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Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity, underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life histories still exist, despite reductions in spawning habitat and hatchery practices that have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River. To understand this diversity, we collected migration timing data and GREB1L genotypes from hook-and-line, acoustic tagging, and carcass surveys of Chinook salmon in the Yuba River between 2009 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in Californias Central Valley. We found that the date Chinook salmon crossed the lowest barrier to Yuba River spawning habitat (Daguerre Point Dam) was tightly correlated with their GREB1L genotype. Importantly, our study confirms that ESA-listed spring-run Chinook salmon are spawning in the Yuba River, promoting a portfolio of life history and genetic diversity, despite the highly compressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems, to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

Ecosystem management and governance of cross-scale dependent systems require integrating knowledge about ecological connectivity in its multiple forms and scales. Although scientists, managers, and policymakers are increasingly recognizing the importance of connectivity, governmental organizations may not be currently equipped to manage ecosystems with strong cross-boundary dependencies. Managing the different aspects of connectivity requires building social connectivity to increase the flow of information, as well as the capacity to coordinate planning, funding, and actions among both formal and informal governance bodies. We use estuaries in particular the San Francisco Estuary, in California, in the United States, as examples of cross-scale dependent systems affected by many intertwined aspects of connectivity. We describe the different types of estuarine connectivity observed in both natural and human-affected states and discuss the human dimensions of restoring beneficial physical and ecological processes. Finally, we provide recommendations for policy, practice, and research on how to restore functional connectivity to estuaries.

Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). The habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.

Altered river flows and fragmented habitats often simplify riverine communities and favor non-native fishes, but their influence on life-history expression and survival is less clear. Here, we quantified the expression and ultimate success of diverse salmon emigration behaviors in an anthropogenically altered California river system. We analyzed two decades of Chinook salmon monitoring data to explore the influence of regulated flows on juvenile emigration phenology, abundance, and recruitment. We then followed seven cohorts into adulthood using otolith (ear stone) chemical archives to identify patterns in time- and size-selective mortality along the migratory corridor. Suppressed winter flow cues were associated with delayed emigration timing, particularly in warm, dry years, which was also when selection against late migrants was the most extreme. Lower, less variable flows were also associated with reduced juvenile and adult production, highlighting the importance of streamflow for cohort success in these southernmost populations. While most juveniles emigrated from the natal stream as fry or smolts, the survivors were dominated by the rare few that left at intermediate sizes and times, coinciding with managed flows released before extreme summer temperatures. The consistent selection against early (small) and late (large) migrants counters prevailing ecological theory that predicts different traits to be favored under varying environmental conditions. Yet, even with this weakened portfolio, maintaining a broad distribution in migration traits still increased adult production and reduced variance. In years exhibiting large fry pulses, even marginal increases in their survival would have significantly boosted recruitment. However, management actions favoring any single phenotype could have negative evolutionary and demographic consequences, potentially reducing adaptability and population stability. To recover fish populations and support viable fisheries in a warming and increasingly unpredictable climate, coordinating flow and habitat management within and among watersheds will be critical to balance trait optimization versus diversification.

The California Central Valley contains the southernmost native populations of Chinook Salmon Oncorhynchus tshawytscha, which inhabit a highly variable, anthropogenically altered environment. To mitigate habitat loss and support fisheries, millions of fall-run hatchery salmon are released each year, often transported downstream to avoid in-river mortality, with consequences not fully understood. We synthesize historical trends in release location and timing (1941–2017), focusing on outcomes influencing stock resilience, adult straying, and ocean arrival timing. Over time, juveniles have been transported increasing distances from the source hatchery, particularly during droughts. Transport distance was strongly associated with straying rate (averaging 0–9% vs. 7–89% for salmon released on site vs. in the bay upstream of Golden Gate Bridge, respectively), increasing the effects of hatchery releases on natural spawners. Decreasing variation in release location and timing could reduce spatiotemporal buffering, narrowing ocean arrival timings and increasing risk of mismatch with peak prey production. Central Valley salmon epitomize the pervasive challenge of balancing short-term (e.g., abundance) against long-term (e.g., stability) goals.

