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Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histories of individual fishes. In this study, we demonstrated that trophic histories reconstructed using eye lenses can resolve key uncertainties regarding diet and trophic habitat shifts. Clear Lake hitch (Lavinia exilicauda chi), a threatened cyprinid, inhabits a single lake (Clear Lake, Lake County, California) and utilizes tributary streams for reproduction. Bayesian mixing models applied to δ13C and δ15N recorded in eye lenses uncovered ontogenetic diet shifts that corresponded with shifts in occupation of habitats providing spawning (tributary streams), rearing (littoral lake), and growth (pelagic lake) functions. The reconstruction of size-structured trophic and habitat information can provide vital information needed to manage and conserve imperiled species such as the Clear Lake hitch.

Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring. Graphical abstract

Context Cross-boundary subsidies create important growth opportunities for a range of taxa. In modified river systems, remnant patches of floodplain and flood bypasses become ephemeral hotspots of zooplankton production, however, the extent to which these prey items are (or could be) transported downstream is unclear. Objectives We investigated the diet of juvenile salmon under varying hydroclimatic conditions to assess the importance of floodplain-produced prey subsidies in an otherwise food-scarce region. Methods Juvenile salmon (n = 3033) and zooplankton were sampled across the California Central Valley Sacramento-San Joaquin River Delta in 2014–2018, incorporating a range of climatic conditions including drought and flood. Salmon stomach fullness and diet composition, and ambient zooplankton densities were used to assess spatiotemporal patterns in prey production and consumption. Results Floodplain-produced cladocerans provided ephemeral food pulses to juvenile salmon in downstream riverine habitats. Salmon had the fullest stomachs in wetter years (2016–2017) and the emptiest stomachs in the final year of a multi-year drought (2015). Cladoceran abundances in the water column and salmon diets were highest during wet periods and below floodplains, and decreased with increasing distance downstream, consistent with flow-mediated trophic subsidies. Conclusions These data emphasize the importance of maintaining diverse, interconnected habitats to support resilient fish populations and the potential for managing floodplains to boost prey production and delivery. Here, the inundation of a flood bypass (or lack of) played a pivotal role shaping the juvenile salmon foodscape. As freshwater ecosystems are increasingly transformed by large-scale engineering, it is important to coordinate infrastructure, habitat and flow modifications to maximize climate resilience and trophic benefits to target species.

Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams. Despite the dominance of late migrants, other strategies played an important role in many years. Our results suggest that further loss of phenotypic diversity will have critical impacts on population persistence in a warming climate. Predicted thermally suitable river conditions for late migrants will shrink rapidly in the future and will be largely relegated above impassable dams. Reconnecting diverse habitat mosaics to support phenotypic diversity will be integral to the long-term persistence of this species. Highlighting the importance of rare phenotypes in population persistence, the authors show that spring-run Chinook salmon late-migrant juveniles were critical for cohort success in drought and ocean heatwave years. Combined further warming and impassable dams threaten these late migrants’ survival.

Predator–prey systems face intensifying pressure from human exploitation and a warming climate with implications for where and how natural resource management can successfully intervene. We hypothesized young salmon migrating to the Pacific Ocean face a seasonally intensifying predator gauntlet when warming water temperature intensifies a multiple predator effect (MPE) from Striped Bass Morone saxatilis and Largemouth Bass Micropterus salmoides. We evaluated this hypothesis using data synthesis and simulation modeling.Contemporary studies based on acoustically tagged fish reaffirmed older observations that Chinook Salmon smolts must transit the Delta before water temperature reaches 20°C or mortality will be nearly 100%. Striped Bass attack rates on tethered smolts were insensitive to distance from shore and water temperature, whereas Largemouth Bass attack rates were highest near shorelines in warm water, supporting the temporal aspect of the hypothesis. Whether the combined effects of the two predators produce an MPE remains unconfirmed due to limitations on quantifying salmon behavior.We used multiple simulation models to try to reconstruct the empirical relationship between smolt survival and water temperature. Simulations reinforced attack rate results, but could not recreate the temperature dependence in smolt survival except at higher than observed temperatures. We propose three hypotheses for why and recommend discerning among them should be a focus of research.We found significant linear relationships between monthly mean inflow to the Delta from each of its two largest tributaries and monthly mean water temperatures along associated salmon migration routes, but these relationships can be nonlinear, with most of the correlation occurring at low inflows when water temperature is largely controlled by air temperature and day length. As the global climate warms, changed circumstances in predator–prey relationships may present important challenges when managing species vulnerable to extinction in addition to presently more abundant species., We build upon previous conceptual models of how intersecting impacts of multiple predators can render former habitats unsuitable to migratory animals and test the conceptual model with a case study. The case study focuses on the potential impacts of two non‐native predators on Chinook Salmon smolts as the young salmon migrate through California's Sacramento‐San Joaquin Delta on their way to the Pacific Ocean.

