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Forage fishes are ecologically and economically important in marine ecosystems worldwide and thus are a focal topic for ecosystem-based fisheries management. In the California Current Large Marine Ecosystem (CCLME), the community dynamics of forage populations have been studied at regional spatial scales, but not across regions. To evaluate indicators of the forage community at the ecosystem-wide scale, we examine temporal variability of forage assemblages in Northern (Oregon/Washington), Central (California; Point Reyes to Monterey Bay) and Southern (southern California) regions of the CCLME from 1998 through 2016 which include years with unprecedented climate variability. Forage communities fluctuated greatly between years within each region owing to regionally low abundances of common taxa in at least some years (e.g., rockfishes Sebastes spp. in each region). Comparison of species assemblages among regions indicate that that temporal shifts in assemblage structure were largely synchronous throughout the CCLME. However, dynamics of most individual taxa were out of phase between regions, indicating that different taxa drove the variability in each region. Within regions, taxa with similar adult ecological niches tended to co-vary, suggesting synchronous responses to environmental forcing. Major changes in forage assemblage structure are descriptively linked to large oceanographic perturbations such as the transition from El Nino to La Nina conditions in 1998, anomalous upwelling in 2005, and the onset of a large marine heatwave in fall-winter 2013–2014. Changes in forage assemblage structure are reflected in prey switching in the diet of California sea lions, Zalophus californianus, in the Southern region. The multivariate forage indices that we develop can serve as effective indicators of regional forage community composition shifts in the CCLME and provide managers with context on spatio-temporal changes in the structure of forage fish communities important to top predators in this system.

Estimating a population's growth rate and year‐to‐year variance is a key component of population viability analysis (PVA). However, standard PVA methods require time series of counts obtained using consistent survey methods over many years. In addition, it can be difficult to separate observation and process variance, which is critical for PVA. Time‐series analysis performed with multivariate autoregressive state‐space (MARSS) models is a flexible statistical framework that allows one to address many of these limitations. MARSS models allow one to combine surveys with different gears and across different sites for estimation of PVA parameters, and to implement replication, which reduces the variance‐separation problem and maximizes informational input for mean trend estimation. Even data that are fragmented with unknown error levels can be accommodated. We present a practical case study that illustrates MARSS analysis steps: data choice, model set‐up, model selection, and parameter estimation. Our case study is an analysis of the long‐term trends of rockfish in Puget Sound, Washington, based on citizen science scuba surveys, a fishery‐independent trawl survey, and recreational fishery surveys affected by bag‐limit reductions. The best‐supported models indicated that the recreational and trawl surveys tracked different, temporally independent assemblages that declined at similar rates (an average of −3.8% to −3.9% per year). The scuba survey tracked a separate increasing and temporally independent assemblage (an average of 4.1% per year). Three rockfishes (bocaccio, canary, and yelloweye) are listed in Puget Sound under the US Endangered Species Act (ESA). These species are associated with deep water, which the recreational and trawl surveys sample better than the scuba survey. All three ESA‐listed rockfishes declined as a proportion of recreational catch between the 1970s and 2010s, suggesting that they experienced similar or more severe reductions in abundance than the 3.8–3.9% per year declines that were estimated for rockfish populations sampled by the recreational and trawl surveys.

Coasts and estuaries contain among the most productive and ecologically important habitats in the world and face intense pressure from current and projected human activities, including coastal development. Seagrasses are a key habitat feature in many estuaries perceived to be in widespread decline owing to human actions. We use spatio-temporal models and a 41-year time-series from 100s of km of shoreline which includes over 160,000 observations from Puget Sound, Washington, USA to examine multi-scale trends and drivers of eelgrass (Zostera spp.) change in an urbanizing estuary. At whole estuary scale (100s of km) we find a stable and resilient eelgrass population despite a more than doubling of human population density and multiple major climactic stressors (e.g. ENSO events) over the period. However, the aggregate trend is not reflected at the site scale (10s of km), where some sites persistently increase while others decline. Site trends were spatially asynchronous; adjacent sites sometimes exhibited opposite trends over the same period. Substantial change in eelgrass occurred at the sub-site (0.1 km) scale, including both complete local loss and dramatic increase of eelgrass. Metrics of local human development including shoreline armoring, upland development (imperviousness), and human density provide no explanatory power for eelgrass population change at any spatial scale. Our results suggest that the appropriate scale for understanding eelgrass change is smaller than typically assumed (approximately 1 to 3 km scale) and contrasts strongly with previous work. Synthesis. Despite ongoing conservation concern over seagrasses worldwide, eelgrass in Puget Sound has been highly resilient to both anthropogenic and environmental change over four decades. Our work provides general methods that can be applied to understand spatial and temporal scales of change and can be used to assess hypothesized drivers of change. This article is protected by copyright. All rights reserved.

