It’s only fitting that the half-million-acre wilderness area running along the crest of the Sierra Nevada, a range John Muir called “the most beautiful of all the mountain chains,” bears the naturalist’s name. Designated as part of the landmark 1964 Wilderness Act, the John Muir Wilderness looks much like it did in the 1870s when Muir first set eyes on its glorious peaks.

The serenity and timeless beauty encountered when hiking the John Muir Trail make it one of the most heavily traveled by backpackers. Crystal-clear, glacier-fed lakes glisten on the mountaintops and still beckon anglers with their abundant trout.

Fishing on the banks of paradise might seem like the quintessential wilderness experience, but just below the surface, the opposite is true.

When Muir first trod into the High Sierra, the lakes he sipped tea beside were fishless. Carved by glaciers, these “isolated gems,” as he called them, are cut off from lower-elevation streams. Muir didn’t find fish in the lakes, but he did encounter ducks, water ouzels, many different beetles, “the larvae of innumerable insects” and “happy frogs.”

“How did the frogs get into them in the first place?” Muir wondered. “Perhaps their sticky spawn was carried in on the feet of ducks—else their progenitors must have made some exciting excursions through the woods and up the sides of the ca–ons.”

Today the presence of fish and the absence of frogs are a subtle yet significant change in the John Muir Wilderness, as well as other parts of the High Sierra. Though trout fishing is associated with the wilderness experience—backcountry guides promise an angler’s paradise—most of the trout are the spawn of semiannual air drops of hatchery fish, courtesy of the California Department of Fish and Game. And these alien predators have made the frogs a lot less happy.

Mountain yellow-legged frogs are falling prey to trout in the Sierra, and they’re not the only amphibians suffering the effects of fish stocking. Over the past century, wilderness lakes all across the West swarm with nonnative trout, mostly brook and rainbow. Although the lakes are protected by federal wilderness legislation, some of the native creatures living within them struggle for survival under a different set of rules.

Even back in the 1920s when the naturalist Joseph Grinnell explored the Sierra, he noted the mountain yellow-legged frog’s avoidance of fish. “It is a commonly repeated observation that frogs, in the tadpole form at least, do not occur in lakes which are stocked with trout,” Grinnell wrote in Animal Life in the Yosemite (coauthored with Tracy Irwin Storer). “The advent of fish in a lake sooner or later nearly or quite eliminates the frogs. It seems probable that the fish prey upon the tadpoles, so that few or none of the latter are able to reach the stage at which they transform.”

Seven decades later, this probability has been confirmed. During frequent forays into the Sierra backcountry, Roland Knapp, a University of California, Santa Barbara fish biologist noticed that “something was going on with mountain yellow-legged frogs,” which are endemic to the range. For one thing, there seemed to be a lot more of them in national parks than in national forests. Knapp suspected this might be related to the fact that the National Park Service stopped stocking trout during the 1970s, while the U.S. Forest Service allowed the practice to continue.

Following up on research conducted during the 1980s by David Bradford, an Environmental Protection Agency scientist, Knapp collaborated with Forest Service research scientist Kathleen Matthews on a wide-ranging study of mountain yellow-legged frogs. They surveyed more than 2,000 alpine lakes and ponds in both the John Muir Wilderness and Kings Canyon National Park. The sites are similar in almost every way—altitude, geology, vegetation, UV exposure, pollution. “The big difference between the two areas is historic and current stocking regimes,” Knapp says. In the John Muir Wilderness, about 90 percent of the lakes contain nonnative trout, but trout are found in only 50 percent of Kings Canyon’s lakes.

Knapp began to realize that the impact of stocking on mountain yellow-legged frogs was worse than he initially feared. “The picture got bleaker and bleaker,” he says. “The frogs are in a much more precarious state than we thought.”

The species is particularly vulnerable to introduced fish because it shares the same habitat requirements. Unlike other amphibians in the Sierra, the mountain yellow-legged frog spends multiple seasons as a tadpole. This restricts it to deeper lakes throughout the year, where it cannot escape from alien invaders.

The study by Knapp and Matthews found frogs in 35 percent of the lakes in the national park, but only in 5 percent of the lakes in the national forest. The mountain yellow-legged frog had disappeared from more than 90 percent of its historic range.

As populations disappear from each lake and basin, the chances for recolonization and recovery diminish. “They were the most common vertebrate up there,” says Matthews. “There are places where they’re just gone.”

