invasives Research, $203,292. (rejected).

2. Research Proposals pending (as in B.1., above)

Farrell, J. M., D. J. Leopold, M. Mitchell, J. Gibbs, K. Schulz. 7/2009-6/2012, Recovery Act – Fisheries Habitat Restoration in the St. Lawrence River. NOAA Coastal and Marine Habitat Restoration Project Grants

under the American Recovery and Reinvestment Act ($1,552,471, submitted 4/09 as subcontract with Ducks Unlimited).

IV. PUBLICATIONS(Full bibliographic citation, i.e., do not use "with Jones," or "Jones, et al."; please list only

publications published, in press, or actually submitted ---do not list manuscripts in preparation).

  1. Refereed Publications

B.F. Kelder and J.M. Farrell. 2009. A spatially-explicit model to predict walleye spawning in a Eastern Lake Ontario tributary. North American Journal of Fisheries Management (revised, pending decision).

Farrell,J.M., K.T. Holeck, E.L. Mills, C.E. Hoffman, and V.J. Patil. 2009. 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 (In review).

Farrell,J.M., B.A. Murry, D.J. Leopold, A. Halpern, M. Rippke, K.S. Godwin, and S.D. Hafner. 2009. Water level regulation and coastal wetland vegetation in the upper St. Lawrence River: Inferences from historical aerial imagery, seed banks, and Typha dynamics. Hydrobiologia (In review).

J. Toner, J. M. Farrell, and J.V. Mead. 2009. Muskrat house abundance responses to regional-scale water regulation within freshwater coastal wetlands. Wetlands (In review).

B.Non-refereed Publications

Farrell. J.M. 2009. Research at Governors Island. Thousand Islands Life Magazine. March 2009.

Farrell, J.M., R.T. Colesante, D.E. Dittman, and J.H. Johnson. 2009. Lakesturgeon population enhancement as a strategy for improvement of ecosystem function and controlling invasive species. Final Report. Fish Enhancement Mitigation and Research Fund, US Fish and Wildlife Service, New York Field Office, CortlandNY.

  1. Papers Presented at Science Meetings (give title, date, occasion, and location)

J.M. Casselman, T. Lusk, J. M. Farrell, and C. Lake. 2008. Muskellunge die-off in the upper St. Lawrence River caused by viral hemorraghic septicemia, 2005-2008: Impacts and consequences. American Fisheries Society Annual Meeting, Ottawa, Canada.

G.E Eckerlin, J.M. Farrell, Casey RN, Hope KM, Bowser PR, Casey J and Groocock GH. 2008. Round goby mediated viral distribution and impacts to smallmouth bass in the St. Lawrence River. American Fisheries Society Annual Meeting, Ottawa, Canada.

K.L. Woodside and J.M. Farrell. 2008. Development and application of models predicting young of the year muskellunge presence and abundance from nursery features. American Fisheries Society Annual Meeting, Ottawa, Canada.

B.F. Kelder and J.M. Farrell. 2008. A spatially-explicit model to predict walleye spawning in an Eastern Lake Ontario tributary. 2008American Fisheries Society Annual Meeting, Ottawa, Canada.

J. M. Farrell, Long term research and management of St. Lawrence River muskellunge (Esox masquinongy). 2008. Queen’s University Biological Station Seminar Series, August 2008 (Invited speaker).

G.E Eckerlin, JM Farrell, Casey RN, Hope KM, Bowser PR, Casey J and Groocock GH. 2009. Great Lake Research Consortium's Great Lakes Goes to Albany Day 2009, Outstanding Student Poster entitled, "A New Great Lakes Virus (VHSV) in St. Lawrence River Sportfish: Monitoring Lessons and Linkages to an Invasive Species. April 2009 (won Best Student poster award).

G.E Eckerlin, JM Farrell, Casey RN, Hope KM, Bowser PR, Casey J and Groocock GH. 2009. A New Great Lakes Virus (VHSV) in St. Lawrence River Sportfish: Monitoring Lessons and Linkages to an Invasive Species. SUNY-ESF Student-Faculty Conference (poster presentation).

G.E Eckerlin, JM Farrell, Casey RN, Hope KM, Bowser PR, Casey J and Groocock GH. 2009. Viral hemorrhagic septicemia virus among smallmouth bass and round goby in the St. Lawrence River: Monitoring implications and potential reservoir hosts. 16th Annual International Conference on the Great Lakes/St. Lawrence River Ecosystem, St. Lawrence Institute, Cornwall, Ont, Canada.

D.Public Service Presentations (lectures, seminars, etc. to and for the public; give group or occasion, date(s), and

attendance)

J. M. Farrell, The Thousand Islands Biological Station: A Great Lakes Research Link in the upper St. Lawrence River. SeaGrant, LakeGuardian Class. (July 2008, 25 attendees).