Long-term mechanistic research and monitoring provides integral science support for ecosystem-based management (EBM) of resources, activities and services. Decades of oceanographic and ecological research by Bill Peterson and colleagues along the Newport Hydrographic Line (NH Line) provides essential context for understanding and managing Pacific salmon Oncorhynchus spp. and other marine resources in the California Current ecosystem. This research program helped federal scientists convey the significance of the northeast Pacific marine heatwave (2013–2016) to fisheries managers and stakeholders. Particularly illustrative were shifts in the composition of the copepod community, which reflected feeding conditions for Pacific salmon and other consumers. We identify six traits of the dataset produced by Peterson and colleagues that have made it especially valuable for informing management: (i) it has generated robust ecosystem indicators; (ii) it is long-term; (iii) it is associated with meaningful ecological mechanisms; (iv) it relates to ecosystem components of high societal value; (v) it can represent processes and lags at meaningful temporal scales; and (vi) it is part of a broader, integrative science effort. This research effort underscores the importance of developing and sustaining long-term mechanistic research and monitoring along the U.S. West Coast and elsewhere in the world.

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

The broadnose sevengill shark (Notorynchus cepedianus) is a high-order marine predator distributed worldwide in shallow coastal waters of temperate seas. Recent reports have suggested it may be a prevalent component of Pacific Northwest coastal estuarine communities, although biological characteristics of the shark population remain undocumented despite growing interest in recreational harvest of the species. Longline sampling was conducted in Willapa Bay and Grays Harbor, Washington, USA seasonally during 2003–2006 to collect sevengill shark size, maturity, and sex ratio data, and establish some baseline catch rate information. Sevengill sharks were collected on 65% of longline sets and catches were composed of subadult and mature individuals (122–283 cm TL) of both sexes. Most male sevengill sharks were large sexually mature adults, based on external clasper calcification levels, whereas most comparably sized females were considered subadults, based on literature-based size-at–maturity estimates. Neonates and young sharks

In Puget Sound, WA (USA), rockfish (Sebastes spp.) have significantly declined in abundance, with multiple petitions to list individual species under the Endangered Species Act. In order to better understand the ecological legacy of rockfish fishing to the Puget Sound ecosystem, the local history of rockfish exploitation was reviewed, focusing on the socioeconomic forces and management decisions which influenced the trajectory of landings. Rockfish have always been harvested for human consumption in the region, but over time exploitation patterns have changed from an opportunistic subsistence activity by indigenous peoples, to a year-round target of commercial and recreational interests. Annual commercial and recreational harvests together peaked (almost 400 mt) in the early 1980s as anglers’ attitudes changed, gear technology improved, rockfish became more familiar to the market, human population increased, and agency programs promoted fisheries to sustain employment. Rockfishes were generally not managed intensely or with conservation goals in mind until the late 1980s, in part due to scientific shortcomings and a lack of resources. By the time management actions were deemed necessary, the greatest harvest had already occurred. However, the low intrinsic productivity of most rockfish species suggests that the legacy of fishing will remain for years to come. As managers strive to restore the integrity and resilience of Puget Sound, they must realize the significance of historical fishery removals to the ecosystem and use the proper social and economic incentives to drive individual behavior toward these ecosystem goals.

The bluntnose sixgill shark Hexanchus griseus is a wide-ranging marine predator and the largest predatory shark in Puget Sound. Biological characteristics of the Puget Sound bluntnose sixgill shark population remain largely undocumented, despite a recent escalation in recreational angling for the species. Standardized longline sampling, supplemented with other opportunistic collections, was used to collect size, sex ratio, and relative catch rate data at three locations during 2006–2008. Fishing trials were also used to examine the effect of soak time, fishing depth, and time of day on catch rates. Captured bluntnose sixgill sharks were exclusively subadults (175–315 cm total length) found in approximately equal sex ratios in all seasons. Catch rates were highest in Elliott Bay, the urbanized port of Seattle, Washington, and were not affected by sampling season. Catch information derived from hook timers implies that the sharks locate and encounter baited hooks relatively rapidly (

The development of targets is foundational in conservation. Although progress has been made in setting targets, the diverse linkages among ecological and social components make target setting for coupled social-ecological systems extremely challenging. Developing integrated social-ecological targets is difficult because it forces policy makers to consider how management actions propagate throughout social-ecological systems, and because ultimately it is society, not scientists, that defines targets. We developed an interdisciplinary approach for identifying management targets and illustrate this approach using an example motivated by Puget Sound, USA. Our approach blends ecological modeling with empirical social science to articulate trade-offs and reveal societal preferences for different social-ecological states. The framework aims to place information in the hands of decision makers and promote discussion in the appropriate forums. Our ultimate objective is to encourage the informed participation of citizens in the development of social-ecological targets that reflect their values while also protecting key ecosystem attributes.