Riverine ecosystems in their natural state are complex mosaics of habitats whose conditions vary across space and time as landscape features filter prevailing hydrologic forcing. Yet, through anthropogenic alteration many large river systems have become simplified through the construction of levees and dams that reduce lateral connectivity and flow variability. The extent to which shifts in habitat mosaics create conditions that support different trophic responses that manifest in differences in fish growth across the landscape remains largely untested. This is primarily due to limitations in linking habitat features, dynamic physical processes, and trophic transfer of energy to higher taxa at the landscape scale. Here, we conducted large-scale enclosure experiments across varying habitats on a fluvial floodplain as a model system to measure factors that influence habitat-specific growth rates in multiple Chinook Salmon (Oncorhynchus tshawytscha) stocks important to fisheries and of conservation concern. Using an ecosystem approach, we reveal that landscape context, water residence time, and habitat type (agricultural, wetland, river channel) result in different hot-spots of primary and secondary food production. This variation in the aquatic foodscape resulted in significant variation in salmon growth rates and ultimate size and morphology across the landscape. Floodplain habitats generally exhibited higher water residence times as highlighted by higher specific conductance, salinity, and chlorophyll-a values. Pelagic invertebrate abundance was 10 to 100 times more abundant in the off-channel habitats compared to the river channels. The average daily growth rates of the juvenile Chinook Salmon ranged from 0.15 mm day−1 and 0.01 g day−1 in the riverine habitat to 0.55 mm day−1 and 0.07 g day−1 in the off-channel habitat. These data were used to build mixed effects models that showed the influence of chlorophyll-a concentration, water temperature and pelagic invertebrate composition on fish growth across locations throughout the experiment. As landscapes become increasingly simplified there is increased risk of losing the mosaic of habitats necessary to achieve enhanced fish growth and phenotypically diverse and sustainable salmon populations. This in-situ experimental and modeling approach can be applied to other systems to develop ecosystem indicators such as habitat-specific fish growth rates to manage landscapes and processes to support resilient fish populations.

Fish face many anthropogenic stressors. Authorities in marine, estuarine, and freshwater realms often share interdependent fisheries management goals, but address singular stressors independently. Here, we present a case study suggesting that coordinating stressor relief across management realms may synergize conservation efforts, especially to actualize restoration benefits. Major efforts are underway to restore juvenile salmon habitat across California’s Central Valley landscape, but it is unclear how fisheries and flow management will influence juvenile salmon occupancy of restored sites. Leveraging monitoring data, we find that for juvenile salmon (

Aquatic ecosystems worldwide face growing threats from elevated levels of contaminants from human activities. Toxic levels of selenium (Se) shown to cause deformities in birds, fish, and mammals can transfer from parents to progeny during embryonic development or accumulate through Se-enriched diets. For migratory species that move across landscapes, tracking exposure to elevated Se is vital to mitigating vulnerabilities. Yet, traditional toxicological investigations resolve only recent Se exposure. Here, we use a novel combination of X-ray fluorescence microscopy and depositional chronology in a biomineral to reveal for the first time provenance, life stage, and duration of toxic Se exposure over the lifetime of an organism. Spinal deformities observed in wild Sacramento Splittail (Pogonichthys macrolepidotus), an imperiled migratory minnow, were attributed to elevated Se acquired through maternal transfer and juvenile feeding on contaminated prey. This novel approach paves the way for diagnosing sources, pathways, and potential for a cumulative exposure of Se relevant for conservation.

