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New Vessel Fills Great Lakes Research Niche

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The 69-year-old research vessel (R/V) Chinook was fast approaching retirement. After years of generating valuable research data on the Great Lakes fishery for the Michigan Department of Natural Resources (MDNR), it was nearing the end of its useful life. Enter the R/V Tanner, a state-of-the-art 57-foot aluminum-hulled vessel with all the modern equipment its crew could hope for. This new member of the fleet, named after former MDNR Fisheries Division chief and director Dr. Howard A. Tanner, was funded in part by a grant from the Great Lakes Fishery Trust (GLFT). Although the Chinook will be missed, the Tanner is a welcome replacement that will enhance data collection and management decisions for years to come.

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New Method Available for Estimating Relative Recruitment Levels

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Thanks to a recent GLFT project, fisheries managers now have two computer models, developed by a team of researchers who wondered if they could find a better way to determine relative recruitments of spawning populations in a mixed environment. The researchers maintained that if they could identify that certain vulnerable populations contributing individuals to a mixture had declining recruitment levels, then fisheries managers could better employ appropriate conservation measures.

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The Role of Tributaries and River Plumes as Nursery Areas for Yellow Perch and Round Gobies in Lake Michigan

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In the warmer waters of spring, yellow perch lay their eggs in long, gelatinous strands, usually among the thick vegetation found in the shallow waters of rivers and along the shores of lakes. A single female can lay more than 20,000 eggs; however, the vast majority of fish that come from these eggs will die very early, primarily due to predation and starvation.
To cultivate self-sustaining stocks of fish, fisheries managers need to understand how best to help young fish survive. For example, among all the different habitats in and around Lake Michigan, are there particular ones where larval and juvenile yellow perch—as well as other species, like round gobies and alewives—can find the food and water conditions they need to thrive? And how do these fish use different habitats as they grow?

The Angle

A team of researchers hypothesized that river plumes—which have unique thermal, light, nutrient, and biological properties—would provide an excellent place for larval yellow perch, round gobies, and alewives to grow. They also wondered how the three species used river mouths, river plumes, and the nearshore waters of southeastern Lake Michigan. Did the young fish function the same regardless of their environment, or were there important differences among habitats?

The Nitty-Gritty

To test their hypotheses, researchers (1) collected water samples from river plumes and adjacent nonplume areas in southeastern Lake Michigan to compare their physical, chemical, and biotic conditions; (2) estimated the movement of larval fish from tributaries into Lake Michigan; (3) compared the densities, diets, and growth rates of the three species in different areas; and (4) evaluated the extent to which later-stage fish used tributaries and river plumes as early life habitats.

The interdisciplinary research team—which included, among others, a fish ecologist, a physical scientist, and a water isotope specialist—used a number of different tools and methods (including otolith isotopic analysis) to better understand fish movement, as well as habitat contributions and linkages.

The Results Are In…

The researchers found that, while river plumes in southeastern Lake Michigan present a somewhat different environment than open lake waters (they are a little bit warmer and more turbid), they are very small and not the hotspots of production that researchers anticipated. Data do suggest, however, that river mouths have greater potential for production, particularly for alewives.

Perhaps the most important finding, though, is that there was a clear distinction between river mouth and nearshore populations of yellow perch and round gobies, but not alewives. An analysis of diets, fatty acids, and stable isotopes, as well as isotopic analyses of otoliths, show that alewives move back and forth between the habitats (the river and the open lake water) with some regularity, while yellow perch and round gobies stay mostly in the same habitat for life.

What Does It All Mean?

Although river plumes were not as productive as researchers originally surmised, river mouths show some promise as production hotspots and, therefore, warrant further study. They may be particularly good environments for larval alewives. Given recent concerns about the considerable year-to-year variations in the alewife population, and their important role as prey for other valuable fish, river mouths may hold some management answers.

