Science in the Thorofare: Researching Cutthroat Trout in the Most Remote Area of the Lower 48

Editor’s Note: Award-Winning Scientists

A recent Fly Fisherman article played a role at the 57th annual meeting of the Montana Chapter of the American Fisheries Society held in Lewistown Feb. 20-23.

Dr. Chris Guy–whose research was part of this article from the Feb-Mar 2024 issue–used a large PDF from the story on screen as part of his presentation about cutthroat recovery efforts in Yellowstone Lake. His presentation was voted by attendees as the best at this year’s conference out of the 50-plus presentations that were given over three days.

At the conference, Dr. Todd Koel won the award for the 2024 Outstanding Fisheries Professional. Koel is Yellowstone National Park’s lead fisheries biologist, and his efforts to restore Yellowstone’s native cutthroat trout were the main subject of Weamer’s story.

 

August 15, 2022 began like many other days for Michelle Briggs in Yellowstone National Park. Her alarm rang at 5:15 A.M. She made coffee, and 45 minutes later she boarded the Northwester and departed from Bridge Bay Marina to begin her daily Montana State University dissertation work on Yellowstone Lake. On this chilly morning—all mornings on the lake are chilly due to its 7,733-foot elevation and frigid water temperatures that induce hypothermia in minutes—Briggs was checking the trap nets used to capture Yellowstone cutthroat trout for her study. Her boat stopped at the Pumice Point trap net, and her team began the work of measuring, tagging, and releasing the captured fish, including one beautiful but otherwise unremarkable native cutthroat specimen she identified with Floy tags numbered 4809.

The exact number of spawning-size Yellowstone cutthroats (from 18 to 24 inches) in Yellowstone Lake is currently unknown; Michelle Briggs is working to formulate an abundance estimation. But their numbers appear to be growing. Some of these fish begin life in tributaries that are accessible from nearby roadways, while others come from a remote, roadless area known as the Thorofare.

The primary reason there are any Yellowstone cutthroats here at all—after the lake was infected by nonnative lake trout 40 years ago—can be credited to the work directed by Yellowstone National Park’s Lead Fisheries Biologist Dr. Todd Koel. Koel is also leader of the Yellowstone Native Fish Conservation Program, and a member of Michelle Briggs’s graduate committee. He’s one of the world’s leading fisheries biologists, and a good friend who also happens to be my boss in my role as the coordinator of the Yellowstone Fly Fishing Volunteer Program.

Koel invited me to join him, Michelle Briggs, and a team of biologists, students, and horse wranglers to ride into the Thorofare region in late June 2023. We were going there to obtain cutthroat DNA, both as part of Briggs’s research work and also to see how the fish population is faring. The excursion was fascinating and beautiful but also dangerous, uncomfortable, and at times stressful. It was a 19th century Wild West adventure playing out in the 21st century.

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The Science

Yellowstone Lake is the largest high-elevation lake in North America. Before being invaded by lake trout, it was believed to be a near-impenetrable stronghold for Yellowstone cutthroats. The lake provides everything these fish need: an excellent food base; cold, clean water; and access to the vast roadless Thorofare region where virginal riverine pathways lead to clean, abundant spawning gravel.

Before the lake trout arrival, Yellowstone Lake held millions of cutthroats in all age classes. Then the lake trout ate 90% of the spawning population. The first sign of trouble occurred in 1994, when an angler reported catching a lake trout in Yellowstone Lake, but it is now believed that these invaders arrived there sometime in the 1980s. The 1990s and early 2000s were dire decades that witnessed meteoric lake trout expansion and the real possibility of total cutthroat extirpation.

Some outfitters ceased their late spring Thorofare trout-guiding operations because there were so few fish to catch that it wasn’t worth the effort it takes to get there. Many hardcore hikers packing fly rods stopped venturing to the region. A spawning migration that was equally as miraculous as the wildebeests’ journey through the Serengeti was nearly erased from the earth.