Rare phenotypes and behaviors adopted by only few individuals in a population are often overlooked, yet they may serve a heightened role for many organisms coping with warming climates. In threatened spring-run Chinook salmon spawning at the edge of the species range (Central Valley, CA USA), late-migrating juveniles were critical to cohort success in years characterized by multi-year droughts and ocean heatwaves. Late migrants rely on cool over-summer river temperatures, and are thus increasingly rare due to the combined effects of warming and dam construction. Yet our results suggest, the further loss of this within-population diversity could have critical impacts to their persistence in a warming climate. Our modeling predicts that thermally appropriate river conditions to support this phenotype will shrink rapidly in the future, and will primarily occur above impassable dams. Importantly, while late migrants dominated returns in some years, interannual variability in individual growth rates and migratory strategies suggests the importance of portfolio effects for these at-risk populations. Reconnecting and maintaining diverse habitat mosaics to support phenotypic and phenological diversity will be integral to the long term persistence of this species.

Floodplains represent critical nursery habitats for a variety of fish species due to their highly productive food webs, yet few tools exist to quantify the extent to which these habitats contribute to ecosystem-level production. Here we conducted a large-scale field experiment to characterize differences in food web composition and stable isotopes (δ¹³C, δ¹⁵N, δ³⁴S) for salmon rearing on a large floodplain and adjacent river in the Central Valley, California, USA. The study covered variable hydrologic conditions including flooding (1999, 2017), average (2016), and drought (2012–2015). In addition, we determined incorporation rates and tissue fractionation between prey and muscle from fish held in enclosed locations (experimental fields, cages) at weekly intervals. Finally, we measured δ³⁴S in otoliths to test if these archival biominerals could be used to reconstruct floodplain use. Floodplain-reared salmon had a different diet composition and lower δ13C and δ³⁴S (δ¹³C = -33.02±2.66‰, δ³⁴S = -3.47±2.28‰; mean±1SD) compared to fish in the adjacent river (δ¹³C = -28.37±1.84‰, δ³⁴S = +2.23±2.25‰). These isotopic differences between habitats persisted across years of extreme droughts and floods. Despite the different diet composition, δ¹⁵N values from prey items on the floodplain (δ¹⁵N = 7.19±1.22‰) and river (δ¹⁵N = 7.25±1.46‰) were similar, suggesting similar trophic levels. The food web differences in δ13C and δ³⁴S between habitats were also reflected in salmon muscle tissue, reaching equilibrium between 24–30 days (2014, δ¹³C = -30.74±0.73‰, δ³⁴S = -4.6±0.68‰; 2016, δ¹³C = -34.74 ±0.49‰, δ³⁴S = -5.18±0.46‰). δ³⁴S measured in sequential growth bands in otoliths recorded a weekly time-series of shifting diet inputs, with the outermost layers recording time spent on the floodplain (δ³⁴S = -5.60±0.16‰) and river (δ³⁴S = 3.73±0.98‰). Our results suggest that δ¹³C and δ³⁴S can be used to differentiate floodplain and river rearing habitats used by native fishes, such as Chinook Salmon, across different hydrologic conditions and tissues. Together these stable isotope analyses provide a toolset to quantify the role of floodplains as fish habitats.