More important, however, is that fish managers now have a clearer understanding of the yellow perch,  round goby, and alewife populations. This information could be of great value when making decisions about regulations for managing these species and helping more larval and juvenile fish survive.

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Study Prompts New Thinking About Yellow Perch, Round Gobies, and Alewives

“The fascinating thing about research,” says Jon Beard, grant manager for the Great Lakes Fishery Trust (GLFT), “is that it’s not just about proving or disproving a hypothesis. Sometimes the most interesting results come from other knowledge gained along the way.”

This was true of a recent GLFT-funded project, which aimed to determine how tributaries and river plumes serve as nursery areas for certain fish species.

“One of the most interesting findings in this project from a fisheries management perspective is not that river plumes weren’t hotspots of production, but that researchers found that yellow perch and round gobies in nearshore Lake Michigan and river mouths rely on distinct trophic pathways and do not appear to move frequently between the two habitats,” Beard says. “This information has real potential for use by management agencies.”

In fact, the GLFT has already funded another study to expand understanding of the topic.

Alewife (Alosa pseudoharengus).

Originally, the research team focused its attention on evaluating the production potential of river plumes. In the process of characterizing and evaluating them, researchers asked two other important questions: How do juvenile yellow perch, round gobies, and alewives use different habitats (including river mouths and the open lake)? And how do those habitats support fish growth?

To answer these questions, the research team looked at the diets of the fish and at different bio-chemical indicators. These indicators included fatty acids and stable isotopes, which scientists use to assess the type of production pathways that support fish growth.


Yellow perch (Perca flavescens).

Tomas Höök, associate professor in the Department of Forestry and Natural Resources at Purdue University and one of the grant’s principal investigators says, “We found distinct signatures in the stable isotope ratios and fatty acids of yellow perch and round gobies in the open lake versus those in the river mouth.” That means that, for the most part, those fish do not go back and forth between the lake and the river; instead, they stay primarily in the habitat where they were caught.

“We saw the isotopic values we would expect to see of fish that have spent their lives almost entirely in the lake or almost entirely in the river mouth,” says Höök. The same was not true, however, of alewives. Because they are more migratory by nature (alewives live in the lake and run into the river to spawn), their fatty acid and isotopic signatures were similar, regardless of the habitat in which they were found.

These findings were reinforced when researchers examined the otoliths in the three species. As Höök explains, “Otoliths are a more or less biologically inert structures in the heads of fish that grow like crystals. They start as very small crystals and, as the fish grow, material is deposited onto the otoliths. Once material is deposited, it’s not sequestered back into the body, so it can give us an idea of the different environments a fish has experienced over time.”

With each of the three species, the research team analyzed the isotopic makeup of the edge and the middle part of the otolith to determine where it had lived. Not surprisingly, in most cases, when it came to yellow perch and round gobies, the core otolith signature was similar to the environment in which the fish were caught, whereas the otolith signatures of alewives were not.

“These findings suggest that yellow perch and round gobies may have a more complex spawning stock structure than alewives in Lake Michigan, which has important management implications,” says Carl Ruetz, professor with the Annis Water Resources Institute at Grand Valley State University. “For example, if yellow perch are composed of numerous subpopulations along the periphery of the lake, managers will need to recognize and account for that diversity when formulating regulations related to yellow perch management.”

More research is needed to determine whether this is the case.

Another finding managers may find useful is that while river plumes were not hotspots of production, as researchers first hypothesized, river mouths appear to hold more promise. “The conditions in the river mouth seem to be good for some fish,” explains Höök. “It’s warmer, it’s turbid, and we found that larval alewives, in particular, are growing better there than in the open lake.”

Given recent concerns about the high variability in alewife populations from year to year, as well as their role as important prey for other valuable fish, river mouths may hold some management answers.

