From summer steelhead secrets to decoding Dean River Chinook, Dr. Tasha Thompson previews cool new research from our science team.

It’s a blistering August afternoon in the hills above Oregon’s North Umpqua River. Dr. Tasha Thompson’s family is out getting ice cream. She’s at home on her laptop, sitting as close as possible to the A/C unit. 

Dr. Thompson, a world-renowned salmon geneticist with Wild Salmon Center, has updates to share—and in the world of conservation science, they’re pretty much as cool as it gets.

“The tools that we’re developing are helping us unlock some fascinating insights about salmon,” she says. “But whether you’re looking at brook trout, or tigers, or spider monkeys, you can also use these tools.”

“The tools that we’re developing are helping us unlock some fascinating insights about salmon. But whether you’re looking at brook trout, or tigers, or spider monkeys, you can also use these tools.”

Wild Salmon Center Salmon Geneticist Dr. Tasha Thompson

These advances come courtesy of three soon-to-be-published studies coauthored by Dr. Thompson. One of these groundbreaking new studies suggests future possibilities for spring Chinook across their range. Another presents a new genetic approach designed to improve salmon analysis—but that’s equally applicable to any species. And the third, focused tightly on North Umpqua summer steelhead, could help this world-famous wild run regain its long-term competitive advantage. 

Below, we ask Dr. Thompson to share early takeaways from this new research.

Wild Salmon Center: For several years, you’ve been mapping wild Chinook salmon genetics across the North Pacific. Where are we with that project?

Dr. Tasha Thompson: We’ve completed data collection, now that we have final sample sets in from places like the Taku and Karluk. Now, we’re incorporating all the data into our wider analysis. We’re also refining our main case study, which centers on Dean River Chinook run timing and demographics, and also presents our new genetic method. Because this new method is so cool and potentially useful on its own, we’ve already submitted that as a separate paper for publication. For the larger analysis on range-wide Chinook genetics, we aim to submit that study for publication within the next couple of months.

I should note that even as we wait for the first paper to go through peer review, it is already out in the world and publicly available on a preprint server. We thought these tools could help other conservation genetics researchers. And indeed, we’ve already been contacted by folks who want to know more—an East Coast researcher, for example, working on brook trout conservation.

“We thought these tools could help other conservation genetics researchers. And indeed, we’ve already been contacted by folks who want to know more.”

Wild Salmon Center Salmon Geneticist Dr. Tasha Thompson

Why do we need a range-wide genetic map for Chinook salmon?

Dr. Thompson: Chinook salmon are perhaps the most culturally and commercially prized of all salmon species. They range from the Central Valley in California to Alaska and across to Kamchatka, and each of these runs is adapted to unique environments. The problem is that many of those environments are changing rapidly, due to climate change and other factors.

Genetics help us see the adaptive potential that already exists within these populations. A population might carry a genetic variation that could help it adapt to new conditions. Some studies on adaptive variation already exist, but most to date have focused on southern Chinook runs. If we want to focus on overall strategies for Chinook conservation, however, we need big picture data.

There are a lot of benefits to a publicly-available, range-wide genomic dataset like this. It can dramatically reduce the cost of applying discoveries made in one population to other parts of the range. And it makes it possible to test things that we need to know about Chinook on a broad scale. An example of this is the genetic marker, Greb1L, that dictates the very different run timing of spring Chinook versus fall Chinook.

We wanted to know if in northern rivers like the Dean, where these runs converge more closely—they can be more like one extended summer run—that variation in Greb1L is still present. And we found that yes, variation in Greb1L is both present and continuing to play a key role in run timing. That matters because climate change is now rapidly altering northern salmon watersheds like the Dean. 

“There are a lot of benefits to a publicly-available, range-wide genomic dataset like this.”

Wild Salmon Center Salmon Geneticist Dr. Tasha Thompson

Eventually, watersheds like the Dean might be more like southern salmon rivers, where the environment tends to select for more clearly defined spring and fall runs. If these northern rivers harbor some of the same early and late migration alleles—or versions—of GREB1L that southern rivers do, that’s a good sign for the adaptive potential of those populations.  