Author(s): Lehman, Brendan M.; Johnson, Rachel C.; Adkison, Mark; Burgess, Oliver T.; Connon, Richard E.; Fangue, Nann A.; Foott, J. Scott; Hallett, Sascha L.; Martinez–Lopez, Beatriz; Miller, Kristina M.; Purcell, Maureen K.; Som, Nicholas A.; Valdes–Donoso, Pablo; Collins, Alison L. | Abstract: Chinook Salmon (Oncorhynchus tshawytscha) are increasingly vulnerable to anthropogenic activities and climate change, especially at their most southern species range in California’s Central Valley. There is considerable interest in understanding stressors that contribute to population decline and in identifying management actions that reduce the impacts of those stressors. Along the west coast of North America, disease has been linked to declining numbers of salmonids and identified as a key stressor resulting in mortality. In the Central Valley, targeted studies have revealed extremely high prevalence of infectious agents and disease. However, there has been insufficient monitoring to understand the effect that disease may have on salmon populations. In order to inform future research, monitoring, and management efforts, a two-day workshop on salmon disease was held at UC Davis on March 14-15, 2018. This paper summarizes the science presented at this workshop, including the current state of knowledge of salmonid disease in the Central Valley and current and emerging tools to better understand its impacts on salmon. We highlight case studies from other systems where successful monitoring programs have been implemented. First, in the Klamath River where the integration of several data collection and modeling approaches led to the development of successful management actions, and second in British Columbia where investment in researching novel technologies led to breakthroughs in the understanding of salmon disease dynamics. Finally, we identify key information and knowledge gaps necessary to guide research and management of disease in Central Valley salmon populations.

Bar-built coastal lagoons are dynamic ecosystems at the land-sea interface that are important habitats for a variety of species. This study examined the habitat ecology of two lagoon species, the endangered Tidewater Goby (Eucyclogobius newberryi) and the Prickly Sculpin (Cottus asper) by reconstructing individual life histories from patterns in the concentration of the element Sr (as ratioed to Ca; Sr:Ca) in otoliths. Specific objectives were to (1) elucidate any movements of individual fishes among three primary habitat components of typical bar-built lagoon systems: coastal ocean, brackish lagoon, and freshwater watershed streams, and (2) determine if either species exhibited a consistent life history as defined by a stereotypical otolith Sr:Ca chronology, which could be indicative of a consistent range of salinity or temperature occupied through ontogeny. Results suggested that Tidewater Goby was a lagoon resident and that Prickly Sculpin exhibited migrations between lagoon and watershed stream habitats. There was no strong evidence in either species of ocean occupancy or of a stereotypical Sr:Ca chronology, the latter suggesting the full range of available lagoon habitat in terms of salinity and temperature was likely utilized at all life stages. These findings add to the body of evidence that bar-built lagoons are not isolated habitats, and holistic management of these habitats with adjoining watershed and marine environments could increase habitat connectivity across the landscape, with potential benefits to fishes.

Estuarine food webs are complex, as marine, freshwater, and terrestrial inputs combine and contribute variable amounts of organic material. Seasonal fluctuations in precipitation amplify the dynamism inherent to estuarine food webs, particularly in lagoonal estuaries, which can be seasonally closed and disconnected from the ocean in low-runoff periods (bar-built lagoons). Despite their abundance along coastlines in Mediterranean climates, the organic matter sources fueling bar-built lagoon food webs are poorly understood, particularly with respect to seasonal hydrologic variability, episodic marine connections, and internal nutrient cycling. In this study, we evaluate the food web of a bar-built lagoon with respect to seasonal differences in lagoon water quality, the sources of organic matter which support consumers, and the trophic ecology of resident fishes. Observed water quality conditions reflected biogeochemical processes associated with salinity-driven stratification and high lagoon residence times and were associated with strong seasonal differences in the contribution of different organic matter sources to lagoon consumers. A variety of organic matter sources supported consumers; marine inputs were important to lagoon food webs in spring when the lagoon was open, while summer food webs were largely driven by phytoplankton which was likely fueled by internal nutrient cycling. Fish diets were largely comprised of crustaceans and fish eggs, with clearly defined trophic niches in spring but high overlap in summer. This study demonstrates that the seasonal changes in bar-built lagoon food webs are largely dependent on ocean connectivity and internal cycling within the lagoon, rather than watershed processes as is typical for many estuaries.

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 (87Sr/86Sr) 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.