Our understanding of fish feeding interactions at Tijuana Estuary was improved by incorporating estimates of spatial and temporal variability into diet analyses. We examined the stomach contents of 7 dominant species (n=579 total fish) collected between 1994 and 1999. General feeding patterns pooled over time produced a basic food web consisting of 3 major trophic levels: (1) primary consumers (Atherinops affinis, Mugil cephalus) that ingested substantial amounts of plant material and detritus; (2) benthic carnivores (Clevelandia ios, Hypsopsetta guttulata, Gillichthys mirabilis, and Fundulus parvipinnis) that ingested high numbers of calanoid copepods and exotic amphipods (Grandidierella japonica); and (3) piscivores (Paralichthys californicus and Leptocottus armatus) that often preyed on smaller gobiids. Similarity-based groupings of individual species' diets were identified using nonmetric multidimensional scaling to characterize their variability within and between species, and in space and time. This allowed us identify major dietary shifts and recognize events (i.e., modified prey abundance during 1997–98 El Ni no floods) that likely caused these shifts.

We used expert elicitation to examine potential responses of eelgrass to several restoration strategies in Puget Sound. Restoration strategies included shoreline armor removal and modification, removal and modification of overwater structures, and efforts to improve water clarity via reductions in anthropogenic nutrient and sediment loadings. Expert responses indicated a general belief that reducing stressors would increase eelgrass cover; however, responses varied greatly among stressors. Our analyses revealed that removal of overwater structures, nutrient loading and shoreline armoring will have significantly larger effects on eelgrass recovery than would removal of sediment loading, with removal of overwater structures having the largest effect. We then used a probabilistic model to estimate what actions, singularly or in combination, could yield a large increase in eelgrass cover. Reducing single stressors could, in theory, result in recovery of eelgrass in Puget Sound; however, the magnitude of actions required would be so great that it is likely not practical. In contrast, we identified combinations of smaller reductions of stressors that could achieve significant eelgrass recovery. For example, a 40% reduction in overwater structures, combined with 20% reductions in shoreline armor, and nutrient and sediment loadings, was predicted to be one of the more feasible combinations of actions for meeting the target. The importance of eelgrass to Puget requires prompt input of scientific advice, and this work fills an important knowledge gap in the face of rapidly approaching legislative deadlines. While coded expert opinion of the sort we use here is a weak substitute for data, our work clarifies the current extent of scientific uncertainty that can guide management action in the near term and scientific research in the long term.

We developed, tested, and applied a bioenergetics model for the California killifish, Fundulus parvipinnis , to estimate the benefits of vegetated salt marsh habitats to killifish growth. Three independent statistical tests indicated that the model accurately estimated killifish growth. Predicted growth differed on average by only 14% from observed values. Field estimates of food consumption show that killifish can potentially double their daily food intake by adding marsh surface foods to their diet during each 2–3 h period of marsh access. Our model predicts that killifish grow from 20 to 44% faster if they add intertidal marsh surfaces to their subtidal feeding areas, despite higher metabolic costs and lower food assimilation during marsh feeding. Killifish may potentially grow up to 100% faster if energy costs associated with marsh access are minimized. During March–May, daytime tides are not high enough to permit marsh access. At water temperatures above 20°C, growth of adult killifish (>3.5 g wet mass, >60–62 mm, TL) is more adversely affected than that of juveniles by lack of marsh access. Killifish that are spawned early (April) develop under thermal regimes and periods of marsh access that differ from those spawned late (September), leading to large differences in the mass that could be achieved by the next spawning season. At age 1 year, early-spawned (ES) fish are 35–50% larger than late-spawned fish. Bioenergetics model are useful for determining the value of vegetated areas for fish (an important mitigation issue), designing for coastal wetland restoration (e.g. inclusion of marshes), and maintaining salt marshes as important fish habitat in southern California.

Fish assemblages from small intertidal creeks (first-order) and from larger subtidal creeks (third- and fourth-order) were sampled seasonally for 1 year at Tijuana Estuary and Sweetwater Marsh in southern California, USA. First-order creeks were dominated by Gillichthys mirabilis, Fundulus parvipinnis, and Clevelandia ios at both sites. At Sweetwater Marsh, species composition and species richness differed between creek orders, as did size structure of F. parvipinnis, one of the most abundant marsh residents; a greater proportion of small juveniles was collected from first-order creeks. At Tijuana Estuary, the larger system, elevations of first-order creeks were higher and fish use of creeks was lower than at Sweetwater Marsh. Shallow habitats are used extensively by several marsh residents, and may provide nursery habitat for juvenile F. parvipinnis. Intertidal creeks should be considered in designs of marsh restoration projects where the creation of habitat for resident fishes is a priority.

