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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.

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.

SummaryAssessing the degree to which at-risk species are regulated by density dependent versus density independent factors is often complicated by incomplete or biased information. If not addressed in an appropriate manner, errors in the data can affect estimates of population demographics, which may obfuscate the anticipated response of the population to a specific action.We developed a Bayesian integrated population model that accounts explicitly for interannual variability in the number of reproducing adults and their age structure, harvest, and environmental conditions. We apply the model to 41 years of data for a population of threatened steelhead troutOncorhynchus mykissusing freshwater flows, ocean indices, and releases of hatchery-born conspecifics as covariates.We found compelling evidence that the population is under strong density dependence, despite being well below its historical population size. In the freshwater portion of the lifecycle, we found a negative relationship between productivity (offspring per parent) and peak winter flows, and a positive relationship with summer flows. We also found a negative relationship between productivity and releases of hatchery conspecifics. In the marine portion of the lifecycle, we found a positive correlation between productivity and the North Pacific Gyre Oscillation. Furthermore, harvest rates on wild fish have been sufficiently low to ensure very little risk of overfishing.Synthesis and applications.The evidence for density dependent population regulation, combined with the substantial loss of juvenile rearing habitat in this river basin, suggests that habitat restoration could benefit this population of at-risk steelhead. Our results also imply that hatchery programs for steelhead need to be considered carefully with respect to habitat availability and recovery goals for wild steelhead. If releases of hatchery steelhead have indeed limited the production potential of wild steelhead, there are likely significant tradeoffs between providing harvest opportunities via hatchery steelhead production, and achieving wild steelhead recovery goals.

Long‐term datasets can be particularly useful for parsing out factors influencing populations, yet few studies have utilized continuous datasets to quantify population dynamics in bivalve molluscs. We used dynamic factor analysis on a clam biomass dataset spanning 28 yr and five distinct regions in the southern Salish Sea to determine (1) if native intertidal clam populations exhibit synchrony and (2) what environmental covariates may be correlated with these population trends. Once covariates were accounted for, the model with the most data support included three predominant trends to describe multidecadal change in clam biomass. Intraspecific synchrony was highest among Saxidomus gigantea and Leukoma staminea populations, with no clear evidence of covariance in Clinocardium nuttallii. Specifically, we quantified a pronounced decadal decline in L. staminea and an increase in S. gigantea biomass on most beaches. No beaches showed synchrony in trends across all three species, indicating that species‐specific trends (regardless of location) were more common than beach‐specific trends (regardless of species). Seven environmental covariates were evaluated in their capacity to explain variability in annual mean biomass. Of these, the North Pacific Gyre Oscillation lagged 4 yr prior to the observation year was most supported by the data in the best fitting model, implying that 4 yr old clam biomass is partially determined by oceanographic processes affecting larval clams. Although results suggest large‐scale density‐independent factors play a role in venerid clam population dynamics, it is also likely local factors account for variability not explained by our model.

Vertical heterogeneity in the physical characteristics of lakes and oceans is ecologically salient and exploited by a wide range of taxa through diel vertical migration to enhance their growth and survival. Whether analogous behaviors exploit horizontal habitat heterogeneity in streams is largely unknown. We investigated fish movement behavior at daily timescales to explore how individuals integrated across spatial variation in food abundance and water temperature. Juvenile coho salmon made feeding forays into cold habitats with abundant food, and then moved long distances (350-1300 m) to warmer habitats that accelerated their metabolism and increased their assimilative capacity. This behavioral thermoregulation enabled fish to mitigate trade-offs between trophic and thermal resources by exploiting thermal heterogeneity. Fish that exploited thermal heterogeneity grew at substantially faster rates than did individuals that assumed other behaviors. Our results provide empirical support for the importance of thermal diversity in lotic systems, and emphasize the importance of considering interactions between animal behavior and habitat heterogeneity when managing and restoring ecosystems.

SUMMARY 1. Pacific salmon (Oncorhynchus spp.) returning to streams deliver substantial quantities of nutrients (nitrogen and phosphorus) that may stimulate primary production. Salmon can also affect the phytobenthos negatively via physical disturbance during nest excavation, a process that may counteract the positive effects of salmon-derived nutrients on benthic algae. The ability of salmon to disturb benthic habitats may be a function of substratum particle size, and therefore, the geomorphology of streams could determine the net effect of salmon on benthic communities. 2. Based on surveys of 17 streams in southwest Alaska before the salmon run and during peak salmon density, we identified size thresholds for the disturbance of substratum particles by salmon and classified particles as vulnerable ( 110 mm) or transitional (61–110 mm). At the scale of individual rocks, algal biomass on vulnerable substrata decreased at peak spawning (relative to values before the run) as a power function of salmon density; transitional and invulnerable substrata showed no quantifiable pattern. However, invulnerable substrata in streams with more than 0.11 salmon m )2 showed net algal accrual, or relatively smaller declines in algal biomass, than vulnerable substrata, indicating that large rocks provide refuge for benthic algae from salmon disturbance. 3. We expected that streams with proportionally larger rocks would respond positively to salmon at the whole-stream scale, after accounting for the relative abundance of rocks of different sizes within streams. Invulnerable rocks made up only 0–12% of the total substratum particle size distribution in salmon-bearing streams, however, and algal accrual on invulnerable substrata did not outweigh the strong disturbance effects on the more spatially extensive vulnerable substrata. The change in whole-stream benthic algal biomass among streams was negatively related to salmon density. 4. Stable isotopes of nitrogen (d 15 N) were used to track nutrients from salmon into benthic biota. Periphyton d 15 N on rocks of all size classes was higher at peak salmon spawning than before the salmon run, indicating the uptake of salmon-derived nitrogen. Peak d 15 N values were positively related to salmon abundance and followed a two-isotope mixing relationship. The per cent of N from salmon in periphyton was also related to salmon density and was best explained by a saturating relationship. Spring d 15 N was unrelated to salmon returns in the previous year, suggesting little annual carryover of salmon nutrients.

