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Water temperature plays a critical role in mediating energy budgets and influencing the behavior of marine ectotherms. Previous research has demonstrated that marine ectotherms such as sea turtles conserve energy by decreasing activity levels in colder water—often at or near the latitudinal limits of their range. San Diego Bay is near the northern edge of the range for eastern Pacific green turtles and is home to a year-round foraging population. Turtles in San Diego Bay experienced a significant decrease in ambient water temperature following the closure of a fossil-fuel-based power plant and corresponding loss of the plant’s warm-water effluent. Time-depth recorders were placed on 13 turtles before (n = 5) and after (n = 8) the closure of this plant to determine how changing water temperature influenced dive duration. Deployments lasted 2-25 d, with a mean deployment of 7.5 d. Green turtle behavior in different thermal regimes revealed a strong relationship between dive duration and water temperature; dive duration was significantly longer when water temperatures were colder, especially when water was below 14.4°C. Establishing the inactivity threshold for this population is critical to future management in light of temperature variability in coastal habitats and the impacts this may have on sea turtle energetics. Understanding organismal response to relatively rapid shifts in thermal conditions is relevant to assessments of the direct and indirect anthropogenic effects on aquatic environments.

Disease plays a major role in shaping wildlife populations worldwide, and changes in landscape conditions can significantly influence risk of pathogen exposure, a threat to vulnerable wild species. Three viruses that cause hemorrhagic disease affect cervid populations in the USA (Odocoileus hemionus adenovirus, bluetongue virus, and epizootic hemorrhagic disease virus), but little is known of their distribution and prevalence in wild populations. We explored the distribution and co-occurrence of seroprevalence of these three pathogens in southern mule deer (Odocoileus hemionus fuliginatus), a subspecies of conservation concern and a harvested species native to southern California, to evaluate the distribution of exposure to these pathogens relative to landscape attributes. We found that habitat type, level of development, and proximity to livestock may affect hemorrhagic disease seroprevalence in southern mule deer. Continued monitoring of hemorrhagic disease-causing viruses in areas where deer are in proximity to cattle and human development is needed to better understand the implications of future outbreaks in wild populations and to identify opportunities to mitigate disease impacts in southern mule deer and other cervid species.

Forecasting habitat suitability and connectivity can be central to both controlling invasive species expansion and promoting native species conservation, especially under changing climate conditions. This study aimed to identify and prioritize areas in Spain to control the expansion of one of the most harmful invasive species in Europe, while conserving its counterpart, the endangered European mink, under current and future conditions. We used dynamic ensemble habitat suitability and connectivity models to predict species ranges and movement routes considering likely climate change under three emission scenarios. Then, using habitat availability metrics, we prioritized areas for invasive mink control and native mink conservation and classified them into different management zones that reflected the overlap between species and threat from American to European minks. Results suggest that both species are likely to experience declines in habitat and connectivity under climate change scenarios with significantly larger declines by the end of the century for European minks (72 and 80% respectively) than for American minks (41 and 32%). Priority areas for management of both species varied over time and across emission scenarios, with a general shift in priority habitat towards the North-East of the study area. Our findings demonstrate how dynamic habitat suitability and connectivity approaches can guide long-term management strategies to control invasive species and conserve native species while accounting for likely landscape changes. The simultaneous study of both invasive and native species can support prioritized management action and inform management planning of the intensity, extent, and techniques of intervention depending on the overlap between species.

Protective legislation and management have led to an increase in California’s sea otter Enhydra lutris nereis population. While sea otter recovery has been linked to ecosystem benefits, sea otter predation may negatively affect commercially valuable species. Understanding the potential influence of sea otters is of particular importance as their range expands into estuaries that function as nurseries for commercially valuable species like Dungeness crab Metacarcinus magister. We consider how sea otter predation has affected the abundance and size of juvenile Dungeness crab in Elkhorn Slough, California, USA, and analyzed cancrid crab abundance and size across 4 California estuaries with and without sea otters to understand how biotic and abiotic factors contribute to observed variation in crab size and abundance. We compared trends in southern sea otters relative to Dungeness crab landings in California to assess whether increasing sea otter abundance have negatively impacted landings. In Elkhorn Slough, juvenile Dungeness crab abundance and size have declined since 2012, coinciding with sea otter population growth. However, the impact of sea otters on juvenile Dungeness crab size was habitat-specific and only significant in unvegetated habitat. Across estuaries, we found that cancrid crab abundance and size were negatively associated with sea otter presence. While abiotic factors varied among estuaries, these factors explained little of the observed variation in crab abundance or size. Although we found evidence that sea otters can have localized effects on cancrid crab populations within estuaries, we found no evidence that southern sea otters, at recent population sizes, have negatively impacted Dungeness crab landings in California from 2000-2014.

