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People seek reliable natural resources despite climate change. Diverse habitats and biologies stabilize productivity against disturbances like climate, prompting arguments to promote climate-resilient resources by prioritizing complex, less-modified ecosystems. These arguments hinge on the hypothesis that simplifying and degrading ecosystems will reduce resources' climate resilience, a process liable to be cryptically evolving across landscapes and human generations, but rarely documented. Here, we examined the industrial era (post 1848) of California's Central Valley, chronicling the decline of a diversified, functional portfolio of salmon habitats and life histories and investigating for empirical evidence of lost climate resilience in its fishery. Present perspectives indicate that California's dynamic, warming climate overlaid onto its truncated, degraded habitat mosaic severely constrains its salmon fishery. We indeed found substantial climate constraints on today's fishery, but this reflected a shifted ecological baseline. During the early stages of a stressor legacy that transformed the landscape and -- often consequently -- compressed salmon life history expression, the fishery diffused impacts of dry years across a greater number of fishing years and depended less on cool spring-summer transitions. The latter are important given today's salmon habitats, salmon life histories, and resource management practices, but are vanishing with climate change while year-to-year variation in fishery performance is rising. These findings give empirical weight to the idea that human legacies influence ecosystems' climate resilience across landscapes and boundaries (e.g., land/sea). They also raise the question of whether some contemporary climate effects are recent and attributable not only to increasing climate stress, but to past and present human actions that erode resilience. In general, it is thus worth considering that management approaches that prioritize complex, less-modified ecosystems may stabilize productivity despite increasing climate stress and such protective actions may be required for some ecological services to persist into uncertain climate futures.

SteelheadOncorhynchus mykisssmolts must migrate through distinct freshwater, estuarine, and coastal habitats, each with unique biological and physical characteristics, on their route from natal streams to the ocean to complete their life cycle. Fewer than 15% of steelhead smolts survived their migration from the Nisqually River through Puget Sound to the Pacific Ocean from 2006 to 2009 and in 2014. Rapid smolt migration coupled with evidence of smolt mortality at harbor sealPhoca vitulinahaulouts during 2014 indicated that predation by pinnipeds was an important source of mortality. When Puget Sound temperatures increased with the Northeast Pacific heat wave from late 2014 to 2016, steelhead smolt survival probabilities increased to 38% in 2016 and 2017, then decreased again as Puget Sound water temperatures cooled. Many ecological changes accompanied the increased marine temperatures, including the increased abundance of northern anchovyEngraulis mordaxin Puget Sound. The years of lowest smolt mortality coincided with abundant larval and post-larval anchovy during the previous year; and we provide data from telemetered harbor seals and steelhead indicating that the resulting high abundance of age-1+ anchovy provided an alternative prey source for predators of migrating steelhead smolts. Identification of ecological mechanisms that drive patterns in the survival of Endangered Species Act-threatened steelhead provides critical understanding of the systems within which management strategies must operate.

We examined historical and contemporary trends for a suite of groundfish species in Puget Sound, Washington, USA, to ask how the groundfish community has responded following shifts in fishing regulations, climate, food web, and a growing human population in the surrounding watershed. We used contemporary data (1990-2017) from a standardized annual bottom trawl survey with historical logbook information (1948-1977) from a research vessel. We standardized data to account for spatial and temporal effects on catch rate by first fitting a Bayesian model to the contemporary data, and then using the posterior distributions of the covariates as prior distributions when fitting models to the historical data. We found that most of the 15 species chosen for analysis had highly variable population dynamics within both time periods, and that patterns of variability were similar in the contemporary and historical time period. Surprisingly, there was little evidence of community-wide recovery following regulations that first limited and then banned commercial bottom trawling in the late 1980s to mid-1990s. Spotted ratfish and English sole dominated catches in both time periods, and species that were common in the historical time period were also common in the contemporary time period. The absence of coherent community changes in response to fisheries regulations and other major social and ecological changes may signal the complex dynamics of an urban estuary that is subject to multiple external drivers, and speaks to the need to consider long-term dynamic behavior of populations and communities when establishing ecological indicators.

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 (

Preseason abundance forecasts drive management of US West Coast salmon fisheries, yet little is known about how environmental variability influences forecast performance. We compared forecasts of Chinook salmon (Oncorhynchus tshawytscha) against returns for (i) key California-Oregon ocean fishery stocks and (ii) high priority prey stocks for endangered Southern Resident Killer Whales (Orcinus orca) in Puget Sound, Washington. We explored how well environmental indices (at multiple locations and time lags) explained performance of forecasts based on different methods (i.e. sibling-based, production-based, environment-based, or recent averages), testing for nonlinear threshold dynamics. For the California stocks, no index tested explained >50% of the variation in forecast performance, but spring Pacific Decadal Oscillation and winter North Pacific Index during the year of return explained >40% of the variation for the sibling-based Sacramento Fall Chinook forecast, with nonlinearity and apparent thresholds. This suggests that oceanic conditions experienced by adults (after younger siblings returned) have the most impact on sibling-based forecasts. For Puget Sound stocks, we detected nonlinear/threshold relationships explaining >50% of the variation with multiple indices and lags. Environmental influences on preseason forecasts may create biases that render salmon fisheries management more or less conservative, and therefore could motivate the development of ecosystem-based risk assessments.

