Trout Rescue

A new hope for westslope cutthroat in Montana

In the Mission Mountain Range of Western Montana, Herrick Run flows in the shadow of Lindy Peak. The small, snow-bound stream tumbles down a series of steep drops into Lindbergh Lake and eventually the Swan River. But here above the lake is a population of stranded westslope cutthroat trout and the home of an important experiment aimed at saving them.

How the fish ended up here is unknown, since fish cannot make their way up the steep cascade. Somehow, the small populations in the creek as well as in nearby Meadow Lake and Bunyan Lake are hanging on. But stagnant population growth and a lack of genetic diversity leave the trout at risk of disappearing.

It’s the kind of situation Gordon Luikart, a conservation geneticist at the University of Montana, needs to develop to boost the population of fish through a process called genetic rescue. Above his desk in his office overlooking the shoreline at the Flathead Lake Biological Station are two large fish prints, one a bull trout, the other a cutthroat. As both a fisherman and biologist, these are two fish he cares about.

Across Montana and the West, there are thousands of small fish populations that have been isolated by shrinking habitats. Scientists until now have seen habitats disappear, as populations get thinner. There is now a movement to start actively helping the fish survive and restore them to new areas.

“Right now the mindset in salmonid fish at least, they home to their natal [birthing] streams and they are very locally adapted,” says Luikart. “You don’t dare move them.”

But that thinking may have to change as ecosystem changes place the fish in hotter water. Luikart is one of the scientists leading that charge.

Among the boulders of the trickling Herrick Run and the closed-in lakes are a few fish that otherwise might have been forgotten. To help the declining population, Luikart and his research team are testing the effectiveness of introducing small numbers of trout to enrich the genetic diversity of the isolated fish. Adding new fish genes into the population may help the entire population fight disease and perhaps to adapt more easily to changing conditions.

Westslope cutthroat trout reside on both sides of the Continental Divide from the Upper Missouri watershed to the Columbia River Basin. But the westslope’s range is shrinking as waters warm. They are estimated to occupy 10 percent of their historic range.

These trout have also struggled to compete with species like brook and rainbow trout that were introduced widely for sport fishing.

As a result, westslope were considered several times for listing under the Endangered Species Act and still remain a potential candidate for listing.

Further up the rutted road from Herrick Run is Bunyan Lake. The sky above the tiny lake swirls with snow and swath of fog hanging in the air in the nearing dark of a winter evening.

The lake, though quiet, is an active laboratory to gauge how effective introducing a less inbred fish into the population might be, thus enlarging its gene pool and increasing overall survival.

The researchers hope introducing new fish into the population will change the close relations, or “cousin problem,” for the remaining trout by injecting new blood into the stream.

In 2014 Luikart and his team collected eight trout from Herrick Run and crossbred them with westslope from a remote and genetically pure population in the South Fork of the Flathead River.

The breeding was done at the small Sekokini Springs hatchery, where biologist Matthew Boyer and Montana Fish Wildlife and Parks fisheries technicians work diligently to fertilize the eggs.

Amid the roar of rushing water from circulating pumps in fish rearing tanks, Luikart and his students from a summer conservation biology class watch the slicing and squeezing of each westslope to remove its eggs or sperm before combining the two into bowls. In a process that resembles a strange cooking show, the year-old fish, carried to the hatchery from distant mountain lakes are sacrificed for future generations of healthy fish. The team then carefully places the eggs in trays to develop for a few weeks.

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The hope is that, once released, the crossbred fish will restore healthy genetic diversity to Herrick Run and surrounding lakes. Boyer knows that if a small population can be helped this way there are other fish that will benefit as well. 

“East of the Divide, the cutthroat populations almost invariably are at very low levels of genetic variation,” Boyer says, “but what we need to know and this experiment will hopefully help validate or inform is where, when and how often do we need to have assisted migration and genetic rescue and then how do we quantify the results?”

With an excitement equal to that of his students, Luikart peeks at the tiny salmon-colored eggs that will eventually grow into fish in Herrick Run.

For the past two summers, scientists raised new batches of cross-bred fish and moved them into the stream.

The effects of introducing new genes over the last few years should be immediate, but so far the crossed fish they have introduced are elusive, and only a few have reappeared in follow-up surveys. But the researchers are confident that the population will improve as they continue the work. Over time, researchers believe, they will be able to recognize the different genetic traits of the introduced fish working their way into the populations naturally, and hopefully increasing the population size.

But they also know they need to be careful.

If they introduce a new population of fish too quickly, they may overwhelm the already localized population’s ability to adapt to the local temperature and environment. Done wrong, these introductions could easily erase good genes.

It’s a balancing act that Luikart has performed before. He first used genetic rescue to stabilize a population of Bighorn sheep at the National Bison Range in Moiese, Mont. The effort strengthened the herd and helped researchers understand how populations can be increased through introducing more diverse genes.

“We are darn good at moving fish around, in fact we are suffering from it.”

Fish, he finds, are a bit easier to deal with. Moving fish around the state is a far less onerous bureaucratic task, as long as there is little potential for further damage to an already imperiled fish. Plus, their work may help fishery managers in the entire westslope region.

On the western side of the Continental Divide, there is a focus on conserving and maintaining the populations, but east of the divide the situation is more dire and fish introductions like those at Herrick Run to increase the populations are needed.