Spatial and temporal heterogeneity interact to make the foraging rates of individuals more variable than expected from models assuming that spatial and temporal dimensions of habitat conditions operate independently. For example, trophic resource pulses produce temporal patches of prey superabundance, yet little is known about how spatial heterogeneity in habitat conditions mediates the ability of consumers to exploit these high-quality foraging opportunities. We studied how spatial variation in water temperature regulates the potential for juvenile coho salmon to exploit a seasonal pulsed subsidy of eggs produced by anadromous sockeye salmon. Streams within the Wood River watershed, southwestern Alaska, USA, ranged in mean summer temperature from 3.6 degrees to 14.5 degrees C. Growth of juvenile coho prior to the arrival of the seasonal egg subsidy was positively related to water temperature among streams. An in situ experiment combined with field samples of diets revealed a size threshold for egg consumption; only individuals longer than approximately 70 mm could consume eggs due to gape limitation of smaller individuals. A bioenergetics simulation demonstrated that water temperature regulated whether age-0 coho salmon could grow large enough to exceed the size threshold for egg consumption. Coho salmon that consumed eggs had energy rations that were five times higher than fish that did not consume eggs, resulting in a positive feedback of water temperature on their integrated seasonal growth. Across this landscape, heterogeneity in water temperature mediates individual- and population-level responses to seasonally available resource pulses. Our study illustrates that ecological mechanisms, such as size-based foraging asymmetries, can magnify the effects of climate change compared to predictions based on physiology alone.

Habitat heterogeneity can generate intraspecific diversity through local adaptation of populations. While it is becoming increasingly clear that population diversity can increase stability in species abundance, less is known about how population diversity can benefit consumers that can integrate across population diversity in their prey. Here we demonstrate cascading effects of thermal heterogeneity on trout-salmon interactions in streams where rainbow trout rely heavily on the seasonal availability of anadromous salmon eggs. Water temperature in an Alaskan stream varied spatially from 5 degrees C to 17.5 degrees C, and spawning sockeye salmon showed population differentiation associated with this thermal heterogeneity. Individuals that spawned early in cool regions of the 5 km long stream were genetically differentiated from those spawning in warmer regions later in the season. Sockeye salmon spawning generates a pulsed resource subsidy that supports the majority of seasonal growth in stream-dwelling rainbow trout. The spatial and temporal structuring of sockeye salmon spawn timing in our focal stream extended the duration of the pulsed subsidy compared to a thermally homogeneous stream with a single population of salmon. Further, rainbow trout adopted movement strategies that exploited the multiple pulses of egg subsidies in the thermally heterogeneous stream. Fish that moved to track the resource pulse grew at rates about 2.5 times higher than those that remained stationary or trout in the reference stream with a single seasonal pulse of eggs. Our results demonstrate that habitat heterogeneity can have important effects on the population diversity of dominant species, and in turn, influence their value to species that prey upon them. Therefore, habitat homogenization may have farther-reaching ecological effects than previously considered.

Understanding how abundance regulates the effects of organisms on their ecosystems remains a critical goal of ecology, especially for understanding inter-ecosystem transfers of energy and nutrients. Here we examined how territoriality and nest-digging by anadromous salmon mediate trophic subsidies to stream fishes. Salmon eggs become available for consumption primarily by the digging of salmon that superimpose their nests on previous nests. An individual-based model of spawning salmon predicted that territoriality and habitat saturation produce a nonlinear effect of salmon density on numbers of available eggs to resident predators. Field studies in Alaskan streams found that higher densities of salmon produce disproportionately more eggs in stream drift and in diets of resident fishes (Arctic grayling and rainbow trout). Bioenergetics model simulations indicated that these subsidies produce substantially enhanced growth rates of trout. These results demonstrate that small changes in salmon abundance can drive large changes in subsidies to stream food webs. Thus, the ecological consequences of population declines of keystone species, such as salmon, will be exacerbated when behavior generates nonlinear impacts.

Pulsed resource subsidies generate ephemeral fluxes of nutrients and energy among ecosystems. The effects of pulsed subsidies should depend on the magnitude of the pulse, the in situ productivity of the recipient system, and the ability of consumers to capitalize on the resources, yet empirical data on these relationships are limited. We assessed the ecological consequences of variation in resource pulse magnitude, as represented by anadromous salmon returns, for the foraging and growth responses of two species of stream-dwelling salmonids in two streams that vary in productivity in southwestern Alaska. Over 11 years and across a greater than 10-fold variation in sockeye salmon (Oncorhynchus nerka) density, both rainbow trout (O. mykiss) and Arctic grayling (Thymallus arcticus) exhibited a relatively similar, but mechanistically different, non-linear saturating growth response to increasing salmon density. This growth response was driven by both an increase in consumption of salmon eggs and also a decrease in dietary overlap between the two species. However, the relative change in growth from low to high salmon densities was different between streams and depended on in situ stream productivity. In low salmon density years the growth of resident consumers fell 46–68% relative to high years in the low productivity stream, but only by 26–34% in the high productivity stream. Our study provides strong evidence that understanding of both the foraging ecology of consumers and the in situ productivity of recipient ecosystems, which together regulate the ecological consequences of variation in resource subsidies, is required for successful implementation of ecosystem-based management in systems dependent on pulsed resource subsidies.