Saving North America’s Rarest Trout

By Dan Hottle
November 14, 2016

It is believed that the loss of the Paiute cutthroat trout, North America’s rarest and most imperiled trout, from its historic range of an 11-mile stretch of rugged, eastern Sierra wilderness stream began as far back as the early 1900s when William Howard Taft was president and the newly-minted Ford Model T was puttering around on 22 cents per gallon gasoline.

Today, efforts led by the California Department of Fish and Wildlife and its partners, the U.S. Fish and Wildlife Service and U.S. Forest Service, to restore the Paiute cutthroat trout (Oncorhynchus clarkii seleniris) to its native home waters remain every bit as challenging for the team as they were back in 1967 when the species was first listed as endangered, six years before the passage of the Endangered Species Act (ESA), and as when it was later upgraded as threatened under the ESA in 1975.

“The Paiute cutthroat is the rarest and yet most recoverable trout in the U.S. It has evolved with a sparkling, iridescent purplish coloration that provides it with camouflage in the higher elevation streams where it lives,” said CDFW fish biologist William Somer. “But in restoring this beautiful trout we are challenged with the impacts of climate change, along with the California drought, which have left the source populations severely reduced in numbers.”

The Paiute cutthroat trout, one of 14 cutthroat trout subspecies, is physically and genetically similar to the much larger Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) that has inhabited the region as early as the Pleistocene. But when the two species diverged perhaps 10,000 years ago following the drying of Lake Lahontan, the Paiutes were isolated to an 11.1-mile section of Silver King Creek and its three associated tributaries between Llewellyn Falls and Silver King Canyon within what is now the Carson-Iceberg Wilderness, Humboldt-Toyaibe National Forest, in Alpine County, California.

Silver King Creek is a tributary of the East Fork Carson River, which drains into the Lahontan Basin. Like most all other western salmonid species, Paiutes need cool, flowing, well-oxygenated waters throughout all their life stages. Adult fish are not known to be migratory and prefer stream pool habitat in low-gradient meadows with undercut or overhanging banks and abundant riparian vegetation.

Pools are also important rearing habitats for juveniles and act as refuge areas during the long harsh winters.

Paiute cutthroat trout have long suffered from a combination of threats including habitat fragmentation, unregulated angling and overgrazing, climate change and wildfire. However, the primary reason for their extirpation from Silver King Creek was the introduction of non-native trout into the watershed.

Over the past 100 years at least four other species of trout have been introduced into the Paiute’s waters including Lahontan cutthroat, rainbow, California golden and brook trout.

Hybridization between Paiutes and non-native trout was first documented below Llewellyn Falls in the mid-1920s, and despite decades worth of concerted measures to eradicate them, non-native trout still occupy the Paiute’s historic range.

Fortunately, the desire to conserve this unique fish began as early as 1912 when a roaming Basque sheepherder named Joe Juansaras transported Paiutes above the falls in a bucket, perhaps establishing the first, most genetically “pure” source population outside of the historic range that is now monitored and maintained for modern restoration efforts. The progeny of those early day transplants were later introduced into several other surrounding lakes and streams, but many were not successful.

The most recent data show that about 800 source Paiutes now occupy about 23.5 miles of stream in formerly fishless areas of the Silver King Creek drainage and in four out-of-basin watersheds above fish passage barriers. Studies suggest that to ensure long-term persistence of the species, a population of around 2,500 fish would need to be established in at least 5.8 miles of habitat.

“Paiute cutthroat are the only trout that currently only occurs outside of its historic habitat, and we have the unique and rare challenge to restore this fish back to 100 percent of its native range,” said Chad Mellison, USFWS fish biologist. “Achieving that level of restoration for an imperiled fish species is a conservation biologist’s dream because there’s usually some portion of historic habitat that has degraded past the point of recovery or simply ceased to exist at all due to human or other factors.”

“Fortunately for us, the remoteness of Silver King combined with decades-worth of forward-looking conservation work by the State of California and U.S. Forest Service to preserve and protect the stream from overfishing and grazing has provided us this incredible opportunity,” he said.

