High resolution assessment of commercial fisheries activity along the US West Coast using Vessel Monitoring System data with a case study using California groundfish fisheries.

Commercial fisheries along the US West Coast are important components of local and regional economies. They use various fishing gear, target a high diversity of species, and are highly spatially heterogeneous, making it challenging to generate a synoptic picture of fisheries activity in the region. Still, understanding the spatial and temporal dynamics of US West Coast fisheries is critical to meet the US legal mandate to manage fisheries sustainably and to better coordinate activities among a growing number of users of ocean space, including offshore renewable energy, aquaculture, shipping, and interactions with habitats and key non-fishery species such as seabirds and marine mammals. We analyzed vessel tracking data from Vessel Monitoring System (VMS) from 2010 to 2017 to generate high-resolution spatio-temporal estimates of contemporary fishing effort across a wide range of commercial fisheries along the entire US West Coast. We identified over 247,000 fishing trips across the entire VMS data, covering over 25 different fisheries. We validated the spatial accuracy of our analyses using independent estimates of spatial groundfish fisheries effort generated through the NOAA's National Marine Fisheries Service Observer Program. Additionally, for commercial groundfish fisheries operating in federal waters in California, we combined the VMS data with landings and ex-vessel value data from California commercial fisheries landings receipts to generate highly resolved estimates of landings and ex-vessel value, matching over 38,000 fish tickets with VMS data that included 87% of the landings and 76% of the ex-vessel value for groundfish. We highlight fisheries-specific and spatially-resolved patterns of effort, landings, and ex-vessel value, a bimodal distribution of fishing effort with respect to depth, and variable and generally declining effort over eight years. The information generated by our study can help inform future sustainable spatial fisheries management and other activities in the marine environment including offshore renewable energy planning.

Microbiome composition and function within the Kellet's whelk perivitelline fluid.

Microbiomes have gained significant attention in ecological research, owing to their diverse interactions and essential roles within different organismal ecosystems. Microorganisms, such as bacteria, archaea, and viruses, have profound impact on host health, influencing digestion, metabolism, immune function, tissue development, and behavior. This study investigates the microbiome diversity and function of Kellet's whelk (Kelletia kelletii) perivitelline fluid (PVF), which sustains thousands of developing K. kelletii embryos within a polysaccharide and protein matrix. Our core microbiome analysis reveals a diverse range of bacteria, with the Roseobacter genus being the most abundant. Additionally, genes related to host-microbe interactions, symbiosis, and quorum sensing were detected, indicating a potential symbiotic relationship between the microbiome and Kellet's whelk embryos. Furthermore, the microbiome exhibits gene expression related to antibiotic biosynthesis, suggesting a defensive role against pathogenic bacteria and potential discovery of novel antibiotics. Overall, this study sheds light on the microbiome's role in Kellet's whelk development, emphasizing the significance of host-microbe interactions in vulnerable life history stages. To our knowledge, ours is the first study to use 16S sequencing coupled with RNA sequencing (RNA-seq) to profile the microbiome of an invertebrate PVF.IMPORTANCEThis study provides novel insight to an encapsulated system with strong evidence of symbiosis between the microbial inhabitants and developing host embryos. The Kellet's whelk perivitelline fluid (PVF) contains microbial organisms of interest that may be providing symbiotic functions and potential antimicrobial properties during this vulnerable life history stage. This study, the first to utilize a comprehensive approach to investigating Kellet's whelk PVF microbiome, couples 16S rRNA gene long-read sequencing with RNA-seq. This research contributes to and expands our knowledge on the roles of beneficial host-associated microbes.

Understanding park visitors' soundscape perception using subjective and objective measurement.

Environmental noise knows no boundaries, affecting even protected areas. Noise pollution, originating from both external and internal sources, imposes costs on these areas. It is associated with adverse health effects, while natural sounds contribute to cognitive and emotional improvements as ecosystem services. When it comes to parks, individual visitors hold unique perceptions of soundscapes, which can be shaped by various factors such as their motivations for visiting, personal norms, attitudes towards specific sounds, and expectations. In this study, we utilized linear models and geospatial data to evaluate how visitors' personal norms and attitudes, the park's acoustic environment, visitor counts, and the acoustic environment of visitors' neighborhoods influenced their perception of soundscapes at Muir Woods National Monument. Our findings indicate that visitors' subjective experiences had a greater impact on their perception of the park's soundscape compared to purely acoustic factors like sound level of the park itself. Specifically, we found that motivations to hear natural sounds, interference caused by noise, sensitivity to noise, and the sound levels of visitors' home neighborhoods influenced visitors' perception of the park's soundscape. Understanding how personal factors shape visitors' soundscape perception can assist urban and non-urban park planners in effectively managing visitor experiences and expectations.

