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Did a legendary trout really ride the rails from California to Missouri?

Scientists use DNA to solve genetic puzzles in waters around the world. But in Crane Creek, the mystery got deeper.

By Matt Crossman

Crane Creek flows right to left in front of me, spring-fed and uncommonly clear and cool, slicing through trees that line both banks. Shallow and thin, it runs 25 miles through thick forests in southwest Missouri, at some points no farther across than a fishing pole is long. You could walk across it and never get your knees wet.

I arrive here on a Tuesday with my friend Aaron, two fishing poles, and the hope that in two days here we will see (never mind catch) a mysterious fish that has fascinated anglers for generations — one of the beautiful rainbow trout that hide under the ledges and logs in the water.

They are fireworks with fins: Their green freckles, pink stripe, and silver body pop far more vividly than rainbow trout found in other Missouri streams. These rainbows are a coveted trophy in the fly-fishing community, not just because of their beauty, but because of their wildness, how difficult it is to get one on the line, and how hard they fight once you do.

Also: their backstory. You won’t catch another fish with an ancestral heritage like this one. According to legend, the rainbow trout in Crane Creek represent a genetically pure strain of McCloud River redband trout, originally from California and now thriving in this hard-to-reach spot and only a few other places on Earth. To catch one is to come face to face with a mystery: Is the legend true? Are the trout pure? What am I supposed to call these fish?

This is a question not just for the people who fish in Crane Creek, but for every scientist working to name every living thing on Earth — and discovering, with technology’s help, that there are more and more things to name.

Naming is one of the fundamental powers of language: All parents labor over what to name their children. We name stars in the heavens and cars in our driveways and storms in our skies. Until something has a name, it’s as if we don’t know what it is. To give it a name is to define it, understand it, place it in context of human knowledge.

So I’m frustrated by these fish in Crane Creek: Every time I get close to pinning down the legend and thus verifying their name, the story jumps off my hook and swims away. My efforts to name them take me from the locomotives of 1800s America to advanced DNA technology that has opened up an ocean’s worth of knowledge, and right back to the side of Crane Creek.

This story begins in the years after the Civil War, when fish provided an important source of protein in many Americans’ diets — so much so that fish populations were depleted. Instead of curtailing fishing, the newly created U.S. Fish Commission and many state governments restocked rivers with fish from other areas, according to the book From Northern California to the Ozarks of Missouri: How Trout Came to the Show-Me State by Rik Hafer, an avid fisher and economics professor at Lindenwood University in St. Charles, Missouri.

While humans migrated west, the fish migrated east. Among the fish chosen for relocation were McCloud River redband rainbow trout, who were native to their namesake river in California. In the late 1800s, Hafer writes, Livingston Stone, a Harvard graduate and former preacher turned fish biologist, sent McCloud River redband rainbow trout across the country in milk jugs. Once they arrived, fishery officials sprinkled them into waterways in a process one expert called “Johnny Troutseed.”

Until something has a name, it’s as if we don’t know what it is.

If that fish story wasn’t good enough on its own, a legend about how the trout got into Crane Creek has emerged. A train carrying the fish broke down at Crane Creek, the legend goes, and the fish were thrown in from a bridge, because they otherwise would have died.

It is a story too good to check, but Francis Skalicky, a media specialist at the Missouri Department of Conservation, did. He spent hours in 2019 digging through newspapers and official documents, hoping to find evidence it was true. It’s not. His investigation came up as empty as a baitless cast.

The trout in Crane Creek eventually became self-sustaining — a rare phenomenon, because the habitat in most Missouri creeks is not hospitable to fish from California. An attempt to create a salmon run from Missouri to the Gulf of Mexico failed, and most other trout populations in Missouri are stocked frequently because they can’t reproduce enough in natural environments.

A United Nations report two years ago found that up to 1 million plant and animal species are in danger of becoming extinct, more than at any time in human history. In far too many cases, human intervention has destroyed habitats and the animals that live there. With the trout in Crane Creek, almost the opposite has happened. We gave them a new home, and they have, apparently, thrived there.

The “apparently” is part of the mystery, because no one knows for sure whether the Crane Creek trout are truly the descendants of the McCloud fish. There is only anecdotal evidence, and it’s the kind of information that draws people to Crane Creek: These fish are a challenge.

When fish raised in hatcheries — which is most other trout in Missouri — see water disturbed by human feet, they think it’s feeding time. That’s a Pavlovian response, built from their time “growing up” in ponds where humans provided their food. Not the trout in Crane Creek. If you splash, they dash. They disappear into their hidey-holes if they even think they see you. Whatever bait you bring to catch them has to look and behave exactly like what they normally eat, or they won’t bite.

In other words, they are only tricked by authenticity.