Protecting habitats for imperiled species is central to conservation efforts. However, for migratory species, identifying juvenile habitats that confer success requires tracking individuals to reproduction. Here, we used otolith strontium isotope ratios (87Sr/86Sr) to reconstruct juvenile habitat use by endangered Sacramento River winter-run Chinook salmon that survived to adulthood. The isotope data revealed that 44–65% of surviving adults reared in non-natal habitats, most of which is not designated as critical habitat under the Endangered Species Act. Juveniles entered these non-natal habitats at small sizes, yet left freshwater at a similar size to those that reared in the mainstem Sacramento River, suggesting these alternate rearing habitats provide suitable growth conditions. These findings indicate Sacramento River winter-run Chinook salmon rely on rearing habitats across a broader geographic region than previously known, potentially opening up greater restoration and conservation opportunities for species recovery.

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., In a heavily dammed Californian river, lower, less variable stream flows were associated with reduced salmon production, and suppressed winter flow cues with reduced early emigration of fry. Otolith records in the returning adults revealed strong selection against early and late migrants, likely resulting from degradation of downstream habitats and increasingly hot summers. Conversely, managed reservoir releases appeared to benefit spring migrants. Yet even with this weakened portfolio, maintaining a broad migratory window increased adult production and reduced variance. This study highlights the importance of freshwater flow and habitat management to recover salmon populations in an increasingly unpredictable climate.

The ability of salmon to navigate from the ocean back to their river of origin to spawn acts to reinforce local adaptation and maintenance of unique and heritable traits among salmon populations. Here, the extent to which Chinook salmon Oncorhynchus tshawytscha from the same freshwater breeding groups associate together in the ocean at regional and smaller-scale aggre- gations prior to homeward migration is evaluated. Natural variation in salmon otolith daily growth bands, strontium isotopes ( 87 Sr/ 86 Sr), and microsatellite DNA were used as intrinsic tags to link the distributions of fish caught in the ocean with their freshwater origins. Adults were caught from vessels by hook and line in small aggregations (7�18 ind.) at the same geographic location (1�24 km of coastline) and time (4�36 h) from 3 ocean regions along central California, USA. Salmon caught together in aggregations were from the same genetic group, and to a lesser extent, of the same natal origin (individual rivers or hatcheries). However, at regional scales, adult salmon mixed. Central Valley winter-run Chinook salmon caught together in the ocean varied in the duration of freshwater rearing for up to 2�3 mo prior to seaward migration, suggesting associa- tions within the group were not established in freshwater or maintained over the lifetime of the fish. Our findings are consistent with coarser information indicating stocks are distributed differ- ently in time and space, but larger sample sizes are required to evaluate the consistency of pat- terns at smaller spatial scales. This study uncovers freshwater associations prior to homeward migration, a principle and undocumented prerequisite of the collective navigation hypothesis.

Estuaries provide critical habitat for a vast array of fish and wildlife but are also a nexus for core economic activities that mobilize and concentrate contaminants that can threaten aquatic species. Selenium (Se), an essential element and potent reproductive toxin, is enriched in parts of the San Francisco Estuary (SFE) to levels known to cause toxicity, yet the risk of Se to species that inhabit the SFE is not well understood. We quantified Se concentrations in muscle, liver and ovary of the demersal cyprinid Sacramento Splittail from six regions in the SFE at three time points to evaluate Se exposure risk. Selenium levels exceeded proposed EPA criteria in ovary and thresholds of concern for liver in 15% and 20%, respectively, of fish collected in the fall of 2010, preceding the discovery of juvenile Splittail displaying a high incidence (>40%) of spinal deformities characteristic of Se toxicity, and again in 2011. No exceedances were detected in muscle tissue. Selenium concentrations varied significantly among regions for muscle (F5,113 = 20.49, p

