Trout Changes

Clint Muhlfeld, a researcher with UM’s Flathead Lake Biological Station, studies trout hybridization. (Photo by Noah Clayton)

Trailblazing Study Guides Actions to Save Montana’s State Fish

By Deborah Richie

Montana’s state fish idles in a crystalline tributary of the North Fork Flathead River. Golden fins catch the sunlight. A trace of a red-colored slash on the lower jaw identifies this foot-long trout. It’s a westslope cutthroat and an angler’s dream to catch, but a trout that’s getting more difficult to find. UM researchers recently discovered a rapid acceleration of hybridizing between native westslope cutthroat and non-native rainbow trout that is linked to climate change.

Within this particular cutthroat is a tiny radio telemetry tag that’s giving Clint Muhlfeld and other fishery researchers a wealth of information. Before inserting the tag, they also clipped a piece of fin the size of a pencil eraser to send to the UM genetics lab. Capturing, tagging and releasing trout to study continues to inform scientists in a quest to save westslope cutthroat.

The rangy and youthful Muhlfeld is equally at home in hip waders or conducting interviews with NBC and NPR reporters who have covered the significant research.

“For the first time, we found a strong relationship between climatic change in both space and time with the advance of invasive hybridization in nature,” says Muhlfeld, who is an assistant research professor at UM’s Flathead Lake Biological Station. He also serves as a research ecologist with the U.S. Geological Survey’s Northern Rocky Mountain Science Center stationed in Glacier National Park.

The study, based on 30 years of research, demonstrates that warming streams and lower spring flows during that time period contributed to rainbow trout expanding their range across the vast Flathead River system into havens for westslope cutthroat and then hybridizing with high rates of success. Rainbows tolerate the climate-induced changes better than cutthroats, and the conditions likely improved spawning success for rainbows, he said.

The findings appear in the article, “Invasive hybridization in a threatened species is accelerated by climate change,” published in Nature Climate Change. Muhlfeld is the lead author, with Ryan Kovach (UM), Leslie Jones (USGS), Robert Al-Chockhachy (USGS), Matthew Boyer (FWP), Winsor Lowe (UM), Gordon Luikart (UM) and Fred Allendorf (UM).

Most climate and wildlife studies look at current patterns of change but simply do not have the ability to go back in time to quantify what’s happened, Muhlfeld says. Fortunately, the 6-million-acre Flathead Basin contains a wealth of fishery genetic information that can be coupled with precise stream temperature and flow data. From 1978 to 2008, the rate of air temperature warming almost tripled in the Flathead Basin, leading to earlier spring runoff, periods of lower spring floods and flows (e.g., drought in the early 2000s) and both warmer and lesser summer flows. The streams that suffered the most from changes showed the highest increases in hybridized trout.

While experts have predicted climate change will lead to more invasive species crossbreeding with natives, this is the first study to give tangible evidence and is helping scientists understand how climate change influences evolutionary processes.

Allendorf, UM biology professor emeritus and another study co-author, is one of the world’s leading experts in fishery genetics. His early research with westslope cutthroat trout dates to the 1970s, when he was still a graduate student at the University of Washington. Then, there were only a few genetic markers to give clues as to whether a westslope cutthroat trout carried genes of a rainbow. Today, there are some 3,000 markers that give key information on how rainbow trout affect the fitness of westslope trout.

“Westslope cutthroats are in big trouble,” Allendorf says. “Hybridization is just so difficult. It’s like pouring black and white paint together to become gray, and there’s no going back to the original colors.”

Muhlfeld, who works closely with Allendorf and fellow geneticists Robb Leary and Gordon Luikart, is passionate about the importance of sharing and applying science to help solve the most challenging of problems. He first became aware of the hybrid threat as a fisheries research technician for Montana Fish, Wildlife and Parks out of Libby in 1994. Since then, he’s dedicated his academic studies and professional career to cracking the case of invasive species, habitat destruction and climate change in one of the most intact ecosystems remaining in North America, the Crown of the Continent/Glacier Park region.

Today, FWP managers rely on each scientific advance to preserve a pivotal part of Montana’s blue-ribbon trout fishing heritage that’s valued at $250 million annually. For example, certain radio-tagged westslope cutthroats that carry the genes of rainbows have led biologists straight to the hybrid swarms that are the sources of upstream invasion.