As for the original hypothesis, Höök and the other members of the research team thought that river plumes might be a productive environment for yellow perch, round gobies, and alewives, because they (1) concentrate diverse abiotic (e.g., sediment) and biotic constituents (e.g., bacteria, phytoplankton, zooplankton, and larval fish), (2) stimulate primary and secondary production, and (3) provide thermally suitable conditions. In fact, earlier research on yellow perch in western Lake Erie found that larval survival was, indeed, higher in the Maumee River plume than in surrounding nonplume waters, due to high levels of turbidity (or murkiness). That research suggested that the turbidity of the water probably reduced the ability of predators to find young fish, which increased their survival rate. Höök and his fellow researchers thought they might see similar results in the river plumes of southeastern Lake Michigan.

Mean Densities of Larval Alewife and Yellow Perch

This is a caption.

Mean densities of larval alewife and yellow perch during May through August 2011 and 2012. Alewife densities were generally higher at river sites, while yellow perch tended to be more dense at lake sites.

After collecting samples from five tributaries over the course of two years, the research team did find that river plumes present a somewhat different set of environmental conditions than the open lake. According to Höök, the plumes “are a little bit warmer and the water is a little bit murkier, which may facilitate foraging and protect young fish from predators. You also see a higher concentration of nutrients in plume versus nonplume areas.”

Unfortunately, the plumes in southeastern Lake Michigan are very small, even in the St. Joseph River, which is the third largest river system in the state and the largest river included in the study. The size of the plumes—or more specifically the length of time that critical materials stay in them—matter.

“We found that resident time of water spent in a plume, at the longest, is about day,” explains Höök. “On most occasions, it’s much shorter. So, even though the environment is somewhat distinct, it’s really quite limited.”

In the end, says Höök, “this really is a habitat issue. You have to understand habitat utilization in order to make predictions about the fish population and to figure out how to manage them.”

Because of this GLFT grant, managers now have a better understanding of the yellow perch, round goby, and alewife populations themselves, as well as how they move, how they use different environments, what resources support their growth, and the relative contribution of different habitats to survival. This is important information for managers to have as they work to help more larval and juvenile fish survive.

GLFT Aquatic Connectivity Workshop Proceedings Document Available

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In 2014, the Great Lakes Fishery Trust convened an aquatic connectivity workshop to identify the types of decision-support tools that resource managers and regulators need and would use to guide decisions on where to improve fish passage or remove dams in the Great Lakes basin.

The workshop convened over 50 participants representing 23 entities from federal, state, tribal, and local agencies; binational organizations; universities; and nonprofits. Participants reviewed existing decision-support tools and discussed their information needs and processes used when developing, evaluating, and implementing aquatic connectivity projects.

The discussion helped identify research needs and information gaps and ways to enhance existing tools to support more effective and efficient decision making.

The proceedings document is available for download below:

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Exploring Life History Characteristics of Naturalized Versus Stocked Chinook

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Since the 1960s, the state has been stocking Lake Michigan with Chinook salmon to help maintain the lake’s ecosystem and provide diverse fishing opportunities to anglers. As a result, more than half of the Chinook in Lake Michigan today are naturalized. But how has the salmon population changed over time? And are there significant differences between naturally produced and hatchery-stocked populations—differences that could upset the delicate balance of the state’s fisheries?

Since Michigan depends on the economic benefits of recreational fishing—and since the health of the lakes depends on making sound management decisions—the Great Lakes Fishery Trust (GLFT) funded a research project to (1) better understand the state’s more naturalized Chinook salmon population, (2) assess potential differences between naturalized and hatchery-stocked fish, and (3) use the results to inform decisions about cultivating self-sustaining stocks of desirable introduced species.

The Angle

To better understand how the Chinook salmon population has changed over time, a team of researchers from five organizations first looked at historical trend data. Then, the team conducted field studies to gather more information on the life-history characteristics of naturalized versus hatchery-stocked populations. Among other things, researchers hypothesized that age and size at maturity would diverge over time (because many life history traits are heritable), and naturalized fish would spawn at later ages and times of the year.