Just as collectors traffic in rare finds, anglers and scientists alike are drawn to fish who live in only one place or very few places. There is, it turns out, a robust network of biologists who travel the world, answering the same question I’m trying to answer in Crane Creek: “What is that?”

Bernie Kuhajda, a biologist at the Tennessee Aquarium Conservation Institute, has studied a fish that lives in a cave in northern Alabama and nowhere else in the world. Now he’s searching for evidence of a species of sturgeon that lives only in the Syr Darya, a river in Kazakhstan. Casey Dillman, the curator of fishes, amphibians and reptiles at Cornell University, is studying “new” eels found in Brazil. One of them produces an electric discharge of 860 volts, or roughly 60 times the power that a car battery puts out when the car is running.

The pace of these discoveries — and the resulting need for new names — has sped up significantly over the past 20 years, as we’ve discovered and refined the ability to track what’s known as environmental DNA, or eDNA.

Like jewelry thieves who covered their fingers in flour, all living creatures shed scales, excrement or other pieces that contain DNA. To uncover that evidence via eDNA is relatively quick, easy and non-invasive.

Using a device that looks like a leaf blower, scientists suck water out of a river or lake into a device strapped to their backs. The eDNA machine (for lack of a better name to call it) extracts DNA from the water sample and then purifies it. The final step involves analyzing DNA found in the water to see if it matches what scientists thought they would find.

“You don’t expect in the 21st century to have a discovery of this level. You think we know everything there is to know in the streams and rivers that have been explored.”

Brooke Penaluna, research fish biologist for the U.S. Forest Service

eDNA can show not only what fish are present, but how many. Sometimes the eDNA confirms that the scientists found what they were looking for. Sometimes eDNA has uncovered secrets below the surface. In 2019, a team of scientists studying Fall Creek, a tributary of the Alsea River in Oregon, found evidence of fish that had never been known before.

“For days it was like, oh my gosh, this is awesome,” says Brooke Penaluna, a research fish biologist for the U.S. Forest Service, who was part of the team that detected the new species. “You don’t expect in the 21st century to have a discovery of this level. You think we know everything there is to know in the streams and rivers that have been well-fished and explored.”

Penaluna and her co-authors of the study dubbed one of these new-to-science fish “prickly-like sculpin” because it looks similar to prickly sculpin. But the difference is obvious when you hold one. A prickly sculpin earns its name. A prickly-like sculpin feels smooth.

My desire to know and understand the rainbow trout in Crane Creek is a small example of what is writ large at Northeastern University’s Ocean Genome Legacy Center in Nahant, Massachusetts. The OGL, which works to preserve the biological diversity of the sea, has collected a genome bank of 28,000 DNA samples from oceans around the world, with more added regularly.

Even with that, there’s a sense that we have merely stuck our faces nose-deep into a bottomless pool. Every fact I uncover about the trout in Crane Creek opens more questions. Imagine that sense of discovery, only with an ocean full of creatures instead of one trout in one creek.

“If you find 10 new questions for every answer that you get, that means the more you work, the less you know,” says biologist Dan Distel, the center’s director. “We’re expanding our knowledge of our ignorance much faster than we’re expanding our knowledge.”

As evidence, I offer a recent headline on the center’s website: “A newly discovered clam eats rock, and no one knows why.” The story under that headline reports that these rock-eating clams poop sand. That prompts so many questions I don’t even know where to begin. But at least I know that rock-eating, sand-pooping clam’s name: Lithoredo abatanica, which translates loosely as “rock shipworm from the Abatan River.”

Our ability to track more aquatic DNA hasn’t just expanded our understanding of the underwater world and given us new things to name. It also has several real-world applications. In Oregon, eDNA has shown that fish swim farther upstream than scientists previously thought. In Brazil, eDNA found a frog previously believed to have been extinct since 1968. Similar discoveries could lead to new habitat protections.

Some even hope eDNA can solve enduring mysteries in the depths. In 2019, researchers ran water from Scotland’s Loch Ness through an eDNA machine in search of DNA that would reveal the identity of the Loch Ness Monster. They didn’t find monster DNA, but they discovered eel DNA in every sample, so much that they think some eels might be big enough to explain decades of Nessie sightings.

The trout in Crane Creek aren’t nearly as famous as Nessie, but their story has fueled a little corner of the tourism industry. In Missouri, the legend is passed down through the fishing community, described on fishing websites and generally treated like any secret fishing hole: You want to share it, but not so much that a ton of people show up to catch them.

When I talk to state wildlife officials, they seem to delight in the origin theory — and for years, some have tried to confirm the legend. When Dillman worked for the Missouri Department of Conservation in 2006, he worked on a study that conducted DNA tests on trout in streams across the state, and found that trout within Crane Creek had unique DNA compared to others from elsewhere in the state. It was a tantalizing hint, but far from proof, that those trout are actually descended from the McCloud River redband rainbow trout of the 1880s.         

