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To assess the risk of aerosol transmission of SARS-CoV-2, measurements of the airborne viral concentrations in proximity to infected individuals, the persistence of the virus in aerosols, and the d...

Developing a comprehensive portfolio of theoretically sound indicators is fundamental to effective place-based management of coastal ecosystems at a wide range of scales. We reviewed indicator deve...

Restoration of degraded coastal and estuarine habitats owing to human activities is a major global concern. In Puget Sound, Washington, U.S.A., removal of hard armor from beaches and intertidal zones has become a priority for state and local agencies. However, the effectiveness of these shoreline restoration programs for subtidal habitats and fish is unknown. We surveyed six restoration sites in Puget Sound over 2 years to evaluate associations between shoreline restoration and subtidal fish abundance. We measured the abundance of juvenile salmonids and forage fishes along armored, restored, and reference shorelines. Bayesian generalized linear models showed limited support for associations between shoreline restoration and these fishes in the 3-7 years since armor removal. Pacific herring were more abundant at reference shorelines; the shoreline effect for surf smelt varied by survey site. Shoreline restoration was not an important predictor of salmonid abundance; the best models for Chinook and chum salmon included predictors for survey site and eelgrass, respectively. The retention of survey site in several species' top models reveals the influence of the broader landscape context. We also found seasonal variation in abundance for chum salmon and surf smelt. Our results suggest that juvenile forage fish and salmonids in estuaries likely have unique responses to shoreline features, and that the positive effects of armor removal either do not extend into subtidal areas or are not detectable at local scales. To be most effective, coastal restoration programs should consider broader landscape patterns as well as species-specific habitat needs when prioritizing investments.

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.

The complexity of ecosystem-based management (EBM) of natural resources has given rise to research frameworks such as integrated ecosystem assessments (IEA) that pull together large amounts of diverse information from physical, ecological, and social domains. Conceptual models are valuable tools for assimilating and simplifying this information to convey our understanding of ecosystem structure and functioning. Qualitative network models (QNMs) may allow us to conduct dynamic simulations of conceptual models to explore natural–social relationships, compare management strategies, and identify tradeoffs. We used previously developed QNM methods to perform simulations based on conceptual models of the California Current ecosystem's pelagic communities and related human activities and values. Assumptions about community structure and trophic interactions influenced the outcomes of the QNMs. In simulations where we applied unfavorable environmental conditions for production of salmon (Oncorhynchus spp....

Improved understanding and management of social-ecological systems (SES) requires collaboration between biophysical and social scientists; however, issues related to research philosophy and approaches, the nature of data, and language hinder interdisciplinary science. Here, we discuss how we used conceptual models to promote interdisciplinary dialogue in support of integrated ecosystem assessments (IEAs) in the California Current ecosystem. Initial con-ceptualizations of the California Current IEA were based on the Driver-Pressure-State-Impact-Response framework. This initial framing was biophysically centered, with humans primarily incorporated as impacts on the system. We wished to move from a conceptualization that portrayed an antagonistic relationship between humans and nature to one that integrated humans and social systems into the IEA framework. We propose a new conceptualization of the California Current that functions across temporal and spatial scales, captures the diverse relationships...

Despite the significant advances in making monthly or seasonal forecasts of weather, ocean hypoxia, harmful algal blooms and marine pathogens, few such forecasting efforts have extended to the ecology of upper trophic level marine species. Here, we test our ability to use short-term (up to 9 months) predictions of ocean conditions to create a novel forecast of the spatial distribution of Pacific sardine, Sardinops sagax. Predictions of ocean conditions are derived using the output from the Climate Forecast System (CFS) model downscaled through the Regional Ocean Modeling System (ROMS). Using generalized additive models (GAMs), we estimated significant relationships between sardine presence in a test year (2009) and salinity and temperature. The model, fitted to 2009 data, had a moderate skill [area under the curve (AUC) = 0.67] in predicting 2009 sardine distributions, 5–8 months in advance. Preliminary tests indicate that the model also had the skill to predict sardine presence in August 2013 (AUC = 0.85) and August 2014 (AUC = 0.96), 4–5 months in advance. The approach could be used to provide fishery managers with an early warning of distributional shifts of this species, which migrates from the U.S.–Mexico border to as far north as British Columbia, Canada, in summers with warm water and other favorable ocean conditions. We expect seasonal and monthly forecasts of ocean conditions to be broadly useful for predicting spatial distributions of other pelagic and midwater species.