Marine mammal bycatch poses a particular challenge in developing countries, where data to document bycatch and its effects are often lacking. Using the Bycatch Risk Assessment (ByRA) toolkit, based on InVEST open-source models, we chose 4 field sites in Southeast Asia with varying amounts of data on marine mammals and fishing occurrence: Trat province in the eastern Gulf of Thailand, the Sibu-Tinggi Islands and Kuching Bay, Malaysia, and Kien Giang Biosphere Reserve in southwestern Vietnam. These field sites have similar species of coastal marine mammals, small-scale and commercial fisheries, and support for research from universities and/or management. In Thailand and Kuching, results showed changing patterns of fishing and Irrawaddy dolphin Orcaella brevirostris habitat use across seasons, showing how bycatch risk could change throughout the year. Risk maps for dugongs Dugong dugon in peninsular Malaysia highlighted patterns of bycatch risk concentrated around a mainland fishing pier, and revealed high risk in a northern subregion. In Vietnam, first maps of bycatch risk for the Irrawaddy dolphin showed the highest risk driven by intensive use of gillnets and trawling gear. ByRA pinpointed areas of spatial and seasonal bycatch exposure, and estimated the consequence of bycatch on local species, providing managers with critical information on where to focus bycatch mitigation and meet new global standards for US Marine Mammal Protection Act and other international regulation (e.g. Official Journal of the European Union 2019; Regulation 2019/1241) compliance. The toolbox, a transferable open-source tool, can be used to guide fisheries management, marine mammal conservation, spatial planning, and further research. KEY WORDS: Incidental bycatch · Marine mammals · Spatial risk assessment · Open-source GIS toolkit · Small-scale fisheries · Southeast Asia

For depleted wildlife populations, understanding and effectively mitigating the direct and indirect impacts of roads can be a key component of recovery efforts. The ocelot is a federally endangered wild felid at risk of local extinction in south Texas, where vehicle collisions are their largest known source of mortality. To support road mortality mitigation, we evaluated mortality risk across the south Texas road network. We also assessed whether a sympatric carnivore, the bobcat, could serve as a surrogate to inform mortality risk. We used several presence-only species distribution models to evaluate a suite of candidate landscape and road attributes and identify those associated with elevated road mortality risk using a 35-year wild felid road mortality dataset. Consensus predictions among models identified high-risk road segments for ocelots and bobcats. We compared predictions between species to determine overlap of high-risk areas. Areas where core ocelot habitat intersected roadways represented the greatest mortality risk, reflecting ocelot reliance on intact habitat and avoidance of degraded and fragmented landscapes. Bobcat road mortality risk had similar relationships to landscape features, with nearly all areas classified as high-risk for ocelots also identified as high-risk for bobcats. Ocelots are vulnerable to road mortality in areas where roads intersect their intact scrub habitat. Bobcats, with appropriate data filters in place, are an acceptable surrogate for informing ocelot road mortality, particularly when ocelot mortality data are limited and for time-sensitive conservation decision-making. For ocelots and other fragmentation-intolerant carnivore species, wildlife underpasses and fencing in focused areas where roads and intact habitat intersect may be feasible options to reduce road mortality.

In human-dominated landscapes, habitat fragmentation and barriers to movement can interrupt gene flow. While often considered at a local extent, regional analyses are also needed to reveal broader landscape-mediated population processes. To explore the relationship between patterns of gene flow and fragmentation resulting from urbanization across southern California, we used the bobcat as an indicator species. We assembled data for a landscape level genetic analysis across southern California from both archived and new samples, including two northern Californian populations for comparison, to identify local and regional areas affected by isolation. Our regional analyses focused on a dataset of 19 microsatellite loci for 118 individuals and a dataset of 422 individuals genotyped at 11 loci. We examined population genetic structure and examined how pairwise genetic distance of all population clusters aligned with geographic distance. We employed a landscape genetic analysis based on resistance to determine which features of the landscape likely play a role in determining the patterns of genetic structure we observed. Study populations generally exhibited a pattern of isolation by distance and localized areas of genetic isolation. The landscape genetic analysis suggested that, in southern California, these patterns are driven by overall landscape permeability. Although local studies are key to examining the effects of urbanization and habitat fragmentation on populations, we demonstrate the importance of combining local and regional analyses for wide-ranging species to understand and maintain connectivity at local scales, while also improving and establishing sustainable linkages to habitats at the regional scale.