Efforts to understand causes of declines in productivity of species of concern often involve retrospective evaluation of multiple possible causes based on trends in relevant ecological indicators. We describe a hypothesis testing framework for examining declines in marine survival for coho and Chinook salmon in the Salish Sea. Independent populations of both anadromous species have declined over the last 50 years, prompting extensive examination of mortality in different life stages. Previous studies have identified declining trends in marine survival, and we re-evaluated these trends in light of a number of possible hypotheses for declines. We laid out seven potential explanations for declines: changes in predator buffering related to abundance and timing, density-dependent or -independent food availability, water quality, timing of freshwater delivery to Puget Sound, and anthropogenic impacts. We compiled ecosystem indicators relevant to these hypotheses and used generalized additive models (GAMs) to examine multivariate relationships with survival from multiple coho and Chinook salmon stocks. We also developed additional models using the most informative indicators based on variable importance weighting (VIW) from the seven hypothesis groups. We examined how these models explained overall trends in marine survival, as well as survival in three temporal stanzas (before, during, and after a major decline, based on statistical breakpoint analysis). Across the entire time series, best fitting models explained 30–40% of the variation in the survival data. Best fitting models were from multiple hypotheses, including predation (abundance and timing), competition, water quality, and anthropogenic impacts; the freshwater delivery hypothesis was the least supported. Different models performed best (lowest error) during different stanzas of the coho salmon marine survival time series and the two VIW models were generally the top performing models, but performance varied in different years. Indicators with the strongest support included seal abundance, herring abundance, timing of hatchery salmon releases, and indicators related to water properties like stratification and temperature. These findings suggest that multiple processes embedded in several of our hypotheses influence marine survival but that an ecological “smoking gun” for Salish Sea salmon declines will remain elusive.

Species of conservation interest are often rare or elusive, and often require labor-intensive population surveys for management. Sampling genetic traces of such species from environmental media such as water, air, or soil (environmental DNA; eDNA) can provide noninvasive and cost-effective means of monitoring. However, eDNA results may not align with traditional survey methods (e.g., visual, net) making it difficult to interpret eDNA results. We present the results of parallel beach seine and quantitative-PCR (qPCR) surveys of a threatened Chinook salmon (Oncorhynchus tshawytscha) from Skagit Bay, an estuary in Washington, USA. Our replicated design and hierarchical statistical model assesses the abundance, biomass, and DNA concentration at two spatial scales (site- and population-) over five months. We find both eDNA- and seine-derived abundance indices reflect the seasonal migration of salmon; at the population-scale, eDNA and seines provide virtually identical quantitative information. At the site scale, the methods are less correlated, suggesting the methods reveal different information about a patchily distributed species. Environmental DNA may act to smooth otherwise patchy biological signals in space and time. Reduced within-site variability for eDNA relative to seines suggests that eDNA may offer more precise population estimates. We partition sources of variability in space and time and compare eDNA and seine surveys – a first, to our knowledge – and so reveal the behavior of eDNA in the field. Our results underscore the value of using eDNA in conjunction with traditional surveys. Combining eDNA and seine estimates should improve the population data on which management of threatened species depends.

Many small pelagic fish species exhibit dramatic fluctuations in abundance accompanied by range expansions during periods of favorable environmental conditions. The location and extent of suitable habitats also shift in response to both short term variability and long term trends in climate. Near the margins of a contemporary range, trends in abundance may reflect a continuation of historical variability but may also foreshadow future changes in distribution. The Salish Sea (all inland marine waters of Washington State and southern British Columbia; made up of the Strait of Georgia, Strait of Juan de Fuca, and Puget Sound) is a highly productive estuarine system at the northern end of the distribution of Northern Anchovy (Engraulis mordax). An apparent recent (2014–2016) increase in Northern Anchovy abundance has generated interest in the dynamics of this species in the Salish Sea. We compiled recent and historical data to understand spatiotemporal patterns of distribution and fluctuations in abundance over the last century. Spatially-consistent occurrence of eggs, larvae, and juveniles, and year-round presence of multiple age classes, confirm that successful spawning and recruitment of Northern Anchovy occurs within the Salish Sea. Most periods of elevated Northern Anchovy abundance in the last century have corresponded to, or lagged, periods of elevated ocean temperatures. While a 2005 peak in abundance within the Salish Sea also corresponded to higher abundance of Northern Anchovy in adjacent regions of the coastal Pacific Ocean, it seems unlikely that Salish Sea abundance is controlled primarily by advection or migration from external populations. Persistence of elevated ocean temperatures like those observed from 2014 to 2016 could lead to consistently high abundance of Northern Anchovy within the Salish Sea, with implications for trophic relationships and ecosystem function.

SUMMARYCoho salmon (Oncorhynchus kisutch), Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) in Puget Sound and the Strait of Georgia have exhibited declines in marine survival over the last 40 years. While the cause of these declines is unknown, multiple factors, acting cumulatively or synergistically, have likely contributed. To evaluate the potential contribution of a broad suite of drivers on salmon survival, we used qualitative network modelling (QNM). QNM is a conceptually based tool that uses networks with specified relationships between the variables. In a simulation framework, linkages are weighted and then the models are subjected to user-specified perturbations. Our network had 33 variables, including: environmental and oceanographic drivers (e.g., temperature and precipitation), primary production variables, food web components from zooplankton to predators and anthropogenic impacts (e.g., habitat loss and hatcheries). We included salmon traits (survival, abundance, residence time, fitness and size) as response variables. We invoked perturbations to each node and to suites of drivers and evaluated the responses of these variables. The model showed that anthropogenic impacts resulted in the strongest negative responses in salmon survival and abundance. Additionally, feedbacks through the food web were strong, beginning with primary production, suggesting that several food web variables may be important in mediating effects on salmon survival within the system. With this model, we were able to compare the relative influence of multiple drivers on salmon survival.