The recovery of predators has the potential to restore ecosystems and fundamentally alter the services they provide. One iconic example of this is keystone predation by sea otters in the Northeast Pacific. Here, we combine spatial time series of sea otter abundance, canopy kelp area, and benthic invertebrate abundance from Washington State, USA, to examine the shifting consequences of sea otter reintroduction for kelp and kelp forest communities. We leverage the spatial variation in sea otter recovery to understand connections between sea otters and the kelp forest community. Sea otter increases created a pronounced decline in sea otter prey—particularly kelp-grazing sea urchins—and led to an expansion of canopy kelps from the late 1980s until roughly 2000. However, while sea otter and kelp population growth rates were positively correlated prior to 2002, this association disappeared over the last two decades. This disconnect occurred despite surveys showing that sea otter prey have continued to decline. Kelp area trends are decoupled from both sea otter and benthic invertebrate abundance at current densities. Variability in kelp abundance has declined in the most recent 15 years, as it has the synchrony in kelp abundance among sites. Together, these findings suggest that initial nearshore community responses to sea otter population expansion follow predictably from trophic cascade theory, but now, other factors may be as or more important in influencing community dynamics. Thus, the utility of sea otter predation in ecosystem restoration must be considered within the context of complex and shifting environmental conditions.

Nearshore habitats play a vital role in the life cycles of many marine fishes. These habitats are particularly important for Pacific herring Clupea pallasii, which rely on submerged vegetation in the shallow subtidal for spawning habitat and egg incubation. However, little is known about spatial or temporal variation in egg success or how spawning habitat may affect herring early life history. We estimated herring egg loss rates across multiple spawning vegetations in 5 subpopulations of Pacific herring in Puget Sound (USA), an urbanized estuarine system. We found enormous variation in herring egg loss among subpopulations (range of daily loss rates: 5 to 70%) and in egg loss of eggs reared under common garden conditions (range of cumulative loss: 20 to 100%). Egg loss varied by subpopulation but not by spawning vegetation type. Exploratory analyses suggest both wave height and land use patterns may affect hatch success. Using historical survey data, we found that a large proportion of spawning habitat available to Puget Sound herring remains unused each year. Furthermore, we found limited evidence that eggs were deposited dis- proportionally on particular vegetation types; only the non-indigenous brown algae Sargassum mu- ticum was spawned on more than expected by chance. Our results demonstrate that Puget Sound herring are not limited by the amount of available suitable spawning vegetation, and that native vegetation is not preferred over other vegetation types for herring spawning. Rather, it appears that other terrestrial or marine variables are likely determinants of herring egg loss.

Stable isotopes are used to address a wide range of ecological questions and can help researchers and managers better understand the movement and trophic ecology of sharks. Here, we review how shark studies from the Northeast Pacific Ocean (NEP) have employed stable isotopes to estimate trophic level and diet composition and infer movement and habitat-use patterns. To date, the number of NEP shark studies that have used stable isotopes is limited, suggesting that the approach is underutilized. To aid shark researchers in understanding the strengths and limitations of the approach, we provide a brief overview of carbon and nitrogen stable isotope trophic discrimination properties (e.g., change in δ

