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1. An information theory-based approach to characterize drivers of upstream salmon migration

   https://doi.org/10.1371/journal.pone.0269193  

   Goodwell, Allison; Campbell, Nicholas (June 2022, PLOS ONE)

   Fujiwara, Masami (Ed.)

   The migration timing of Pacific salmon in the Columbia River basin is subject to multiple influences related to climate, human water resource management, and lagged effects such as oceanic conditions. We apply an information theory-based approach to analyze drivers of adult Chinook salmon migration within the spring and fall spawning seasons and between years based on salmon counts at dams along the Columbia and Snake Rivers. Time-lagged mutual information and information decomposition measures, which characterize lagged and nonlinear dependencies as reductions in uncertainty, are used to detect interactions between salmon counts and lagged streamflows, air and water temperatures, precipitation, snowpack, climate indices and downstream salmon counts. At a daily timescale, these interdependencies reflect migration timing and show differences between fall and spring run salmon, while dependencies based on variables at an annual resolution reflect long-term predictability. We also highlight several types of joint dependencies where predictability of salmon counts depends on the knowledge of multiple lagged sources. This study illustrates how co-varying human and natural drivers could propagate to influence salmon migration timing or overall returns, and how nonlinear types of dependencies between variables enhance predictability of a target. This information-based framework is broadly applicable to assess driving factors in other types of complex water resources systems or species life cycles. 

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2. Interactions between life history and the environment on changing growth rates of Chinook salmon

   https://doi.org/10.1139/cjfas-2022-0116  

   Buckner, Jack H.; Satterthwaite, William H.; Nelson, Benjamin W.; Ward, Eric J. (April 2023, Canadian Journal of Fisheries and Aquatic Sciences)

   Fish in all the world's oceans exhibit variable body size and growth over time, with some populations exhibiting long-term declines in size. These patterns can be caused by a range of biotic, abiotic, and anthropogenic factors and impact the productivity of harvested populations. Within a given species, individuals often exhibit a range of life history strategies that may cause some groups to be buffered against change. One of the most studied declines in size-at-age has been in populations of salmon; Chinook salmon in the Northeast Pacific Ocean are the largest-bodied salmon species and have experienced long-term declines in size. Using long-term monitoring data, we develop novel size and growth models to link observed changes in Chinook size to life history traits and environmental variability. Our results identify three distinct trends in size across the 48 stocks in our study. Differences among populations are correlated with ocean distribution, migration timing, and freshwater residence. We provide evidence that trends are driven by interannual variation in certain oceanographic processes and competition with pink salmon. 

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3. Assessing the Role of Incubation Temperature as a Barrier to Successful Establishment of Coho Salmon ( Oncorhynchus kisutch ) in a Rapidly Warming Arctic

   https://doi.org/10.1002/ece3.70797  

   Lindley, Elizabeth D; Dunmall, Karen M; Westley, Peter_A H (January 2025, Ecology and evolution)

   ABSTRACT Warming associated with climate change is driving poleward shifts in the marine habitat of anadromous Pacific salmon (Oncorhynchusspp.). Yet the spawning locations for salmon to establish self‐sustaining populations and the consequences for the ecosystem if they should do so are unclear. Here, we explore the role of temperature‐dependent incubation survival and developmental phenology of coho salmon (Oncorhynchus kisutch) as a potential early life history barrier to establishment in an Arctic stream. We exposed embryos to temperatures previously recorded in the substrate of an Arctic groundwater spring‐fed spawning environment. Using a common garden experimental design, coho salmon embryos were exposed to treatments that thermally mimicked four spawning dates from August 1 to October 1 (AUG1, SEPT1, SEPT15, and OCT1). Spawning temperatures were 6°C at the warmest (AUG1) and 1.25°C at the coldest (OCT1). We observed low survival rates in SEPT1 (41%) and OCT1 (34%) and near complete mortality in the other treatments. While far below what is considered normal in benign hatchery‐like conditions, these rates suggest that temperatures experienced at these spawning dates are survivable. We detected differences in developmental rates across treatments; embryos developed 1.9 times faster in the warmest treatment (AUG1, 120 days) compared to the coldest (OCT1, 231 days). Differences in accumulated thermal units (ATUs) needed for hatching ranged from 392 ATUs in AUG1 to 270 ATUs in OCT1, revealing compensation in developmental requirements. Given these findings, the most thermally suitable spawning dates within our study are between September 15 and October 1, which facilitates hatching and projected nest emergence to occur in spring warming conditions (March–September). Broadly, our findings suggest that spawning sites within thermal tolerances that can support the survival and development of coho salmon exist in the North American Arctic. Whether the habitat is otherwise suitable for transitions through other life stages remains unknown. 

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4. An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity

   https://doi.org/10.3389/fnana.2022.945344  

   Eilertsen, Mariann; Davies, Wayne Iwan; Patel, Dharmeshkumar; Barnes, Jonathan E.; Karlsen, Rita; Mountford, Jessica Kate; Stenkamp, Deborah L.; Patel, Jagdish Suresh; Helvik, Jon Vidar (July 2022, Frontiers in Neuroanatomy)

   Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), Chinook salmon ( Oncorhynchus tshawytcha ), coho salmon ( Oncorhynchus kisutch ), rainbow trout ( Oncorhynchus mykiss ), and sockeye salmon ( Oncorhynchus nerka )] compared to the northern pike ( Esox lucius ), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λ max values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision. 

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5. Prey tell: what quillback rockfish early life history traits reveal about their survival in encounters with juvenile coho salmon

   https://doi.org/10.3354/meps13300  

   Fennie, HW; Sponaugle, S; Daly, EA; Brodeur, RD (June 2020, Marine Ecology Progress Series)

   Predation is a major source of mortality in the early life stages of fishes and a driving force in shaping fish populations. Theoretical, modeling, and laboratory studies have generated hypotheses that larval fish size, age, growth rate, and development rate affect their susceptibility to predation. Empirical data on predator selection in the wild are challenging to obtain, and most selective mortality studies must repeatedly sample populations of survivors to indirectly examine survivorship. While valuable on a population scale, these approaches can obscure selection by particular predators. In May 2018, along the coast of Washington, USA, we simultaneously collected juvenile quillback rockfish Sebastes maliger from both the environment and the stomachs of juvenile coho salmon Oncorhynchus kisutch . We used otolith microstructure analysis to examine whether juvenile coho salmon were age-, size-, and/or growth-selective predators of juvenile quillback rockfish. Our results indicate that juvenile rockfish consumed by salmon were significantly smaller, slower growing at capture, and younger than surviving (unconsumed) juvenile rockfish, providing direct evidence that juvenile coho salmon are selective predators on juvenile quillback rockfish. These differences in early life history traits between consumed and surviving rockfish are related to timing of parturition and the environmental conditions larval rockfish experienced, suggesting that maternal effects may substantially influence survival at this stage. Our results demonstrate that variability in timing of parturition and sea surface temperature leads to tradeoffs in early life history traits between growth in the larval stage and survival when encountering predators in the pelagic juvenile stage. 

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