Lightning on a Bobber

The Hunter’s Moon rises as the evening hours set in. The cool autumn air is a sharp contrast to the warmer temps from earlier in the day. Full of high spirits and angling optimism, Trevor Fey and his nephew Derek prep a boat at the Lake Sarah public water access in southwestern Minnesota. The pair have walleye on the brain. Derek’s success on Lake Sarah just two days earlier, when he caught a lavish number of walleye, including a 29-incher, bolsters their confidence. “I’m surprised this lake isn’t on more people’s radar,” says Trevor, who has fished the lake for years. “In my experience, this lake is one of the best in the state to catch both quality and number of walleye.”

By the light of the first full moon in October, the duo catches and releases 87 walleye, a banner day by any angler’s measure. Though the walleye look and act like the ones you’d catch up north, they are a genetically unique version of the fish, known as the Lower Mississippi strain. The strain is a relatively new, and exciting, discovery for fish biologists, though it has long swum in an area that covers most of the southern third of Minnesota, including all drainages below St. Anthony Falls on the Mississippi River.

Thanks to DNA sequencing, a bit of historical sleuthing, and present-day research trials, Minnesota’s Lower Mississippi strain is benefiting walleye conservation, fish stocking operations, and anglers like Trevor and Derek Fey.

Stocking the State Fish. Minnesotans love their walleye. The state fish is fun to catch and delicious to eat. And while many anglers may picture the central and northern regions when they think of walleye fishing in Minnesota, the species is also native to lakes and rivers in the south.

Due to the fish’s popularity and distribution around the state, the Minnesota Department of Natural Resources stocks more walleye than any other fish species, loading the state’s waters with an annual average of more than 250 million walleye fry (newly hatched walleye) and 1 million walleye fingerlings (walleye at the end of their first year of growth). Walleye are stocked to restore depleted populations, provide angling opportunities where spawning habitat may be limited or where young walleye have trouble growing to adult sizes, and to supplement when natural reproduction alone is unable to sustain a walleye population.

Minnesota’s history of walleye stocking began in the late 1800s with haphazard attempts by early federal and state fish commissions. Over time, as fisheries science was established and field practices evolved, stocking became more grounded in experimental design and scientific evaluation. In 1984, the DNR initiated the first lake management plans that prescribed fish stocking, including those for walleye. In 1996, the agency released guidelines that recommended stocking walleye within the state’s major watersheds, noting that the watersheds likely held genetically unique strains of walleye. Fisheries managers were instructed to stock each watershed, when possible, with its corresponding walleye strain to preserve genetics.

But with no active wild spawning operations in place in southern Minnesota, walleye stocking efforts in the region relied on fertilized eggs and hatched walleye fry shipped down from big lakes in northern Minnesota. The practice was largely a matter of scale, as northern lakes could produce millions of fertilized walleye eggs in a short period of time, something the southern region wasn’t equipped to do.

Eventually, this would change.

A Persistent Strain. Over time, increasingly sophisticated genetic analysis and walleye surveys showed even more clearly the benefits of stocking local strains in their corresponding watersheds. A breakthrough in this avenue of research came in December 2014, at a meeting of DNR fisheries staff from southern Minnesota. At the gathering in New Ulm, research geneticist Loren Miller presented a series of slides showing the genetic makeup of walleye in a handful of lakes in southern Minnesota. To the surprise of the audience, these slides revealed that a local walleye strain—what would later become known as the Lower Mississippi strain—had persisted in some of the sampled lakes and was outperforming stocked northern strain walleye in others. Tetonka Lake in Waterville, as well as other lakes on the Cannon River, had high levels of the Lower Mississippi strain. So did Lake Sarah.

Miller’s research built on earlier research. In 1991, a report by DNR fisheries researcher Mike McInerny and others described genetic differences of walleye stocks in Minnesota and noted that these differences appeared to line up with geographic isolation caused by glaciation. Put simply, watersheds create a natural confinement that has allowed for the emergence of different walleye strains.

