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Humans interact with the oceans in diverse and profound ways. The scope, magnitude, footprint and ultimate cumulative impacts of human activities can threaten ocean ecosystems and have changed over time, resulting in new challenges and threats to marine ecosystems. A fundamental gap in understanding how humanity is affecting the oceans is our limited knowledge about the pace of change in cumulative impact on ocean ecosystems from expanding human activities – and the patterns, locations and drivers of most significant change. To help address this, we combined high resolution, annual data on the intensity of 14 human stressors and their impact on 21 marine ecosystems over 11 years (2003–2013) to assess pace of change in cumulative impacts on global oceans, where and how much that pace differs across the ocean, and which stressors and their impacts contribute most to those changes. We found that most of the ocean (59%) is experiencing significantly increasing cumulative impact, in particular due to climate change but also from fishing, land-based pollution and shipping. Nearly all countries saw increases in cumulative impacts in their coastal waters, as did all ecosystems, with coral reefs, seagrasses and mangroves at most risk. Mitigation of stressors most contributing to increases in overall cumulative impacts is urgently needed to sustain healthy oceans.

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.

Assessing the geographic structure of populations has relied heavily on Sewell Wright's F‐statistics and their numerous analogues for many decades. However, it is well appreciated that, due to their nonlinear relationship with gene flow, F‐statistics frequently fail to reject the null model of panmixia in species with relatively high levels of gene flow and large population sizes. Coalescent genealogy samplers instead allow a model‐selection approach to the characterization of population structure, thereby providing the opportunity for stronger inference. Here, we validate the use of coalescent samplers in a high gene flow context using simulations of a stepping‐stone model. In an example case study, we then re‐analyze genetic datasets from 41 marine species sampled from throughout the Hawaiian archipelago using coalescent model selection. Due to the archipelago's linear nature, it is expected that most species will conform to some sort of stepping‐stone model (leading to an expected pattern of isolation by distance), but F‐statistics have only supported this inference in ~10% of these datasets. Our simulation analysis shows that a coalescent sampler can make a correct inference of stepping‐stone gene flow in nearly 100% of cases where gene flow is ≤100 migrants per generation (equivalent to F ST = 0.002), while F‐statistics had mixed results. Our re‐analysis of empirical datasets found that nearly 70% of datasets with an unambiguous result fit a stepping‐stone model with varying population sizes and rates of gene flow, although 37% of datasets yielded ambiguous results. Together, our results demonstrate that coalescent samplers hold great promise for detecting weak but meaningful population structure, and defining appropriate management units.

This work was assisted through participation in “Next Generation Genetic Monitoring” Investigative Workshop at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Hawaiian fish community data were provided by the NOAA Pacific Islands Fisheries Science Center's Coral Reef Ecosystem Division (CRED) with funding from NOAA Coral Reef Conservation Program. O.E.G. was supported by the Marine Alliance for Science and Technology for Scotland (MASTS). A. C. and C. H. C. were supported by the Ministry of Science and Technology, Taiwan. P.P.-N. was supported by a Canada Research Chair in Spatial Modelling and Biodiversity. K.A.S. was supported by National Science Foundation (BioOCE Award Number 1260169) and the National Center for Ecological Analysis and Synthesis. All data used in this manuscript are available in DRYAD (https://doi.org/dx.doi.org/10.5061/dryad.qm288) and BCO-DMO (http://www.bco-dmo.org/project/552879). Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organisation (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap we present a unifying framework for the measurement of biodiversity across hierarchical levels of organisation. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon’s entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.) we applied the framework to a real dataset on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics, and eco-evolutionary dynamics. Publisher PDF

