Climate impacts on biological systems are typically considered in isolation, but they are exacerbated by other human stressors. This suggests that alleviation of human stressors may recover lost biological climate resilience. However, real-world examples that document such interventions are rare. Coho salmon in California are an iconic species that requires cool, wetted habitat in a warm, drought-prone region. Extensive beaver trapping in previous centuries has left this landscape unnaturally lacking in wetlands that maintain cool, wetted habitats resilient to drought. Loss of climate resilience is especially concerning because California is both warming and experiencing severe droughts. Here, we restored wetlands using beaver dam analogues, which increased estimated coho salmon habitat capacity and coincided with increased juvenile survival and adult returns. Moreover, adult returns were less impacted by drought when juveniles used restored habitats. Remarkably, these responses coincided with a severe drought that collapsed coho salmon populations in neighboring, unrestored systems and the total adult returns of four monitored tributaries in the Klamath basin became dominated by the Scott River population. These data suggest that restoration of once abundant slow-water wetland habitat increased population performance overall and mitigated impacts of climate stress. Broadly, these results underscore the need to consider the land use history of ecosystems to recognize changes that have increased climate sensitivity to certain species and, by implication, paths to bolster systems against climate stress.

Literature linking phenology to climate has proliferated in recent decades and shows that climate change has reorganized seasonal opportunities worldwide. However, this literature often quantifies changes in point measures of timing (e.g., beginnings and peaks) without context about duration (e.g., rearing season length) or performance (e.g., juvenile development). Consequently, phenological studies often cannot discern whether climate change truncates biological processes or merely recenters them intact around different dates, which limits the utility of these studies for climate vulnerability assessments. Showing how research may bridge this gap, we quantified links between temperature and coastal nursery rearing phenology in threatened Chinook salmon (Oncorhynchus tshawytscha, Walbaum 1792). Long nursery rearing periods are crucial to enabling growth that promotes survival and life-history diversity that spreads risk. Because salmon can express diverse, climate-influenced phenologies and our study region warmed but remained temperate, we sought to discern whether nursery rearing was intact or truncated amid potential phenological change. Leveraging ∼170,000 observations across three decades and three basins, we found that warm years generally advanced populations' seasonal trajectories of habitat use and growth and that they did not reduce annual 95th percentile body lengths. Additionally, warm years did not consistently compress or expand habitat use in rivers or deltas but consistently expanded habitat use in nearshore marine waters. Overall, there was substantial evidence that warm years advanced nursery rearing intact and little evidence of truncation. Thus, climate change shifted when populations reared but did not prevent populations from completing rearing. Global research on phenological change has begun to transcend descriptions of patterns to consider biological consequences. Simultaneously, efforts to assess populations' climate vulnerabilities have become widespread. Studies that inspect phenological change to distinguish intact processes from truncated processes could provide insights into climate vulnerabilities. Coastal nursery rearing is one process that may especially befit this framework.

Estuaries are productive ecosystems facing anthropogenic pressures, prompting widespread conservation efforts. However, assessing and protecting entire species assemblages is challenging. The “umbrella species” concept — protecting a focal species to protect a sympatric assemblage indirectly — offers a practical surrogate approach, yet it remains underexplored in estuaries. We evaluated the potential for Chinook salmon, an iconic species that rears in estuaries, to function as an umbrella species in the Skagit River estuary (Washington, USA). From nine years of monitoring delta and nearshore waters, we quantified the occurrence, phenology, and environmental associations (depth, salinity, temperature, velocity) of the fish assemblage. Chinook salmon occupied diverse habitats throughout the estuary from February to August and ranked among the most frequently observed species. Their presence corresponded to increased occurrence for 11 of 12, 11 of 14, and 22 of 25 common species in delta blind channels, distributary channels, and nearshore waters, respectively, alongside elevated assemblage diversity, richness, and total abundance. Chinook salmon overlapped with all species, especially other anadromous species, which showed similar phenologies and relationships with local environments. Conservation that targets Chinook salmon may therefore extend an “umbrella” of protection over a diverse, sympatric estuarine fish assemblage. Estuaries commonly support nursery habitats for fish that seasonally move throughout estuarine seascapes and share basic habitat requirements (e.g., predator refuge, prey availability). This overlap in spatial, temporal, and ecological terms is desirable in umbrella species, suggesting potential to apply umbrella conservation approaches in estuaries elsewhere.