Although tidal wetland vegetation patterns are typically related to elevation, we hypothesized that the vertical range of a species may shift where the topography is more heterogeneous. We examined plant species occurrences in relation to elevation, proximity to the bay, and proximity to tidal creeks at a near-pristine wetland in San Quintin Bay, Baja California, Mexico. At the whole-wetland scale, most species occurred primarily within a 30-cm elevation band (the marsh plain). However, Spartina foliosa occurred only at the bayward margin, even though “suitable” elevations were present further inland. A similar pattern was found in San Diego Bay. At the microtopographic scale, three species on the marsh plain were strongly influenced by elevation, whereas four species responded to both elevation and proximity to tidal creeks. The latter species tended to “avoid” the lower 10 cm of the marsh plain except near a tidal creek. Species richness was thus greater (by 0.6 species at the lowest 10-cm class) at the tidal creek margin. Better drainage near creeks is the hypothesized cause. Our results help explain why species that are transplanted to constructed wetlands do not always grow at the full range of elevations they occupy in natural wetlands. We recommend that species be introduced to their modal elevation (determined from nearby reference marshes) and that salt-marsh construction designs include topographic heterogeneity (complex tidal creek networks). The analysis of broad-scale and fine-scale patterns of occurrence also suggests new habitat nomenclature. Elevation-based terms (“low,”“middle,” and “high” marsh) should be replaced by a system that considers elevation, landscape position, and conspicuous species. We suggest three habitat designations: (a) the high marsh—a 30- to 70-cm elevation range with Salicornia subterminalis; (b) the marsh plain—a 30-cm elevation range with heterogeneous topography and up to nine common species; and (c) cordgrass habitat—the bayward portion of the marsh plain and lower elevations, all occupied by Spartina foliosa. Although these habitats do not have discrete boundaries, separate terms are needed for wetland restoration plans and these designations will improve recognition that vegetation patterns respond to horizontal, as well as vertical, position.

The performance of two intertidal wetland mitigation projects constructed by the California Department of Transportation (Caltrans) in the Sweetwater Marsh National Wildlife Refuge (SMNWR) in San Diego Bay was evaluated over 5 years. Most of the Sweetwater wetland complex has been altered this century, including diking (with subsequent subsidence), filling, modification of the tidal regime, freshwater inflow and sediment fluxes. The mitigation project goals included a range of functional criteria intended to support two endangered bird species (light-footed clapper rail and California least tern) and one endangered plant (salt marsh bird's-beak). While the mitigation projects have achieved some of the performance criteria established in the regulatory permits (particularly, those related to fish), vegetation criteria for one of the bird species have not been met. The initial grading (in relation to local tidal datums) should support the target plant species, but growth has been less than required. Shortcomings of the habitat include elevated soil and groundwater salinity, low nutrient levels (especially nitrogen, which is readily leached from the coarse substrate), and eroding topography (where a single oversized and overly sinous channel and the lower-than-natural marshpalin result in high velocity surface water flow and erosion). The failure to achieve a large plain at low-marsh elevations highlights the importance of a more complete understanding of the relationship between the site physical processes (topography, hydrology, climate, geomorphology), substrate conditions, and biotic responses.

This study evaluated the use by fish of restored tidal wetlands and identified links between fish species composition and habitat characteristics. We compared the attributes of natural and constructed channel habitats in Sweetwater Marsh National Wildlife Refuge, San Diego Bay, California, by using fish monitoring data to explore the relationships between channel environmental characteristics and fish species composition. Fishes were sampled annually for 8 yr (1989–1996) at eight sampling sites, four in constructed marshes and four in natural marshes, using beach seines and blocking nets. We also measured channel habitat characteristics, including channel hydrology (stream order), width and maximum depth, bank slope, water quality (DO, temperature, salinity), and sediment composition. Fish colonization was rapid in constructed channels, and there was no obvious relationship between channel age and species richness or density. Total richness and total density did not differ significantly between constructed and natural channels, although California killifish (Fundulus parvipinnis) were found in significantly higher densities in constructed channels. Multivariate analyses showed fish assemblage composition was related to channel habitat characteristics, suggesting a channel’s physical properties were more important in determining fish use than its restoration status. This relationship highlights the importance of designing restoration projects with natural hydrologic features and choosing proper assessment criteria in order to avoid misleading interpretations of constructed channel success. We recommend that future projects be designed to mimic natural marsh hydrogeomorphology and diversity more closely, the assessment process utilize better estimates of fish habitat function (e.g., individual and community-based species trends, residence time, feeding, growth) and reference site choice, and experimental research be further incorporated into the restoration process.