While individual growth ultimately reflects the quality and quantity of food resources, intra and interspecific interactions for these resources, as well as individual size, may have dramatic impacts on growth opportunity. Out‐migrating anadromous salmonids make rapid transitions between habitat types resulting in large pulses of individuals into a given location over a short period, which may have significant impact on demand for local resources. We evaluated the spatial and temporal variation in IGF‐1 concentrations (a proxy for growth rate) and the relationship between size and concentration for juvenile Chinook salmon in Puget Sound, WA, USA, as a function of the relative size and abundance of both Chinook salmon and Pacific herring, a species which commonly co‐occurs with salmonids in nearshore marine habitats. The abundance of Chinook salmon and Pacific herring varied substantially among the sub‐basins as function of outmigration timing and spawn timing, respectively, while size varied systematically and consistently for both species. Mean IGF‐1 concentrations were different among sub‐basins, although patterns were not consistent through time. In general, size was positively correlated with IGF‐1 concentration, although the slope of the relationship was considerably higher where Pacific herring were more abundant than Chinook salmon; specifically where smaller individual herring, relative to Chinook salmon, were more abundant. Where Pacific herring were less abundant than Chinook salmon, IGF‐1 concentrations among small and large Chinook salmon were more variable and showed no consistent increase for larger individuals. The noticeable positive effect of relative Pacific herring abundance on the relationship between size and individual growth rates likely represents a shift to predation based on increased IGF‐1 concentrations for individual Chinook salmon that are large enough to incorporate fish into their diet and co‐occur with the highest abundances of Pacific herring.

Identifying factors that influence anadromous Pacific salmon (Oncorhynchus spp.) population dynamics is complicated by their diverse life histories and large geographic range. Over the last several decades, Chinook salmon (O. tshawytscha) populations from coastal areas and the Salish Sea have exhibited substantial variability in abundance. In some cases, populations within the Salish Sea have experienced persistent declines that have not rebounded. We analyzed a time series of early marine survival from 36 hatchery Chinook salmon populations spanning ocean entry years 1980–2008 to quantify spatial and temporal coherence in survival. Overall, we observed higher inter-population variability in survival for Salish Sea populations than non-Salish Sea populations. Annual survival patterns of Salish Sea populations covaried over smaller spatial scales and exhibited less synchrony among proximate populations relative to non-Salish Sea populations. These results were supported by multivariate autoregressive state space (MARSS) models which predominantly identified region-scale differences in survival trends between northern coastal, southern coastal, Strait of Georgia, and Puget Sound population groupings. Furthermore, Dynamic Factor Analysis (DFA) of regional survival trends showed that survival of southern coastal populations was associated with the North Pacific Gyre Oscillation, a large-scale ocean circulation pattern, whereas survival of Salish Sea populations was not. In summary, this study demonstrates that survival patterns in Chinook salmon are likely determined by a complex hierarchy of processes operating across a broad range in spatial and temporal scales, presenting challenges to the management of mixed-stock fisheries.

Identifying causes of structural ecosystem shifts often requires understanding trophic structure, an important determinant of energy flow in ecological communities. In coastal pelagic ecosystems worldwide, increasing jellyfish (Cnidaria and Ctenophora) at the expense of small fish has been linked to anthropogenic alteration of basal trophic pathways. However, this hypothesis remains untested in part because baseline description of fish–jellyfish trophic dynamics, and the environmental features that influence them are lacking. Using stable isotopes of carbon (δ13C) and nitrogen (δ15N), we examined spatiotemporal patterns of fish and jellyfish trophic structure in greater Puget Sound, an urbanizing fjord estuary in the NW United States. We quantified niche positions of constituent species, niche widths and trophic overlap between fish and jellyfish assemblages, and several community‐level trophic diversity metrics (resource diversity, trophic length, and niche widths) of fish and jellyfish combined. We then related assemblage‐ and community‐level measures to landscape gradients of terrestrial–marine connectivity and anthropogenic influence in adjacent catchments. Relative niche positions among species varied considerably and displayed no clear pattern except that fish generally had higher δ15N and lower δ13C relative to jellyfish, which resulted in low assemblage‐level trophic overlap. Fish assemblages had larger niche widths than jellyfish in most cases and, along with whole community trophic diversity, exhibited contrasting seasonal patterns across oceanographic basins, which was positively correlated to landscape variation in terrestrial connectivity. In contrast, jellyfish niche widths were unrelated to terrestrial connectivity, but weakly negatively correlated to urban land use in adjacent catchments. Our results indicate that fish–jellyfish trophic structure is highly heterogeneous and that disparate processes may underlie the trophic ecology of these taxa; consequently, they may respond divergently to environmental change. In addition, spatiotemporal variation in ecosystem connectivity, in this case through freshwater influence, may influence trophic structure across heterogeneous landscapes.

Understanding ecosystem drivers of fish stock performance is essential to improving conservation and management. We used a hypothesis-driven approach to identify potential ecosystem indicators and developed a retrospective analysis using regression models of steelhead trout marine survival in Puget Sound, an urban estuary in Washington State, USA, over a 30-year time series. Indicators related to predator abundance, the presence of hatchery Chinook salmon in the system, salinity of marine waters, and timing of cumulative river discharge explained the most variance in smolt survival. Seal abundance was the strongest predictor, showing a strong negative relationship with steelhead marine survival, indicating that predation pressure may influence marine survival. Several other predictors were supported in our models, but with much less individual explanatory power. Our results support the conclusion that a combination of factors with differing mechanisms have likely contributed to declining survival of steelhead in inland marine waters. This study emphasizes the importance of collecting long-term survival and environmental data, taking a hypothesis-based approach to understanding ecosystem drivers related to marine survival, and evaluating the mechanisms associated with survival for species with complex life histories like anadromous steelhead trout.