The Nitty-Gritty

Researchers began their work by examining 23 years of data. Then, they conducted field studies for two years to collect biological data on three different spawning populations in northwestern Lake Michigan: (1) a hatchery-stocked population, (2) a naturalized population, and (3) a mixed population whose origins could not be discerned. For each population, researchers evaluated age at maturity, weight and length at maturity, fecundity, egg size, and the months in which fish spawned. They also analyzed the total thiamine concentrations in Chinook egg subsamples to determine whether egg and larval survivability differed among the populations.

The Results Are In…

Much to their surprise, researchers found only minor differences in the life-history traits of the Chinook salmon population. Even as the population became more naturalized, data show that maturity at age did not change; length at maturity remained consistent; and the average weight at maturity declined, but only slightly. There also was a decrease over time in the ratio of males to females, but the decline was not as significant as expected.

When using more current field data to compare the three Chinook populations, researchers found no support for concerns about differing ages and sizes at maturity, fecundity, or the times at which the fish spawned. They did, however, find that mixed populations had the largest and heaviest eggs, whereas naturalized populations had the smallest.

One of the most interesting and unexpected findings was that egg thiamine concentrations, on average, were above the ED50 threshold (concentrations below the threshold are associated with 50 percent larval mortality). In fact, concentrations were higher than those previously reported, and there was no indication of high occurrences of thiamine deficiency. This finding is noteworthy because Chinook salmon now consume alewives, the primary driver of thiamine deficiency in Great Lakes salmonids.

What Does It all Mean?

While divergences between hatchery and naturalized Chinook salmon populations have become a serious concern in other areas of the country, this project data suggest there is no need to be overly worried about differences in the Great Lakes region, at least at this time. The life-history characteristics of the overall Chinook salmon population have remained fairly stable, and the characteristics of naturalized populations are similar to those of hatchery-produced populations. Therefore, the results suggest that an increasingly naturalized Chinook salmon population has neither adversely affected the salmon fishery nor will it do so in the future.

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Research Shows Few Differences Between Naturalized and Stocked Salmon

Mark Rogers, a research fishery biologist with the U.S. Geological Survey and one of the primary investigators on a recent project funded by the Great Lakes Fishery Trust (GLFT), posed this fundamental question: As the population structure of Chinook salmon in Lake Michigan changes, should we expect the fishery to change, too? Project results suggest the answer might be no, or least not as much as we might expect. Given current concerns about the vulnerability and sustainability of the Chinook salmon population, this could be an important finding.

For their GLFT-funded project, Rogers and a team of researchers attempted to answer his question by looking at life-history characteristics in two ways. First, they examined 23 years of historical data to determine whether average life-history parameters changed as the Chinook salmon population became increasingly naturalized. (Naturalized fish now comprise more than 50 percent of the total Chinook salmon population in Lake Michigan.)

Second, the team conducted two years of field studies to gather data that might support or call into question what the trend data suggested. For the field study, researchers looked at spawning populations in northwestern Lake Michigan that were naturalized, hatchery-stocked, and mixed (e.g., their origins could not be discerned).


In a third part of the project, researchers analyzed the total concentrations of thiamine, a vitamin B structure, in Chinook eggs, which has implications for egg and larval survivability. Specifically, they wanted to understand whether naturalized salmon were less inclined toward thiamine deficiencies, which, at certain levels, can lead to early mortality syndrome.

Many of the team’s findings were entirely unexpected, Rogers says. For example, researchers were fairly confident that naturalized fish would reach maturity later, which would cause them to spawn at later ages and at later times of the year (perhaps in October and November instead of August or September). Neither the trend data nor the field study data supported this hypothesis. Age at maturity did not change, length at maturity remained the same, and the time of year at which fish spawned showed no significant differences.

Randy Claramunt of the Charlevoix Fisheries Research Station, who served as a collaborator on the project, was surprised with this finding.