The Marianas Trench Marine National Monument (MNM) currently extends policy-based protection to deep-sea ecosystems contained within it, but managers require better understanding of the current knowledge and knowledge gaps about these ecosystems to guide decision-making. To address this need, we present a case study of the Marianas Trench MNM using in-depth interviews to determine scientists’ (1) current understanding of anthropogenic drivers of change and system vulnerability in deep-sea ecosystems; and (2) perceptions of the least understood deep-sea ecosystems and processes in the Marianas Trench MNM, and which of these, if any, should be research priorities to fill knowledge gaps about these systems and the impacts from anthropogenic drivers of change. Interview respondents shared similar views on the current knowledge of deep-sea ecosystems and potential anthropogenic drivers of change in the Marianas Trench MNM. Respondents also identified trench and deep pelagic (bathyal, abyssal, and hadal zones) ecosystems as the least understood, and highlighted climate change, litter and waste, mining and fishing, and interactions between these drivers of change as critical knowledge gaps. To fill key knowledge gaps and inform conservation decision-making, respondents identified the need for monitoring networks and time-series data. Our approach demonstrates how in-depth interviews can be used to elicit knowledge to inform decision-making in data-limited situations.

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.

The growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision-making. Yet there is no clear-cut guidance on how genetic features can be incorporated into conservation planning processes, with multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns also differ between species, but the potential trade-offs amongst genetic objectives for multiple species in conservation planning are currently understudied. This study compares spatial conservation prioritizations derived from two metrics of both genetic diversity (nucleotide and haplotype diversity) and genetic isolation (private haplotypes and local genetic differentiation) for mitochondrial DNA for five marine species. The findings show that conservation plans based solely on habitat representation noticeably differ from those additionally including genetic data, with habitat-based conservation plans selecting fewer conservation priority areas. Furthermore, all four genetic metrics selected approximately similar conservation priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, the results suggest that multi-species genetic conservation objectives are vital to create protected area networks that appropriately preserve community-level evolutionary patterns. This article is protected by copyright. All rights reserved.

Ecosystems often shift abruptly and dramatically between different regimes in response to human or natural disturbances. When ecosystems tip from one regime to another, the suite of available ecosystem benefits changes, impacting the stakeholders who rely on these benefits. These changes often create some groups who stand to incur large losses if an ecosystem returns to a previous regime. When the participation cost in the decision-making process is extremely high, this can “lock in” ecosystem regimes, making it harder for policy and management to shift ecosystems out of what the majority of society views as the undesirable regime. Public stakeholder meetings often have high costs of participation, thus economic theory predicts they will be dominated by extreme views and often lead to decisions that do not represent the majority viewpoint. Such extreme viewpoints can create strong inertia even when there is broad consensus to manage an ecosystem towards a different regime. In the same manner that reinforcing ecological feedback loops make it harder to exit an ecosystem regime, there are decision-making feedback loops that contribute additional inertia.

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.

As climatic changes and human uses intensify, resource managers and other decision makers are taking actions to either avoid or respond to ecosystem tipping points, or dramatic shifts in structure and function that are often costly and hard to reverse. Evidence indicates that explicitly addressing tipping points leads to improved management outcomes. Drawing on theory and examples from marine systems, we distill a set of seven principles to guide effective management in ecosystems with tipping points, derived from the best available science. These principles are based on observations that tipping points (1) are possible everywhere, (2) are associated with intense and/or multifaceted human use, (3) may be preceded by changes in early‐warning indicators, (4) may redistribute benefits among stakeholders, (5) affect the relative costs of action and inaction, (6) suggest biologically informed management targets, and (7) often require an adaptive response to monitoring. We suggest that early action to preserve system resilience is likely more practical, affordable, and effective than late action to halt or reverse a tipping point. We articulate a conceptual approach to management focused on linking management targets to thresholds, tracking early‐warning signals of ecosystem instability, and stepping up investment in monitoring and mitigation as the likelihood of dramatic ecosystem change increases. This approach can simplify and economize management by allowing decision makers to capitalize on the increasing value of precise information about threshold relationships when a system is closer to tipping or by ensuring that restoration effort is sufficient to tip a system into the desired regime.