J. M. Farrell, The Thousand Islands Biological Station: A Great Lakes Research Link in the upper St. Lawrence River. Antique Boat Muesum Board of Directors Meeting, Chippewa Bay, NY (September 2008, 20 attendees)

J. M. Farrell. Update on VHSV effects on muskellunge and status in the St. Lawrence River: Save The River 18th Annual Winter Weekend Conference (February 2009; 60 attendees).

J. M. Farrell, G. Avruskin, and J. Hughes. A Conservation Strategy of Enhancement of St. Lawrence River Native Fish Populations. US Fish and Wildlife Service, Cortland Field Office, Informational Session, Cortland, NY (March 2009; 15 attendees).

G. E. Eckerlin, P. Bowser, J. M. Farrell, and GGroocock, Round Goby Mediated Viral Distribution among Smallmouth Bass in the St. Lawrence River.Save The River 18th Annual Winter Weekend Conference (February 2009; 60 attendees).

V. PUBLIC SERVICE

A. Funded Service (include consulting activities)

1. Government Agencies (Federal, State, Local):

IJC St.Lawrence River Board of Control – invited expert to workshop regarding development of criteria for water levels regulation for environmental interest.

NYSDEC Great Lakes Water Levels Management- advised DEC on issues related to IJC Water Levels management and effects on public resources, produced proposal for monitoring wetlands with Gibbs, Leopold, Distler, Schulz and Mitchell.

2. Industrial and Commercial Groups, etc.

NY Power Authority – assisted on walleye spawning habitat enhancement project by providing resources and laboratory space at ESF to process samples taken at recently created spawning bed.

B. Unfunded Service to Governmental Agencies, Public Interest Groups, etc.

Thousand IslandsLand Trust: Community site tour on wetlands (August 2008; 15 attendees).

Thousand Islands Land Trust Zenda Farms Picnic, Provided live fish and poster displays as part of community event (June 2008; ~250 attendees)

Save The River, Clayton, NY, Winter Environmental Weekend Invited Speaker, Board of Directors, advisory roles on environmental issues.

Other groups served:

Ontario Ministry of Natural Resources, NYS Fish and Wildlife Management Board, Cornell Veterinary College, The Nature Conservancy, US Fish and Wildlife Service, Lake Ontario Sportfish Coalition, Natural Resources Conservation Service, Ducks Unlimited, SeaGrant.

VI. PROFESSIONAL DEVELOPMENT

A.Professional Honors and Awards (for teaching, research, outreach, etc.)

B.1. Activities in Professional Organizations (Offices held, service as chairman, member, participant or consultant)

Associate Editor, Wetlands (resigned 1/09).

Board of Directors, Save The River Inc. – 1200 member Environmental Advocacy organization on the St. Lawrence River.

Chair, International Esocid Working Group – Fisheries Management group created under the Great Lakes Fisheries Commission

Advisory Board Member, Central Michigan University Biological Station – Worked with committee of noted scientists in development of recommendation document at request of CMU Dean.

Advisory Board Member, Cornell University Biological Station – Met in April to discuss future of the CBFS.

2. Professional Society Membership

American Fisheries Society, International Association of Great LakesResearchers, Great Lakes Research Consortium, Society of Wetland Scientists

3. Other Professional Activities

a. Editorial activity

Journal(s)Responsibility

Wetlands Associate Editor (resigned 1/2009)

Other (books, symposia, etc.)

b. Reviewer

Journal(s) No. of manuscripts

Wetlands3

Hydrobiologia1

Agency No. of proposals

Other

c. Participation (workshops, symposia, etc.)

Name of workshop, etc.DatePlace

C. Further Education/Re-training Undertaken, Leaves, Workshops, etc.

Genetics for Fisheries Professionals: Tools and Decisions, NY Chapter American Fisheries Society (February 2009- Certificate of Completion)

Cornell University Limnology 100th Anniversary Celebration – one day lecture series and event.

IJC St.Lawrence River Board of Control Environmental Workshop, OswegoNY.

D. Foreign Travel (Where, When, Purpose)

Ottawa, Canada, August 2008, American Fisheries Society Annual Meeting.

VII. ADMINISTRATIVE AND SERVICE RESPONSIBILITIES (include committee participation)

A. Department-level

  • Chair of Building Advisory Committee–produce memo to EFB Chair with guidance for building improvements. Assisted with management of EFB Boston Whaler
  • Member, Field Programs Committee
  • Mentor for an Assistant Professor in EFB
  • Held TIBS open house for EFB faculty including tour

College-level

  • Served as Director of the Thousand Islands Biological Station.
  • Led facility improvementsimplementation at TIBS including Main Lodge renovations.
  • Worked on development initiative for new TIBS multipurpose building with Bob Quinn.
  • Committee memberfor the ESF Scientific Diving ProgramChaired by Mark Teece of Chemistry
  • Helped secure $40,000 in private gifts to TIBS with Bob Quinn of development office.

