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The Rio Grand cutthroat trout has dwindled in its native habitat. A multi-agency effort to restore it still can inspire anger and concern. (Provided by Colorado Fish and Wildlife)

On a beautiful early September day, Ken Gierhart hiked a trail familiar since boyhood to Music Pass in the Sangre de Cristo mountains above Westcliffe. As he dropped off the saddle toward the Sand Creek lakes, he noticed people heading the opposite direction with fishing poles.

“How’s the fishing?” he asked one woman.

“They’re all dead,” she replied, saying nothing more as she passed.

Puzzled, Gierhart came upon another woman heading away from the lakes and tried his question again.

“There is no fishing,” she said. “They’re all dead.”

This time, the angler paused to explain that Colorado Parks and Wildlife, according to signs posted in the area, had used a chemical called rotenone to kill all the fish in the lakes and Sand Creek, which meanders south down the mountain before veering west to eventually disappear, after 13 miles, into the depths of the Great Sand Dunes. 

The project is part of a long-planned strategy to restore the native Rio Grande cutthroat trout to waters where its numbers have dwindled toward the edge of extinction.

The Rio Grand cutthroat trout has dwindled in its native habitat. A multi-agency effort to restore it still can inspire anger and concern. (Provided by Colorado Fish and Wildlife)

Increasingly scarce in a dwindling native range and hybridized with other species like non-native cutthroats, which had been stocked alongside it many years ago, the Rio Grande cutthroat eventually will be reintroduced to the mountain lakes and streams where it once thrived. But the process can be disconcerting — especially to an unsuspecting hiker like Gierhart.

It wasn’t until he got closer to Lower Sand Creek Lake that he saw the informational signs for himself. Then he headed toward the upper lake, following the trail that crosses the creek several times along the way. He said piles of dead earthworms filled seemingly every crevice in the rocks. And then it got worse. 

“It was horrifying at that level to see what had been done to the lake,” Gierhart said. “When I got to the lake I saw fish belly-up, carcasses on the bank where animals or birds had pulled them out.”

Gierhart, a 54-year-old wholesale tree grower, hadn’t heard anything about the fish management plan, and he stewed all the way back to his home in Westcliffe. There, he fired up his Facebook account and vented in a post that estimated “thousands” of dead fish and that attracted nearly 100 comments, most expressing concern over an undertaking they, too, seemed unaware of.

“I”ve always been preservation conscious,” Gierhart said, still steamed a couple weeks later, “but to see aquatic life dead like that, I started thinking about the watershed, the lasting effects, side effects.”

The rant and its response caught the attention of CPW officials, who expressed frustration over response to a broad regional project that has been years in the making and which framed its intent in a compact signed in 2003 — and renewed in 2013 by six federal entities, state agencies in Colorado and New Mexico and three American Indian tribal agencies. The agreement also received non-signatory support from two Trout Unlimited groups.

The Sand Creek drainage was officially listed in a 2013 strategy document.

In 2019, meetings on both the Westcliffe and Alamosa sides of the mountain yielded no opposition — other than concern over the temporary loss of fishing — and little public comment. The project moved ahead, though a year later than originally scheduled due to a late fish spawn.

“It’s something we need to do,” said John Alves, the Durango-based senior aquatic biologist for CPW’s Southwest Region. “With only 11% of its historic range left, the Rio Grande cutthroat trout is always susceptible to petitions to list it as endangered, and also to extrication if there are events like fire. It’s a constant process for us.”

Joe Lewandowski, spokesman for CPW’s Southwest Region, which includes the Sand Creek drainage, notes that the state agency has done similar projects before and will do more of them throughout Colorado. 

“We don’t get a great deal of pleasure having to poison a stream, but it is necessary to restore native species,” he said in an email to The Colorado Sun. “This has been done in waters to restore the Rio Grande, greenback and the Colorado River cutthroat; and these projects will continue.

“We know people are not happy to see dead fish, and it is confusing. It’s very difficult — often impossible — to explain to the general public why we have to do these projects.”

The intersection of history, science and politics of wildlife management can be complex. And while in this case the ultimate goal — to restore the Rio Grande cutthroat to its native range — is mostly a shared interest, the path to achieving it can be challenging.

After the 2003 conservation agreement, federal and state authorities started doing reconnaissance in 2004 to determine if the drainage could be restored. Geography that essentially isolated water flow, and therefore fish migration, proved fortuitous.