“Anglers often ask us if we have to manage wild salmon separately from stocked fish because wild fish are thought to spawn at older ages and later in the year,” he says. “The findings from this study show that wild and stocked salmon likely are not distinct subpopulations. Therefore, our current models on salmon abundance adequately reflect the mixed population.”

The only noticeable change in the salmon population over time was a slight decline in average weight. The decline, researchers learned, was not related to something inherent to the population, or even to stocking density (e.g., too many fish going after too few prey). Instead, they found that weight variations had a stronger relationship with prey fish abundance.

“In years where more prey was available, the fish were heavier,” Rogers says.


Chinook salmon (Oncorhynchus tshawytscha).

Another unexpected finding was that the ratio of males to females did not decline as precipitously as anticipated. The assumption that the population would reach a male/female balance over time is based on the fact that hatchery-stocked fish grow very fast during the first year of life. As a result, male fish reach maturity at age one or two instead of the expected age of three or four. These early maturing males are called “jacks.” Researchers surmised that as naturalized fish contributed more to the salmon population, there would be fewer jacks, thereby equalizing the number of males and females in the spawning population. The trend data from the GLFT project suggests that, while there has been some shift over 23 years, it is not as strong as expected. The Chinook salmon population in Lake Michigan is still male biased.

Yet another surprising finding relates to fecundity. As Rogers explains, “There is an evolutionary paradigm that the number and size of eggs a fish produces should be optimized for the habitat in which they are laid to maximize their survival. So, if you’re in a stable habitat—like a hatchery—the fish will invest its energy in making small eggs and a lot of them. But, if the fish is in a less stable habitat—maybe one with high and low water levels or other stressful conditions—it will invest its energy in laying fewer eggs that are larger.”

Ironically, researchers found that naturalized Chinook salmon, who live in less stable environments than hatchery-stocked fish, laid the smallest eggs. The mixed population had the largest, heaviest eggs, and the eggs of the hatchery-stocked population were in the middle. Among the three populations, however, there were no differences when comparing the total number of eggs laid to a female’s weight.

“If the naturalized fish had much larger eggs than the hatchery-stocked fish, that would imply the naturalized females were putting more energy into their eggs,” Rogers says. “If that energy comes from prey resources, the current prey biomass levels we’re experiencing in the lake, which are lower than in previous decades, could hurt the naturalized Chinook population. Since that’s not the case, we probably don’t have to worry.”

The final, and perhaps most unexpected, finding was that, on average, Chinook salmon egg thiamine concentrations were above the ED50 threshold (egg thiamine concentrations below ED50 are associated with 50 percent larval mortality).

“Thiamine is a vitamin B structure. Thiaminase is a vitamin B blocker that some prey fish have, like alewives. When the salmon consume the alewives with thiaminase, it inhibits thiamine production, which is important to egg and larval survival. So, having higher than expected levels of thiamine in salmon is good.”

While the findings of this study shed valuable light on the Chinook salmon population, Rogers cautions that they do not tell the whole story. The study only looked at fish in northwestern Lake Michigan; therefore, the results do not necessarily represent lakewide patterns. Furthermore, the study focused primarily on the increasing contribution of wild fish to the population. But as Rogers points out: “A lot has been going on in Lake Michigan since the conclusion of our study … that could affect the dynamic of the salmon fishery. So, while our results don’t suggest that the fishery is going to change, there are other things that could change it.”

Field Study Area and Survey Location Maps

Map of field study areas and creel survey locations for Lake Michigan salmon life history conducted during the fall of 2012 and 2013 (left). Map of rivers and creeks where Chinook Salmon samples were collected for historical analyses (right).

Mark Coscarelli, trust manager for the GLFT, agrees with Rogers.

“While the data suggest that there are far fewer differences among naturalized and stocked fish than we imagined, the project underscores that life history characteristics are only one piece of a complex puzzle that drives salmon production in Lake Michigan,” he says. “As we witnessed with Lake Huron, the changing food web brought about by invasive species likely has far greater implications for the fishery.”