Summary 1. Ecosystem-based management of coral reef fisheries aims to sustainably deliver a diverse portfolio of ecosystem services. This goal can be undermined if the ecosystem shifts into a different state, with altered ecosystem functions and benefits to people. If levels of drivers that cause transitions between states are identified, management measures could be aimed at maintaining drivers below these levels to avoid ecosystem shifts. 2. Analysing data from a large number of Caribbean coral reefs (N = 2001), suites of nonlinear thresholds were identified between metrics of coral reef processes and structure along a gradient of total fish biomass (a proxy for fishing pressure). Several metrics (macroalgal cover, invertivorous fishes and fish species richness) associated with coral-dominated reefs exhibited thresholds at relatively high fish biomass levels (50–88% of unfished biomass). Other metrics (urchin biomass, ratio of macroalgal to coral cover, herbivorous fishes and coral cover) showed thresholds at lower fish biomass levels (28–37% of unfished biomass). 3. Ratios of total fish biomass in fishing areas to closed areas (unfished biomass) in the Caribbean indicate that reefs may generally be at risk for change at ratios between 05 (coral dominated) and 03 (macroalgal dominated). Similar relationships were found for coral reefs in the Indian Ocean. While these results illustrate thresholds at the scale of the entire Caribbean, assessing local reefs is advisable because biomass levels vary within the region, and reef trajectories depend on past, present and future local conditions. 4. Synthesis and applications. If the thresholds in this study are generalizable to scales relevant to management, it may be possible to produce sustainable yield while simultaneously maintaining coral-dominated reefs by restricting fishing mortality to levels that result in biomass ratios near 05. Fishing down to biomass ratios near 03 may increase the risk of overfishing (resulting in lower long-term yields) and transition to macroalgal-dominated reefs. Thresholds offer a simple and powerful way for managers to operationalize precautionary ecosystem-based fishery management by adaptively limiting fishing pressure in order to (i) maintain desirable coral reef conditions, (ii) establish a system-specific target for generating pretty good yield and (iii) maintain sustainable multi-species fishery yields.

Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental and applied research questions in various research fields, including ecology, evolution, and conservation biology. However, the unique combination of different scientific disciplines and analytical approaches also constitute a challenge to most researchers wishing to apply landscape genomics. Here, we present an introductory overview of important concepts and methods used in current landscape genomics. For this, we first define the field and explain basic concepts and methods to capture different hypotheses of landscape influences on neutral genetic variation. Next, we highlight established and emerging genomic tools for quantifying adaptive genetic variation in landscape genomic studies. To illustrate the covered topics and to demonstrate the potential of landscape genomics, we provide empirical examples addressing a variety of research question, i.e., the investigation of evolutionary processes driving population differentiation, the landscape genomics of range expanding species, and landscape genomic patterns in organisms of special interest, including species inhabiting aquatic and terrestrial environments. We conclude by outlining remaining challenges and future research avenues in landscape genomics.

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (''unplugged'') approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches.

Targeted conservation and management programs are crucial for mitigating anthropogenic threats to declining biodiversity. Although evolutionary processes underpin extant patterns of biodiversity, it is uncommon for resource managers to explicitly consider genetic data in conservation prioritization. Genetic information is inherently relevant to management because it describes genetic diversity, population connectedness, and evolutionary history; thereby typifying their behavioral traits, physiological climate tolerance, evolutionary potential, and dispersal ability. Incorporating genetic information into spatial conservation prioritization starts with reconciling the terminology and techniques used in genetics and conservation science. Genetic data vary widely in analyses and their interpretations can be challenging even for experienced geneticists. Therefore, identifying objectives, decision rules, and implementations in decision support tools specifically for management using genetic data is challenging. Here, we outline a framework for eight genetic system characteristics, their measurement, and how they could be incorporated in spatial conservation prioritization for two contrasting objectives: biodiversity preservation vs maintaining ecological function and sustainable use. We illustrate this framework with an example using data from Tridacna crocea (Lamarck, 1819) (boring giant clam) in the Coral Triangle. We find that many reefs highlighted as conservation priorities with genetic data based on genetic subregions, genetic diversity, genetic distinctness, and connectivity are not prioritized using standard practices. Moreover, different characteristics calculated from the same samples resulted in different spatial conservation priorities. Our results highlight that omitting genetic information from conservation decisions may fail to adequately represent processes regulating biodiversity, but that conservation objectives related to the choice of genetic system characteristics require careful consideration.

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.

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.

We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.

Seafood is widely considered to be either fished or farmed. In contrast to this perception, many types of seafood are produced by enterprises using a combination of techniques traditionally ascribed to either fisheries or aquaculture. Categorizing seafood as either fished or farmed obfuscates the growth potential and environmental impacts of global seafood production. To better capture seafood data, national and international record-keeping organizations should add a new hybrid category for seafood produced using both fisheries and aquaculture methods.