The first federal recovery plan governing these efforts was formulated in 1985. Subsequent Paiute range-wide habitat assessments were conducted by the state of California in 1992 and 2002, but at the time those assessments did not address the ESA listing status for the species.

A revised recovery plan was adopted in 2004, and an initial five-year review was completed in 2008. A second five-year review was published in 2013. The recovery plan addressed the Paiute’s listing status under the ESA’s rigorous, five-factor analysis, which determines threats to a species including: habitat damage or destruction; commercial, recreational or scientific overutilization; disease and predation; adequacy of regulatory mechanisms and other human factors.

The analysis revealed that over the years human impacts no longer pose a considerable threat to the species, specifically because of the state’s regulations on angling and the implementation of federally-managed objectives for – or outright elimination of -- livestock grazing in the region. Disease and predation are also not believed to be significant threats, and existing regulatory mechanisms have been deemed adequate. What remains are habitat fragmentation, the impacts of drought, hydrologic changes, wildfire and other climate change factors and the muddying of the Paiute’s genetics through hybridization.

It will only be after all non-native trout species are completely eliminated from Silver King Creek and a viable population of Paiutes are returned and maintained under a long-term conservation plan that the species can be considered for de-listing under the ESA. The Paiute Cutthroat Trout Restoration Project outlined in the recovery plan details specific actions such as stream treatments that have been completed to accomplish those two goals.

Although mechanical methods to remove non-natives from the stream have been used in the past, the most common method of removal involves the use of chemical treatments, specifically a fish poison called rotenone. The team was stalled in 2010 due to legal pressures concerning the safety of deploying rotenone in the stream system, and the project’s compliance with Wilderness Act protections was called into question.

A California court, however, found no basis to support the dispute in 2013 and agencies were allowed to continue implementing the project over the next two years.

State and federal partners have worked in concert since the 1960s to preserve the Paiute’s unique genetic characteristics in the outlying source population, which will eventually be used to restock them back into Silver King Creek. But preserving those traits has proven to be just as slippery as the spotless, pastel colored trout itself.

Paiute cutthroat have limited genetic variability due to their isolation, and there is no documented population that currently possesses all of the genetic alleles -- variant forms of a specific gene -- known to the species. Therefore, all surviving populations are considered as a single management unit. All eventual re-stocking efforts will involve using large numbers of fish from multiple donor populations with as much genetic variation as possible to help minimize the loss of diversity and the effects of inbreeding in the species.

Simply gathering population estimates for the Paiutes can be difficult due to the remote location of the source population streams along with the wildly varying characteristics of the streams themselves. Fish biologists have traditionally used fly rod depletion methods, snorkeling surveys and triple-pass depletion electrofishing, or “e-fishing,” since the 1960s to count Paiutes, and estimates can fluctuate significantly due to a number of contributing environmental factors.

E-fishing can be done by boat, but on small streams it involves carrying a heavy backpack attached to a long pole and length of wire cord containing an anode and a cathode. The apparatus is placed in the water and any fish caught between the two electrical points receives a small shock sufficient to stun it long enough that it can be handled for monitoring and returned to the water.

An emerging new technology called Environmental DNA, or eDNA, testing is also frequently being used to sample for the presence of non-native trout. Environmental DNA is genetic material given off by all organisms into their environment, whether it is skin cells, mucus, sperm, eggs or feces. This DNA can persist in streams for weeks. Biologists collect water samples that are tested in a lab to determine if any non-natives remain in a stream segment after chemical treatments have been applied.

Moving forward, eDNA technology will continue to be a valuable tool that the team will use to determine whether their efforts to remove non-native trout removal have been successful. They cannot afford to be overly-eager and take chances by restocking Paiutes too early. After all, according to biologists, one rainbow in the Paiute’s historic range is one too many.

In the meantime, the partners will continue to implement the restoration project, develop a genetics management plan, re-evaluate habitat conditions and work to improve population estimates so that more can be known about the species.

When America’s rarest trout is finally returned to its historic home in Silver King Creek, it probably won’t care much about who is president, or that automobiles can now run on electricity.

Dan Hottle is the public affairs officer for the Reno Fish and Wildlife Office.