By 2002, William Eldridge—then a graduate student in the University of Minnesota’s fisheries program—and others published a paper on their efforts to stock five southern Minnesota lakes with walleye fry from two northern Minnesota fisheries stations, comparing their survival to the lakes’ naturally reproduced walleye. Over two summers of evaluation, the study showed that local walleye proportionally increased while the proportion of stocked northern walleye dropped. Around that same time, the Illinois Natural History Survey completed a multistate study describing differences in walleye genetics from different watersheds. According to Miller, these were all hints and evidence that a distinct strain of walleye was thriving in southern Minnesota.

Saving Genetics and Money. The rewards of stocking the Lower Mississippi walleye strain in southern Minnesota include fish with better adaptability, fitness, and survivorship. And those benefits in turn add up to another: cost savings.

Between 2018 and 2022, DNR fisheries research biologist Dale Logsdon led a comparison study in which he stocked select southern Minnesota lakes with equal amounts of the Lower Mississippi strain and a northern strain known as Upper Mississippi.

During the research period, the southern strain outsurvived the northern one at an astounding ratio of 70:30 or better.
Miller, who was a coauthor of the study, noted its genetic implications. “Because all of the fish in the study were subject to the same environmental conditions,” he says, “seeing the higher survival from Lower Mississippi strain truly indicates that it is a genetics thing.”

From an economic perspective, fisheries staff did the math and quickly realized that although southern Minnesota stocking operations were small scale compared with those in the north, the dramatically higher survivorship of the local strain made it a less expensive stocking option.

“The cost effectiveness of using the Lower Mississippi strain was the real eye-opener,” says Logsdon, adding that southern Minnesota stocking operations were historically viewed as costly and inefficient. “There was a small [stocking operation] on the Cannon River back in the 1980s, and the question was, ‘Why are you wasting time on that when you can get in a single day on Cutfoot Sioux Lake what might take a week down there?’ But we’ve stocked those Cutfoot fish down south and they don’t survive as well, so is it really cost effective? The answer from our study is a clear no.”

Whether anglers fishing lakes stocked with Lower Mississippi strain walleye will see change in their fishing success is yet unknown, but they will still realize a benefit because the same walleye fishery can be produced at a much lower cost, freeing funds for other important work. That is an efficiency win for the local area fisheries office and could help ensure that local anglers have plenty of walleye to target.

How Do They Do It? Though scientists have proven that Lower Mississippi strain walleye have fared well in southern Minnesota, the exact reasons remain a mystery. “There is this genetics and ecology concept of local adaptation and having localized better fitness and better survival,” says Miller. But the exact mechanisms that provide better fitness, survivorship, and reproduction rates for the Lower Mississippi strain are not well understood. Miller is trying to sort all that out.

“We’re doing DNA tests on these remnant walleye in southern Minnesota. And the persistence of the distinct strain, this local ancestry in the south … I merely detect it. My techniques tell me nothing about why those fish persisted. They just tell me that they did.” Miller hopes that the rapidly advancing field of genomics might soon provide some answers.

Keeping It Local. After Miller showed the Lower Mississippi strain’s dominant status in lakes in the Cannon River chain, DNR fisheries offices in the region began changing how they manage walleye in southern Minnesota.

Today, walleye egg hatching rates in southern Minnesota are higher for Lower Mississippi strain walleye than for Upper Mississippi walleye. That means hatcheries in the region have more capacity now that they no longer need as many eggs to offset those lower hatching rates among northern strain walleye. And with more fish hatchery capacity available, stocking of the local strain can expand within the watershed where walleye management and stocking are already underway. Lake Sarah has been the primary egg source for Lower Mississippi strain walleye, but four years ago, the Waterville fisheries office spawned walleye from Tetonka Lake and the Cannon River. And the Hinckley fisheries office began collecting walleye eggs from the Knife River above the St. Croix River in 2023.

While the Lower Mississippi strain has been cultured as a hatchery fish for only 10 years, the early returns have been impressive. It’s not a “super strain” of walleye, but it does well where it’s locally adapted.

The story of the Lower Mississippi strain has a clear takeaway for fisheries managers: Stock local and adhere to watershed boundaries. Conserving the many walleye strains across Minnesota will provide opportunities for genetic conservation in the future and ensure there are plenty of walleye where most anglers want them: on the ends of their lines.