The Yellowstone cutthroat trout that Briggs catches in the lake’s trap nets receive two identical Floy T-bar anchor tags before they’re released. This allows individual fish to be studied and identified upon recapture. In 2022, before our Thorofare trip, Briggs and her team tagged 2,967 cutthroats. Floy tags are cylindrical-shaped monofilament identification devices that are implanted under the fish’s pterygiophores (dorsal fin supporting bones). These “spaghetti tags” are inserted with a tool that looks like a 1980s pricing gun from a retail clothing store. The tags have a plastic “T” on their ends, which holds them in place, and there are two numbers on them. The first is a four-digit numerical code that identifies the fish, where it was caught, and any other notations that the biologists include in their data. The second is a telephone number that anglers can use to report their catch. Dr. Koel receives those texts.

The daunting job of curtailing the lake trout in an effort to save what was left of the native cutthroat fishery also fell to Koel. He oversees a lake trout gillnetting program that has ramped up over the years to reach a massive scale. Koel and his team captured, tagged with transponders, and released some of the lake trout, hoping the fish would lead the biologists to their spawning areas, which were not easily identifiable in such a large body of water.

To reduce lake trout numbers before the fish grow large enough to eat cutthroats, Koel began using the gillnet-caught lake trout flesh to cover the lake trout eggs in their now identified spawning areas. As the dead lake trout bodies deteriorate, oxygen is depleted in the area and the eggs die. When the program ran out of lake trout remains, Dr. Koel devised a soy pellet substitute to use with the same effect. The hope remains that enough lake trout can be removed to allow the cutthroats to grow to spawning age and, as they’ve done for thousands of years, return to their natal tributaries, including those found in the Thorofare.

The Thorofare has long been considered one of the world’s greatest fly-fishing destinations. Before lake trout, huge numbers of spring-spawning Yellowstone cutthroats pushed into the region’s rivers and streams. But some of the lake’s fish do not travel that far. They spawn in other tributaries that require a much shorter migration. Michelle Briggs is trying to determine if there’s a biological reason for this. Are there unique genes within the lake’s Yellowstone cutthroat trout that create subgroup populations, which helps determine where they spawn? Or are the fish only traveling to spawn in the same places they hatched, simply because their ancestors spawned there?

Briggs’s research required that samples be collected from various locations in the Thorofare region’s Atlantic, Open, and Thorofare creeks as well as the Yellowstone River itself. DNA was previously obtained from Atlantic Creek during a previous expedition. That allowed us to focus on the remaining areas. We would need to capture at least 20 fish from each of Briggs’s specific sites to have enough data to validate the science. Each time a fish was caught, a small piece of its tail was clipped to provide DNA for the study. The samples will be compared to each other and also to DNA samples that Briggs has collected from Yellowstone Lake’s trapping program.

Watch a Video of the Trip Here: 

The Thorofare

The region received the name “Thorofare” from the many 19th century fur trappers who traveled through it. Today, it’s the most remote place in the Lower 48 states. There’s a small clearing on the trail to Thorofare Creek where a couple of tiny metal signs hanging from trees delineate the boundary for Yellowstone National Park. At this location, you’re at least 32 miles from a road in any direction. To get there, we traversed along Two Oceans Plateau, where one creek divides into two—Atlantic and Pacific—that flow in opposite directions to drain into the Atlantic and Pacific oceans.

We traveled around 130 miles on horseback and spent approximately 40 hours in the saddle during our trip. Our group of 10 people consisted of fisheries biologists and graduate students from Yellowstone National Park, Montana State University, Wyoming Game and Fish, and Susan Guy, who helped with our meal preparation and gave additional support. There was also one fly-fishing writer whose only purpose was to try to catch fish: That was me. Finally, there were four packers—Brodie, Donny, Jackson, and Cade—from the Triangle X Ranch, who loaded and wrangled our large horse and mule herd, set up camp, provided meals, and got us safely in and out of the Thorofare and the fishing spots we visited.