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk.

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet's whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet's whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

Avoiding critical thresholds through effective monitoring.

A major challenge in sustainability science is identifying targets that maximize ecosystem benefits to humanity while minimizing the risk of crossing critical system thresholds. One critical threshold is the biomass at which populations become so depleted that their population growth rates become negative-depensation. Here, we evaluate how the value of monitoring information increases as a natural resource spends more time near the critical threshold. This benefit emerges because higher monitoring precision promotes higher yield and a greater capacity to recover from overharvest. We show that precautionary buffers that trigger increased monitoring precision as resource levels decline may offer a way to minimize monitoring costs and maximize profits. In a world of finite resources, improving our understanding of the trade-off between precision in estimates of population status and the costs of mismanagement will benefit stakeholders that shoulder the burden of these economic and social costs.

Proteomic changes across a natural temperature gradient in a marine gastropod.

Responses of marine ectotherms to variable environmental temperature often entails maintanence of cellular homeostasis and physiological function through temperature compensation and physiological changes. We investigated the physiological response to thermal stress by examining proteomic changes in the marine kelp forest gastropod and emerging fisheries species Kellet's whelk (Kelletia kelletii) across a naturally-existing thermal gradient that ranges from a warmer-water site inside the species' native range and extends to the northern, cold-water edge of the range. We hypothesized that abundance of cellular stress response and energy metabolism proteins would increase with decreasing temperature in support of cold-compensation. Our exploratory proteomic analysis of whelk gill tissue (N = 6 whelks) from each of the four California Channel Island sites revealed protein abundance changes related to the cytoskeleton, energy metabolism/oxidative stress, and cell signaling. The changes did not correlate consistently with temperature. Nonetheless, whelks from the coldest island site showed increased abundance of energy metabolism and oxidative stress proteins, possibly suggesting oxidative damage of lipid membranes that is ameliorated by antioxidants and may aid in their cold stress response. Similarly, our exploratory analysis revealed abundances of cell signaling proteins that were higher at the coldest site compared to the warmest site, possibly indicating an importance for cell signaling regulation in relatively cooler environments. This study provides protein targets for future studies related to thermal effects in marine animals and may contribute to understanding the physiological response of marine organisms to future ocean conditions.

Designing MPAs for food security in open-access fisheries.

Food security remains a principal challenge in the developing tropics where communities rely heavily on marine-based protein. While some improvements in fisheries management have been made in these regions, a large fraction of coastal fisheries remain unmanaged, mismanaged, or use only crude input controls. These quasi-open-access conditions often lead to severe overfishing, depleted stocks, and compromised food security. A possible fishery management approach in these institution-poor settings is to implement fully protected marine protected areas (MPAs). Although the primary push for MPAs has been to solve the conservation problems that arise from mismanagement, MPAs can also benefit fisheries beyond their borders. The literature has not completely characterized how to design MPAs under diverse ecological and economic conditions when food security is the objective. We integrated four key biological and economic variables (i.e., fish population growth rate, fish mobility, fish price, and fishing cost) as well as an important aspect of reserve design (MPA size) into a general model and determined their combined influence on food security when MPAs are implemented in an open-access setting. We explicitly modeled open-access conditions that account for the behavioral response of fishers to the MPA; this approach is distinct from much of the literature that focuses on assumptions of "scorched earth" (i.e., severe over-fishing), optimized management, or an arbitrarily defined fishing mortality outside the MPA's boundaries. We found that the MPA size that optimizes catch depends strongly on economic variables. Large MPAs optimize catch for species heavily harvested for their high value and/or low harvesting cost, while small MPAs or no closure are best for species lightly harvested for their low value and high harvesting cost. Contrary to previous theoretical expectations, both high and low mobility species are expected to experience conservation benefits from protection, although, as shown previously, greater conservation benefits are expected for low mobility species. Food security benefits from MPAs can be obtained from species of any mobility. Results deliver both qualitative insights and quantitative guidance for designing MPAs for food security in open-access fisheries.