Author(s): Herbold, Bruce; Carlson, Stephanie M.; Henery, Rene; Johnson, Rachel C.; Mantua, Nate; McClure, Michelle; Moyle, Peter B.; Sommer, Ted | Abstract: California’s salmonids are at the southern limits of their individual species’ ranges, and display a wide diversity of strategies to survive in California’s highly variable climate. Land use changes after statehood in 1850 eliminated important habitats, or blocked access to them, and reduced the abundance, productivity, and distribution of California’s salmon. Habitat simplification, fishing, hatchery impacts, and other stressors led to the loss of genetic and phenotypic (life history, morphological, behavioral, and physiological) diversity in salmonids. Limited diversity and habitat loss left California salmon with reduced capacity to cope with a variable and changing climate. Since 1976, California has experienced frequent droughts, as were common in the paleo-climatological record, but rare in the peak dam-building era of 1936–1976. Increasing temperatures and decreasing snowpacks have produced harsher conditions for California’s salmon in their current habitats than they experienced historically. The most likely way to promote salmon productivity and persistence in California is to restore habitat diversity, reconnect migratory corridors to spawning and rearing habitats, and refocus management to replenish the genetic and phenotypic diversity of these southernmost populations.

Ecologists are pressed to understand how climate constrains the timings of annual biological events (phenology). Climate influences on phenology are likely significant in estuarine watersheds because many watersheds provide seasonal fish nurseries where juvenile presence is synched with favorable conditions. While ecologists have long recognized that estuaries are generally important to juvenile fish, we incompletely understand the specific ecosystem dynamics that contribute to their nursery habitat value, limiting our ability to identify and protect vital habitat components. Here we examined the annual timing of juvenile coldwater fish migrating through a seasonally warm, hydrologically managed watershed. Our goal was to (1) understand how climate constrained the seasonal timing of water conditions necessary for juvenile fish to use nursery habitats and (2) inform management decisions about (a) mitigating climate‐mediated stress on nursery habitat function and (b) conserving heat‐constrained species in warming environments. Cool, wet winters deposited snow and cold water into mountains and reservoirs, which kept the lower watershed adequately cool for juveniles through the spring despite the region approaching its hot, dry summers. For every 1°C waters in April were colder, the juvenile fish population (1) inhabited the watershed 4–7 d longer and (2) entered marine waters, where survival is size selective, at maximum sizes 2.1 mm larger. Climate therefore appeared to constrain the nursery functions of this system by determining seasonal windows of tolerable rearing conditions, and cold water appeared to be a vital ecosystem component that promoted juvenile rearing. Fish in this system inhabit the southernmost extent of their range and already rear during the coolest part of the year, suggesting that a warming climate will truncate rather than shift their annual presence. Our findings are concerning for coldwater diadromous species in general because warming climates may constrain watershed use and diminish viability of life histories (e.g., late springtime rearing) and associated portfolio benefits over the long term. Lower watershed nurseries for coldwater fish in warming climates may be enhanced through allocating coldwater reservoir releases to prolong juvenile rearing periods downstream or restorations that facilitate colder conditions.

Summary 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.

The Sacramento splittail (Pogonichthys macrolepidotus) is a relatively large (400 mm), long-lived (8 years) demersal cyprinid of conservation importance endemic to the San Francisco Estuary (SFE), California, USA. It exhibits a semi-anadromous life cycle spending adult life in low to moderate salinity (0-12) habitat with migrations into upstream freshwater rivers and floodplains for spawning during winter-spring. The species persists as two genetically distinguishable populations — one dominant and one subordinate — separated by discrete spawning habitats that we suggest resemble an island-mainland metapopulation structure. The populations overlap in distribution in the SFE, yet segregation is maintained with individuals tending to aggregate or school with others of similar population heritage and natal origin. The populations are spatially connected via dispersal of the dominant population into the subordinate population's spawning habitat when climate patterns produce freshwater outflow sufficient to form a bridge of suitable low salinity habitat across the upper SFE. Habitat affinities of the two populations, hydrodynamic modeling studies, and historical outflow records together suggest such conditions occur in approximately 1/3 of years overall with an irregular frequency. This dynamic pattern of spatial connectivity controlled by climate variability may be an important driver of gene flow between the two populations. Resume : Pogonichthys macrolepidotus est un cyprinide demersal longevif (8 ans) relativement grand (400 mm) d'importance pour