Stable isotopes are used to address a wide range of ecological questions and can help researchers and managers better understand the movement and trophic ecology of sharks. Here, we review how shark studies from the Northeast Pacific Ocean (NEP) have employed stable isotopes to estimate trophic level and diet composition and infer movement and habitat-use patterns. To date, the number of NEP shark studies that have used stable isotopes is limited, suggesting that the approach is underutilized. To aid shark researchers in understanding the strengths and limitations of the approach, we provide a brief overview of carbon and nitrogen stable isotope trophic discrimination properties (e.g., change in δ15N between predator and prey), tissue sample preparation methods specific to elasmobranchs, and methodological considerations for the estimation of trophic level and diet composition. We suggest that stable isotopes are a potentially powerful tool for addressing basic questions about shark ecology and are perhaps most valuable when combined and analysed with other data types (e.g., stomach contents, tagging data, or other intrinsic biogeochemical markers).

SUMMARYAs human population size and demand for seafood and other marine resources increase, understanding the influence of human activities in the ocean and on land becomes increasingly critical to the management and conservation of marine resources. In order to account for human influence on marine ecosystems while making management decisions, linkages between various anthropogenic pressures and ecosystem components need to be determined. Those linkages cannot be drawn until it is known how different pressures have been changing over time. This paper identifies indicators and develops time series for 22 anthropogenic pressures acting on the USA's portion of the California Current ecosystem. Time series suggest that seven pressures have decreased and two have increased over the short term, while five pressures were above and two pressures were below long-term means. Cumulative indices of anthropogenic pressures suggest a slight decrease in pressures in the 2000s compared to the preceding few decades. Dynamic factor analysis revealed four common trends that sufficiently explained the temporal variation found among all anthropogenic pressures. This reduced set of time series will be a useful tool to determine whether links exist between individual or multiple pressures and various ecosystem components.

Systematic scenario analysis is increasingly being used as an approach to evaluate ecosystem-based management options, often using “storylines” communicated through computer-generated (CG) images or visualizations. To explore potential issues associated with using CG imagery for conveying scenarios of habitat restoration we performed experiments in the Puget Sound, Washington region in which we asked whether respondents could differentiate among images of varying seagrass density and spatial extent, and if the presence of humans in the images affected these assessments and their perceptions of ecosystem health. Respondents were able to grossly determine relative seagrass density in the images, but only about 50% of them were able to determine this perfectly. Most errors occurred when the difference in density was small: approximately 20 shoot m −2 . The ability to correctly distinguish among images was inversely correlated with educational level. The presence or absence of people in the imagery did not influence the ability of respondents to correctly sort images, nor did it affect perceptions of ecosystem “health”. Taken together, the results suggest that such imagery can be useful as basis for communicating large differences in ecological conditions, but may be less informative as means to convey marginal changes in ecological structure. This work begins to highlight some of the pitfalls, but also the promise, of the use of CG visualization in marine resource management.

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.

Resource managers at the state, federal, and tribal levels make decisions on a weekly to quarterly basis, and fishers operate on a similar timeframe. To determine the potential of a support tool for these efforts, a seasonal forecast system is experimented with here. JISAO’s Seasonal Coastal Ocean Prediction of the Ecosystem (J-SCOPE) features dynamical downscaling of regional ocean conditions in Washington and Oregon waters using a combination of a high-resolution regional model with biogeochemistry and forecasts from NOAA’s Climate Forecast System (CFS). Model performance and predictability were examined for sea surface temperature (SST), bottom temperature, bottom oxygen, pH, and aragonite saturation state through model hindcasts, reforecast, and forecast comparisons with observations. Results indicate J-SCOPE forecasts have measurable skill on seasonal timescales. Experiments suggest that seasonal forecasting of ocean conditions important for fisheries is possible with the right combination of components. Those components include regional predictability on seasonal timescales of the physical environment from a large-scale model, a high-resolution regional model with biogeochemistry that simulates seasonal conditions in hindcasts, a relationship with local stakeholders, and a real-time observational network. Multiple efforts and approaches in different regions would advance knowledge to provide additional tools to fishers and other stakeholders.