Parsing human and biophysical drivers of coral reef regimes.

Coral reefs worldwide face unprecedented cumulative anthropogenic effects of interacting local human pressures, global climate change and distal social processes. Reefs are also bound by the natural biophysical environment within which they exist. In this context, a key challenge for effective management is understanding how anthropogenic and biophysical conditions interact to drive distinct coral reef configurations. Here, we use machine learning to conduct explanatory predictions on reef ecosystems defined by both fish and benthic communities. Drawing on the most spatially extensive dataset available across the Hawaiian archipelago-20 anthropogenic and biophysical predictors over 620 survey sites-we model the occurrence of four distinct reef regimes and provide a novel approach to quantify the relative influence of human and environmental variables in shaping reef ecosystems. Our findings highlight the nuances of what underpins different coral reef regimes, the overwhelming importance of biophysical predictors and how a reef's natural setting may either expand or narrow the opportunity space for management interventions. The methods developed through this study can help inform reef practitioners and hold promises for replication across a broad range of ecosystems.

Combining fish and benthic communities into multiple regimes reveals complex reef dynamics.

Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai'i to define reef regimes in terms of both fish and benthic assemblages. Model-based clustering revealed five distinct regimes that varied ecologically, and were spatially heterogeneous by island, depth and exposure. We identified a regime characteristic of a degraded state with low coral cover and fish biomass, one that had low coral but high fish biomass, as well as three other regimes that varied significantly in their ecology but were previously considered a single coral dominated regime. Analyses of time series data reflected complex system dynamics, with multiple transitions among regimes that were a function of both local and global stressors. Coupling fish and benthic communities into reef regimes to capture complex dynamics holds promise for monitoring reef change and guiding ecosystem-based management of coral reefs.

Advancing the integration of spatial data to map human and natural drivers on coral reefs.

A major challenge for coral reef conservation and management is understanding how a wide range of interacting human and natural drivers cumulatively impact and shape these ecosystems. Despite the importance of understanding these interactions, a methodological framework to synthesize spatially explicit data of such drivers is lacking. To fill this gap, we established a transferable data synthesis methodology to integrate spatial data on environmental and anthropogenic drivers of coral reefs, and applied this methodology to a case study location-the Main Hawaiian Islands (MHI). Environmental drivers were derived from time series (2002-2013) of climatological ranges and anomalies of remotely sensed sea surface temperature, chlorophyll-a, irradiance, and wave power. Anthropogenic drivers were characterized using empirically derived and modeled datasets of spatial fisheries catch, sedimentation, nutrient input, new development, habitat modification, and invasive species. Within our case study system, resulting driver maps showed high spatial heterogeneity across the MHI, with anthropogenic drivers generally greatest and most widespread on O'ahu, where 70% of the state's population resides, while sedimentation and nutrients were dominant in less populated islands. Together, the spatial integration of environmental and anthropogenic driver data described here provides a first-ever synthetic approach to visualize how the drivers of coral reef state vary in space and demonstrates a methodological framework for implementation of this approach in other regions of the world. By quantifying and synthesizing spatial drivers of change on coral reefs, we provide an avenue for further research to understand how drivers determine reef diversity and resilience, which can ultimately inform policies to protect coral reefs.

Acoustic environments matter: Synergistic benefits to humans and ecological communities.