doi: https://doi.org/10.15447/sfews.2017v15iss3art1A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winter-run Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Identification of habitats responsible for the successful production and recruitment of rare migratory species is a challenge in conservation biology. Here, a tool was developed to assess life stage linkages for the threatened potamodromous cyprinid Clear Lake hitch Lavinia exilicauda chi. Clear Lake hitch undertake migrations from Clear Lake (Lake County, CA, USA) into ephemeral tributary streams for spawning. An aqueous isoscape of strontium isotopic ratios (87Sr/86Sr) was constructed for Clear Lake and its watershed to trace natal origins and migration histories of adult recruits. Aqueous 87Sr/86Sr differentiated Clear Lake from 8 of 10 key tributaries and clustered into 5 strontium isotope groups (SIGs) with 100% classification success. Otolith 87Sr/86Sr showed all five groups contributed variably to the population. The age at which juveniles migrated from natal streams to Clear Lake ranged from 11 to 152 days (mean±s.d., 43±34 days) and was positively associated with the permanency of natal habitat. This information can be used by resource managers to develop conservation actions for Clear Lake hitch. This study demonstrates the utility of strontium isotopes in otoliths as a tool to identify important freshwater habitats occupied over the lifespan of an individual that would otherwise be challenging or impossible to trace with other methods.A

Selective mortality during early life history stages can have significant population- level consequences, yet critical periods when selective mortality occurs, the strength of selection, and under what environmental conditions can be difficult to identify. Here, we used otolith microstructure and chemistry to examine the factors potentially linked to selective mortality of juvenile fall-run Chinook salmon Oncorhynchus tshawytscha from California's Central Valley during early ocean residence. Back-calculated size and growth rates of the population were com- pared across 3 sample periods: as juveniles exited the San Francisco Bay estuary (estuary-exit), after their first month at sea (summer-ocean) and 5 mo after ocean entry (fall-ocean). We com- pared mortality dynamics during years of exceptional recruitment (addition of individuals to har- vestable population; 2000 and 2001) to a year of poor recruitment (2005). Otoliths from 2005 were also analyzed for sulfur isotopes to discern hatchery from naturally spawned stock. Significant size and growth-rate selective mortality were detected during the first month at sea in the low recruit- ment year of 2005, but not in 2000 and 2001. Individuals that were larger and growing faster dur- ing freshwater and estuarine rearing were more likely to survive to summer and fall in the low recruitment year. There was a slight, but insignificant, increase in the proportion of hatchery to naturally spawned individuals from estuary-exit to fall-ocean, suggesting that fish from neither origin were overwhelmingly favored. Our results suggest that Central Valley Chinook salmon can be subject to significant size and growth-rate selective mortality resulting in low adult abundance, and this mortality appears independent of origin.

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.

Active Galactic Nuclei: Basic Physics and Main Components.- Multiwavelength Evidence of the Physical Processes in Radio Jets.- The Broad-Line Region in Active Galactic Nuclei.- Cold Gas Near Active Galactic Nuclei.- AGN Beyond the 100pc Scale.- The Fueling and Evolution of AGN: Internal and External Triggers.- X-Ray Survey Results on Active Galaxy Physics and Evolution.- The Links Between AGN and Galaxy Formation.

We are carrying out a multiwavelength and spectroscopic study of a volume-limited sample of very nearby galaxies. Our main aim is to assess the prevalence and nature of activity in normal galaxies to the lowest possible level. In this poster we present some results from our multiwavelength imaging and some very preliminary spectroscopic results.

Maintaining viable populations of salmon in the wild is a primary goal for many conservation and recovery programs. The frequency and extent of connectivity among natal sources defines the demographic and genetic boundaries of a population. Yet, the role that immigration of hatchery-produced adults may play in altering population dynamics and fitness of natural populations remains largely unquantified. Quantifying, whether natural populations are self-sustaining, functions as sources (population growth rate in the absence of dispersal, λ>1), or as sinks (λ