Understanding connectivity remains a fundamental challenge to marine ecology due to technical limitations of tracking larval dispersal. Marine population genetic analyses are often used to make inferences about the scale of population connectivity. For species with a larval phase, pelagic larval duration (PLD) is assumed to influence the scale of connectivity. If PLD and genetic metrics are reliable proxies of connectivity, the 2 should be well correlated. Previous tests report conflicting results, with many reports that global FST (Wright's fixation index) correlates poorly with PLD, and one very high correlation of isolation-by-distance (IBD) slope, which is derived from FST, with PLD. First we clarify the expectations for the performance of these different proxies in light of the latest understanding of larval dispersal dynamics. We then test the hypothesis that IBD slope may be a more robust correlate with dispersal scale than global FST with a new dataset of recent marine genetic studies. Re-evaluation of previously published and new datasets revealed a consistent, moderate fit (R 2 ~0.30) between genetic and PLD proxies of dispersal (using either IBD slope or global FST), with significant improvement for small-scale (

Marine species frequently show weak and ⁄or complex genetic structuring that is commonly dismissed as ‘chaotic’ genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet’s whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site-to-site migration probability derived from a high resolution multi-year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information–theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure.

Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management.

Coastal marine ecosystems rank among the most productive ecosystems on earth but are also highly threatened by the exposure to both ocean- and land-based human activities. Spatially explicit information on the distributions of land-based impacts is critical for managers to identify where the effects of land-based activities on ecosystem condition are greatest and, therefore, where they should prioritize mitigation of land-based impacts. Here, we quantify the global cumulative impact of four of the most pervasive land-based impacts on coastal ecosystems—nutrient input, organic and inorganic pollution, and the direct impact of coastal populations (e.g., coastal engineering and trampling)—and identify hotspots of land-based impact using a variety of metrics. These threat hotspots were primarily in Europe and Asia, with the top three adjacent to the Mississippi, Ganges, and Mekong rivers. We found that 95% of coastal and shelf areas (

Quantitative assessment of the spatial patterns of all human uses of the oceans and their cumulative effects is needed for implementing ecosystem-based management, marine protected areas, and ocean zoning. Here, we apply methods developed to map cumulative impacts globally to the California Current using more comprehensive and higher-quality data for 25 human activities and 19 marine ecosystems. This analysis indicates where protection and threat mitigation are most needed in the California Current and reveals that coastal ecosystems near high human population density and the continental shelves off Oregon and Washington are the most heavily impacted, climate change is the top threat, and impacts from multiple threats are ubiquitous. Remarkably, these results were highly spatially correlated with the global results for this region (R2= 0.92), suggesting that the global model provides guidance to areas without local data or resources to conduct similar regional-scale analyses.

Molecular tools perform at their best when integrated with other data and approaches. The value of integrating approaches is especially high when the underlying genetic signal is relatively weak, as occurs in many marine species. Recently, studies combining genetic, oceanographic, behavioural and modelling approaches have provided new insights into the spatial ecology of marine populations, in particular regarding larval migration, barriers to dispersal and source-sink population dynamics. In this perspectives piece, we explore the advantages of a multidisciplinary approach to marine population genetics by (i) providing a synthesis of what has been learned about connectivity from studies that combine genetic data with other tools, (ii) discussing how incorporation of ecological and oceanographic information into alternative hypotheses can boost inference when genetic power is low, and (iii) summarizing recent innovations in statistical population genetics that enable seamless integration of ecological, environmental and genetic data. These topics are covered in the context of how genetic inferences of connectivity and dispersal can contribute to pressing questions facing marine conservation and management.

