Equivocal associations between small-scale shoreline restoration and subtidal fishes in an urban estuary.

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.

From the predictable to the unexpected: kelp forest and benthic invertebrate community dynamics following decades of sea otter expansion.

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.

Stable Isotope Applications for Understanding Shark Ecology in the Northeast Pacific Ocean.

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).

Population assessment using multivariate time-series analysis: A case study of rockfishes in Puget Sound.

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.

Spatial distribution of environmental DNA in a nearshore marine habitat.

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.

A framework for inferring biological communities from environmental DNA.

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.

Genetic signatures of ecological diversity along an urbanization gradient.

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA-which we use here to detect hundreds of taxa simultaneously-as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

Experiments with Seasonal Forecasts of ocean conditions for the Northern region of the California Current upwelling system.

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.

Analysis of muscle creatine kinase regulatory elements in recombinant adenoviral vectors.

Adenoviral gene transfer holds promise for gene therapy, but effective transduction of a large and distributed tissue such as muscle will almost certainly require systemic delivery. In this context, the use of muscle-specific regulatory elements such as the muscle creatine kinase (MCK) promoter and enhancer will avoid potentially harmful ectopic expression of transgenes. We describe here the development and testing of adenoviral vectors containing small, striated muscle-specific, highly active MCK expression cassettes. One of these regulatory elements (CK6) is less than 600 bp in length and is 12% as active as the CMV promoter/enhancer in muscle. A recombinant adenoviral vector containing this regulatory element retains very high muscle specificity, expressing 600-fold higher levels of transgene in muscle than in liver. Muscle-specific regulatory elements may also increase persistence of transduced muscle cells. Adenoviral transduction of dendritic cells has been shown to stimulate cytotoxic T-lymphocyte (CTL) responses directed against transgene epitopes. We show that human dendritic cells infected in vitro with MCK-containing adenoviruses do not express significant levels of transgene. Furthermore, while adenoviral vectors containing nonspecific promoters are normally cleared from muscle tissue within 1 month, we show that MCK-containing vectors express significant levels of transgene 4 months after intramuscular injection.