Great Lakes fish thought extinct for decades rediscovered – in an unexpected place

It's a fish story with a big, unexpected plot twist.

A native Great Lakes whitefish thought extinct for nearly 40 years has been rediscovered by scientists – in the wrong Great Lake.

The Shortnose Cisco was once abundant on the Great Lakes, but overfishing and invasive species such as sea lamprey, zebra and quagga mussels, alewives and round gobies dwindled the fish's numbers and disrupted its habitat. A 2016 Great Lakes Fishery Commission report on ciscoes of the Great Lakes described the Shortnose's historic waters as Great Lakes Michigan, Huron and Ontario.

"Despite more recent sampling using appropriate gear at suitable locations and depths, (the Shortnose Cisco) was last recorded in Lake Ontario in 1964, Lake Michigan in 1982, and Lake Huron in 1985 and is currently believed to be extinct," the report stated.

'Nobody was expecting us to find this'

Not so fast. In 2022, Shortnose Cisco were discovered in scientists' fish surveys on Lake Superior – a lake in which scientists did not believe the fish lived.

U.S. Geological Survey scientists have declined to discuss the Shortnose Cisco find with the Detroit Free Press, part of the USA TODAY Network, citing an agency policy of waiting until peer-reviewed research is published on the topic. But they've discussed it among themselves and their fellow fishery scientists, including in emails obtained by the Free Press.

The Shortnose Cisco "had not been seen" before by any modern scientists on Lake Superior, Owen Gorman, a research fisheries biologist with USGS's Great Lakes Science Center in Ann Arbor, Michigan, said during a panel presentation earlier this year before the Lake Superior Technical Committee, a scientific body helping inform the Great Lakes Fishery Commission.

"It was assumed to be extinct for nearly 40 years on the Great Lakes, so nobody was expecting us to find this," he said. "But apparently, there it is."

The Shortnose Cisco belongs to a class of fish known as coregonines, including as many as 11 species of cisco and whitefish native to the Great Lakes. According to the Fishery Commission, coregonines were abundant in each lake a century ago, occupying diverse habitats – rivers, bays and the deepest parts of the lakes. Some species were key prey for lake trout and burbot, supporting a Great Lakes fishery now valued at $7 billion annually.

Among the coregonines, different species of ciscoes declined dramatically between the 1920s and 1970s because of overfishing, invasive species and habitat loss. At least two species were considered extinct – including the just-rediscovered Shortnose – and several other species no longer appear in several lakes. The whitefish species have been more resilient, but have been undergoing their own declines in the past 20 years, fishery commission officials said.

USGS, working with state and provincial fisheries managers, has undertaken efforts to better understand the various coregonine species and how they live. Using trawler nets along the lake bottom and gill nets farther up the water column, researchers on Lake Superior have been catching coregonines over the past several years, studying both their morphology – the shapes, measurements and characteristics of their bodies – and utilizing advancements in genetics research to better understand just what cisco species are in the lake.

It was during those missions, in July 2022, that three young Shortnose Cisco were identified among the fish collected in trawl nets near the Keweenaw Peninsula.

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In the emails obtained by the Free Press through a U.S. Freedom of Information Act request, scientists expressed surprise at the discovery.

"The fabled Lake Superior Shortnose collected July 12-13, 2022," USGS fishery biologist Mark Vinson emailed to USGS colleagues on Feb. 14, 2023, attaching a photo of three small, silvery fish in labeled plastic bags.

"Wow! Age-0 Shortnose cisco caught!!!!" replied USGS fishery biologist David "Bo" Bunnell.

Further study on Lake Superior found even more Shortnose Cisco, this time adults.

An early fishery researcher is vindicated

Between 2006 and 2021, USGS collected 602 adult fish, from which they could extract genetic material, from around Lake Superior. Morphological characteristics of the fish were measured – the size of their eyes; aspects of their gill rakers, cartilaginous appendages fish use to capture tiny invertebrates; fin lengths, jaw shapes, and more. Simultaneously but separately, researchers also tested the genetics of the caught fish. Their goal: to see if they could find any clusters of particular species in the Lake Superior coregonines, or just an undifferentiated mix of unidentifiable fish.