As global climate change and anthropogenic activities amplify widespread environmental variability, there is a strong need for management strategies that incorporate relationships between ecosystem components. This need is especially apparent when changes in environmental drivers cause threshold responses (abrupt, nonlinear changes) in ecosystems. Such ecological thresholds can provide useful reference points for management decisions. However, methods for detecting thresholds in empirical datasets may fail to find an existing threshold, find one that does not exist, or be biased in their estimates of threshold locations. These types of threshold misspecifications can result in high conservation and socioeconomic costs. Simulation studies can mitigate these risks by providing information about method performance across different scenarios. Here, we constructed a series of simulations to evaluate the robustness of threshold detection with generalized additive models (GAMs) when exposed to a variety of common, real-world data characteristics. GAMs generally performed best when time series were long, observation error was low, thresholds were crossed fairly frequently, and covariates were accounted for. Over realistic ranges of values, observation error and frequency of threshold crossing had stronger effects on threshold detectability than time series length. Importantly, detectability was found to depend on both the shape of the threshold relationship and the statistical definition of the threshold location. As a case study, we applied this threshold detection method to an empirical dataset relating ocean temperature and the spatial distribution of Pacific hake (Merluccius productus), the largest volume fishery on the US West Coast. While the data suggest no statistical evidence for a threshold relationship, our simulations indicated approximately equal chances of true and false threshold detection given currently available data. Our results provide general guidelines for where threshold detection with GAMs is likely to be robust and are useful in the context of indicator development for ecosystem-based management in a variable world.

Estuaries provide many important functions for numerous aquatic species across life stages. However, these habitats have been widely impacted due to their characteristics and features that support agriculture and industrialization. Within Puget Sound, estuary restoration has been a primary tool to support recovery of Chinook salmon which are known to rely heavily on estuaries during early life history. Tracking habitat gains via restoration and evaluating effectiveness of these actions is necessary to ensure recovery targets are met. We used aerial imagery from two distinct time periods to measure estuarine habitat and estimate rates of change over two decades in Puget Sound. In addition, we developed a method to estimate functional trajectories for restoration projects based on allometry of planform geometry features for tidal deltas. A total of 72 restoration actions across nine tidal deltas added ~147 ha and ~410 km of tidal channel habitat in Puget Sound between 1997 and 2018. While positive overall, time series of rearing habitat change for individual tidal deltas varied reflecting the frequency and magnitude of restoration actions as well as the response of individual actions to natural processes. Estimated functional footprints for restoration projects were below total footprints for all deltas. Functional footprints appeared to track total footprint well for some deltas but indicated potential limitations in others that may be related to particular planform geometry metrics for individual sites. Overall restoration of estuarine habitats in Puget Sound since 1997 have added substantial rearing habitat in support of recovery for Chinook salmon populations. While total gains are positive, our estimates of functional trajectories provide additional information that may support adaptive management to ensure efforts remain beneficial to target species. Continuing to accurately track changes to estuarine habitat should benefit recovery efforts and support management decisions in the future.