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring‐run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%–73%) of spawners across six return years (2009–2011, 2018–2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba‐origin spawners, on average, 30% (range 14%–50%) exhibited the spring‐run genotype. The Yuba‐origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early‐migrating fry dominated the returns (mean 59%, range 33%–89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non‐natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in‐river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring‐run are reproducing, surviving, and returning to the Yuba River every year suggests that re‐establishment of an independent population is possible, although hatchery‐wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience. [ABSTRACT FROM AUTHOR]

This article explores the significance of understanding fish habitat ecology in a changing climate and its implications for fisheries stability and ecosystem health. It emphasizes the need for diverse approaches, such as field observations, laboratory experiments, genomics, telemetry, and modeling, to quantify fish habitat needs. The integration of data on fish movement, connectivity, and food webs is crucial for predicting future fish distributions and informing management and conservation efforts. The article also discusses the various stressors faced by fish populations, including warming, hypoxia, and habitat loss, which have led to shifts in fish distributions. Accurately predicting fish population responses to environmental change requires data from various disciplines. The text highlights the importance of building social connectivity and communication between academia, stakeholders, managers, and policymakers for effective fish and habitat management. It emphasizes the need for long-term food security and sustainable fishing practices, as well as the concept of "One Health" to ensure the health of humans, animals, plants, and the environment. The article concludes by expressing pride in hosting the 2023 FSBI Symposium and emphasizes the importance of interdisciplinary collaboration and engaging the public in fisheries science. [Extracted from the article]

European sea bass (Dicentrarchus labrax) is a species of high commercial and recreational value, but it exhibits highly variable recruitment rates and has been subject to recent declines. Emergency management measures put in place to protect spawning stocks include the annual closure of commercial and recreational fisheries over a 2‐month, February–March, window. Whether this protection measure is having the desired outcome for this data‐poor species remains unclear. Otolith microstructural analyses (counts and widths of daily growth rings and check marks indicative of settlement) were used to estimate (1) spawn timing, (2) pelagic larval duration and settlement timing, (3) growth rate and condition, and (4) the otolith‐fish size relationship for juvenile European sea bass caught from two estuaries in Wales (Dwyryd, Y Foryd), located at the northern edge of the species range. We observed a significant mismatch between the timing of fisheries closures and the spawning, with 99.2% of recruits having been spawned after the fishery had reopened (back‐calculated median spawn date = May 5 ± 17 days SD), suggesting that the closure may be too early to adequately protect this population. Further, we present the first empirically derived estimates of pelagic larval duration for sea bass recruits settling in UK habitats, which showed a strong negative relationship with spawn date. Finally, we found significant differences in fish condition between the two estuaries, suggesting local variation in habitat quality. The results suggest that the timing of current fisheries closures may not be adequately protecting the spawners supplying these northernmost estuaries, which are likely to become increasingly important as sea bass distributions shift northward in our climate future. [ABSTRACT FROM AUTHOR]

The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it is necessary to first understand how environmental factors affect their expression and success. We used otolith (87)Sr/(86)Sr in adult Chinook salmon (Oncorhynchus tshawytcha) returning to the Stanislaus River in the California Central Valley (USA) to reconstruct the sizes at which they outmigrated as juveniles in a wetter (2000) and drier (2003) year. We compared rotary screw trap-derived estimates of outmigrant timing, abundance and size with those reconstructed in the adults from the same cohort. This allowed us to estimate the relative survival and contribution of migratory phenotypes (fry, parr, smolts) to the adult spawning population under different flow regimes. Juvenile abundance and outmigration behavior varied with hydroclimatic regime, while downstream survival appeared to be driven by size- and time-selective mortality. Although fry survival is generally assumed to be negligible in this system, >20% of the adult spawners from outmigration year 2000 had outmigrated as fry. In both years, all three phenotypes contributed to the spawning population, however their relative proportions differed, reflecting greater fry contributions in the wetter year (23% vs. 10%) and greater smolt contributions in the drier year (13% vs. 44%). These data demonstrate that the expression and success of migratory phenotypes vary with hydrologic regime, emphasizing the importance of maintaining diversity in a changing climate.

Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento-San Joaquin River system form the backbone of California's salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery-versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope ([sup.87]Sr/[sup.86]Sr) ratios of otoliths collected during carcass surveys from 2002 to 2010. Our results show that prior to the 2007-2008 salmon stock collapse, 55%-67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (~90%) in 2011-2012. Though the rebound in abundance of salmon in the Feather River suggests recovery of the stock postcollapse, our otolith chemistry data document a persistent decline of wild spawners, likely leading to the erosion of locally adapted Feather River salmon populations. Les saumons quinnats (Oncorhynchus tshawytscha) a migration automnale du reseau du fleuve Sacramento et de la riviere San Joaquin forment l'epine dorsale de la peche aux saumons en Californie et sont fortement soutenus par la production en alevinieres. La determination des tendances dans le temps des apports relatifs de saumons issus d'alevinieres et de saumons nes dans la nature est cruciale pour evaluer l'etat et la resilience des populations de saumons sauvages. Nous avons reconstitue la proportion de poissons issus d'alevinieres dans des aires de frai naturelles dans la riviere Feather, un important affluent du fleuve Sacramento, en utilisant les rapports d'isotopes de strontium ([sup.87]Sr/[sup.86]Sr) d'otolites preleves durant des releves de carcasses de 2002 a 2010. Les resultats montrent que, avant l'effondrement des stocks de saumons de 2007-2008, de 55% a 67% des frayeurs dans la riviere provenaient d'alevinieres; toutefois, l'apport d'alevinieres a connu une augmentation tres marquee (89%) en 2010 dans la foulee de l'effondrement. Les donnees tirees d'une campagne recente de marquage en aleviniere corroborent ces resultats, demontrant que les poissons issus d'alevinieres sont toujours predominants (~90%) en 2011-2012. Si la remontee de l'abondance des saumons dans la riviere Feather semble indiquer un retablissement du stock a la suite de l'effondrement, nos donnees sur la chimie des otolites documentent un declin soutenu des geniteurs sauvages, qui mene vraisemblablement a l'erosion des populations de saumons adaptees aux conditions locales de la riviere Feather. [Traduit par la Redaction], Introduction The Sacramento-San Joaquin River system in California's Central Valley (CV) is the foundation of California's water supply, providing water for approximately 35 million residents and supporting a multibillion dollar [...]

Trace element concentrations in fish earstones ('otoliths') are widely used to discriminate spatially discrete populations or individuals of marine fish, based on a commonly held assumption that physiological influences on otolith composition are minor, and thus variations in otolith elemental chemistry primarily reflect changes in ambient water chemistry., We carried out a long-term (1-year) experiment, serially sampling seawater, blood plasma and otoliths of mature and immature European plaice ( Pleuronectes platessa L.) to test relationships between otolith chemistry and environmental and physiological variables., Seasonal variations in otolith elemental composition did not track seawater concentrations, but instead reflected physiological controls on metal transport and biokinetics, which are likely moderated by ambient temperature. The influence of physiological factors on otolith composition was particularly evident in Sr/ Ca ratios, the most widely used elemental marker in applied otolith microchemistry studies. Reproduction also triggered specific variations in otolith and blood plasma metal chemistry, especially Zn/ Ca ratios in female fish, which could potentially serve as retrospective spawning indicators., The influence of physiology on the trace metal composition of otoliths may explain the success of microchemical stock discrimination in relatively homogenous marine environments, but could complicate alternative uses for trace element compositions in biominerals of higher organisms. [ABSTRACT FROM AUTHOR]

Oxygen isotope ratios from fish otoliths are used to discriminate marine stocks and reconstruct past climate, assuming that variations in otolith δ18O values closely reflect differences in temperature history of fish when accounting for salinity induced variability in water δ18O. To investigate this, we exploited the environmental and migratory data gathered from a decade using archival tags to study the behaviour of adult plaice (Pleuronectes platessa L.) in the North Sea. Based on the tag-derived monthly distributions of the fish and corresponding temperature and salinity estimates modelled across three consecutive years, we first predicted annual otolith δ18O values for three geographically discrete offshore sub-stocks, using three alternative plausible scenarios for otolith growth. Comparison of predicted vs. measured annual δ18O values demonstrated >96% correct prediction of sub-stock membership, irrespective of the otolith growth scenario. Pronounced inter-stock differences in δ18O values, notably in summer, provide a robust marker for reconstructing broad-scale plaice distribution in the North Sea. However, although largely congruent, measured and predicted annual δ18O values of did not fully match. Small, but consistent, offsets were also observed between individual high-resolution otolith δ18O values measured during tag recording time and corresponding δ18O predictions using concomitant tag-recorded temperatures and location-specific salinity estimates. The nature of the shifts differed among sub-stocks, suggesting specific vital effects linked to variation in physiological response to temperature. Therefore, although otolith δ18O in free-ranging fish largely reflects environmental temperature and salinity, we counsel prudence when interpreting otolith δ18O data for stock discrimination or temperature reconstruction until the mechanisms underpinning otolith δ18O signature acquisition, and associated variation, are clarified. [ABSTRACT FROM AUTHOR]