Across the Pacific Northwest, at least 17 intensively monitored watershed projects have been implemented to test the effectiveness of a broad range of stream restoration actions for increasing the freshwater production of salmon and steelhead and to better understand fish–habitat relationships. We assess the scope and status of these projects and report on challenges implementing them. We suggest that all intensively monitored watersheds should contain key elements based on sound experimental design concepts and be implemented within an adaptive management framework to maximize learning. The most significant challenges reported by groups were (1) improving coordination between funders, restoration groups, and researchers so that restoration and monitoring actions occur based on the project design and (2) maintaining consistent funding to conduct annual monitoring and evaluation of data. However, we conclude that despite these challenges, the intensively monitored watershed approach is the most reliable me...

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.

While numerous studies have shown that floodplain habitat complexity can be important to fish ecology, few quantify how watershed-scale complexity influences productivity. This scale mismatch complicates population conservation and recovery strategies that evaluate recovery at regional or multi-basin scales. We used outputs from a habitat status and trends monitoring program for ten of Puget Sound's large river systems to examine whether juvenile Chinook salmon productivity relates to watershed-scale habitat complexity. We derived habitat complexity metrics that quantified wood jam densities, side and braid to main channel ratios, and node densities from a remote sensing census of Puget Sound's large river systems. Principal component analysis revealed that 91% of variance in these metrics could be explained by two principal components. These metrics revealed gradients in habitat complexity across Puget Sound which were sensitive to changes in complexity as a result of restoration actions in one watershed. Mixed effects models revealed that the second principle component term (PC2) describing habitat complexity was positively related to log transformed subyearling Chinook per spawner productivity rates from 6-18 cohorts per watershed. Total subyearling productivity (subyearlings per spawner) and fry productivity (subyearling fry per spawner) rates were best described by models that included a positive effect of habitat complexity (PC2) and negative relationships with log transformed peak flow recurrence interval, suggestive of reduced survival due to egg destruction during floods. Total subyearling productivity (subyearlings per spawner) and parr productivity (subyearling parr per spawner) rates were best described by models that included a positive effect of habitat complexity (PC2) and negative relationships with log transformed spawner density, suggestive of density dependent limits on juvenile rearing habitat. We also found that coefficient of variation for log transformed subyearling productivity and subyearling fry productivity rates declined with increasing habitat complexity, supporting the idea that habitat complexity buffers populations from annual variation in environmental conditions. Therefore, we conclude that our watershed-scale census-based approach provided habitat complexity metrics that explained some of the variability in productivity of subyearling juveniles among Chinook salmon populations. Furthermore, this approach may provide a useful means to track and evaluate aggregate effects of habitat changes on the productivity of Endangered Species Act (ESA) listed Chinook salmon populations over time.

Coastal ecosystems face a variety of natural and anthropogenic influences, raising questions about mechanisms by which species abundance and composition change over time. We examined these questions by synthesizing 6 surface-trawling efforts in greater Puget Sound, Washington (USA), spanning 40 yr, and then determining changes in forage fish abundance and composition and jellyfish prevalence. We also assessed whether patterns were associated with potential anthropogenic pressures (human population density and commercial harvest) as well as large-scale climate signals. We found evidence for trends in abundance of all forage species in 4 sub-basins of Puget Sound. Cumulative distribution functions of catch per unit effort indicate that the historically dominant forage fishes (Pacific herring and surf smelt) have declined in sur- face waters in 2 sub-basins (Central and South Puget Sound) by up to 2 orders of magnitude. How- ever, 2 other species (Pacific sand lance and three-spine stickleback) increased in all 4 sub-basins. Consequently, species composition diverged among sub-basins over the last 40 yr. In addition, jelly - fish-dominated catches increased 3- to 9-fold in Central and South Puget Sound, and abundance positively tracked human population density across all basins. The strongest predictors of forage fish declines were human population density and commercial harvest. Climate signals offered additional explanatory power for forage fish but not jellyfish catch. These patterns suggest possi- ble linkages between coastal anthropogenic activities (e.g. development, pollution) and the abun- dance of forage fish and jellyfish in pelagic waters. Our findings also provide a basis for improving indicators for assessment, monitoring, and spatial planning to rehabilitate pelagic ecosystems.

Rising populations around coastal systems are increasing the threats to marine water quality. To assess anthropogenic fecal influence, subtidal waters were examined monthly for human- and ruminant-sourced Bacteroidales markers at 80 sites across six oceanographic basins of the Salish Sea (Washington State) from April through October, 2011. In the basins containing cities with individual populations >190,000, >50% of sites were positive for the human marker, while in the basins with high densities of dairy and cattle operations, ∼30% of sites were positive for the ruminant marker. Marker prevalence was elevated in spring (April and May) and fall (October) and reduced during summer (June through September), corresponding with seasonal precipitation. By logistic regression, the odds of human marker detection increased with percentage of adjacent catchment impervious surface, dissolved nitrate concentration, and abundance of low nucleic acid bacteria, but decreased with salinity and chlorophyll fluorescence. The odds of ruminant marker detection increased with dissolved ammonium concentration, mean flow rate for the nearest river, and adjacent shoreline length. These relationships are consistent with terrestrial to marine water flow as a transport mechanism. Thus, Bacteroidales markers traditionally used for identifying nearby sources can be used for assessing anthropogenic fecal inputs to regional marine ecosystems.

Understanding the factors contributing to declining smolt-to-adult survival (hereafter “smolt survival”) of Coho Salmon Oncorhynchus kisutch originating in the Salish Sea of southwestern British Columbia and Washington State is a high priority for fish management agencies. Uncertainty regarding the relative importance of mortality operating at different spatial scales hinders the prioritization of science and management activities. We therefore examined spatial and temporal coherence in smolt survivals for Coho Salmon based on a decision tree framework organized by spatial hierarchy. Smolt survival patterns of populations that entered marine waters within the Salish Sea were analyzed and compared with Pacific coast reference populations at similar latitudes. In all areas, wild Coho Salmon had higher survival than hatchery Coho Salmon. Coherence in Coho Salmon smolt survival occurred at multiple spatial scales during ocean entry years 1977–2010. The primary pattern within the Salish Sea was a decli...