We developed a food web model of central Puget Sound to provide science-based support for ecosystem-based management and to refine our understanding of bottom-up and top-down trophic forcing. Phytoplankton accounted for a large fraction of total biomass, total throughput, and caused considerable bottom-up effects in most functional groups in a dynamic simulation fit to time series data from 1981 to 2000. Top-down control was most apparent in the case of bald eagles (Haliaeetus leucocephalus), which exhibited keystone tendencies and appeared capable of causing trophic cascades. Increasing top-down control in several predator–prey relationships improved model fits to time series data from 1981 to 2000, but not as much as introducing non-equilibrium dynamics (biomass accumulation terms) to several key vertebrates. Fishing had little effect on system dynamics. Our model appears well-suited for addressing strategic, scenario-based questions of how the community as a whole will respond to management actions.

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

The Restoration Prioritization Framework was designed as a decision-making tool for the Lower Columbia River Estuary Partnership, to help identify the highest-priority sites for restoration. The underlying concepts are derived from regional applications of aquatic restoration theory. The framework uses the conceptual model that physical controlling factors (e.g., light, temperature, hydrology) drive the formation and maintenance of habitats and their ecological functions, and that stressors act on the controlling factors. The framework is two tiered and comprises 1) an overview of the concepts and description of framework tools; 2) a spreadsheet containing detailed data, formulas, and workflow for the actual site prioritization; and 3) a geographic information system (GIS) database containing source and processed geospatial datasets. In Tier I, the framework uses a GIS-based approach to evaluate impacts from a variety of human "stressors" such as diking, agriculture, overwater structures, and flow restrictions. Data processing derives priority scores, which are then relinked to the geographic sites in the GIS. In this manner, all of the data and tools employed can be analyzed and queried in a geospatial context. In addition to the core impact assessment, the framework includes tools to incorporate information on hydrologic connectivity and existing function into the priority screening. Specific restoration project proposals are evaluated in Tier II, using information on cost, expected functional change, site size, and predicted probability of success. Using this framework, the Lower Columbia River Estuary Partnership can screen for impacted areas, prioritize areas based on desired ecological criteria, and evaluate selected projects.

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 estimation of home range size of marine fish has received attention because of its application to the design of marine reserves. How individuals use space may also be important to the management of the species and for understanding behavioral processes like optimal foraging or ter- ritoriality. We used an acoustic tracking system (VRAP) to examine patterns in home range size and movement behavior for 3 demersal fishes in Puget Sound: lingcod Ophiodon elongatus, copper rock- fish Sebastes caurinus and quillback rockfish S. maliger. Data were collected over 8 wk in the sum- mer of 2006 and 3 wk in the winter of 2007. Home ranges were relatively small (~1500 to 2500 m 2 ) and did not differ among species. During the summer, lingcod had larger home ranges during the day than at night. Movement in all 3 species was in some way related to diel and tidal cycles, although individuals within species differed, and there was no general pattern. About half of the lingcod used portions of their home ranges only during the day and on the flood tide. Other individuals made sim- ilar movements on the ebb tide. Some copper rockfish moved to specific areas of their home range on the day ebb tide, while others made these movements on the night flood tide; others showed no pat- tern. Similar results were seen for quillback rockfish. While the arena of resource management often requires us to simplify complex systems, our results illustrate that such simplification may be difficult, and will depend ultimately on detailed behavioral data.

Environmental DNA (eDNA), genetic material recovered from an environmental medium such as soil, water, or feces, reflects the membership of the ecological community present in the sampled environment. As such, eDNA is a potentially rich source of data for basic ecology, conservation, and management, because it offers the prospect of quantitatively reconstructing whole ecological communities from easily obtained samples. However, like all sampling methods, eDNA sequencing is subject to methodological limitations that can generate biased descriptions of ecological communities. Here, we demonstrate parallels between eDNA sampling and traditional sampling techniques, and use these parallels to offer a statistical structure for framing the challenges faced by eDNA and for illuminating the gaps in our current knowledge. Although the current state of knowledge on some of these steps precludes a full estimate of biomass for each taxon in a sampled eDNA community, we provide a map that illustrates potential methods for bridging these gaps. Additionally, we use an original data set to estimate the relative abundances of taxon-specific template DNA prior to PCR, given the abundance of DNA sequences recovered post-PCR-and-sequencing, a critical step in the chain of eDNA inference. While we focus on the use of eDNA samples to determine the relative abundance of taxa within a community, our approach also applies to single-taxon applications (including applications using qPCR), studies of diversity, and studies focused on occurrence. By grounding inferences about eDNA community composition in a rigorous statistical framework, and by making these inferences explicit, we hope to improve the inferential potential for the emerging field of community-level eDNA analysis.

