Using Genetics to Inform Conservation: Spring-Run Chinook Salmon in the Klamath-Trinity River Basin

Featured photo by Jonas Ferlin from Pexels

Article: Prince, D.J., S.M. O’Rourke,T.Q. Thompson, O.A. Ali, H.S. Lyman, I.K. Saglam, T.J. Hotaling, A.P. Spidle, M.R. Miller. 2017. The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. Science Advances 3:8. DOI: 10.1126/sciadv.1603198

Pacific Salmon: A Quick Review

Like many people, I love eating salmon, and I was surprised to learn that many populations of several salmon species are listed as threatened, endangered, or are even extinct from their native ranges along the West Coast. Salmon have been negatively impacted by human activities since the 19th century, including freshwater habitat loss and destruction, overfishing, pollution, warming temperatures due to climate change, and dams that block key freshwater habitat.

All salmon spawn in freshwater and are “anadromous”. This means that to complete their life cycle, juvenile salmon must migrate out to the ocean and return as adults to reproduce in the river where they were born. Because of their strategy of “homing”, a population of salmon will continuously return to the same stream, creating genetically distinct groups that can be listed as threatened or endangered under the Endangered Species Act. This makes restoration of key spawning grounds crucial, as salmon need to be able to return to their birthplace to complete their life cycle and produce offspring. Scientists can track populations of salmon that always return to the same stream and try to figure out why that particular group within the species might be struggling.

Chinook salmon along the west coast can have multiple “runs” in a single river throughout the year, based on the season in which adults return. “Fall-run” Chinook return to their streams in the fall and spawn, while “spring-run” Chinook return to the river in the spring and hang out until they are ready to spawn in the fall. The specific genetic cause of this difference in run timing has been the subject of much debate since the 1990s, and has important implications for the conservation of Chinook salmon.

Upper Klamath-Trinity Spring-Run Chinook

The Klamath River has made the news recently on the West Coast of the United States because four dams along the river have been scheduled for removal in 2020. These dams have been a highly contentious issue in this region for a long time, but one of the reasons for their removal is the potential spawning habitat for salmon that will be made available once the dams are gone.

Klamath Basin map
Figure 1. This map of the Klamath River Basin shows the location of the dams throughout the basin, as well as several key tributaries, including the Trinity River (lower left). The inset map shows the location of the Klamath River Basin on a map of California and Oregon. Source:

The Klamath and Trinity Rivers historically supported large populations of both fall and spring-run Chinook salmon, providing a crucial food source for local indigenous people and supporting commercial and recreational fisheries. Since the 90s, spring-run Chinook numbers have dramatically declined compared to the fall-run. Because fall and spring-run Chinook are grouped within the same Evolutionary Significant Unit under the Endangered Species Act, it is not possible to list the spring-run as threatened or endangered by itself, although there have been three attempts to do so since 1998.

Klamath Salmon Genetics

If spring- and fall-run Chinook evolved through parallel evolution (Figure 2), it is likely that if the spring run goes extinct, it could re-develop from the fall run. However, if the spring and fall runs are genetically distinct due to a single evolutionary event (Figure 2) in their family tree, it is much less likely that the spring-run could rise again from extinction. This article argues that the spring-run Chinook in this basin are genetically distinct from fall-run Chinook based on one key piece of their genetic code. That suggests there was a single evolutionary event that separated the two runs. While it may seem very nit-picky, this distinction is what will help management agencies decide if the runs deserve to be listed separately.

Evolutionary tree
Figure 2. Generalized phylogenetic trees that illustrate the difference between a single evolutionary event and parallel evolution. In this example, A = Fall-run and B = Spring-run Chinook salmon in the Klamath River. Asterisks mark each “evolutionary event”.                  Source: Maddie Halloran
Why is this important?

Spring runs of Chinook salmon in the Klamath basin have drastically declined from historical levels, and are much lower than fall-run Chinook in the same river. These salmon are a crucial source of food and jobs in this remote area, and many stakeholders would like to see additional restoration actions on behalf of the spring-run salmon.

This issue highlights the pitfalls of the Endangered Species Act – there are few legal avenues to proactively protect species in the U.S. Instead, we must spend many years and valuable restoration funds to prove that a group of animals are worthy of protecting on a very particular genetic basis. Currently, the Endangered Species Act only covers distinct populations, while variations within highly connected populations are not necessarily protected. It is well understood that diverse populations are stronger, as individuals can be better adapted to different conditions available in any given year. In order to provide a fighting chance for recovering salmon populations along the Klamath, the impact of genetic differences on conservation must be better understood.

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Maddie Halloran

I am a second year master's student at Humboldt State University in the Fisheries Biology Department. I'm interested in human impacts on the environment and conservation. When I'm not counting fish you can probably find me outside on an adventure or eating ice cream on my porch.

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