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U.S. Geological Survey - Great Lakes Science Center

Population Structure

The USGS-GLSC is aiding Great Lakes fisheries management and restoration by studying spatial and temporal population structure of Great Lakes fishes, including age and metapopulation (subpopulation) structure and genetic diversity. Knowledge of fish population structure is important for management and restoration because fish population growth is affected by the age distribution of the population as well as genetic mixing that occurs within and between subpopulations. USGS-GLSC research on fish population structure includes analysis of genetic diversity in: hatchery strains of lake trout, lake whitefish from Lakes Superior Michigan, Huron, and Erie, preyfish in the upper Great Lakes, and aquatic organisms in Isle Royale. Researchers are also studying age and subpopulation structure of cisco and bloater in the Great Lakes. These assessments provide detailed population information that allows managers to better predict fish population dynamics, thereby improving fishery management and restoration.


Yellow perch is one of two exploited species in Lake Erie that account for over a billion dollars in net economic value. Collaborative genetic and morphometric research has revealed structuring of the Yellow Perch population is at a scale finer than the scale at which the species is managed. Continuing genetics and PIT-tagging work seeks to define the spatial scale of population structuring and how mobile smaller-scale population units are. The ultimate goal is to inform management of yellow perch for long-term sustainability.

Principal Investigator: Patrick Kocovsky

Lake whitefish are one of many fish species that have declined in the Great Lakes region, although populations in Lake Erie have partially recovered and there is a robust commercial fishery in Lake Huron (Chiarappa 2005).  Habitat degradation, overfishing, and competition with exotic species are just some of the reasons why populations declined (Chiarappa 2005).  In the Detroit River, habitat alteration has played a particularly significant role.  At one time lake whitefish spawned at several locations in the Detroit River (Goodyear et al. 1982) and supported a very valuable fishery (Milner 1874; Todd 1986).  In 1905, the United States government began construction on shipping channels intended to improve the passage for large vessels.  Spawning grounds of whitefish and other species were disrupted by the construction.  After construction was complete whitefish did return to the river but the population began to decline.  Since 1925 there have been very few reports of lake whitefish in the Detroit River.  A few larvae were caught during sampling conducted in 1977 and 1978 (Hatcher and Nester 1983) and the authors believed that those fish may have drifted from Lake Huron.

In 2005 and 2006, the first whitefish catches were reported in the Detroit River.  Viable eggs and a male in spawning condition were collected in the fall of 2005 and larvae were collected in the spring of 2006.  The exact location of the spawning grounds is unknown and further research is required to determine the location of the spawning grounds and estimate the size of any spawning populations (Roseman et al. 2007).  Further research is also required to determine if these contemporary lake whitefish are a remnant of stocks that once existed in the Detroit River or if they are fish that had migrated into the river from Lake Erie or possibly Lake Huron.  Whitefish may have migrated between Lake Erie and the Detroit River before the collapse of the fishery (Milner 1874) and walleye have been shown to move along this corridor (Todd and Haas 1993).  Genetic data could be used to test this hypothesis and also to characterize the whitefish populations now in the Detroit River.

Principal Investigator: Wendylee Stott

Lake trout were extirpated from the Great Lakes as a result of habitat alteration, commercial over-harvest, and sea lamprey predation (e.g., Brown et al. 1981; Goodier 1981).  Considerable financial commitments have been made to restore lake trout to the Great Lakes by stocking, habitat restoration, and sea lamprey control.  Today, lake trout rehabilitation is still one of the primary goals of restoration and management programs (e.g., (Ebener 1998).  Since 1969, over 46.5 million lake trout of various ages and strains have been stocked in all areas of Lake Huron (Ebener 1998).  Several hatchery strains of lake trout have been used including:  Jenny Lake, Lewis Lake, Marquette, Seneca Lake, Lake Manitou, Slate Is., Michipicoten Is., Parry Sound (Big Sound), and Iroquois Bay.  In addition, splake have also been stocked.  Although successful natural reproduction of lake trout in the Great Lakes outside of Lake Superior has been limited, reproduction has occurred at six sites in Lake Huron (South Bay, Iroquois Bay, Owen Sound, Parry Sound, Six Fathom Bank and Thunder Bay).  Knowing the origin of naturally produced fish in Lake Huron will provide valuable direction for management efforts.  For example, the information can be used to ensure that future stocking of unsuccessful strains, which could limit any of the success already achieved, does not continue.  A variety of microsatellite DNA markers have been developed for salmonid species (see below) and recent research projects have characterized microsatellite DNA variation in the majority of lake trout hatchery strains stocked into the Great Lakes (e.g., Stott 1998; Page 2001).  Therefore, the required data are available to assess the contribution of different lake trout strains to successful natural reproduction in Lake Huron.

Principal Investigator: Wendylee Stott

Before their collapse between 1950 and 1970, members of the genus Sander (walleye, blue pike, and sauger) from Lake Erie supported a world-class fishery. Blue pike was considered extinct in the U.S. in 1983 and in Canada in 1985, yet reports of the species in both the U.S. and Canada continue to surface.  Although now they are considered to be sub-species of Sander vitreum, questions remain about the taxonomic status of blue pike and walleye that have been difficult to address with genetic techniques due to the scarcity of samples of blue pike that yield DNA of sufficient quality. The changes in the Sander populations of Lake Erie are well documented in scale collections housed at the Great Lakes Science Center  that were identified by experts such as H.J. Deason and J. VanOosten. These scales provide an opportunity to collect genetic data to examine taxonomic and population genetic relationships between sub-species.

Principal Investigator: Wendylee Stott

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

Members of the genus Sander (walleye, blue pike, and sauger) from the western basin of Lake Erie once supported world class fisheries.  Between 1950 and 1970 the blue pike and sauger fisheries collapsed and the walleye fishery was diminished.  The causes and characteristics of the collapse are very similar to the recent loss of other commercial fisheries world wide and in particular on the East Coast of North America (e.g. Hutchings and Myers 1994; Myers et al. 1995).  Blue pike were listed as extinct in 1983, but may have disappeared as early as 1971 in the western basin of Lake Erie.

The Great Lakes Science Center currently houses blue pike, sauger, and walleye spawning populations were collected simultaneously, therefore spatially and temporally cohesive samples are available for analysis. Four locations in Lake Erie were sampled repeatedly for blue pike and walleye between 1929 and 1957 (Parsons 1967). Individuals from the years 1929, 1939, 1949 and 1957 from each sample site will be analyzed. Modern samples from similar areas will also be collected for comparison and to validate sequence data.

Comparisons of historical and contemporary population genetic structure of Sander species will provide natural resource managers with information necessary to evaluate progress in current walleye population rehabilitation and restoration efforts.  Additional information gained in this study about the taxonomic status of Sander species will be useful to management agencies to help management and protect walleye and sauger populations in throughout their range.

Principal Investigator: Wendylee Stott

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