We left from the Turpin Meadow Trailhead on June 25, 2023, guided by two of the packers (the two others had gone ahead with the loaded mules to begin set-up) slowly advancing through some of North America’s most ruggedly beautiful country in Wyoming’s Teton Wilderness toward our intended campsite near the outlet of Bridger Lake, named for the renowned explorer Jim Bridger. It took a great deal of effort to get all of us, our gear and tents, fishing equipment, and camp kitchen into this remote area. Though our horses were wonderful on the trail, they were still horses, and that always means some level of unpredictability.

There were dangers and difficulties to overcome: One horse and rider fell into a quicksand-like hole, other horses bucked and kicked at each other while we were riding. Twice they spooked when grouse erupted from the conifers. Bear sign was abundant; mules broke free of their strings and rampaged into the wilderness, nearly strangling one of our party who was attempting to capture them.

There were other challenges. Would we be too early to find the fish? Would the rivers and streams be swollen with snowmelt, making them too dangerous to cross? Or could a poor fish return make them too isolated for us to find? It rained nearly every day, even days where the forecasters gave a zero percent chance of precipitation. There were lots of mosquitoes, but they weren’t nearly as bad as we feared, though someone mentioned during our stay that they seemed to be growing larger by the day.

After our first fishing day in the Thorofare, several group members—Michelle Briggs, Brian Ertel, Andi Puchany, and Jason Burkhardt—were dropped off at a river crossing where they backpacked into the Open Creek drainage and stayed in a spike camp to get the data there. The rest of us—Todd Koel, Katie Furey, Sadie Ainsworth, Chris and Susan Guy, and I—concentrated on the Yellowstone and Thorofare creek sections.

Some who read this may be concerned about the potential harm caused by fishing for Thorofare cutthroats during their spawning period. But you shouldn’t worry about that, for a few reasons. First, this trip was for science. We need to be able to better understand the Yellowstone Lake cutthroat fishery to help ensure its survival. Catch-and-release fly fishing is much less invasive than capturing the fish through electroshocking or the use of nets. You must capture the specimens you wish to study.

Second, the timing is important. Most of these fish spawn during high flows when much of the Thorofare is inaccessible or unfishable for anglers. I only witnessed a few pairs of actively spawning fish among the hundreds I saw while I was there. Third, this is a very difficult place for anglers to reach and a great deal of the spawning water is very lightly fished, or most likely unfished, due to its remoteness. Formal outfitter licensing and the lack of good, available campsites greatly limits the number of anglers who can stay in the Thorofare to fish. This place is not similar to the average cutthroat fishery in Yellowstone National Park, which sees large numbers of fishermen, so the necessary cutthroat spawning protections there are not needed in the Thorofare.

The Fishing

This wasn’t an ordinary fishing trip. After riding ten hours on horseback to reach our camp, those of us who remained in camp rode again, each morning, from one and a half to three hours to our fishing destination for the day. But getting to the water was only half the problem. From the time we disembarked from our horses and tied them up, we had only three hours to fish before we needed to begin the three-hour ride back to camp. That’s three hours to wade into water we’d never seen before, find the fish in rivers and streams that have almost no resident trout populations (just because the water looked great didn’t mean it was great for fishing), catch 20 fish and record the data, pack our science and angling gear, get back on our horses, and begin the ride back to camp.

So while the fish and scenery were spectacular, these weren’t serene, contemplative days on the water. This was urgent fishing where failure mattered more than just a sore ego. We did see a few fish rising for dry flies, and I spent a couple minutes on Thorofare Creek trying to catch one before the gravity of our mission reemerged in my mind and I returned to nymphing. It would have been great to spend more time trying to coax these cutthroat giants to the surface. But this was a numbers game. We would sometimes bypass fishing areas where we could see only one or two fish. Trying to catch fish in areas that held few of them would take too much time. We only had five fishing days to collect our samples. The clock was ticking.