She says new research shows the decline of the frogs is affecting other native creatures, such as mountain garter snakes, that depend on frogs as a food source. Because the high mountains present a fairly extreme environment, the terrain is species poor, she explains. “If you wipe out one group, it’s really going to affect the system, and it is.”

Hundreds of miles away in the Bighorn Crags of Idaho, graduate student David Pilliod has found a similar pattern. After surveying more than 100 lakes and ponds in the Frank ChurchÐRiver of No Return Wilderness, Pilliod helped chronicle the effects of trout stocking on the Columbia spotted frog and the long-toed salamander.

About 43 percent of the lakes and ponds in the Bighorn Crags contain trout, which the Idaho Department of Fish and Game began stocking in the high country in 1937. “Almost all larger, deeper lakes that can support fish currently have trout and continue to be stocked every three years with fingerling trout,” Pilliod says.

His research indicates that long-toed salamanders are being excluded from lakes with fish. Like mountain yellow-legged frogs, they require two to three years to complete metamorphosis at high altitudes, and so are particularly vulnerable to predation.

Columbia spotted frogs can breed in shallow ponds and the margins of lakes, which offer some protection from fish. But during the winter, they require deeper, ice-free waters. “Because most of these overwintering sites contain fish, predation on metamorphs during winter may limit the reproductive potential of many shallow, fishless breeding ponds,” Pilliod explains. “The only places where spotted frog populations are robust are in areas that still contain some deep, fishless lakes, but these habitats are rare.”

The change in the amount of fishless habitat available in the mountains has only recently come to the fore. In 1992, graduate student Peter Bahls estimated that more than 95 percent of the nearly 16,000 high-elevation lakes in the West had lacked fish historically. Yet state fish and game agencies saw little reason to discontinue stocking.

“Since the 1940’s,” Bahls wrote, “the use of aircraft to stock trout in high mountain lakes has facilitated the widespread and intensive introduction of non-native species throughout the mountain ranges of the western United States. However, the improvement in technology that has permitted fish introductions on a massive scale has far out-paced an understanding of the ecological consequence.”

Bahls found that Oregon had the most stocked lakes (76 percent), and Wyoming, Nevada and Montana had the fewest (20, 22 and 24 percent, respectively). He interviewed more than forty state fish and wildlife managers in eleven states and concluded that most saw their agency’s role as “maximizing a diversity of fishery recreation opportunities.”

Pilliod thinks many state fish and wildlife biologists want to protect ecosystems, but are pressured by anglers to continue stocking.

“There’s no doubt fish eat tadpoles and fish eat larval salamanders,” admits Ed Schriever, fish biologist for the Idaho Department of Fish and Game’s Clearwater Region. “Fish are the top-level predator.” However, he notes that Columbia spotted frogs and long-toed salamanders are widespread species. Unlike mountain yellow-legged frogs in California, they don’t rely on high mountain lakes exclusively. “At the landscape level, we have suitable habitat,” Schriever says.

Even so, Idaho Fish and Game has made some adjustments. Long ago it stopped stocking brook trout, a fish native to the eastern United States, which is particularly troublesome for western species. Instead, the department stocks native westslope cutthroat and rainbow trout. And the state of Idaho has stopped stocking in a number of lakes since Bahls completed his study. Schriever says the agency also is developing a statewide mountain lake management plan.

Even though many mountain lakes are protected in federal wilderness areas, state agencies have the authority to manage their fish and game resources. The Wilderness Act of 1964 states, “Nothing in this Act shall be construed as affecting the jurisdiction or responsibilities of the several States with respect to wildlife and fish in the national forests.” Forest Service policies permit aerial stocking of fish in wilderness if the program was established prior to wilderness designation.

When Forest Service managers want to discontinue stocking to protect native species or preserve wilderness values, state managers tend to defer to the interests of anglers and outfitters.

Pat Van Eimeren, a fish biologist on the Hungry Horse Ranger District in Kalispell, Montana, is working hard to convince Montana Fish, Wildlife and Parks to change its views. He’s managing a joint project in the Bob Marshall Wilderness to chemically treat a number of lakes with rotenone to kill stocked populations of rainbow and Yellowstone cutthroat trout, which are escaping into streams and inlets and hybridizing with native westslope cutthroat. Though the state agency plans to restock the lakes with native trout, Van Eimeren wants to leave some of the lakes fishless.