Conventionally, juvenile salmonids are thought to migrate unidirectionally from freshwater systems to marine systems and therefore only inhabit natal drainages. Although scattered evidence suggests juveniles can move bidirectionally between freshwater rivers and the ocean, including into non-natal drainages, such movements have never been documented with high replication. Here, we detected hundreds of movements of juvenile salmonids between drainages that involved 0-22% of cohort emigrants in Washington State and California. Individuals moved up to nine times and between drainages up to 70 km apart. These findings reveal a life-history type of salmonids whose remarkably complex migrations have gone unnoticed. Implicitly, juveniles may use any coastal freshwater habitat accessible from the sea and may not descend from spawning populations of drainages they inhabit. Consequently, typical conservation focused on natal drainages may overlook freshwater habitat elsewhere. A concept of coastal areas as meta-nurseries formed by multiple watersheds connected by the sea may accurately describe anadromous species' habitat options and better inform management.

Estuaries comprise important but often-degraded fish nursery habitat. People have invested considerable resources into restoring estuaries to rehabilitate habitats, but comparatively little work has evaluated population outcomes for target species. Here, we examined the response of a threatened population of Chinook salmon (Oncorhynchus tshawytscha) to estuary restoration in their natal tidal delta, and observed demographic changes consistent with increasing nursery habitat capacity and quality. We leveraged three decades of monitoring before, during, and after restoration in the Skagit River delta, and compared demographic patterns in restored and unrestored forks within the delta, and in locations landward and seaward of the delta. We hypothesized that restoration in tidal deltas should result in reductions in local densities, and reduced density-dependent spillover of juveniles into nearshore waters. We also examined other predictions that were more ambiguous and depended upon biological mechanisms. We found that (1) delta restoration led to lower juvenile densities overall and greater juvenile densities when conspecific abundances were high, and (2) individual juveniles were smaller overall and their lengths declined less when densities were higher. We also monitored juvenile salmon in nearshore waters seaward of the delta. Following delta restoration, (3) juvenile catches in nearshore marine waters declined relative to delta habitat change, and (4) the prevalence of nearshore fry (<~45 mm) — a phase thought to benefit more from delta nursery habitats — decreased overall. These findings suggest that greater nursery habitat capacity in the delta allowed salmon to spread out and accommodated higher salmon numbers when juvenile outmigrations were especially high. They also suggest that restoration promoted the use of delta habitats by smaller fish while alleviating competitive effects on growth. Furthermore, they suggest that greater delta habitat capacity supported more juveniles, decreasing overflow to nearshore environments, especially for the smallest, most vulnerable salmon that presumably benefit most from growth before entering nearshore waters. Thus, estuary restoration appeared to alleviate density-dependent constraints on rearing and growth. These findings provide empirical support for restoring estuaries in human-stressed landscapes to rehabilitate nursery habitat functions for Chinook salmon and, potentially, other species and life stages.

Human stressors block, eliminate, and simplify habitat mosaics, eroding landscapes’ life history diversity and thus biological resilience. One goal of restoration is to alleviate human stressors that suppress life history diversity, but life history responses to these efforts are still coming into focus. Here, we report life history diversity emerging in threatened salmonids ( Oncorhynchus spp.) repopulating the recently undammed Elwha River (WA, United States) in adjacent but environmentally distinct tributaries. The ~20 km tributaries entered the Elwha River <1 km apart, but one had a colder stream temperature regime and swifter waters due to its high, snow-dominated elevation and steep valley gradient (~3%), while the other had a warmer stream temperature regime and slower waters because it drained a lake, was at lower elevation, and had a lower stream gradient (~1.5%). Following the 2012 removal of Elwha Dam, the tributaries’ salmonids generally became more abundant and expressed diverse life histories within and among species. The warmer, low-gradient tributary produced more age-1+ coho salmon while the colder, steeper tributary produced a notably high abundance of steelhead smolts in 2020. Additionally, salmonids exiting the warmer tributary were older and possibly larger for their age class, emigrated ~25 days earlier, and included age-0 Chinook salmon that were larger. Also, assemblage composition varied among years, with the most abundant species shifting between Chinook salmon and coho salmon, while steelhead abundances generally increased but were patchy. These patterns are consistent with a newly accessible, heterogeneous landscape generating life history diversity against the backdrop of patchy recruitment as salmonids—some with considerable hatchery-origin ancestry—repopulate an extirpated landscape. Overall, dam removal appears to have promoted life history diversity, which may bolster resilience during an era of rapid environmental change and portend positive outcomes for upcoming dam removals with similar goals.