If you’ve fished Great Lakes steelhead runs, you already have a basic understanding of how to fish the Thorofare waters. This is predominantly sight fishing where we could see the cutthroat holding or moving in pools and gravel-bottomed runs a couple feet deep. Most of the time, the fish weren’t especially difficult to catch once we found them. They ate Egg Sucking Leeches, Flashback Pheasant-tail and Hare’s-ear nymphs, Perdigons, and various styles of egg patterns—the same stuff Great Lakes steelhead eat. We fished the eggs and nymphs tied to 9-foot 3X leaders, under indicators, with nontoxic split-shot above them. We used shorter and heavier leaders for streamers. The most important tactic was using enough weight to get the flies to the trout’s level. If the flies weren’t on the bottom, the fish seldom moved to eat them. We watched this all occur in the pristine clear water.

We encountered our initial Thorofare cutthroat minutes after we arrived at the Yellowstone River on our first fishing day. Koel and I climbed down quickly from our horses, and in our cowboy boots, hopped across a small, shallow stream channel. “Do you see anything?” Koel asked me. I didn’t. We walked along the cobbles, peering into the river when Sadie Ainsworth announced, “Here’s one!” It was dead, killed by a predator, most likely by a raptor as the talon marks suggested, and left on the bank. But we knew the fish were there, and this one was fresh enough that DNA could be extracted. Fish number one was in the books.

I began fishing with two egg patterns, and that was the most effective rig for catching Thorofare trout. I did this on the Yellowstone River for the first two days with varying degrees of success. On day three we decided to move to Thorofare Creek, and that’s when something amazing occurred. I could see the dark forms of cutthroat trout in the water before me. My indicator twitched, and I lifted my rod tip to feel the surging connection between angler and fish. I brought the trout into the shallows and gently pulled it into my net when I heard one of our team members exclaim, “The fish is tagged!” There was tremendous excitement in our group as the first tagged Yellowstone Lake cutthroat was caught in the Thorofare. There were only 2,967 of them in all of Yellowstone Lake, and they could have migrated anywhere. I looked at the tag: number 4809. It was the fish that Michelle Briggs tagged on that chilly morning of August 15. I caught it approximately 40 miles from the Pumice Point trap net where she tagged it.

The trip’s final fish was appropriately caught by Briggs in the Yellowstone River, just outside our camp. It was a magnificent hen that ate a black streamer, and I quickly saw its tags as I jumped into the river to net it. It wore the number 2299, from another Pumice Point trap net on July 15, 2022. A little over two weeks shy of a year from the first time Briggs touched the fish, she released it again so it could complete its work replenishing one of the West’s most iconic native fish species. Its capture meant that we had secured all the fish and data we needed; our mission had also been completed. We had an evening to celebrate before the early, pre-light, morning work of tearing down camp and beginning the long ride home.

As we traveled out of the Thorofare, we encountered small groups of hikers, two and three at a time, many with rod tubes protruding from their packs as they trudged into the wilderness. There were also larger groups on horseback, most likely pushing toward the same area around Bridger Lake where we camped. Anglers whose ages ranged from teenagers to well past retirement were slowly pushing, slogging along flooded trails through mosquito-infested, willow-lined marshes, headed toward the promise of the return of one of the world’s greatest native fish migrations. Word is leaking out of the Thorofare—the trout and the fishing have returned.

The parade of anglers reminded me of the line of cars advancing toward the cornfield baseball diamond at the end of the movie Field of Dreams. In that movie, Kevin Costner’s character, Ray Kinsella, hears a heavenly voice that whispers, “If you build it, he will come,” instructing him to build a baseball diamond where miracles occur. Dr. Koel and the amazing team of fisheries biologists, graduate students, techs, commercial fishermen, and volunteers who work with and for him are, against great odds, rebuilding the Thorofare’s native Yellowstone cutthroat fishery. It’s one of the world’s natural wonders. It’s a miracle, and you should come.

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Paul Weamer is the author of Favorite Flies for Yellowstone National Park (Stackpole Books, 2022) and Dry Fly Strategies (Stackpole Books, 2021). He is a program coordinator with the Institute on Ecosystems at Montana State University and runs the Yellowstone Fly Fishing Volunteer Program. He lives in Paradise Valley, Montana.