The general range of westslope cutthroat trout.

Relocating any species can come with a cost; the same part of human nature that is trying to solve the problems of genetic diversity for the fish to Herrick Run is the same that caused the problems though initial alternation of the ecosystem, says Robb Leary, a fisheries geneticist for the Montana Fish, Wildlife and Parks.

“We are darn good at moving fish around,” he pauses and adds, “in fact we are suffering from it.” Rainbow trout and other fish in new locations are a product of once-thought positive introduction goals.

Warming streams can accelerate introduced species’ population growth. Rainbow trout that displace and hybridize with westslope cutthroat have a competitive advantage in warmer climates.

Luikart adds to this, “Go to a fish hatchery and see the fish that are swamping them out.” There is considerably more production in hatcheries to introduce rainbow trout than westslope trout.

Fisheries biologists can only try to correct past mistakes, while not making new ones, and maintain the populations that are surviving.

Leary says, “We are making the best decisions we can with the data we have,” much of the data on hybridization and health of populations in Montana is incomplete. But as new data comes in, Leary says he feels that even in western Montana the situation for cutthroat trout is dire, and immediate action is required.

Where native trout have been pushed to the cooler water, these tributaries are their last refuge.

Leary says, “Isolation is our friend and enemy.”

Researchers like Seth Smith are hoping to minimize the downside for those fish.

At the University of Montana’s Montana Conservation Genetics Lab, in the basement of a small research building in Missoula, Smith is using a household salad spinner to mix a chemical solution.

As he pulls a tray used in DNA testing out of the spinner, he gestures to the expensive, but broken, plate spinner labeled ‘MPL1000’ in the corner. The salad spinner labeled in marker ‘Roto-DNA’ with a skull and crossbones, rarely fails and does much the same job.

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Smith sits at the bench and goes through a series of dilutions lasting many cycles. It’s an exercise in repetition, pulling the bottles of chemical solution from the shelf above the bench and filling the pipette lines with additional chemicals in different dilutions.

He has assembled 96 DNA samples from fin clips or flesh of different fish. Each chip is set into a clear plastic tray are combined with 96 wells of chemical solutions designed to identify different genes, looking for variations in the genetic code.

“It’s like baking 96 times 96 different cakes at once,” says Smith as he looks at the messy lab bench for a calculator and corrects himself, “9216 cakes.”

Each “cake” is a tiny square that looks like a transparent black computer chip on a clear plastic tray. The chip has wells on the side to hold genetic samples and assays that will be combined through tiny, almost invisible tubes in the center. Essentially, once each of the genetic samples is in the chip a photograph is taken that will test for the presence of differing alleles, or versions of gene.

A large blue box opens suddenly, looking and sounding like a CD drive, waits for the tray with samples to be inserted.

This is when skin cells, hair, or dung become a set of data that a geneticist can use to infer what cannot be seen or measured through observation. Once the sample enters what Smith calls the “magic box” you can start to see the invisible fluids come to life.

A few hours later the chip emerges from the box.

The power of the SNP test or Single-nucleotide polymorphism, representing the change of a single molecule in all of the fish genome, is its speed.

Once the tests for thousands of SNP variations are run, the data generated can be instantly viewed and processed. Smith looks over the mountain of numbers in a spreadsheet, but the numbers are combinations of only ones and twos.

‘1’ represents westslope and ‘2’ represents rainbow trout genes in an individual fish. He is looking at a simple test to measure the amount of hybridization between the differing species.

Smith measures the inbred level and hybridization level in these small populations to prepare for introducing a more genetically diverse westslope trout this summer. The fish above Herrick Run have remained 99 percent pure based on genetic testing, which is a positive for the fish.

Often, barriers such as a steep cascade or diversion dams can both help and hinder a population, shielding them from hybridization but also cutting them off from broader gene pool on the other side of an obstacle. Even extremely genetically pure fish populations are walled off intentionally to preserve their genetics by biologists.

Luikart soon hopes to start genetic rescue of westslope populations east of the Continental Divide with the same techniques used in Herrick Run. They also want to gauge the difference between crossing a genetically healthy Missouri River-based trout versus a Columbia River fish, species that have several thousand years of genetic divergence, to gauge which rescuer is more effective. But that might mean moving fish over evolutionary boundaries that would otherwise take ice ages and geologic timescales to cross. Now science can accomplish this with only a few years of hatchery breeding.

When the snow clears, the field crew will go up to Herrick Run to continue genetic testing on the isolated populations of westslope. The introduction of new genes into the small stream may mean a stronger population, but a problem can come from mixing in populations that are not locally adapted to the stream conditions, such as temperature and habitat. Maintaining natural local adaptation that can take thousands of reproductive cycles is tantamount.

Although it’s difficult to reverse the effects of humans altering natural adaptation, it might be the only way to maintain a struggling population.

Still, Luikart believes the technique to correct inbreeding could serve as a model for reviving westslope in areas where they continue to struggle, like across Eastern Montana, by gently introducing new genes that should ensure stronger survival traits into the already imminent future of climate change in Montana’s streams.

“We have to do this slowly and carefully,” says Luikart, without that measure they could do more harm than good.

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Part 2: New Invaders, New Solutions

© KEN RAND 2016 - images and text COPYRIGHTED unless otherwise noted. All rights reserved. (Published May 2016)