Eelgrass meadows provide vital nearshore habitats and ecosystem services, but they have declined from human stressors and conservation efforts are now widespread. Dynamic ecosystems like eelgrass meadows naturally rearrange as disturbance and recruitment unfold across seascapes. However, some decisions that protect eelgrass only consider extant meadows, thus ignoring the potential for change. Here, we report decades of eelgrass dynamics observed across the northeast Pacific. Our observations support conservation expanded to the seascape scale, which includes potentially inhabitable areas along with extant meadows. We found that total seascape meadow area changed over time, and changes within seascapes were often asynchronous. Some meadows rearranged across seascapes over multiple kilometres and decades. Also, some seascapes compartmentalized meadow collapse, which enabled later recovery, or supported local recruitment that substantially increased total meadow area. These observations were consistent with hierarchical patch dynamics, which promote ecosystem persistence over larger space and time scales. Thus, to enable the dynamics that underpin eelgrass persistence, it is necessary to keep many eelgrass habitat options open across seascapes, rather than protect only extant meadows. Given that dynamic, hierarchical ecosystems are common along marine shorelines, this approach may be effective for both nearshore ecosystems in general and for eelgrass in particular.

Ecosystems constantly change, yet managers often lack information to move beyond static habitat assumptions. As human impacts and geographic information systems advance, it is important and feasible to quantify past habitat boundary shifts to inform management decisions (e.g. protective perimeters) robust to near-term habitat changes. This is the case in eelgrass (Zostera spp.), an ecosystem engineer that forms dynamic, often protected meadows. Practitioners protect areas to avoid human stress to eelgrass, but they can lack quantitative descriptions of the near-term potential for eelgrass meadows to shift into unprotected areas. Here, we quantified interannual eelgrass meadow boundary shifts within 23 sites spanning 9 decades and 19 degrees latitude. Eelgrass meadow boundaries typically shifted into areas tens of meters away from previous meadow edges, but sometimes much farther. Also, eelgrass meadows often vacated and later recolonized the same areas. By implication, eelgrass protection efforts may be enhanced by considering that presently vacant areas may be inhabited in the future, especially near currently existing meadows. Additionally, eelgrass meadows changed less over time at sites less modified by people within temperate landscapes compared to sites located within human-dominated, warmer, and drought-prone landscapes with limited water turnover. We thus hypothesize that eelgrass meadows change more over time within landscapes exposed to greater stressor regimes because they more frequently or intensely cycle through disturbance and recovery phases. These results inform tactical decisions seeking to mitigate impacts of human activities to eelgrass and underscore the potential synergy of monitoring, research, and adaptive management approaches to protect dynamic habitats.

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.

Many nearshore ecosystems are modified by aquaculture, including bivalve culture to produce food and restore extirpated populations. Small invertebrates in nearshore ecosystems support fundamental ecological processes, but the effects of bivalve culture on invertebrates are incompletely understood. Here, we compared invertebrate assemblages from multiple studies of bivalve-cultivated and unmodified nearshore habitats along the US west coast. In general, unmodified eelgrass and nearby off-bottom culture habitats with eelgrass present were inhabited by a greater abundance, richness, and diversity of epibenthic invertebrates than bottom culture and bare (mud, sand) habitats that both lacked eelgrass. Findings of individual studies suggested: minor differences in epibenthic invertebrate assemblages associated with various aquaculture practices; restoring native oysters to mudflats did not detectably alter epibenthic invertebrate abundances; epibenthic invertebrates were more abundant on shell hash introduced to mudflats than unmodified mudflats; and benthic invertebrates were less abundant, rich, and diverse in habitats cultured on bottom by Manila clams. Considering the range of these patterns, there appears to be potential for coastal communities to restore extirpated bivalve populations or develop bivalve culture practices that meet objectives to grow food while maintaining nearshore ecosystems' fundamental processes supported by robust invertebrate assemblages.

