A logjam on a river can be a beautiful thing鈥攅specially if you鈥檙e a salmon. Logjams collect the gravel salmon need to lay their eggs.
But if you鈥檙e a spring chinook on the South Umpqua, the slick gray-green sheets of rock that line the course of the river can be a bleak place.
鈥淭he water just rips through it. And because the bedrock offers very little resistance, all the gravel and substrate just move out and don鈥檛 get retained,鈥� Forest Service fisheries biologist Casey Baldwin said.
Baldwin has been working for more than a decade to add logs back to the river and improve its spawning habitat. Logs were pulled from the river by his agency in the 1960s and 鈥�70s in a misguided practice called 鈥渟tream clean out,鈥� where the logjams were removed in an attempt to make it easier for fish to get upstream.
鈥淎 lot of the river鈥檚 pretty much its base or worst state that it can be in. I mean, you really [can] say it鈥檚 a beautiful ditch of bedrock,鈥� he said.
The progress has been slow. The past few years, Baldwin鈥檚 workforce has been busy fighting wildfires instead of being available for restoration work. And funding can be unpredictable from year to year.
Every year the river continues to resemble a massive bedrock waterslide, spring chinook numbers continue to fall. Only about 60 鈥渟pringers鈥� came back this year to the South Umpqua River.
鈥淲e鈥檙e looking at the last breaths of a species,鈥� said Stanley Petrowski, a board member of Umpqua Watersheds.
Petrowski said spring chinook declines on coastal Oregon rivers haven鈥檛 been given the conservation attention they need because the spring and fall fish are lumped together and regarded as a single species. For decades, based on what scientists knew about salmon genetics, wildlife managers in the Pacific Northwest considered chinook salmon that return to deposit and fertilize eggs in the spring and those that return in the fall to be the same fish. So, even though wild spring chinook salmon runs on many rivers in Northern California and Oregon have crashed, there hasn鈥檛 been the urgency to change anything鈥攁s long as the fall runs remain strong.
Wildlife managers thought that if spring chinook salmon disappeared, then fall chinook would just re-evolve to start their homeward migration in spring鈥攔eplenishing that run of fish.
But recently, there鈥檚 been a significant shift in our understanding of salmon genetics. Researchers have found a distinct area in salmon DNA where the spring and fall chinook differ.
鈥淣ow that we know that there鈥檚 a genetic difference, they should be managed as that. And that鈥檚 what we鈥檙e pushing for,鈥� Petrowski said.
Umpqua Watersheds and other groups have recently filed a petition based on this new science. They want to extend Endangered Species Act protections to spring chinook in Oregon coastal rivers roughly between Port Orford and Seaside鈥攁 stretch that covers most of the Oregon coastline.
Genetic Revelations
Being a spring run chinook instead of a fall run chinook can definitely have advantages.
Spring chinook get their name because they enter rivers in spring when water flows are high and rivers are deep. This allows them to move farther inland to access spawning grounds. The fish hang out in cold river pools all summer while they develop the ability to reproduce.
By the time fall run fish leave the ocean, river flows are usually lower. What looked like a speed bump to a spring salmon might be more like a tall, insurmountable waterfall later in the year.
Both runs of fish spawn at roughly the same time (springers generally lay their eggs about a month earlier), but because spring fish access parts of the river fall fish can鈥檛, they reduce the level of competition for spawning grounds.
The genetic difference between fall and spring chinook salmon was first documented in a 2017 paper coauthored by University of California-Davis geneticist Mike Miller. But scientists had been looking into the genetic differences between the fish since the 1970s.
鈥淲hat [had] been found over and over again is that when you look at pairs of spring and fall chinook from the same watershed, they tend to be really related to each other 鈥� they were indistinguishable,鈥� Miller said.
Based on this, scientists concluded that the fish first developed a preference for a specific home river before they evolved to return to that river at a different time of the year.
鈥淚t would suggest that the spring run evolved lots of different times in lots of different places,鈥� he said.
If this change in behavior emerged many times in the past, what鈥檚 to say it couldn鈥檛 reemerge again when conditions are favorable?
Miller decided to look a little closer at the issue using new high-resolution genetic analysis technology.
鈥淲e were really surprised we found that there was one region of the genome that was basically 鈥� perfectly correlated with whether individuals were either spring run or fall run,鈥� he said.
They did the same analysis for winter and summer runs of steelhead and found the same genetic variation between the two runs.