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.

The enantiomerically pure acyl complexes were converted to the corresponding enantiomerically pure carbene complexes (S Fe )- and (R Fe )-C 5 H 5 (CO)(PR 3 )Fe=CHCH 3 + by using standard techniques. Enantioselective ethylidene transfer from these complexes to styrene, vinyl acetate, and isopropenyl acetate gave methylcyclopropanes in high optical yields. A mechanistic analysis of the transfer reaction is presented by using the stereochemical results obtained coupled with deuterium labeling and relative reactivity studies. It is concluded that the most likely mechanism for carbene transfer involves reaction of the olefin with the minor but more reactive synclinal isomer of C 5 H 5 (CO)(PR 3 )Fe=CHCH 3 + followed by backside attack of the developing electrophilic center at Cγ on the Fe-Cα bond. A rationale is offered for the differing diastereoselectivities of ethylidene transfer from C 5 H 5 (CO)(PR 3 )Fe=CHCH 3 + versus C 5 H 5 (CO) 2 Fe=CHCH 3 + to various olefins

Meat and poultry processing facilities are an essential component of our food supply system. Like most agri-industrial production facilities, meat processing facilities have a number of unique design requirements. Design information, to date, has been limited. In an effort to summarize state of the art design procedures for meat processing facilities constructed in the United States, an overview of accepted standards and procedures has been assembled and discussed. With this paper engineers should become more familiar with specific design considerations for meat and poultry processing production facilities and develop appropriate references to expand their knowledge base. Educators may find this paper useful too. This paper discusses structural, layout, planning, construction, and sanitation of meat processing facilities and their effects on plant operation.

Flour milling facilities have been the cornerstone of agricultural processing for centuries. Like most agri-industrial production facilities, flour milling facilities have a number of unique design requirements. Design information, to date, has been limited. In an effort to summarize state of the art design procedures for flour milling facilities constructed in the United States, an overview of accepted standards and procedures has been assembled and discussed. With this paper engineers should become more familiar with specific design considerations for flour milling production facilities and develop appropriate references to expand their knowledge base. Educators may find this paper useful too.

Faculty of the Biological Systems Engineering Department at the University of Wisconsin- Madison are considering modifications to their undergraduate engineering curriculum that will result in graduates who are better prepared for positions as agri-industrial facility designers.

This paper summarizes educational needs for agri-industrial facility designers and mangers. Relevant skills required for the design, planning, and operation of agri-industrial facilities are discussed. Continuing and University educational needs for facility designers and managers are also presented.

Feed milling facilities represent an important segment of our food production system, because they manufacture the majority of products used to meet the nutritional needs of livestock in our meat supply chain. Agri-industrial facilities such as feed mills have a number of unique design requirements. In an effort to summarize state of the art design procedures for feed milling facilities constructed in North America, an overview of these procedures and accepted standards has been assembled. Specifically, this paper focuses on process engineering considerations. Consequently, engineers and designers should become familiar with the distinctive design process for these facilities and develop an appropriate reference base from which to work.

This paper defines North American Agri-Industry. Using the North American Industry Classification System and the definition of agri-industry industry segments are identified. Major areas of agri-industry include food, beverage and tobacco manufacturing, wood, leather and fiber processing, and Wholesaling and storage of non-durable goods. Current Gross Domestic Product and projected industry growth are discussed.