Trout Unlimited, a conservation organization, is planning a similar study to compare wild Missouri trout to each other and to existing populations in the source river. The study is not designed to specifically answer the question of the Crane Creek rainbow trout’s origin. But it could find an answer in a roundabout way.

“If we can identify that multiple isolated redband populations in Missouri share a genetic affinity that is distinct from stocked populations, that would indicate that those populations are direct descendants of those original stockings,” says Ed Heist, a professor of zoology and associate director of the Center for Fisheries, Aquaculture, & Aquatic Sciences at Southern Illinois University Carbondale, who will work on the proposed study.

There are a lot of ifs embedded in that. We might never know the full truth. Early in my quest to learn the origin of this trout, I thought I would reach a denouement via DNA testing. I would catch a fish, clip a fin, send it off for testing and uncover a match to the McCloud River redband rainbow trout. The only problem with that: Nobody has McCloud River redband rainbow trout DNA to compare it to. The stretch of the McCloud River that originally provided the fish has since been restocked with different trout, which diluted the gene pool. The pure strain is no longer pure.

Before my first daughter was born, my wife and I spent weeks kicking around names. My wife insisted we wait to see her before making a final decision, to see if she looked appropriately like the name we had chosen. When she was born, I was stunned by how much she looked like my dad, and I wondered if we were going to have the only little girl in the world named Richard.

My naïve hope is that by catching a trout in Crane Creek and laying eyes on it, I will similarly have some idea of what to call these fish. The descriptions — vivid colors on adults, specific patterns on younger ones — seem specific enough. But for most of the two days Aaron and I spend on Crane Creek, the trout flash and disappear in my peripheral vision, there and gone in a blink, like flickering candles doused by sudden wind. Those views are all too fleeting.

When Aaron says, “I got one,” I run my eyes down his line and below the water’s surface, and I am rewarded with my first extended view of this fish that has so captured my imagination. I’m disappointed at first. It looks muted and gray, far from the amazing technicolor dreamtrout I’ve read so much about. But soon I realize that’s because the water has dulled its color, like a flashlight covered by a tissue.

Suddenly it leaps out of the water, a green, pink, and silver lightning bolt, striving to be free from the hook. I howl in surprise, shattering the silence of Wire Road Conservation Area. The fish crashes the surface, performs another world-class high jump, and splashes back into the water.

Aaron’s shoulders remain square, his eyes intent. The fish jumps again and flops like it’s hooked to electrodes. Aaron holds the line tight enough to keep the hook set, but not so tight the line breaks. More than five minutes later, the fish tires. Aaron scoops it into his net.

Aaron shows me the fish. I study its freckles and pink stripe. Maybe I have fish goggles on, but its sharp colors jump out of the net; it is more vivid than any rainbow I’ve caught. It’s as beautiful as its reputation and far bigger: 18 inches from nose to tail, a trophy by any standard, and an all-timer considering the place. It’s at least a foot bigger than any other fish we see on this trip.

But as much as I’d like to say that seeing it gave me proof that the Crane Creek trout trace back to California, that’s not true. There’s a scientific term for two creatures that look exactly alike but are actually genetically different species: cryptic speciation. Back in Oregon, the prickly-like sculpin looks so much like a prickly sculpin that fish biologists can’t see the difference. Only DNA reveals it. Then there’s the two-barred flasher butterfly, which even to experts’ eyes looks like one butterfly. But DNA has shown there are at least three distinct species of two-barred flashers. Who’s to say what Aaron’s fish is?

I can’t, at least not until I know the full truth, after which I will move on to figuring out why the hell those clams eat rocks.

After a few fruitless hours in Crane Creek on our first day there, I wander back to the car. There I spend 20 minutes talking to a fisherman whose name I didn’t catch, but I’ll name him Zen, because he radiated calm after spending an afternoon knee deep in the creek.

An Air Force veteran, Zen told me he bought into a farm near Crane Creek in part so he could fish it. He got skunked the first four or five times he waded into it with a fly rod, but he has pulled as many as two dozen rainbows out of it on his best days, including a couple of big ones.

Zen loves these rainbow trout, whatever they are, for their wildness, their bright colors, their relentless fights. He knows the legend of their origin and has heard the tales of their purity. He doesn’t know what to believe and is perfectly content letting the mystery remain just that. The fish are beautiful and fun to catch. A DNA study won’t change that. Who cares about the rest? “Just call them Crane Creek trout,” he said.

I guess that’s good enough for now. But I want certainty — to know that I can go to a small corner of Missouri to catch a wild fish from California, and to imagine that our knowledge will eventually overtake our ignorance. That’d be a fantastic fish story.

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Matt Crossman is a writer based in St. Louis. He has written for Sporting News, Sports Illustrated, The Athletic, Men's Health, and The Washington Post.

Illustration by Angela Pyne


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