“It’s an ideal situation in a lot of regards, because it’s a closed system,” said Fred Bunch, chief of resources management for the Great Sand Dunes National Park and Preserve, which takes in the Sand Creek drainage. “The creeks have their headwaters high in the Sangres, they flow into those lakes and the lakes flow out to the dunes. Thirty-four square miles of sand is a pretty substantial fish barrier.” 

Sand Creek flows from its headwaters high in the Sangre de Cristo mountains to the Great Sand Dunes, where it disappears underground. (Provided by Colorado Fish and Wildlife)

Bunch points to several reasons why reintroduction of the Rio Grande cutthroat looms important. First, there’s federal policy that favors native species in national parks and preserves. Another has to do with the essential characteristics of a wilderness area. A third is for preservation of the species.

“This is an ideal opportunity to restore 13 miles of habitat for the Rio Grande cutthroat trout,” he said.

The stakeholders who signed the conservation agreement meet annually to discuss the status of its efforts. The key thing, Bunch said, is to prevent the listing of the Rio Grande cutthroat as an endangered species and ensure it has robust habitat.

And that’s where politics can come in.

The Center for Biological Diversity, a nonprofit organization, claims roots in the fear that government authority alone will not always protect flora and fauna when powerful business interests can exert political leverage. (The timber industry was its founders’ nemesis.) Now, it contests threats to biodiversity on a range of levels, from climate change to encroachment of off-road vehicles.

The group has petitioned multiple times to place the Rio Grande cutthroat trout on the endangered species list, including one case that’s still pending an appeal.

From the standpoint of state wildlife managers like Alves, who shares the group’s desire to see the native species rebound, the fish’s presence on the list represents another potential layer of bureaucracy that state workers on the ground would have to contend with.

“Once a species is listed by the U.S. Fish and Wildlife Service, local agencies don’t make decisions,” he said. “They’re made by the federal government. For years, since the late ‘90s, there have been petitions to list the Rio Grande cutthroat trout. (The Center for Biological Diversity) sees listing as a way to get timber and mining off public lands.”

That is true, said Noah Greenwald, the center’s Portland, Oregon-based endangered species director.

“Those things present a real threat to their habitat and to the species, so we want to make sure those things are done in a careful way or there’s avoidance of trout habitat or, to the extent that there’s damage, there’s mitigation — which is what the Endangered Species Act requires.”

Aside from territorial concerns stemming from listing the species, both the center and the state agree on some key issues. The center supports and applauds the effort to repopulate the Sand Creek drainage with the native fish. But Greenwald also claims that his organization’s petitions to list the Rio Grande trout “spurred the state to take action to conserve them more than they were before.” 

“We haven’t succeeded in putting them on the protected list, but we’ve pressured the state to do more for them, which is a benefit for the species,” he said. “They’ve done a tremendous amount of surveys and used staffing resources in an effort to avoid listing them. We don’t think that’s the right tradeoff. It makes more sense to list them and work for recovery.”

The center doesn’t even have problems with the kill-to-restock method, or the rotenone compound used to achieve it.

Greenwald calls the CPW a “credible messenger” with regard to the safety of rotenone.

“We don’t love having to use poisons,” he said. “But there’s been a lot of work done on this issue, and there are not other effective means. As chemicals go, rotenone is pretty specific to fish. … We definitely think it needs to be done carefully and we don’t relish the thought of poison being used. But it’s the only way.”

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Although the battle over listing the fish persists, all sides celebrate the ideas that in the case of the Sand Creek drainage, the area could become a refugium for the species, where the fish could naturally multiply and be used as a source for future stocking or restoration if some other habitat experiences problems — say, from wildfire. 

“So we’re doing it for many things,” Bunch said. “One is the philosophy of land managers, but there’s also the species itself. Also there’s a recreational piece. It’s a great situation where a hiker can backpack in and catch native fish. That’s a pretty great situation to have, and that’s what we’re shooting for.”

From the start, the effort to restore the species has been a multipartner project, including federal, state and county agencies and even private groups like Trout Unlimited. Some of the early upfront money came from the National Park Service but functionally, the reintroduction process is a CPW project done in a national preserve. Cost of a helicopter, boats and other equipment is covered mostly by the state.

This year, phase one of the process got underway. But before fish and wildlife authorities took any action, they needed to know exactly how many different species they were dealing with in those waters that stretch from the Sand Creek lakes to the sand dunes.