It didn鈥檛 matter where the spring chinook they analyzed came from, they all had the same genetic marker. This means the genetic mutation happened once, likely tens of thousands of years ago or more and then spread. This was not something that could be counted on to happen again in our lifetime.
This presented a new avenue to argue that spring chinook should be protected separately under the Endangered Species Act.
Matt Sloat, a scientist with the Wild Salmon Center in Portland, said the finding could be the 鈥渂iggest thing to influence how the Endangered Species Act governs salmon in a long time.鈥�
Trailblazers
The mutation that initially was an evolutionary boon for spring chinook salmon has left them particularly vulnerable because of the way humans have changed the rivers.
Dams were built that blocked off large chunks of the upstream habitat springers relied on, pitting them against fall fish in downstream spawning grounds. Wild fish advocates say hatcheries are undermining wild populations. The water quality of the rivers has been altered by land uses like logging, grazing and mining, and by communities withdrawing water for agriculture, drinking supplies and industrial use. River levels are lower and water temperatures are warmer, affecting spring fish that need cold water habitat to get them through the hot summer months.
This is the case on the Klamath River, which drains parts of Southern Oregon and Northern California. Once springers were the dominant run of fish, and very important to the Native American tribes in the region. Now the only stronghold of wild spring chinook left is found on a tributary called the Salmon River鈥攊f 161 fish can be considered a stronghold.
Amy Fingerle of the Salmon River Restoration Council wears a full black wetsuit, felt-soled boots and snorkel gear as she prepares to push off the rocks into a deep hole on the Salmon River. She points to the spot where Wooley Creek cascades into the larger river.
鈥淚鈥檇 recommend that we go off to the side where the water is eddying out so we don鈥檛 disturb the fish as we鈥檙e popping in,鈥� she said above the rushing water.
A few steps ahead, Craig Tucker, who works with the Karuk Tribe, called out in unabashed dad-joke glory: 鈥淲ho鈥檚 this Eddie guy we keep looking for?鈥�
鈥淭hey like to nose into these creek mouths where the cold water is mixing with the river water,鈥� Fingerle said, referring to the salmon, not Eddie. 鈥淲e鈥檒l hope that they鈥檙e there.鈥�
Fingerle and Tucker slip into the pool, initially swept upstream by the force of Wooley Creek flowing in. They then make a wide circle on the surface and briefly rest in the calm of the eddy. The visibility is only about 10 feet in the turbid pool and they have to dive to see the bottom.
Underwater, they follow the cold water to the mouth of the creek, just like the spring chinook do.
Dive after dive, then pool after pool moving up Wooley Creek, they see small trout, a steelhead, some juvenile fish鈥攂ut no returning adult spring chinook salmon.
鈥淭hat鈥檚 disappointing,鈥� Tucker said, emerging from a pool.
鈥淭here was no doubt in my mind that we鈥檇 come here and see spring chinook. This is prime habitat,鈥� Fingerle said. 鈥淏ut you have 161 fish that have returned, spread throughout the watershed. It鈥檚 almost becoming like a needle in a haystack.鈥�
The Karuk Tribe and Salmon River Restoration Council were the first to use the new genetic science to try to get spring chinook listed as threatened or endangered. That petition is currently awaiting action from the National Marine Fisheries Service, which was supposed to issue a decision at the end of 2018.
A NMFS spokesperson said the decision is now expected before the end of this year. With this decision will come the first clue whether salmon conservation will change to reflect the expanding understanding of salmon genetics.
The Eyes Have It?
Not all scientists working in the field of salmon genetics agree on the interpretation of the new genetic data. In fact, a group of scientists working with Miller on the 2017 paper, removed their names before it was published.
NOAA Fisheries ecologist Carlos Garza was one of those scientists, although he agrees the underlying work showing the genetic difference between spring and fall chinook was good (and has subsequently been confirmed by his own, as yet unpublished, work).
Garza says the genes that mark spring run salmon only correlate with the time they enter rivers, not any other physical or developmental difference. And he says people are going too far with the interpretation of what the genetic difference means.
鈥淚f you鈥檙e proposing that we change the way that we label these fish to focus on something that is not descriptive of the way that they are actually existing in nature, then that 鈥� becomes an issue of anthropogenically categorizing things in a way that is not consistent with their biology,鈥� he said.
In addition, through research on the Salmon River, Garza has learned that spring and fall chinook occupy the same spawning grounds鈥攖hey interbreed, which helps conserve the genetic variation.