The California sheephead Semicossyphus pulcher and the kelp bass Paralabrax clathra- tus are members of a suite of nearshore reef species that have subtropical taxonomic affiliations and important fisheries in the Southern California Bight (SCB). This suite shows high interannual fluctu- ation in recruitment success in the SCB, with no known cause. One hypothesis gaining mention in management literature is the idea that recruitment booms in the SCB originate from larvae swept poleward from Mexico during El Nino flow-reversal events. If true, SCB stocks may be reliant on Mexican sources. We used 3 diverse sources of data to investigate the likelihood of El Nino-driven recruitment success and connectivity for S. pulcher and P. clathratus. Time series of larval abundance revealed that neither species shows synchrony with El Nino Southern Oscillation (ENSO) cycles that would suggest influx of Mexican larvae during El Nino flow reversals. P. clathratus age structure data show that recruitment strength is unrelated to ENSO cycles but correlates to spring sea surface tem- perature in the SCB, indicating that local environmental factors drive interannual variation in local production. Genetic analyses of 14 populations of P. clathratus with 7 microsatellite loci revealed dis- tinct patterns of genetic structure in the SCB and Baja California that reflect localized connectivity patterns and contradict patterns that would be expected if dispersal primarily occurred during El Nino flow reversals. While these results support the importance of protecting local sources in the SCB, continued study of dispersal and recruitment at large scales will help characterize the causes of interannual variation and the exact scale of cross-border connectivity.

Marine ecosystems are threatened by a suite of anthropogenic stressors. Mitigating multiple threats is a daunting task, particularly when funding constraints limit the number of threats that can be addressed. Threats are typically assessed and prioritized via expert opinion workshops that often leave no record of the rationale for decisions, making it difficult to update recommendations with new information. We devised a transparent, repeatable, and modifiable method for collecting expert opinion that describes and documents how threats affect marine ecosystems. Experts were asked to assess the functional impact, scale, and frequency of a threat to an ecosystem; the resistance and recovery time of an ecosystem to a threat; and the certainty of these estimates. To quantify impacts of 38 distinct anthropogenic threats on 23 marine ecosystems, we surveyed 135 experts from 19 different countries. Survey results showed that all ecosystems are threatened by at least nine threats and that nine ecosystems are threatened by >90% of existing threats. The greatest threats (highest impact scores) were increasing sea temperature, demersal destructive fishing, and point-source organic pollution. Rocky reef, coral reef, hard-shelf, mangrove, and offshore epipelagic ecosystems were identified as the most threatened. These general results, however, may be partly influenced by the specific expertise and geography of respondents, and should be interpreted with caution. This approach to threat analysis can identify the greatest threats (globally or locally), most widespread threats, most (or least) sensitive ecosystems, most (or least) threatened ecosystems, and other metrics of conservation value. Additionally, it can be easily modified, updated as new data become available, and scaled to local or regional settings, which would facilitate informed and transparent conservation priority setting.

In the face of growing human impacts on ecosystems, scientists and managers recognize the need to better understand thresholds and non-linear dynamics in ecological systems to help set management targets. However, our understanding of the factors that drive threshold dynamics, and when and how rapidly thresholds will be crossed is currently limited in many systems. In spite of these limitations, there are approaches available to practitioners today—including ecosystem monitoring, statistical methods to identify thresholds and indicators, and threshold-based adaptive management—that can be used to help avoid reaching ecological thresholds or restore systems that have crossed them. We briefly review the current state of knowledge and then use real-world examples to demonstrate how resource managers can use available approaches to avoid crossing ecological thresholds. We also highlight new tools and indicators being developed that have the potential to enhance our ability to detect change, predict when a system is approaching an ecological threshold, or restore systems that have already crossed a tipping point.

Human pressures on the ocean are thought to be increasing globally, yet we know little about their patterns of cumulative change, which pressures are most responsible for change, and which places are experiencing the greatest increases. Managers and policymakers require such information to make strategic decisions and monitor progress towards management objectives. Here we calculate and map recent change over 5 years in cumulative impacts to marine ecosystems globally from fishing, climate change, and ocean- and land-based stressors. Nearly 66% of the ocean and 77% of national jurisdictions show increased human impact, driven mostly by climate change pressures. Five percent of the ocean is heavily impacted with increasing pressures, requiring management attention. Ten percent has very low impact with decreasing pressures. Our results provide large-scale guidance about where to prioritize management efforts and affirm the importance of addressing climate change to maintain and improve the condition of marine ecosystems., Human pressure on the ocean is thought to be increasing globally, yet the magnitude and patterns of these changes are largely unknown. Here, the authors produce a global map of change in cumulative human pressures over the past 5 years, and show that ∼66% of the ocean has experienced elevated human impact.

