USGS - science for a changing world

U.S. Geological Survey - Great Lakes Science Center

Jeffrey Schaeffer


Research Fishery Biologist Great Lakes Science Center Email: Phone: (734) 214-7250 Fax: (734) 994-8780


B.S. (Fisheries Management), The Ohio State University, 1980
M.S. (Zoology), The Ohio State University, 1984
Ph.D. (Natural Resources), The University of Michigan, 1994

Current Studies

Ecological Consequences of Altered Lotic Flows

The presence of water is of course necessary to support aquatic organisms. The quantity, quality, and dynamic conditions of water in lotic systems also influence populations and communities of aquatic organisms. Human exploitation of water resources can greatly affect flow of water through lotic systems, but the specific responses of fish and other aquatic organisms to altered flow regimes is poorly understood. This study investigates effects of water throughput in a lotic system and its variability on the biodiversity, community structure, and abundance of fish populations and communities.

Principal Investigator: James E. McKenna, Jr.
Maumee River

The Maumee River has been designated an Area of Concern (AOC) due to legacy contaminants, sedimentation, and habitat loss that have resulted in beneficial use impairments. Although progress toward delisting has been achieved, some intractable impairments remain, especially in the lower river. Remediation of impairments has been made difficult because no master habitat plan exists to guide restoration and incorporate recent findings on how Great Lakes Rivermouths function. This information is needed to more rapidly achieve delisting, and to apply immediately toward remediation of impairments.

Principal Investigator: Jeff Schaeffer
Genetic Population Structure of Lake Whitefish in Lake Huron

Coregonids are an important native species in historical and present day fisheries in the Great Lakes. They are a forage species for top predators and as such, play an important role in the trophic transfer of energy. While most coregonid populations in the Great Lakes have been greatly depleted from historical levels, lake whitefish (Coregonus clupeaformis) populations have increased in Lake Huron during the late 1900s, possibly as a consequence of the restoration of top predators. However, recent declines in biomass and condition of lake whitefish (particularly in the main basin) have raised concerns about the overall health of the resource. The Great Lakes Fishery Commission's Lake Huron committee has embraced an ecosystem approach to management. This approach recognizes that diversity among fish stocks is important to the diversity of the fish community as a whole. Management actions should strive to maintain genetic diversity by recognizing stocks and protecting them as needed. A first step in this process is to delineate stock boundaries. Lake whitefish are currently managed as 33 stocks (8 in Michigan waters and 25 in Ontario waters). However, little genetic information exists to support these stock designations. Previous genetic studies sampled the northern of portions lakes Huron and a few sites in lakes in Superior and Ontario and there is a recent more comprehensive study of Lake Michigan, but little is known about the genetic diversity and stock structure of main basin and major spawning grounds on Lake Huron. Therefore, we propose to analyze lake-wide stock structure by analyzing microsatellite DNA variation of lake whitefish in Lake Huron. We will test the null hypothesis that lake whitefish in Lake Huron exist as a single population. Secondary hypotheses will test correspondence of the observed genetic structure with existing stock designations and the results of an ongoing tagging study. Results of this study will provide information that is required for scientifically sound management and will help with the continued resurgence of lake whitefish in Lake Huron. Comparisons with data from other studies will also provide insight into the evolution of coregonids in North America.

Principal Investigator: Wendylee Stott
Rivermouths and Fishes: Understanding Structure and Function of Coastal Habitats, Fish Communities, and Application Toward Restoration

There is a critical need for science describing rivermouth ecosystems--the places where tributaries meet wetland and coastal processes to form productive freshwater estuaries; these habitats link riverine (landscape) and Great Lakes nearshore (and ultimately deepwater) systems. For example, it is generally agreed that rivermouths are key nurseries for migratory fishes; however this dynamic is poorly understood for most species. Rivermouths are also the hubs of human interaction with the Great Lakes proper, in terms of both impacts and appreciation. Yet despite their ecological and human importance, these key ecosystems are poorly understood and little studied. We are studying Great Lakes Rivermouths to learn about the processes that make them important as sites of fish and wildlife production, with special emphasis on their role in providing ecosystem services that could help coastal communities achieve economic revitalization. Our most important finding to date is that many rivers experience flow reversal during seiches; this moves lake water far upstream and creates a complex mixing zone that provides critical nutrients for the organisms living there. Nutrient availability is likely enhanced by mixing, but also highly dependent on watershed characteristics.

Principal Investigator: Jeff Schaeffer

Recent Publications

Lizhu Wang, Catherine M. Riseng, Lacey A. Mason, Kevin E. Wehrly, Edward S. Rutherford, James E. McKenna Jr., Chris Castiglione, Lucinda B. Johnson, Dana M. Infante, Scott Sowa, Mike Robertson, Jeff Schaeffer, Mary Khoury, John Gaiot, Tom Hollenhorst, Colin Brooks, and Mark Coscarelli 2015. A spatial classification and database for management, research, and policy making: The Great Lakes aquatic habitat framework. Elsevier . Journal of Great Lakes Research . 41 (2). 584-596.
Contribution #1914
Jeffrey S. Schaeffer, Mark W. Rogers, David G. Fielder, Neal Godby, Anjanette Bowen, Lisa O'Connor, Josh Parrish, Susan Greenwood, Stephen Chong, and Greg Wright 2014. Designing long-term fish community assessments in connecting channels: Lessons from the Saint Marys River. Elsevier . Journal of Great Lakes Research . 40 (Supplement 2). 15-22.
Contribution #1831
James E. McKenna, Jr., Jeffrey S. Schaeffer, Jana S. Stewart, and Michael T. Slattery 2014. Development of a spatially universal framework for classifying stream assemblages with application to conservation planning for Great Lakes lotic fish communities. John Wiley & Sons, Inc. . Restoration Ecology . 23 (2). 167-178.
Contribution #1873
Edward F. Roseman, Jeffrey S. Schaeffer, Ethan Bright, and David G. Fielder 2014. Angler-Caught Piscivore Diets Reflect Fish Community Changes in Lake Huron. Taylor & Francis . Transactions of the American Fisheries Society . 143 (6). 1419-1433.
Contribution #1872
Stott, Wendylee, Ebener, Mark P., Mohr, Lloyd, Schaeffer, Jeff, Roseman, Edward F., Harford, William J., Johnson, James E., and Cherie-Lee Fietsch. 2012. Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron. Fundamental and Applied Limnology. Special Issues. Advances in Limnology . 63 241-260.
Contribution #1619

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