What do you hope will be the long-term impact of your research, and the public database you’re making available?

Dr. Thompson: I have three main hopes. The first is that once this range-wide database is out in the world, these prove to be tools that we can use for a long time—and by many different researchers.

Second, I’m excited that we’re learning more about the fine-tuning of the Greb1L genetic markers, which has been core to my research for years now. I think what we learn from this marker now that we have a range-wide map could help unlock some really prescient conservation strategies for salmon.

A third big hope that I have is that this marks the start of more research on adaptive variation in northern Chinook salmon runs, which, as I’ve noted, has been understudied in comparison with southern runs.

Okay, let’s shift to your work with North Umpqua summer steelhead. Can you describe this project for us?

Dr. Thompson: This is a project that I’ve been moving forward that expands on the research of Michelle Pepping, a UC-Davis graduate student. It’s personal for me in that this work focuses on my home river here in Oregon, the North Umpqua. It also expands on my research on the Greb1L genetic marker, which dictates run timing for summer steelhead, much like it does for spring Chinook salmon.  

What’s the problem here that this research could help resolve?

Dr. Thompson: Well, the North Umpqua is known all over the world for its summer steelhead run. It drives a robust recreational fishing economy. The fact that we have historically had such a strong summer steelhead run means that our steelheading season goes for many months longer than it otherwise would. The problem is that North Umpqua summer steelhead have seen steep declines in the last ten years, and answers have been hard to find. 

We have a core hypothesis about why summer run steelhead exist in the first place: they can access habitat that winter steelhead can’t. It’s really hard to be a summer steelhead. They stop eating once they enter freshwater, and they can be in freshwater for up to 10 months before they spawn. That’s a long time to go without eating! And they also have to sexually develop during that time, which takes a lot of energy. Because of the challenges they already face, summers are at a serious disadvantage when they have to compete directly with winter steelhead for spawning habitat. But low river flows in the summer allow summer steelhead to get up over steep cascades and waterfalls that become impassable barriers in the winter when flows are much higher. That means the summer run can access exclusive habitat where they don’t have to compete with winter steelhead.  

 To test this, we wanted to know where summer steelhead were showing up in the North Umpqua, where winter steelhead were, and what, if any, true flow dependent barriers were keeping them separate. To create our map, we sampled extensively throughout the basin for the and tested the samples at GREB1L. 

“We have a core hypothesis about why summer run steelhead exist in the first place.  To test this, we wanted to know where summer steelhead were showing up in the North Umpqua, where winter steelhead were, and what, if any, true flow dependent barriers were keeping them separate.”

Wild Salmon Center Salmon Geneticist Dr. Tasha Thompson

And what did you find?

Dr. Thompson: We found that Steamboat Creek may actually be one of the only truly exclusive summer steelhead habitats in the North Umpqua. In some years, other creeks might have semi-exclusive habitat, but the barriers on Steamboat Creek were the only ones we found that had exclusively summer run steelhead above them. So this one creek is critical for the North Umpqua’s summer steelhead run. That puts a lot of pressure on Steamboat Creek. 

This paper might be out in the world even sooner than your range-wide Chinook study. What could be some applications for this research that you’d like to see? 

Dr. Thompson: Well, I think that for a salmon conservationist interested in protecting North Umpqua summer steelhead, one obvious takeaway from our work is that this run needs as many opportunities as possible to make use of its genetic advantage. 

Certainly work to make sure Steamboat Creek continues to provide viable habitat for steelhead generally will benefit the summer run. But there may be additional opportunities to help the summer run specifically. 

For example, a dam on the upper mainstem North Umpqua blocked steelhead from passing between 1952 and 2012 when a fish ladder was installed. Now steelhead are beginning to recolonize habitat above the dam. There’s a tributary up there with 30-40 miles of great habitat, and it has a barrier on it that we’re sure is impassable in the winter. We’re currently working to understand whether summer steelhead are recolonizing that tributary, and evaluating potential management approaches that might help that upper basin area harbor some exclusive summer steelhead habitat.