And that’s where science played a big role.

John Wood founded Pisces Molecular more than 20 years ago, just a few years before efforts began in earnest to restore the Rio Grande cutthroat trout. 

Though it has just four people on staff, the Boulder-based biotech lab has clients all over the world, not to mention right in its backyard. Wood’s lab has worked with Colorado Parks and Wildlife on multiple different fish projects, including when in 2007, in conjunction with University of Colorado post-doc Jessica Metcalf, it discovered that CPW’s stock of supposed greenback cutthroat trout — which happens to be Colorado’s state fish — were actually Colorado River cutthroat trout.

How do scientists figure out what species are in a waterway? One method is simply catching a sample of fish, clipping off the tiniest bits of their fins, and sending the material to a lab for DNA sequencing. Wood notes that can be laborious and difficult to get an accurate representation of the species makeup of a waterway. 

John Wood, owner and founder of Pisces Molecular, discusses how the lab can find genetic markers of different fish species in a tiny sample of water. (Lucy Haggard, The Colorado Sun)

The other option is environmental DNA testing. Just as humans regularly shed skin, hair, saliva and other sources of DNA, so do fish. Field researchers can collect a sample of water, filter out all the bits from the water, and send the gunked-up, DNA-laden filter to the lab for testing. These results will indicate the presence of species upstream of where the sample was taken.

Regardless of the type of sample, once it gets to the lab, Wood’s team uses polymerase chain reactions, also known as PCR, to check for species-specific genetic markers. For reference, this is the same kind of procedure used in the SARS-CoV-2 coronavirus test; Wood says it’s become “a very sexy technique” since the patent on PCR expired in the 2000s. And it’s remarkably precise; if one-tenth of a drop of a fish’s DNA solution were mixed into an Olympic-sized swimming pool, Wood said, “we would pick it up.” 

“The only technical field that is changing as fast as computers is molecular genetics, so the sort of techniques that we use now are incredibly more sophisticated than when I was in graduate school, and I find that really fun,” Wood said.

Theoretically, this could happen all in the field, but Wood says that it requires “a lot of coordination, because you don’t keep wild fish outside of their water body for very long.” More often, it’s an iterative process between the lab and the wildlife managers — testing the waterway, analyzing the results for the percent purity for individual fish or the population at large, then removing or restocking fish as needed, and doing it all over again. 

Though Pisces was not directly involved with last month’s rotenone treatment, it has generally worked on identifying species in the Upper Sand Creek Lake drainage. In 2015, Wood’s team found evidence that the drainage had native Rio Grande cutthroat trout that were hybridizing with other subspecies, including Yellowstone cutthroat, greenback cutthroat and Colorado River cutthroat.

Wood called CPW’s attitude on restoring native species “enlightened,” especially when compared to previous practices. Much of the 20th century was spent stocking the state’s waterways with outside fish such as rainbow trout, which are especially susceptible to whirling disease; when that struck the state in the 1990s, the rainbow trout population quickly spread it to other fish species, including native cutthroats. And this wasn’t just in one or two rivers; in the process of moving fish around from waterway to waterway, stocking and other efforts inadvertently introduced the disease to 15 of the 17 hydrographic drainages in the state.

John Wood, owner and founder of Pisces Molecular, shows a DNA Away solution designed to rid a surface of any remnants of DNA. This is a critical tool in his lab, which deals primarily with analyzing the genomes of a variety of different animals. (Lucy Haggard, The Colorado Sun)

Along Sand Creek, the CPW found ponds on private property that harbored the parasites that transmit whirling disease. But the ponds were removed with stimulus funds during the Great Recession. Since they qualified as gravel pits, they could be remediated as abandoned mines. The whirling disease went away and the reintroduction plans moved forward.

“Humans, when we mess with ecology, we generally make a mess,” Wood said. “So it’s probably philosophically better to do less interventions and strive to maintain what’s there than presume that we’re smarter than Mother Nature.”

That said, it’s not like leaving the river to rebound on its own would work. Part of it has to do with the different life cycles of fish species: brook trout, for example, spawn in the fall, giving them a full six months’ head start to grow before cutthroats spawn in the spring. And while rainbow trout spawn in the spring, like cutthroats, Wood notes that the jury’s still out as to the impact of the two species interbreeding freely.

In other words: humans made this mess, and only humans can clean it up.