Since the mid-2000s, FWP started removing hybrids at these key locations. Their aim is to prevent them from migrating upriver to infect the last bastions of pure westslope cutthroats. The biologists transplant the hybrids to kids’ fishing ponds, so there’s a recreational benefit.

“The control efforts are promising, because the spread of hybridization is slowing,” Muhlfeld says. Those management actions especially are important, he adds, given predictions that climate warming will further increase rainbow and westslope cutthroat crossbreeding. Suppressing the source population offers managers a buffer for developing more tools to address the threat.

Historically, westslope cutthroat trout swam the cold, connected, complex and clean rivers of Montana west of the Continental Divide, as well as the upper Missouri and Hudson rivers. Of the 12 cutthroat species, the westslope range remains the largest in Montana. Genetically pure populations of cutthroat trout are known to inhabit less than 10 percent of their historical range. The fortresses lie in wilderness and roadless tributaries protected from the intrusions of invasive rainbows and habitat degradation. The native populations, however, are increasingly isolated from each other, and without genetic mixing their chances for long-term survival are dramatically lower.

Westslope cutthroat trout are threatened by encroaching rainbow trout, whose range has expanded with the effects of climate change. (Courtesy of Clint Muhlfeld)The problem is multifaceted. Rainbow trout introduced into the lower Flathead River system as far back as the 1800s have long hybridized with westslope cutthroat, mostly below Columbia Falls. As Allendorf notes, once a rainbow breeds with a westslope, you can’t go back to a native strain. What you’ve lost is the genetic vigor of a fish that’s supremely suited to the natural dynamic ecosystems of fire, flood and drought.

To understand how ideally configured these native fish are to their homes takes stepping back 12,000 years, Muhlfeld says. That’s about how long westslope trout in the Flathead Basin have navigated the extremes of fires, drought, flooding and small glacial periods. The origin of the westslope cutthroat lineage itself goes back 1 million to 2 million years.

Over time, westslope cutthroat have become perfectly tuned to thrive in a dynamic ecosystem. The trout lay their eggs in streambeds in late May up through early July, when the peak spring floods are ebbing to protect their redds (nests) from washing away and giving their young, called fry, the best chance of survival.

In contrast, rainbow trout that originally hailed from Pacific watersheds lack the innate savvy to lay their eggs at the best time. Instead, they spawn too early, from March through May. That means the big spring floods can come through and wash away their eggs and fry, limiting the ability of the rainbow offspring to pioneer the upper watersheds.

This natural barrier might explain why the 20 million rainbow trout planted in the lower Flathead River system from the late 1800s until the late 1960s did not eliminate the westslope cutthroats through crossbreeding.

“There were railroad cars designed just to carry fish that brought rainbow, brook and brown trout into Montana in the early 1900s,” Muhlfeld says. “What’s remarkable is that the Flathead River still remains a stronghold of connectivity and the full expression of their life history – with some fish staying in a stream their entire lives, others moving from streams to rivers and still others growing in lakes and returning to the streams they were born in, like inland salmon.”

However, the rainbow trout in the lower watershed were there “like a time bomb waiting to go off given the right environmental conditions,” he says.

The bomb has gone off. Resampling the same populations of hybrids existing in the late 1970s shows that, especially in the past 15 years, the crossed rainbow-westslopes are streaking as far as 50 miles upriver from their old homes with nothing to stop them. Even in the headwaters where all trout used to be natives, nearly half of those resampled are hybrids.

“There was a window of opportunity through which rainbow expanded massively in the system, irreversibly corrupting the native gene pools that are linked to the adaptive traits, which have allowed the cutthroat trout to adapt and persist to environmental change for thousands of years,” Muhlfeld says.

Across western North America, aquatic ecosystems are predicted to experience increasingly earlier snowmelt in spring, reduced late spring and summer flows, warmer and drier summers and increased water temperatures – all bad news for keeping hybridization at bay.

It sounds dire, yet Muhlfeld is an optimist and points especially to FWP’s promising efforts. First, the agency was forward-thinking in the late 1960s and stopped stocking rainbow trout. Soon after, they pursued the genetics for early detection of crossing between westslope and cutthroats. Then, FWP took action, even with some uncertainty, to slow the spread of hybrids.

“The Flathead is still recognized as a range-wide stronghold for cutthroat,” he says. “You can still catch beautiful cutthroat that move from lakes to rivers, and that’s the fishery that people are drawn to. It’s the last of the best, and worth all our efforts to save it.”

For more information email Muhlfeld at

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