Steelhead Oncorhynchus mykiss smolts 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 seal Phoca vitulina haulouts during 2014 indicated that predation by pinnipeds was an important source of mortality. When Puget Sound temperatures increased with the Northeast Pacific marine 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 anchovy Engraulis mordax in 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.

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 (<55 mm) to actualize benefits of restored habitats will likely require maintaining spawner abundances and flows at or above intermediate values, especially in less-connected portions of the landscape. Furthermore, restoration efforts may prioritize more connected regions to promote use of restored areas, considering that less connected areas are often uninhabited when water and spawners are scarcer. This ecosystem-based framework that evaluates interdependencies of management decisions may be applied to realize natural productivity and enhance conservation in many systems.

Kelp forests are an important ecological component of temperate coastal systems that are sensitive to anthropogenic disturbance and are in decline in many locations globally. In the northeastern Pacific Ocean off the coast of Washington, USA, bull kelp Nereocystis luetkeana forests are seasonally used by juvenile salmonids and forage fishes; however, details on ecosystem functional linkages for forage fishes and salmonids are not well quantified. Using a zooplankton drop net and snorkel surveys for fishes, we sampled two bull kelp forests across multiple years. Our goal was to quantify differences in the communities of zooplankton, juvenile salmonids (Chinook Salmon Oncorhynchus tshawytscha and Coho Salmon O. kisutch), and forage fishes (Pacific Herring Clupea pallasii, Surf Smelt Hypomesus pretiosus, and Pacific Sand Lance Ammodytes hexapterus) between kelp forests and adjacent nonkelp (open-water) habitats. We tested the hypothesis that zooplankton common in the diets of surface-oriented forage fishes and juvenile salmonids would be more abundant in kelp than in open water. At the overall assemblage level of organization, kelp and open-water habitats had similarly abundant and diverse zooplankton communities. However, decapods and phytal-associated harpacticoid copepods within this assemblage (i.e., groups that are an important component of fish diets) were significantly more abundant in kelp forests than in open-water habitat. Greater presence and abundance of zooplankton, juvenile salmonids, and forage fishes in kelp forests compared to adjacent open-water habitats suggest that kelp forests are important for culturally and economically valuable forage fishes and salmonids and warrant further study to define and conserve their ecosystem function.

Ecology is often governed by nonlinear dynamics. Nonlinear ecological relationships can include thresholds-incremental changes in drivers that provoke disproportionately large ecological responses. Among the species that experience nonlinear and threshold dynamics are Pacific salmon (Oncorhynchus spp.). These culturally, ecologically, and economically significant fishes are in many places declining and management focal points. Often, managers can influence or react to ecological conditions that salmon experience, suggesting that nonlinearities, especially thresholds, may provide opportunities to inform decisions. However, nonlinear dynamics are not always invoked in management decisions involving salmon. Here, we review reported nonlinearities and thresholds in salmon ecology, describe potential applications that scientists and managers could develop to leverage nonlinear dynamics, and offer a path toward decisions that account for ecological nonlinearities and thresholds to improve salmon outcomes. It appears that nonlinear dynamics are not uncommon in salmon ecology and that many management arenas may potentially leverage them to enable more effective or efficient decisions. Indeed, decisions guided by nonlinearities and thresholds may be particularly desirable considering salmon management arenas are often characterized by limited resources and mounting ecological stressors, practical constraints, and conservation challenges. More broadly, many salmon systems are data-rich and there are an extensive range of ecological contexts in which salmon are sensitive to anthropogenic decisions. Approaches developed to leverage nonlinearities in salmon ecology may serve as examples that may inform analogous approaches in other systems and taxa.

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.

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.