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Using genetics to conserve life history strategies in California steelhead (Oncorhynchus mykiss)

About the author: Dr. Alexandra DeCandia is a postdoctoral fellow at Smithsonian’s National Zoo and Conservation Biology Institute. Her research applies diverse molecular techniques to wildlife conservation and disease management of North American mammals. Alexandra received her Ph.D. from Princeton University in 2020 and her B.A. from Columbia University in 2015. For her career, she strives to work along the intersection of scientific research, wildlife conservation, and science communication. For more information, please visit her personal website.



Oncorhynchus mykiss in the Eel River watershed. Image credit: Shaun Thompson.

Steelhead (Oncorhynchus mykiss) inhabit both cultural and ecological niches in northern California and the Pacific Northwest. Culturally, steelhead provide an important food source to indigenous communities and represent abundance, wealth, prosperity, and determination in traditional art and religious ceremonies (Squamish Lil’Wat Cultural Center). Ecologically, migratory steelhead transport key nutrients between marine and freshwater environments (and the organisms that inhabit them) and serve as indicator species for ecosystem health.

Figure 1. Simple schematic of summer-run and winter-run migration timing. Figure created by A. DeCandia with BioRender.

Diverse life history strategies adopted by steelhead are critical to the fulfillment of these niches. Perhaps most emblematic of salmonid life history strategies concerns migration. Steelheads are classified into two primary groups: residents and migrants. Resident individuals inhabit streams, rivers, lakes, and reservoirs throughout their lives, whereas anadromous steelhead migrate between marine and freshwaters for feeding and spawning, respectively. Within the migrating group, there exist additional strategies regarding the timing of migration from marine to freshwaters (termed “run-timing”; Figure 1). Summer-run steelhead migrate to freshwaters in late spring/early summer to mature during the fall and spawn in winter. In contrast, winter-run steelhead wait until late fall/winter to migrate into freshwaters for spawning.

Although once abundant throughout the region, steelhead have experienced dramatic declines due to anthropogenic activities. Stressors include dams, diversions, development, pollution, run-off, harvest, thermal stress, and reduced stream flow rendering certain migratory routes impassable. In addition to causing the loss of individuals, these threats jeopardize the complex life history strategies exhibited by steelhead in the region. Summer-run steelhead are particularly vulnerable and at risk of local extirpation.

Figure 2. Map of study area (Figure 1 in Kannry et al. 2020).

In their recent study, Samantha Kannry et al. (2020) examined the distribution of life history strategies in the southernmost river system containing summer-run steelhead: the Eel River in northern California (Figure 2). More specifically, the authors used genetic techniques to examine population structure, demography, and ecology throughout the Eel River watershed. Their dataset consisted of genome-wide loci genotyped through Rapture sequencing, as well as markers previously associated with migration (OMY5) and run-timing (GREB1L) life history strategies. Their sample set included more than two thousand steelheads sampled for this and a previous study in the Eel River watershed.

Samantha Kannry in the field looking for fish. Image credit: Ethan Bertz.

Principal component analysis revealed three genetic clusters within the watershed. Interestingly, steelhead primarily clustered by sampling basin rather than life history phenotype. Summer-run and winter-run individuals sharing the same sampling basin (e.g., Van Duzen) therefore clustered more closely together than summer-run steelheads sampled across basins. This result supported the presence of two independent populations of summer-run steelhead in the Van Duzen and Middle Fork Eel Rivers. Critically, this overturned the previous assumption that all summer-run steelhead derived from the same subpopulation.

Kannry et al. (2020) next considered potential barriers to steelhead passage found throughout the watershed. Through examination of migration allele frequencies, they reported that Eaton Falls in the Van Duzen River does not present a complete barrier to anadromous steelhead, as previously hypothesized. This result contrasts the South Fork barrier in Yager Creek, and is supported by estimates of population differentiation across no barrier (mean pairwise FST=0.059), the partial Eaton Falls barrier (0.094), and the confirmed South Fork barrier (0.219). Within migrating steelhead, they also identified barriers between winter-run and summer-run steelhead in both the Van Duzen (Salmon Falls barrier) and Middle Fork Eel (Osbourne Roughs barrier) Rivers, suggesting habitat segregation between the two run-timing phenotypes. This result found its extreme in the South Fork Eel River, where no summer-run alleles were identified, thus indicating the absence of this phenotype from this part of the watershed.

Samantha Kannry in the field sampling a fish. Image credit: Ethan Bertz.

The final barrier considered by the authors was Scotts Dam, a hydropower facility that has diverted water into the nearby Russian River watershed for roughly 100 years. Constructed without a fish passage, Scotts Dam presents a formidable barrier to anadromous steelhead. As this dam is up for relicensing in 2022, Kannry et al. considered whether the migration phenotype could be recovered above the dam. Through population genetic surveys, the authors identified both anadromous and summer-run alleles in the resident steelhead population sampled above Scotts Dam. This suggests that steelheads may be able to naturally recover this important phenotype without additional human intervention, should the dam be removed.

Oncorhynchus mykiss. Image credit: Timothy Knepp – U.S. Fish and Wildlife Service – This image originates from the National Digital Library of the USFWS 

In summary, the authors identified distinct population segments, mixed and distinct anadromous and nonanadromous waters, candidate areas for habitat restoration, and potential source populations for the natural recovery of phenotypes. Considered together, these insights can directly inform the conservation and management of steelhead in the Eel River watershed, particularly with regard to the Scotts Dam relicensing in 2022. In addition to these implications, the analytical approach described by Kannry et al. provides a roadmap for conducting similar analyses in other river systems in northern California and the Pacific Northwest. By better understanding the ecology and distribution of life history strategies throughout the region, the authors demonstrate that phenotypic complexity can be preserved. Given steelhead’s significance, these analyses and resulting management recommendations can enable steelhead to occupy important cultural and ecological niches indefinitely.



Samantha H Kannry, Sean M O’Rourke, Suzanne J Kelson, Michael R Miller (2020) On the Ecology and Distribution of Steelhead (Oncorhynchus mykiss) in California’s Eel River. Journal of Heredity, 111, 548–563.

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