Stable isotopes (δ15N and δ13C) offer one representation of an individual’s trophic niche and are important tools for elucidating ecological patterns and testing a diversity of hypotheses. Because δ15N and δ13C values are often obtained from the same sample, they compose a bivariate response that researchers commonly analyze using multivariate statistical methods. However, stable isotope data sets often exhibit hierarchical structure whereby samples may be clustered or grouped at multiple levels either as an artifact of sampling design or due to structure inherent in the sampled population (e.g., samples from individuals grouped according to life history stages, social groups, ages, or sizes classes). Ignoring such structure can result in overly optimistic confidence intervals and heighten the risk of observing significant differences where none exist. To address these issues, we suggest researchers utilize multivariate hierarchical models, which are a simple extension of univariate hierarchical methods. The models account for potential dependencies between δ15N and δ13C values, permit valid predictions of shifts in δ15N–δ13C space related to predictor variables, provide more accurate estimates of parameter uncertainty, and improved inferences on coefficients that correspond to groups with small to moderate quantities of data. We demonstrate advantages of multivariate hierarchical models by examining size-dependent shifts in δ15N–δ13C space in outmigrating post-smolt Chinook salmon sampled from an estuarine habitat. Given the prevalence of complex structure in ecological stable isotope data sets, multivariate hierarchical models should hold considerable value to food web and stable isotope ecologists.

A key step in identifying global change impacts on species and ecosystems is to quantify effects of multiple stressors. To date, the science of global change has been dominated by regional field studies, experimental manipulation, meta-analyses, conceptual models, reviews, and studies focusing on a single stressor or species over broad spatial and temporal scales. Here, we provide one of the first studies for coastal systems examining multiple stressor effects across broad scales, focused on the nursery function of 20 estuaries spanning 1,600 km of coastline, 25 years of monitoring, and seven fish and invertebrate species along the northeast Pacific coast. We hypothesized those species most estuarine dependent and negatively impacted by human activities would have lower presence and abundances in estuaries with greater anthropogenic land cover, pollution, and water flow stress. We found significant negative relationships between juveniles of two of seven species (Chinook salmon and English sole) and estuarine stressors. Chinook salmon were less likely to occur and were less abundant in estuaries with greater pollution stress. They were also less abundant in estuaries with greater flow stress, although this relationship was marginally insignificant. English sole were less abundant in estuaries with greater land cover stress. Together, we provide new empirical evidence that effects of stressors on two fish species culminate in detectable trends along the northeast Pacific coast, elevating the need for protection from pollution, land cover, and flow stressors to their habitats. Lack of response among the other five species could be related to differing resistance to specific stressors, type and precision of the stressor metrics, and limitations in catch data across estuaries and habitats. Acquiring improved measurements of impacts to species will guide future management actions, and help predict how estuarine nursery functions can be optimized given anthropogenic stressors and climate change scenarios.

Effective conservation and restoration of estuarine wetlands require accurate maps of their historical and current extent, as well as estimated losses of these valued habitats. Existing coast-wide tidal wetland mapping does not explicitly map historical tidal wetlands that are now disconnected from the tides, which represent restoration opportunities; nor does it use water level models or high-resolution elevation data (e.g. lidar) to accurately identify current tidal wetlands. To better inform estuarine conservation and restoration, we generated new maps of current and historical tidal wetlands for the entire contiguous U.S. West Coast (Washington, Oregon, and California). The new maps are based on an Elevation-Based Estuary Extent Model (EBEEM) that combines lidar digital elevation models (DEMs) and water level models to establish the maximum historical extent of tidal wetlands, representing a major step forward in mapping accuracy for restoration planning and analysis of wetland loss. Building from this new base, we also developed an indirect method for mapping tidal wetland losses, and created maps of these losses for 55 estuaries on the West Coast (representing about 97% of historical West Coast vegetated tidal wetland area). Based on these new maps, we estimated that total historical estuary area for the West Coast is approximately 735,000 hectares (including vegetated and nonvegetated areas), and that about 85% of vegetated tidal wetlands have been lost from West Coast estuaries. Losses were highest for major river deltas. The new maps will help interested groups improve action plans for estuarine wetland habitat restoration and conservation, and will also provide a better baseline for understanding and predicting future changes with projected sea level rise.

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.

Marine hydrokinetic power projects will operate as marine environments change in response to increased atmospheric carbon dioxide concentrations. We considered how tidal power development and stressors resulting from climate change may affect Puget Sound species listed under the U.S. Endangered Species Act (ESA) and their food web. We used risk tables to assess the singular and combined effects of tidal power development and climate change. Tidal power development and climate change posed risks to ESA-listed species, and risk increased with incorporation of the effects of these stressors on predators and prey of ESA-listed species. In contrast, results of a model of strikes on ESA-listed species from turbine blades suggested that few ESA-listed species are likely to be killed by a commercial-scale tidal turbine array. We applied scenarios to a food web model of Puget Sound to explore the effects of tidal power and climate change on ESA-listed species using more quantitative analytical techniques. To simulate development of tidal power, we applied results of the blade strike model. To simulate environmental changes over the next 50 years, we applied scenarios of change in primary production, plankton community structure, dissolved oxygen, ocean acidification, and freshwater flooding events. No effects of tidal power development on ESA-listed species were detected from the food web model output, but the effects of climate change on them and other members of the food web were large. Our analyses exemplify how natural resource managers might assess environmental effects of marine technologies in ways that explicitly incorporate climate change and consider multiple ESA-listed species in the context of their ecological community. Estimacion de los Efectos de Proyectos de Energia de las Mareas y el Cambio Climatico sobre Especies Marinas Amenazadas y en Peligro y su Red Alimentaria.