The scales of population structure in marine species depend on the degree to which larvae from different populations are mixed in the plankton. There is an intriguing trend in marine population genetic studies of significant genetic structure for larvae, recruits, or populations at fine scales that is unpatterned across space and changes through time. This "chaotic genetic patchiness" suggests that larval pools are not well mixed in the plankton. However, few studies have been able to distinguish among potential causes of spatial and temporal genetic heterogeneity: changes in larval migration patterns, changes in environmental selection, or stochasticity caused by "sweepstakes" reproductive success of spawners creating detectable family structure. Here we use microsatellite markers to show that significant allele frequency shifts occurred sporadically in space and time for cohorts of recruits of Paralabrax clathratus (kelp bass) collected once every two weeks over two years from five sites in the Santa Barbara Channel, California, USA. We found that the pattern of genetic differentiation among cohorts was explained by a combination of (1) family structure in some cohorts, evidenced by half and full siblings, and (2) an indication of changes in larval delivery. It is unlikely but possible that environmental selection also plays a role. Although sampling of potential source populations was incomplete, cohorts arriving during western current flows show most genetic similarity with a population sample collected in the west, and cohorts arriving during current flows from the southeast show similarity with population samples collected in the south and east. Despite the family structure apparent in some cohorts, these "sweepstakes" events occur on too fine a scale to create lasting year class genetic structure. The results corroborate oceanographic models of larval dispersal, which suggest that larval mixing in the plankton is less extensive than previously believed.

Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists' ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike.

Enric Sala ...et al. -- 13 pages, 5 figures, 4 tables, Historical exploitation of the Mediterranean Sea and the absence of rigorous baselines makes it difficult to evaluate the current health of the marine ecosystems and the efficacy of conservation actions at the ecosystem level. Here we establish the first current baseline and gradient of ecosystem structure of nearshore rocky reefs at the Mediterranean scale. We conducted underwater surveys in 14 marine protected areas and 18 open access sites across the Mediterranean, and across a 31-fold range of fish biomass (from 3.8 to 118 g m−2). Our data showed remarkable variation in the structure of rocky reef ecosystems. Multivariate analysis showed three alternative community states: (1) large fish biomass and reefs dominated by non-canopy algae, (2) lower fish biomass but abundant native algal canopies and suspension feeders, and (3) low fish biomass and extensive barrens, with areas covered by turf algae. Our results suggest that the healthiest shallow rocky reef ecosystems in the Mediterranean have both large fish and algal biomass. Protection level and primary production were the only variables significantly correlated to community biomass structure. Fish biomass was significantly larger in well-enforced no-take marine reserves, but there were no significant differences between multi-use marine protected areas (which allow some fishing) and open access areas at the regional scale. The gradients reported here represent a trajectory of degradation that can be used to assess the health of any similar habitat in the Mediterranean, and to evaluate the efficacy of marine protected areas, This study was funded by the Oak Foundation, the Pew Charitable Trusts, Spain's National Council for Scientific Research (CSIC) and the Lenfest Ocean Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Although seafood is the most highly traded food internationally, it is an often overlooked component of global food security. It provides essential local food, livelihoods, and export earnings. Although global capture fisheries production is unlikely to increase, aquaculture is growing considerably. Sustaining seafood's contributions to food security hinges on the ability of institutions, particularly in developing countries, to protect and improve ecosystem health in the face of increasing pressures from international trade.