Protected areas are critical locations worldwide for biodiversity preservation and offer important opportunities for increasingly urbanized humans to experience nature. However, biodiversity preservation and visitor access are often at odds and creative solutions are needed to safeguard protected area natural resources in the face of high visitor use. Managing human impacts to natural soundscapes could serve as a powerful tool for resolving these conflicting objectives. Here, we review emerging research that demonstrates that the acoustic environment is critical to wildlife and that sounds shape the quality of nature-based experiences for humans. Human-made noise is known to affect animal behavior, distributions and reproductive success, and the organization of ecological communities. Additionally, new research suggests that interactions with nature, including natural sounds, confer benefits to human welfare termed psychological ecosystem services. In areas influenced by noise, elevated human-made noise not only limits the variety and abundance of organisms accessible to outdoor recreationists, but also impairs their capacity to perceive the wildlife that remains. Thus soundscape changes can degrade, and potentially limit the benefits derived from experiences with nature via indirect and direct mechanisms. We discuss the effects of noise on wildlife and visitors through the concept of listening area and demonstrate how the perceptual worlds of both birds and humans are reduced by noise. Finally, we discuss how management of soundscapes in protected areas may be an innovative solution to safeguarding both and recommend several key questions and research directions to stimulate new research.

Drivers of redistribution of fishing and non-fishing effort after the implementation of a marine protected area network.

Marine spatial planning (MSP) is increasingly utilized to sustainably manage ocean uses. Marine protected areas (MPAs), a form of spatial management in which parts of the ocean are regulated to fishing, are now a common tool in MSP for conserving marine biodiversity and managing fisheries. However, the use of MPAs in MSP often neglects, or simplifies, the redistribution of fishing and non-fishing activities inside and outside of MPAs following their implementation. This redistribution of effort can have important implications for effective MSP. Using long-term (14 yr) aerial surveys of boats at the California Channel Islands, we examined the spatial redistribution of fishing and non-fishing activities and their drivers following MPA establishment. Our data represent 6 yr of information before the implementation of an MPA network and 8 yr after implementation. Different types of boats responded in different ways to the closures, ranging from behaviors by commercial dive boats that support the hypothesis of fishing-the-line, to behaviors by urchin, sport fishing, and recreational boats that support the theory of ideal free distribution. Additionally, we found that boats engaged in recreational activities targeted areas that are sheltered from large waves and located near their home ports, while boats engaged in fishing activities also avoided high wave areas but were not constrained by the distance to their home ports. We did not observe the expected pattern of effort concentration near MPA borders for some boat types; this can be explained by the habitat preference of certain activities (for some activities, the desired habitat attributes are not inside the MPAs), species' biology (species such as urchins where the MPA benefit would likely come from larval export rather than adult spillover), or policy-infraction avoidance. The diversity of boat responses reveals variance from the usual simplified assumption that all extractive boats respond similarly to MPA establishment. Our work is the first empirical study to analyze the response of both commercial and recreational boats to closure. Our results will inform MSP in better accounting for effort redistribution by ocean users in response to the implementation of MPAs and other closures.

Upstream solutions to coral reef conservation: The payoffs of smart and cooperative decision-making.

Land-based source pollutants (LBSP) actively threaten coral reef ecosystems globally. To achieve the greatest conservation outcome at the lowest cost, managers could benefit from appropriate tools that evaluate the benefits (in terms of LBSP reduction) and costs of implementing alternative land management strategies. Here we use a spatially explicit predictive model (InVEST-SDR) that quantifies change in sediment reaching the coast for evaluating the costs and benefits of alternative threat-abatement scenarios. We specifically use the model to examine trade-offs among possible agricultural road repair management actions (water bars to divert runoff and gravel to protect the road surface) across the landscape in West Maui, Hawaii, USA. We investigated changes in sediment delivery to coasts and costs incurred from management decision-making that is (1) cooperative or independent among landowners, and focused on (2) minimizing costs, reducing sediment, or both. The results illuminate which management scenarios most effectively minimize sediment while also minimizing the cost of mitigation efforts. We find targeting specific "hotspots" within all individual parcels is more cost-effective than targeting all road segments. The best outcomes are achieved when landowners cooperate and target cost-effective road repairs, however, a cooperative strategy can be counter-productive in some instances when cost-effectiveness is ignored. Simple models, such as the one developed here, have the potential to help managers make better choices about how to use limited resources.

Offshore aquaculture: Spatial planning principles for sustainable development.

Marine aquaculture is expanding into deeper offshore environments in response to growing consumer demand for seafood, improved technology, and limited potential to increase wild fisheries catches. Sustainable development of aquaculture will require quantification and minimization of its impacts on other ocean-based activities and the environment through scientifically informed spatial planning. However, the scientific literature currently provides limited direct guidance for such planning. Here, we employ an ecological lens and synthesize a broad multidisciplinary literature to provide insight into the interactions between offshore aquaculture and the surrounding environment across a spectrum of spatial scales. While important information gaps remain, we find that there is sufficient research for informed decisions about the effects of aquaculture siting to achieve a sustainable offshore aquaculture industry that complements other uses of the marine environment.