Variation in growth and body size during critical life history stages can have important implications for life history schedules and survivorship. For Pacific herring (Clupea pallasii), there is still debate as to whether juvenile body size is governed by density-dependent or -independent processes and few have evaluated whether the relative importance of either process shifts over the course of early ontogeny. We used a unique data set consisting of seasonal measurements of abundance, body size, and spatial distribution within a semi-enclosed basin of Puget Sound (Washington State, U.S.A.) to measure the relative importance of temperature and cohort abundance on body size at distinct time periods, and evaluated whether density-dependent habitat shifts might be responsible for density-dependent growth. Over the 9 years of sampling (2001–2010) midsummer body size was positively related to temperatures experienced during the egg/yolk sac and larval stages and unrelated to cohort abundance. However, fall body size was negatively correlated with abundance and uncorrelated with both midsummer body size and temperature, indicating a shift from density-independent to density-dependent control over the course of the growing season. Thus, density-dependent effects may supplant density-independent effects exhibited early in herring life history. Our data on spatial distributions of herring and their zooplankton prey indicate that density-dependent reductions in growth may be explained by density-dependent habitat shifts that lead to reduce overlap of herring with zooplankton. Evidence of density-dependent growth in marine fish populations is often attributed to exploitative competition, but our results suggest that these patterns may partly be mediated by density-dependent distribution expansions in to prey-poor habitat.

We explored patterns of small pelagic fish assemblages and biomass of gelatinous zooplankton (jellyfish) in surface waters across four oceanographic subbasins of greater Puget Sound. Our study is the first to collect data documenting biomass of small pelagic fishes and jellyfish throughout Puget Sound; sampling was conducted opportunistically as part of a juvenile salmon survey of daytime monthly surface trawls at 52 sites during May–August 2003. Biomass composition differed spatially and temporally, but spatial differences were more distinct. Fish dominated in the two northern basins of Puget Sound, whereas jellyfish dominated in the two southern basins. Absolute and relative abundance of jellyfish, hatchery Chinook salmon Oncorhynchus tshawytscha, and chum salmon O. keta decreased with increasing latitude, whereas the absolute and relative abundance of most fish species and the average fish species richness increased with latitude. The abiotic factors with the strongest relationship to biomass ...

Disease epidemiology requires information about ecological and environmental condi- tions to identify factors that can influence disease progression. Bacterial kidney disease (BKD) is an endemic disease among Pacific Northwest salmonids that causes significant morbidity and mortality in artificially propagated stocks, but risk factors for infection among free-living salmon are unknown. We evaluated infection by the causative agent of BKD, Renibacterium salmoninarum, in 1752 fish across 52 sampling sites monthly from May to November 2003 as a component of a broader study of neritic habitat use in Puget Sound by juvenile Chinook salmon Oncorhynchus tshawytscha. Infection intensity was ≤10 cells per slide for 77% of the fish. Correlations between the density of Chinook salmon with infection prevalence and with infection intensity were observed across multiple spatial scales. Capture location was a stronger predictor of infection than fish origin (based on coded wire tags) or genetic stock. Influential risk factors by logistic regression were temperature, densities of marked and unmarked Chinook salmon, and density of river lamprey Lampetra ayresis. Renibac- terium salmoninarum were found in gut contents and kidney of river lamprey, suggesting this species may be a transmission vector. The low infection intensity, lack of an effect of fish origin, effect of capture bay, and strong associations with Chinook salmon density are consistent with horizontal transmission of R. salmoninarum during the juvenile neritic phase, posing a potential for infectious interaction between sympatric hatchery and wild fish.

We examined how local- and regional-scale environmental drivers affect patterns ofabundance and recruitment in 2 abundant and ecologically significant forage fishes (Pacific herring Clupea pallasi and surf smelt Hypomesus pretiosus) in the Skagit River estuary (Puget Sound, Wash-ington, USA). We identified associations between survey catch rates and environmental conditions at2 scales: within-season distributional shifts in response to local environmental conditions, and inter-annual patterns of relative year class strength related to both local- and regional-scale drivers. Usingmonthly data that spanned a 9 yr period, we found that a small proportion (

This study focuses on the use by juvenile Chinook salmon Oncorhynchus tshawytscha of the rarely studied neritic environment (surface waters overlaying the sublittoral zone) in greater Puget Sound. Juvenile Chinook salmon inhabit the sound from their late estuarine residence and early marine transition to their first year at sea. We measured the density, origin, and size of marked (known hatchery) and unmarked (majority naturally spawned) juveniles by means of monthly surface trawls at six river mouth estuaries in Puget Sound and the areas in between. Juvenile Chinook salmon were present in all months sampled (April–November). Unmarked fish in the northern portion of the study area showed broader seasonal distributions of density than did either marked fish in all areas or unmarked fish in the central and southern portions of the sound. Despite these temporal differences, the densities of marked fish appeared to drive most of the total density estimates across space and time. Genetic analysis and ...

Stream flow affects many aspects of freshwater fish biology, but the extent to which variation in stream flow influences productivity of anadromous salmonid populations across their entire life cycle is not well known. We compared relationships of stream flow and productivity for Chinook salmon (Oncorhynchus tshawytscha) from two systems in the Salmon River basin in Idaho: the Lemhi River, a watershed subjected to intensive water use for irrigation, and Marsh Creek, a drainage with a natural hydrograph. We estimated rates of productivity based on monitoring at four life stages: the number of eggs initiating each cohort, juveniles migrating from the natal tributary past an outmigrant trap, smolts surviving to the Snake River, and adults returning to spawn. Using model selection techniques, we examined whether river flow experienced during these life stages explained variation above and beyond predictors of climate associated with each stage. In the Lemhi River, tributary stream flow during early residence exhibited strong correlations with egg–trap, egg–smolt, and egg–adult return rates, and was consistently a better predictor of productivity than stream flow occurring during late summer. Model selection indicated that early rearing flow was the single best predictor of both egg–trap and trap–smolt transition rates in the Lemhi River, and path analysis revealed a strong set of pathways linking rearing flow to adult return rate primarily through egg–trap productivity. These patterns were much less strongly exhibited or nonexistent in Marsh Creek. However, for both populations, migration flow in the Columbia River was the best predictor of smolt–adult return rates. Potentially confounding climatic variables exhibited relatively weak effects upon both early life histories and tributary flow, but were included in the best models of migration flows and smolt–adult return rate. These results suggest that effects of stream flow on juvenile salmonids in flow-altered systems can have substantial impacts on returning adults.