Keywords Mendelian Microsatellite Mitochondrial Paralabrax SerranidaeWhile molecular tools have transformed fisheries biology,their development and implementation can necessitate theuse of delicate equipment, be expensive, and requireextensive optimization [1]. Counting only consumables, wehave calculated that in-house sequencing of 500–700 baseson a Beckman CEQ 8000 (Beckman Coulter, Fullerton,CA, USA) costs *$4–5 per sample under ideal conditions.It is a process not amenable to isolated or rudimentary labconditions and is not easily performed as a quick-returnassay. Loci scored as dye-labeled fragments on an auto-mated sequencer are also expensive [2]; they requiredevelopment of a microsatellite library and cost commer-cially *US$12,500 [3]. Confirmation of Mendelianinheritance in the marker set is yet another cost burden andrepresents an important but infrequently performed pre-requisite for statistical testing. A recent survey found 1 in15 microsatellite loci, as expressed in their data scores, hadnon-Mendelian patterns [4].The reporting of methodologies and inheritance studiesthat are cost effective and have minimal equipmentrequirements can therefore be invaluable to a new researchprogram or a monitoring effort that requires fast turn-around times. A set of markers will be available for thespecies in question and frequently its congeners; thestrategies for developing the markers, such as our inheri-tance methodology below, can have even widerapplication. Based on this rationale, this short paper pre-sents genetic methods developed for the kelp bass,Paralabrax clathratus, that confirm the robustness ofmarkers and allow for economical and expeditious assays.Kelp bass are a temperate serranid found abundantly fromPoint Conception, CA, to just south of Punta Eugenia,Mexico [5], and are an important component of the$300 million California sport fishing industry [6, 7]. P.clathratus occurs in current and proposed southern Cali-fornia marine reserves and has been the subject of adiversity of research [8–11].We document a restriction fragment length polymor-phism (RFLP) assay of the mitochondrial control regionthat can assess a substantial amount of the sequencediversity with only a thermal cycler and an agarose gel box.We also present a series of controlled crosses to confirmMendelian inheritance for previously published microsat-ellite markers [12], a task generally difficult to performwith many marine fish [13].Development of RFLPsSequences for the mitochondrial control region of 105 kelpbass from ten locations (Genbank accession numbersDQ192295–DQ192399) were used. Sequences werealigned in Sequencher 4.5 (Gene Codes, Ann Arbor, MI,USA) and surveyed with the program’s restriction enzymelibrary. Pairwise U

Kelp bass, Paralabrax clathratus, is an important sport fishery of California, USA and Baja, Mexico. Here we describe eight microsatellite loci developed for this species. Two loci were derived from known primers for other species in the family, Serranidae and six were developed anew using a clone enrichment protocol. Loci were arranged into three multiplex PCR (polymerase chain reaction) sets for fast throughput; 564 individuals from nine populations across the species’ range were genotyped. Polymorphism ranged from four to 47 alleles and all populations at all loci displayed Hardy–Weinberg and linkage equilibrium.

We present a novel method for designing marine reserves that trades off three important attributes of a conservation plan: habitat condition, habitat representation, and socioeconomic costs. We calculated habitat condition in four ways, using different human impacts as a proxy for condition: all impacts; impacts that cannot be managed with a reserve; land-based impacts; and climate change impacts. We demonstrate our approach in California, where three important tradeoffs emerged. First, reserve systems that have a high chance of protecting good condition habitats cost fishers less than 3.1% of their income. Second, cost to fishers can be reduced by 1/2-2/3 by triaging less than 1/3 of habitats. Finally, increasing the probability of protecting good condition habitats from 50% to 99% costs fishers an additional 1.7% of their income, with roughly 0.3% added costs for each additional 10% confidence. Knowing exactly what the cost of these tradeoffs are informs discussion and potential compromise among stakeholders involved in protected area planning worldwide.

More than 38% of the world’s population lives within 100 km of the coast, and the coastal zone is becoming more heavily populated each year (Small and Cohen 2004). More and more human activities depend upon and compete for coastal and marine ecosystem goods and services. This intensification of use is necessitating a shift toward more comprehensive and integrated approaches to management – a shift that is already underway via approaches such as ecosystem-based management and ocean zoning (Day 2002; McLeod et al. 2005; Crowder et al. 2006; Douvere et al. 2007; Douvere 2008; Office of the President 2010). Given the diversity of human uses and natural resources that converge in coastal waters, understanding the potential independent and cumulative impacts of those uses and associated stressors on marine ecosystems can be very challenging. Little empirical data is available to weigh the relative vulnerability of the range of ecosystem types to the full set of human stressors (Halpern et al.

Eleven microsatellites were characterized for Semicossyphus pulcher (California sheephead) using an enrichment protocol. The number of alleles varied from three to 14 for a sample of 40 individuals from two populations. Expected heterozygosities ranged from 0.311 to 0.891. All loci but one were in Hardy-Weinberg equilibrium. No evidence for linkage disequilibrium was observed. These polymorphic microsatellites will be useful for genetic diversity and connectivity analyses of S. pulcher.

Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as 'chaotic' genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet's whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site-to-site migration probability derived from a high resolution multi-year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information-theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure.

A panel of 64 experts ranked 30 scenarios of human activities according to their impacts on coastal ecosystems. Experts were asked to rank the five scenarios posing the greatest threats and the five scenarios posing the least threats. The goal of this study was to find weights for criteria that adequately model these stakeholders’ preferences and can be used to predict the scores of other scenarios. Probabilistic inversion (PI) techniques were used to quantify a model of ecosystem vulnerability based on five criteria. Distinctive features of this approach are: 1. A model of the stakeholder population as a joint distribution over the criteria weights is obtained. This distribution is found by minimizing relative information with respect to a noninformative starting distribution, but makes no further assumptions about the interactions between the weights for different criteria. Criteria distributions with dependence emerge from the fitting procedure. 2. The multicriteria preference model can be empirically validated with expert preferences not used in fitting the model.

The management and conservation of the world's oceans require synthesis of spatial data on the distribution and intensity of human activities and the overlap of their impacts on marine ecosystems. We developed an ecosystem-specific, multiscale spatial model to synthesize 17 global data sets of anthropogenic drivers of ecological change for 20 marine ecosystems. Our analysis indicates that no area is unaffected by human influence and that a large fraction (41%) is strongly affected by multiple drivers. However, large areas of relatively little human impact remain, particularly near the poles. The analytical process and resulting maps provide flexible tools for regional and global efforts to allocate conservation resources; to implement ecosystem-based management; and to inform marine spatial planning, education, and basic research.

Scientists and resource managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressors. However, a growing body of literature demonstrates that many relationships are-non-linear, where small changes in a driver prompt a disproportionately large ecological response. We aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focused our analyses on one of the best-studied marine systems, pelagic ecosystems, which allowed us to apply robust statistical techniques on a large pool of previously published studies. In this synthesis, we (1) conduct a wide literature review on single driver-response relationships in pelagic systems, (2) use statistical models to identify the degree of non-linearity in these relationships, and (3) assess whether general patterns exist in the strengths and shapes of non-linear relationships across drivers. Overall we found that non-linearities are common in pelagic ecosystems, comprising at least 52% of all driver-response relation- ships. This is likely an underestimate, as papers with higher quality data and analytical approaches reported non-linear relationships at a higher frequency (on average 11% more). Consequently, in the absence of evidence for a linear relationship, it is safer to assume a relationship is non-linear. Strong non-linearities can lead to greater ecological and socioeconomic consequences if they are unknown (and/or unanticipated), but if known they may provide clear thresholds to inform management targets. In pelagic systems, strongly non-linear relationships are often driven by climate and trophodynamic variables but are also associated with local stressors, such as overfishing and pollution, that can be more easily controlled by managers. Even when marine resource managers cannot influence ecosystem change, they can use information about threshold responses to guide how other stressors are managed and to adapt to new ocean conditions. As methods to detect and reduce uncertainty around threshold values improve, managers will be able to better understand and account for ubiquitous non-linear relationships.

Our results provide an important first step toward a full assessment of how human activities act cumulatively to affect the condition of the oceans. Fisheries (and climate change) impacts are some of the hardest to map and measure accurately. Consequently, species-specific considerations and fine-scale analyses should be left to more nuanced regional-scale replicates of our mapping framework.

Huntington's and Kennedy's disease are autosomal dominant neurodegenerative diseases caused by pathogenic expansion of polyglutamine tracts. Expansion of glutamine repeats must in some way confer a gain of pathological function that disrupts an essential cellular process and leads to loss of affected neurons. Association of huntingtin with vesicular structures raised the possibility that axonal transport might be altered. Here we show that polypeptides containing expanded polyglutamine tracts, but not normal N-terminal huntingtin or androgen receptor, directly inhibit both fast axonal transport in isolated axoplasm and elongation of neuritic processes in intact cells. Effects were greater with truncated polypeptides and occurred without detectable morphological aggregates.