“We now know more about genetics, we can discern finer level details, we have a longer history of how our attempts to alter ecologies tend not to work very well, so let’s see if we can remediate some of the damage that we’ve done,” Wood said. 

In June, weeks before implementation of the first phase of the Rio Grande cutthroat project began, the CPW declared a fish “emergency public salvage” in the Sand Creek drainage. That tactic, which allows anglers to catch an unlimited number of fish from the waterways, has been used more times this summer, for a variety of reasons, than in the past 10 years.

On this occasion, the CPW wanted to let anglers help make best use of the fish before the chemical rotenone was administered to kill any that remained.

Alves, of the CPW’s Southwest Region, noted that removing the bag limit seemed to be a particularly effective strategy in the lakes.

“Get enough anglers out there,” he said, “they do a pretty good job.”

The rest is left to rotenone, a plant-based compound effective only on gill-breathing organisms — primarily fish and insects. The CPW workers secured the necessary permissions and trained to use it. During the first week of September, they began the process in the two high mountain lakes and the creeks below — up to a point where waterfalls along Sand Creek provide a natural barrier to fish migration. Phase 2 of the operation will involve clearing Sand Creek from below the waterfalls to the Great Sand Dunes.

A helicopter from the Colorado Division of Fire Protection and Control had been busy fighting wildfires, but eventually was freed up to transport boats, motors, pumps and the 5-gallon buckets of rotenone itself to the lakes. Workers mixed the chemical with water.  It was administered from a boat throughout the lake, in volumes dictated by the water’s depth. The mixture shaded the water slightly white, a change that diminishes within several hours.

Workers use a drip process to administer rotenone to moving water in a stream. The chemical, which carries an organic green dye to mark its path, kills all fish in preparation to reintroduce the native Rio Grande cutthroat trout. (Provided by Colorado Parks and Wildlife)

To apply rotenone to streams, workers spread out drips that added the rotenone/water solution to the flow every 15 seconds. A four-hour drip produced the desired solution throughout the streams.

The chemical works quickly. At one of the drip stations, Alves noticed that as soon as the organic green dye marker reached him from a drip point upstream, fish started dying. Workers also sprayed backwaters where fish might be lurking.

Rotenone, though extremely toxic to fish and some insects, is “harmless to man and all warmblooded vertebrates,” according to the journal Nature. Alves notes that it breaks down quickly in streams, but in lakes, at a water temperature of 50 degrees, takes about 28 days to decompose.

Then, the waiting begins. The dead fish decompose and, if all goes perfectly, the waterways will be clear for stocking. First, the water is tested — environmental DNA sampling comes in handy here — to make sure no fish survived that could taint the reintroduction of the native Rio Grande.

“You’ve got to wait and see,”Alves said. “We’ll do a lot of sampling, electrofishing in the streams, gill netting in the lakes, probably use environmental DNA, and test to see if there are genetic markers. We use that as a confirming tool.”

If any fish remain, CPW will come back and repeat the process.

“If there’s zero live fish,” Alves said, “we’ll start to restock in the fall.”

The view from Music Pass in the Sand Creek drainage, where a multi-agency effort is unfolding to restore the Rio Grande cutthroat trout. (Provided by Colorado Parks and Wildlife)

Typically, CPW uses airplanes to stock the high mountain lakes. Workers on foot or on horseback, and sometimes by helicopter, stock the streams. By stocking fish in a variety of age groups, managers can hasten the turnaround.

The Sand Creek drainage, with its hiking trails and beautiful vistas, is a highly used area, Alves said. Though remote, it’s only about an hour-and-a-half hike in from the trail head. What he wants people to understand is that what the CPW is doing “is definitely the right thing.” Yes, the fish are all gone — but that’s only temporary.

“As soon as we can, we’ll put in Rio Grande cutthroat trout, really a pretty fish, growing to the same size they’re used to catching, a 15- or 16-inch fish,” he said. “So they’re temporarily losing their opportunity, but it’ll come back. I predict within five years, they’ll see really good cutthroat trout in the lakes.”

Lucy Haggard was a TRENDS Reporting Fellow from August 2020 to May 2021 with The Colorado Sun. Email: Twitter: @lucy_haggard

Kevin Simpson is a co-founder of The Colorado Sun and a general assignment writer and editor. He also oversees the Sun’s literary feature, SunLit, and the site’s cartoonists. A St. Louis native and graduate of the University of Missouri’s...