The objective of this study was to develop guidance for tagging methods for juvenile Chinook salmon Oncorhynchus tshawytscha in their first ocean year by evaluating the effects of tagging during this critical life stage. We compared survival over 42 d among juvenile hatchery Chinook salmon receiving surgically implanted dummy ultrasonic transmitters (equivalent to VEMCO V7-1 L tags) ranging from 2.6% to 8.8% of body mass with that of fish receiving gastrically implanted tags. Survival was significantly lower in fish receiving gastrically implanted transmitters (21%) than for the gastric-sham (66%), surgery (61%), surgery-sham (58%), and control treatments (90%). Survival was also significantly higher in the control treatment than in all other treatments. The results of this study indicate that surgical insertion into the peritoneal cavity is the preferred method of transmitter implantation in juvenile Chinook salmon in their first ocean year and that the transmitters should be less than 5.8% of t...

Salmon carcasses provide a marine derived nutrient (MDN) subsidy to river systems, but the extent to which it affects juvenile salmon growth is unclear. To evaluate temporal and spatial nutrient contributions from watershed sources and MDNs using stable isotopes, Skagit River (Washington, USA) juvenile coho salmon (Oncorhynchus kisutch) were collected. Muscle samples were taken from fry through smolts to measure temporal changes in δ15N and δ13C. δ15N and δ13C levels declined from emergence until fall, when they approached values for resident cutthroat trout (Oncorhynchus clarkii) collected above anadromous barriers. Muscle δ13C was highly variable and did not increase subsequently. However, coho salmon δ15N increased during the winter. March coho salmon parr δ15N levels suggested high variability in carcass availability for consumption. During the next spring, δ15N levels again declined. In Griffin Creek, a Snoqualmie River tributary, a significant relationship between carcass density and δ15N and δ13C levels was found in March coho salmon parr. At high spawner densities, some parr δ15N exceeded carcass values; however, parr δ13C increased moderately. These findings show that stable isotope data provide insights on seasonal sources of nutrients. In addition, results indicate that March coho salmon parr δ15N levels would be a useful index of carcass availability for overwintering juvenile consumption.

Lotic ecosystems are made up of numerous tributary streams forming a complex branching network. The point where smaller tributaries flow into larger rivers, or tributary junctions, may be sites in the network where spatial discontinuities or “hot spots” are created and maintained, because small streams funnel important materials captured from the surrounding landscape and carry them by gravity downstream. We hypothesized that habitat complexity, environmental productivity, and abundance of primary consumers and predators peak in mainstem rivers at or downstream of tributary junctions. We conducted surveys in three river basins and 13 reaches to examine interdependence between tributary streams and the larger rivers they enter. Wood abundance and volume, variability in median substrate size (i.e., substrate heterogeneity), concentrations of nitrogen and phosphorus in water, algal biomass, and abundance of consumers and predators peaked with a higher frequency at or downstream of tributary junctions. For several variables, the size of the tributary relative to the main stem contributed to the strength of tributary affect. These findings suggest that some tributary streams have fundamental effects on the larger rivers they enter. We argue that maintaining the integrity of connections among and between ecosystems is essential for promoting habitat complexity and community structure within river networks.

Incorporating parameter uncertainty into a Monte Carlo procedure for estimating spawning habitat capacity helped determine that spawning habitat availability is unlikely to limit recovery of six populations of Chinook salmon (Oncorhynchus tshawytscha) in Puget Sound. Spawner capacity estimates spanned up to four orders of magnitude, yet there was virtually no overlap of distributions of capacity estimates with distributions of current spawner abundance (

We predicted 22 years of return rates for wild Chinook salmon Oncorhynchus tshawytscha as a function of environmental conditions experienced during residency in freshwater, tidal delta, bay, and ocean habitats as well as as an indicator of density dependence (based on egg production) across life stages. The best predictors of return rate included the magnitude of floods experienced during incubation, a principal components factor describing environmental conditions during bay residency, a similar factor describing conditions experienced during the third ocean year, and an estimate of egg production. Our models explained up to 90% of the variation in return rate and had a very high forecasting precision, yet environmental conditions experienced during ocean residency explained only 5% of the variation. Our results suggest that returns of wild Chinook salmon can be predicted with high precision by incorporating habitat residency and that freshwater and nearshore environmental conditions strongly in...

Restoring salmon populations depends on our ability to predict the consequences of improving aquatic habitats used by salmon. Using a Leslie matrix model for chinook salmon (Oncorhynchus tshawytscha) that specifies transitions among spawning nests (redds), streams, tidal deltas, nearshore habitats, and the ocean, we compared the relative importance of different habitats under three density-dependent scenarios: juvenile density independence, density-dependent mortality within streams, delta, and nearshore, and density-dependent migration among streams, delta, and nearshore. Each scenario assumed density dependence during spawning. We examined how these scenarios influenced priorities for habitat restoration using a set of hypothetical watersheds whose habitat areas could be systematically varied, as well as the Duwamish and Skagit rivers. In all watersheds, the three scenarios shared high sensitivity to changes in in nearshore and ocean mortality and produced similar responses to changes in other parameters controlling mortality (i.e., habitat quality). However, the three scenarios exhibited striking variation in population response to changes in habitat area (i.e., capacity). These findings indicate that nearshore habitat relationships may play significant roles for salmon populations and that the relative importance of restoring habitat area will depend on the mechanism of density dependence influencing salmon stocks.