Both the body characteristics studies and the genetic testing revealed four distinct coregonine species among the Lake Superior fish: Cisco, Bloater, Kiyi and, most surprisingly, Shortnose. The two studies matched the findings of one another "to the 97th percentile," Gorman told fellow fisheries scientists at the Lake Superior Technical Committee.

The work provided some vindication to one of the forefathers of coregonine research, Walter Koeltz. A whitefish researcher at the University of Michigan's Institute for Fisheries Research in the 1920s, Koeltz published the seminal "Coregonid Fishes of the Great Lakes" in 1929, based on his observations.

"Anyone who is a student of ciscoes becomes a student of Koeltz," Gorman said. "Koeltz's book on the Great Lakes coregonid fishes is kind of like a bible; you can talk about chapter and verse. You have to go back over and over to this work."

But among the coregonids Koeltz identified on Lake Superior was the Shortnose Cisco. When subsequent researchers, over decades, did not make similar findings, it was presumed Koeltz got it wrong.

The confirmed genetic and morphologic findings of Shortnose Cisco, some 100 years after Koeltz said they were there, means, "in a sense, we have rediscovered Shortnose Cisco in Lake Superior," Gorman said.

Restoring ciscoes points to Great Lakes health

Restoring native cisco species to the Great Lakes may help turn the tide on a Great Lakes ecosystem disrupted over generations by significant invasive species, changing nutrient dynamics and other stresses, said Randall Claramunt, fisheries chief for the Michigan Department of Natural Resources.

The DNR since 2018 has collected gametes – fertilized eggs – from a remaining population of wild cisco near Drummond Island in far northern Lake Huron, raised the fish at a U.S. Fish and Wildlife Service hatchery on the Jordan River in Antrim County, and then released 1 million young fish in the spring and fall into Saginaw Bay – a place where the cisco long ago thrived but were wiped out.

"We know if you catch a cisco in Saginaw Bay, it's likely from the stocking," Claramunt said.

"To see survival has been huge, because people thought, there's a lot of walleye in Saginaw Bay; there are a lot of predators on Lake Huron; and there are not a lot of prey fish."

But DNR officials have seen young, stocked cisco fish surviving, reaching adulthood, finding habitat.

"We are waiting for the last piece, which is: Are they successfully reproducing?" Claramunt said. "The next couple of years will be key to being able to detect successful reproduction."

The DNR considered a similar assist to cisco populations on the Lake Michigan side, he said. But in a surprise, the populations there have adapted to alewives and other invasive species and habitat changes and have begun a recovery on their own.

"They have just learned to adapt their life history to coexist with alewife," Claramunt said.

Fisheries managers around the Great Lakes have undertaken similar coregonine restoration efforts. In New York, state and federal researchers are attempting to restore bloater, using eggs collected from northern Lake Michigan. Next year, cisco will also be experimentally reintroduced in the New York waters of Lake Erie, where the fish was once abundant but has since been wiped out.

While some anglers grumble that they would like to see more effort placed on prized sports fish over ciscoes, Claramunt said the effort complements the Great Lakes' vital sports fishery.

"The Great Lakes will never go back to what they were 200 years ago," he said. "After 60 or 70 years of trying to control sea lamprey, we control them every year, but we still haven't eradicated them, along with the other invasive species.

"The idea is these native fish are very flexible; they occupy all of these different habitats and these different life strategies. Bringing them back now strategically will provide more stability for the Great Lakes in the future, and more resilience to future threats."

Contact Keith Matheny: kmatheny@freepress.com.

This article originally appeared on Detroit Free Press: 'Extinct' Great Lakes Shortnose Cisco fish discovered in Lake Superior