“If we can keep some of these lakes fishless, we can improve our limits-of-acceptable-change standards [in the wilderness],” he says.

Because a 1986 memorandum of understanding between state and federal wildlife agencies in Montana gives the state authority to manage wildlife on federal lands, Forest Service biologists must use persuasion to make the case for native ecosystems.

However, a new report by Peter Landres and Shannon Meyer of the Aldo Leopold Wilderness Research Institute, indicates that legal precedents give more leverage to federal managers. “Despite state claims to the contrary,” they write, “case law over the last century supports an active federal role in wildlife management. The Supreme Court has ruled that Congress may enact legislation governing wildlife on federal lands. When conflicting state law exists, the supremacy clause ensures that federal legislation will prevail.”

Though the Forest Service might be allowed legally to exercise more authority in wilderness lake management—as the National Park Service does—the agency often lacks the political will to do so. “We as an agency are not willing to push that,” Van Eimeren says. For now, he’ll try to work cooperatively with the states in hopes of making modest gains.

In California, however, the Department of Fish and Game has been forced to pick up the pace of reform. The mountain yellow-legged frog is likely to be listed under the Endangered Species Act, as a result of petitions by environmental groups. Knapp says the threat of listing lit a fire under state managers. “As soon as the listing package hit the ground, my phone was ringing off the hook,” he says.

In March, the department issued a rather cryptic press release, stating that it will continue stocking only if the following two criteria are met: “first, the stocking must fulfill a valid fishery management purpose; and second, there must be no significant environmental harm to native amphibian populations from stocking activities.”

Ed Pert, the department’s inland fisheries science adviser, says this means most high mountain lakes will not see stocking until the agency surveys them, looks at where frog populations still are found and assesses the stocked trout’s importance to recreation interests. He says, “We’re trying to make decisions based on sound scientific information.”

Matthews says the scientific evidence is overwhelming. “We really don’t need to be doing any more studies to determine if trout impact mountain yellow-legged frogs. We already know that they do,” she says. “Fish and Game is reluctant to do much because they’re afraid of the public response.”

Knapp says that state officials need not worry so much. Even without stocking, many trout populations would be self-sustaining. He points out that 80 percent of the formerly stocked lakes in Kings Canyon still support fisheries, even though the lakes haven’t been stocked in more than twenty years. In fact, fishing often improves in a lake that’s not inundated regularly by fingerlings. The trout get bigger and healthier.

The resistance to change, Knapp says, has less to do with fishing than with relinquishing old paradigms. “Fish and Game could walk away from their stocking airplane today,” he says, “and most anglers would never know the difference.”

Some fishing groups are even beginning to advocate an end to nonnative stocking. “Fishermen are definitely a house divided,” Steve Trafton, California policy coordinator for Trout Unlimited, says. “There are a lot of people out there who don’t mind going out and having their fishing experience. They catch hatchery trout, and they take those home and eat them.” But there are others, he says, “who don’t want to just accept a handout. They want to catch something wild.”

In the John Muir Wilderness, Knapp and others have begun to experiment with trout removal, and the results are promising. In one lake that had a very small population of mountain yellow-legged frogs, Knapp used gill nets to remove the fish. Within three years, the frog population went from twenty adults and twenty tadpoles to 120 adults and 1,400 tadpoles. The population was isolated, so this increase is the result of more successful reproduction, without fish eating all the progeny.

In another part of the wilderness, Curtis Milliron, a Fish and Game biologist, has been removing trout from two mountain lakes as part of an experiment designed to improve fisheries and restore habitat for native fauna. Since gill netting more than 9,000 nonnative trout in the lakes, Milliron says he’s seen the frog population jump from two to sixty-five in one season. The increase is due to migration from adjacent streams, not reproduction, which will likely increase the frog population quite a bit more, as long as the fish stay out.

If you put the results of such projects together, it’s easy to see how amphibians could be recovered in key areas. Of course, removing trout is expensive: it took a two-person crew from the Milliron’s Bishop, California, field office two years to do it. And gill netting fish, or chemically treating them, doesn’t really line up with John Muir’s idea of wilderness. But it might be the only way to restore some wilderness lakes to a more pristine condition.

“We wilderness advocates should be thanking our lucky stars that the solutions here are so straightforward—and will allow us to continue to provide recreation opportunities in wilderness,” Trafton says. “The potential is there to cut a win-win deal for both trout and frogs.”