Animal communication systems have become closely tuned to local habitat conditions as populations have adjusted to different long-term environmental pressures. However, many habitats are now rapidly changing because of anthropogenic modification. Maintenance of effective communication systems in greatly altered environments will depend on communicative responses on both evolutionary and ontogenetic time scales. Consideration of potential acoustic challenges caused by human-generated habitat modification has important implications for basic research and conservation biology. First, the observed signal structure of individuals in altered environments may not match the normally hypothesized call structure. Second, species that either possess little ability to adapt quickly on an evolutionary time scale or have little plasticity in their communicative systems may be unable to respond to large anthropogenic alterations in their acoustic environment.

Much of current habitat-selection theory assumes that individual fitness monotonically declines as a function of density, and that social interactions among settlers are entirely competitive. However, when animals settle at low densities, other fitness distributions (e.g., Allee effects) and positive interactions among settlers (e.g., conspecific cueing) are possible. We developed an individual-based simulation model to explore how habitat selection at low densities is influenced by three factors: (1) the relationship between density and fitness (negative density-dependence vs. Allee distributions), (2) intrinsic habitat quality, and (3) settlement costs. When two habitat patches are identical in quality, Allee and negative density-dependent models differ in two respects: in Allee models, (1) all individuals initially settle in one habitat patch, and (2) some individuals switch habitats as soon as the alternative habitat begins to be colonized. These patterns are accentuated if habitats differ in quality, and in this situation, Allee distributions and differences in habitat quality have comparable effects on settlement patterns. Settlement costs reduce the number of individuals switching habitat patches in Allee models, and if settlement costs decline as a function of density (as in conspecific cueing), settlers aggregate even if fitness declines monotonically with density after settlement is complete. Our results show that many of the patterns currently construed as supporting negative density-dependent habitat-selection models are also predicted by models that incorporate Allee effects or settlement costs and, more generally, suggest new approaches to habitat selection at low population densities.

In three experiments, a new reference memory procedure was used to examine how male rats search for consistently located food in a cue-controlled spatial environment. The animals searched the tops of 24 poles for six hidden baits in an enclosed circular arena containing a fixed configuration of six object landmarks. In Experiment 1, acquisition was faster and overall performance better for theconsistent group (10 rats), in which the six baited poles were fixed relative to the landmarks for each session, than for therandom group (4 rats), in which baited poles were randomly configured. Cue-control tests and computer simulations suggested that the consistent group relied on the landmarks to directly go to the baited poles, whereas the random group used them to employ a response strategy for searching the arena. Experiments 2 and 3 revealed that the number, identity, and geometric configuration of the landmarks were important to the consistent group’s search performance. Overall, these results are most consistent with the use of a geometric representation by male rats which includes information about both the identity and the relative geometry of discrete landmarks in the surrounding spatial environment.

Marine hydrokinetic power projects will operate as marine environments change in response to increased atmospheric carbon dioxide concentrations. We considered how tidal power development and stressors resulting from climate change may affect Puget Sound species listed under the U.S. Endangered Species Act (ESA) and their food web. We used risk tables to assess the singular and combined effects of tidal power development and climate change. Tidal power development and climate change posed risks to ESA-listed species, and risk increased with incorporation of the effects of these stressors on predators and prey of ESA-listed species. In contrast, results of a model of strikes on ESA-listed species from turbine blades suggested that few ESA-listed species are likely to be killed by a commercial-scale tidal turbine array. We applied scenarios to a food web model of Puget Sound to explore the effects of tidal power and climate change on ESA-listed species using more quantitative analytical techniques. To simulate development of tidal power, we applied results of the blade strike model. To simulate environmental changes over the next 50 years, we applied scenarios of change in primary production, plankton community structure, dissolved oxygen, ocean acidification, and freshwater flooding events. No effects of tidal power development on ESA-listed species were detected from the food web model output, but the effects of climate change on them and other members of the food web were large. Our analyses exemplify how natural resource managers might assess environmental effects of marine technologies in ways that explicitly incorporate climate change and consider multiple ESA-listed species in the context of their ecological community. Estimación de los Efectos de Proyectos de Energía de las Mareas y el Cambio Climático sobre Especies Marinas Amenazadas y en Peligro y su Red Alimentaria.

The presence of locally abundant wildlife raises questions about natural regulation and ecological consequences of overpopulation. We sought to establish precise information about population size, structure, and productivity to examine the role of natural regulation in a closed tule elk (Cervus elaphus nannodes) population at Point Reyes National Seashore, California, USA. We estimated an instantaneous exponential growth rate of 0.19 with an adjusted R 2 = 0.98 during 1998, 20 years after the elk were introduced. We estimated annual survival for adult cows of nearly 0.95. Calf survival from birth through the rut ending during October-November was 0.85. Male calves exhibited higher mortality than female calves. Cow mortality was associated with the calving season. We measured a 42% increase in cow:calf density from 0.733 ha -1 to 1.043 ha -1 during 1996-1998. We observed a density-correlated reduction in the rate of increase and in the cow:calf ratios prior to high precipitation El Nino Southern Oscillation years, 1993, 1996, and 1997, precipitation >1.23 m year -1 . Given the high population growth rate and model evaluation of management scenarios, park managers will need to use a suite of approaches, such as contraception and removal, to maintain the elk population at levels at or near the closed-range carrying capacity for years between El Nino events.