鈥淭hat means that effectively in the Salmon River, spring and fall chinook are part of one population,鈥� he said.
Garza doesn鈥檛 see spring and fall fish as being any more different than siblings with different colored eyes.
鈥淥ne can have a very simple genetically controlled trait lead to a cascade of phenotypic [observable characteristics] changes that cause people to perceive what could be two full siblings as being dramatically different organisms,鈥� he said.
This interpretation could affect whether the Endangered Species Act is evoked to bring additional protections for spring chinook salmon.
And the stakes are big. Restoring populations of spring chinook can be more complicated than restoring fall fish because they rely on favorable river conditions for several months. Spring chinook need a larger portion of each river to be in habitable condition for a longer period of time. And this involves more than just science. It brings in politics and the economy and ideological allegiances and federal agencies stretched thin by the conservation and restoration work already on their plates.
And the question raised by the new genetic analysis might ultimately have a much larger impact.
In 2018 two other NOAA Fisheries scientists, Robin Waples and Steven Lindley, published a paper in the journal Evolutionary Applications that suggests changes in management may be warranted.
鈥淚n at least some of these cases it might be necessary to consider whether to revise existing conservation units based on the genomics data, and if so how best to do so,鈥� they wrote.
They suggest that salmon won鈥檛 be the last species where a more nuanced understanding of genetics will trigger challenges to how different animals and plants are managed.
Coming Together
Leaf Hillman looks like a man who鈥檚 ready to sleep in his own bed. He sits on a bench on his front porch, slightly slouched, slightly dazed. He reaches slowly for the beer that鈥檚 offered by Craig Tucker and he and his son offer up yard grapes in return.
Hillman is the hereditary owner of White Deerskin Dance at Tishawnik, which was danced by members of the Karuk tribe at this year鈥檚 World Renewal Ceremony. That鈥檚 where he鈥檚 been camping for more than a week. He just got home.
Hillman says this year the ceremony was different.
鈥淔irst year that we never had鈥攏ot one鈥攆resh fish all camp long. We always have fish, even on bad years,鈥� he said.
The fish Hillman speaks of are salmon. There are very few spring chinook in the river, and the fall chinook are late coming back this year.
鈥淲e had a great ceremony,鈥� he said. 鈥淚 think it was just weird not having fish.鈥�
Hillman is also the Karuk tribe鈥檚 director of natural resources. The Karuk are behind the accepted petition for Endangered Species Act protection for spring-run chinook salmon in the Upper Klamath and Trinity rivers.
On a similar petition back in 2011, NMFS found that the spring and fall fish in the Klamath River should be considered as part of the same 鈥渆volutionary significant unit,鈥� the framework wildlife managers use to categorize and protect variation within a species under the ESA. This time around the tribe is citing the new genetic science as a reason to reconsider that decision.
For Hillman though, the recent genetic discovery doesn鈥檛 feel all that new. The tribe, which traditionally relied on salmon as a primary food source, has always considered the two runs to be different fish.
鈥淭hey don鈥檛 show up for the same time of year. So obviously they鈥檙e not the same fish,鈥� he said. 鈥淲e have a different name for them. We call 鈥榚m ishy芒at. We call the other ones 谩ama.鈥�
There a buzz around this idea in the salmon conservation community.
鈥淲hat [the new science] does is it confirms a lot of that traditional ecological knowledge,鈥� said Conrad Gowell, fellowship program director at the Native Fish Society. 鈥淥ur scientific knowledge is starting to catch up with the knowledge of a lot of the tribes who have acknowledged these populations as distinct for a while, since time immemorial.鈥�
Similar observations have entered the zeitgeist around issues of land management and wildfire.
Hillman is a bit saltier in responding to this meeting of the two schools of thinking.
鈥淚鈥檝e always said that if it鈥檚 good science it鈥檒l eventually catch up with what we already know as Indian people, and we鈥檝e always known that spring chinook is a different fish,鈥� he said. 鈥淲estern science finally caught up to that. Bully for them 鈥� Maybe we can do something different.鈥�
Jes Burns is the Southern Oregon reporter for Oregon Public Broadcasting鈥檚 Science and Environment Team. She鈥檚 based at 老夫子传媒 and works collaboratively with JPR鈥檚 newsroom to create original journalism that helps citizens examine how environmental issues unfolding in their own backyards intersect with national issues. Her work can be heard and seen on public radio and television stations throughout the Pacific Northwest.