C. University-wide, including Research Foundation

  • Secured twogrants and managed existing contracts through the RF.
  • Helped secure member-item for $100,000 from NYS Sen. Darrel Aubertine with Bob Quinn.
  1. SUMMARY OF SIGNIFICANT ACTIVITIES AND ACCOMPLISHMENTS DURING THIS REPORTING PERIOD, ESPECIALLY THOSE MOST NOTEWORTHY AND RELATIVE TO THE COLLEGE’S AND DEPARTMENT’S MISSION.A paragraph on each of the following would be very helpful: this past year, what have you done for our students, department/college, and self professionally?NOTE: PLEASE CONSIDER THE INFORMATION IN THIS SECTION [along with the supporting specific information elsewhere in this report] AS ESSENTIAL TO HELPING ME DETERMINE DISCRETIONARY RAISES

For the students:

Two of my MS graduate students (Geof Eckerlin and Katie Woodside) graduated during this reporting period and my PhD student (Kevin Kapuscinski) successfully completed his candidacy exam in the spring semester and we brought in a $148,000 grant to support the remainder of his program. I brought on two EFB PhD students, Geof Eckerlin started in January and Derek Crane will begin in June 2009. I worked with undergraduate Dan Zangari (EFB graduate May 2009) on an independent study of round goby in the St. Lawrence River during summer 2008 and fall 2009. Dan presented his research at the EFB Aquabreak seminar during the spring semester. Jennifer Raino and Colby Bowmanboth EFB majors also worked with my research program through the summer. I worked with two American Fisheries Society Hutton Scholars, Carly Fairbanks and Mariah Taylor (now an EFB major) that were High School Seniors in my program. I took these students to the AFS meeting in Ottawa where they were recognized for their accomplishments, each received a plaque at the business meeting, and we attended presentations and events- their excitement was a real highlight for me.

Department/college:

The development of the Thousand Islands Biological Station continues and I led an effort to renovate the main lodge facility at TIBS. I hired three construction workers and with Physical Plant assistance we renovated the kitchen, bathroom and main room in the building. The project is nearly complete and has improved our appearance and facilities. I have initiated a collaborative effort with the AntiqueBoatMuseum in Clayton NY. They have provided a waterfront house for student housing complete with docking and we are improving it as a mainland facility. I will provide a short summer lecture series at the museum and other environmental interpretive activities that showcase our research to the community. I continue to work with theESF Development Office and Bob Quinn to help us with fundraising for the proposed MultipurposeBuilding for TIBS. We have secured gifts and grants totaling $170,000 and continue to meet with private donors. As Chair of the Building Advisory Committee to we continue to work on space, efficiency, and workplace quality concerns. We have met twice this period and developed a memo to the EFB Chair with recommendations to improve Illick Hall.

Professional/self

Our work with the St. Lawrence River habitat restoration strategy for several native coolwater fish species was funded and we continue to design, implementation, and evaluatehabitat enhancements in the St. Lawrence Valley. Gillian Avruskin will continue as our GIS specialist and I hired Eli Polzer (our 2008 Valedictorian) as a Research Support Specialist. I submitted a major $1.5M grant to NOAA through Ducks Unlimited with many partners including four EFB faculty that if funded will result in beginning a major research effort to evaluate the habitat enhancements in a truly holistic way. It would support five graduate students and a post-doc and bring together an analysis of biogeochemistry, lower trophic levels and nutrient chemistry, plant ecology, avifauna, herps, amphibians, mammals and fish in a comprehensive evaluation of habitat enhancements.

IX. A. FUTURE PLANS, AMBITIONS, AND POTENTIAL CONTRIBUTIONS FOR YOUR OWN

PROFESSIONAL DEVELOPMENT AND THE ENHANCEMENT OF THE PROGRAM IN

ENVIRONMENTAL AND FOREST BIOLOGY (brief summary)

B. PROJECTED ACTIVITIES FOR NEXT YEAR.

1. Summer 2009

a. Course(s) to be offered

EFB 388 to be co-taught with Neil Ringler

b. Proposed research activity

Continue research on spatial modeling fish reproductive habitats; Investigations regarding fish disease, muskellunge genetics and habitat study on the St. Lawrence and NiagaraRivers, and walleye habitat modeling. Manage students and staff at TIBS in monitoring and research program.

c. University, professional society, and public service

Service activities related to duties at TIBS including development and fundraising activities for facilities enhancements at TIBS. Participate in several significant community outreach events and work with the AntiqueBoatMuseum on summer lecture series.

2. Fall Semester 2009

a. Course(s) to be offered

I will begin my new title as Associate Professor within EFB this fall semester. I am looking forward to opening course offerings to undergrads and having greater interaction with undergraduates.