Close the high seas to fishing?

The world's oceans are governed as a system of over 150 sovereign exclusive economic zones (EEZs, ∼42% of the ocean) and one large high seas (HS) commons (∼58% of ocean) with essentially open access. Many high-valued fish species such as tuna, billfish, and shark migrate around these large oceanic regions, which as a consequence of competition across EEZs and a global race-to-fish on the HS, have been over-exploited and now return far less than their economic potential. We address this global challenge by analyzing with a spatial bioeconomic model the effects of completely closing the HS to fishing. This policy both induces cooperation among countries in the exploitation of migratory stocks and provides a refuge sufficiently large to recover and maintain these stocks at levels close to those that would maximize fisheries returns. We find that completely closing the HS to fishing would simultaneously give rise to large gains in fisheries profit (>100%), fisheries yields (>30%), and fish stock conservation (>150%). We also find that changing EEZ size may benefit some fisheries; nonetheless, a complete closure of the HS still returns larger fishery and conservation outcomes than does a HS open to fishing.

Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality.

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well as the population genetic characteristics within S. pulcher. While S. pulcher and S. darwini are found in the temperate eastern Pacific regions of the northern and southern hemispheres, respectively, their genetic divergence was very small (estimated to have occurred between 200 and 600 kya). Within S. pulcher, genetic structuring was generally weak, especially along mainland California, but showed weak differentiation between Sea of Cortez and California, and between mainland California and Channel Islands. We highlight the congruence of weak genetic differentiation both within and between species and discuss possible causes for maintenance of high gene flow. In particular, we argue that deep and cooler water refugia are used as stepping stones to connect distant populations, resulting in low levels of genetic differentiation.

Achieving the triple bottom line in the face of inherent trade-offs among social equity, economic return, and conservation.

Triple-bottom-line outcomes from resource management and conservation, where conservation goals and equity in social outcomes are maximized while overall costs are minimized, remain a highly sought-after ideal. However, despite widespread recognition of the importance that equitable distribution of benefits or costs across society can play in conservation success, little formal theory exists for how to explicitly incorporate equity into conservation planning and prioritization. Here, we develop that theory and implement it for three very different case studies in California (United States), Raja Ampat (Indonesia), and the wider Coral Triangle region (Southeast Asia). We show that equity tends to trade off nonlinearly with the potential to achieve conservation objectives, such that similar conservation outcomes can be possible with greater equity, to a point. However, these case studies also produce a range of trade-off typologies between equity and conservation, depending on how one defines and measures social equity, including direct (linear) and no trade-off. Important gaps remain in our understanding, most notably how equity influences probability of conservation success, in turn affecting the actual ability to achieve conservation objectives. Results here provide an important foundation for moving the science and practice of conservation planning-and broader spatial planning in general-toward more consistently achieving efficient, equitable, and effective outcomes.

The value of coordinated management of interacting ecosystem services.

Coordinating decisions and actions among interacting sectors is a critical component of ecosystem-based management, but uncertainty about coordinated management's effects is compromising its perceived value and use. We constructed an analytical framework for explicitly calculating how coordination affects management decisions, ecosystem state and the provision of ecosystem services in relation to ecosystem dynamics and socio-economic objectives. The central insight is that the appropriate comparison strategy to optimal coordinated management is optimal uncoordinated management, which can be identified at the game theoretic Nash equilibrium. Using this insight we can calculate coordination's effects in relation to uncoordinated management and other reference scenarios. To illustrate how this framework can help identify ecosystem and socio-economic conditions under which coordination is most influential and valuable, we applied it to a heuristic case study and a simulation model for the California Current Marine Ecosystem. Results indicate that coordinated management can more than double an ecosystem's societal value, especially when sectors can effectively manipulate resources that interact strongly. However, societal gains from coordination will need to be reconciled with observations that it also leads to strategic simplification of the ecological food web, and generates both positive and negative impacts on individual sectors and non-target species.