Globally, biodiversity has declined at an unprecedented rate, challenging the viability of ecosystems, species, and ecological functions and their corresponding services. Payments for ecosystem services (PES) programs have been established and implemented worldwide to combat the degradation or loss of essential ecosystems and ecosystem services without sacrificing the well-being of people. With an overarching goal of reducing soil erosion, China’s Grain-to-Green program (GTGP) converts cropland to forest or grassland. As one of the largest PES programs in the world, GTGP has great potential to offer biodiversity conservation co-benefits. To consider how GTGP may influence biodiversity, we measured forest structure and plant and wildlife species diversity at both GTGP forest and natural forest sites in Fangjingshan National Nature Reserve, China. We also evaluated the relationship between canopy cover and biodiversity measures to test whether forest cover, the most commonly measured and reported ecological metric of PES programs, might act as a good proxy for other biodiversity related parameters. We found that forest cover and species diversity increased after GTGP implementation as understory and overstory plant cover, and understory and midstory plant diversity at GTGP sites were similar to natural forest. Our results suggest that GTGP may also have been associated with increased habitat for protected and vulnerable wildlife species including Elliot’s pheasant (Syrmaticus ellioti), hog badger (Arctonyx collaris), and wild boar (Sus scrofa). Nevertheless, we identified key differences between GTGP forest and natural forest, particularly variation in forest types and heterogeneity of overstory vegetation. As a result, plant overstory diversity and wildlife species richness at GTGP forest were significantly lower than at natural forest. Our findings suggest, while forest cover may be a good proxy for some metrics of forest structure, it does not serve as a robust proxy for many biodiversity parameters. These findings highlight the need for and importance of robust and representative indicators or proxy variables for measuring ecological effects of PES programs on compositional and structural diversity. We demonstrate that PES may lead to biodiversity co-benefits, but changes in program implementation could improve the return on investment of PES programs to support conservation of biodiversity.

An important component of wildlife management and conservation is monitoring the health and population size of wildlife species. Monitoring the population size of an animal group can inform researchers of habitat use, potential changes in habitat and resulting behavioral adaptations, individual health, and the effectiveness of conservation efforts. Arboreal monkeys are difficult to monitor as their habitat is often poorly accessible and most monkey species have some degree of camouflage, making them hard to observe in and below the tree canopy. Surveys conducted using uninhabited aerial vehicles (UAVs) equipped with thermal infrared (TIR) cameras can help overcome these limitations by flying above the canopy and using the contrast between the warm body temperature of the monkeys and the cooler background vegetation, reducing issues with impassable terrain and animal camouflage. We evaluated the technical and procedural elements associated with conducting UAV-TIR surveys for arboreal and terrestrial macaque species. Primary imaging missions and analyses were conducted over a monkey park housing approximately 160 semi-free-ranging Japanese macaques (Macaca fuscata). We demonstrate Repeat Station Imaging (RSI) procedures using co-registered TIR image pairs facilitate the use of image differencing to detect targets that were moving during rapid sequence imaging passes. We also show that 3D point clouds may be generated from highly overlapping UAV-TIR image sets in a forested setting using structure from motion (SfM) image processing techniques. A point cloud showing area-wide elevation values was generated from TIR imagery, but it lacked sufficient point density to reliably determine the 3D locations of monkeys.

From a conservation perspective, quantifying potential refugial capacity has been predominantly focused on climate refugia, which is critical for maintaining the persistence of species and ecosystems. However, protection from other stressors, such as human-induced changes in fire and hydrology, that cause habitat loss, degradation, and fragmentation is also necessary to ensure that conservation efforts focused on climate are not undermined by other threats. Thus, conceptual and methodological advances for quantifying potential refugia from multiple anthropogenic stressors are important to support conservation efforts. We devised a new conceptual approach, the domains of refugia, for assessing refugial capacity that identifies areas where exposure to multiple stressors is low. In our framework, patterns of environmental variability (e.g., increased frequency of warm summers), thresholds of resilience, and extent and intensity of stressors are used to identify areas of potential refugia from a suite of ongoing anthropogenic stressors (e.g., changes in fire regime). To demonstrate its utility, we applied the framework to a Southern California landscape. Sites with high refugial capacity (super-refugia sites) had on average 30% fewer extremely warm summers, 20% fewer fire events, 10% less exposure to altered river channels and riparian areas, and 50% fewer recreational trails than the surrounding landscape. Our results suggest that super-refugia sites (∼8200 kmMarco Conceptual a para Identificar Refugios de Múltiples Amenazas a Escala de Paisaje Resumen Desde la perspectiva de la conservación, la cuantificación de la capacidad potencial de refugio se ha enfocado principalmente en los refugios climáticos, los cuales son críticos para mantener la persistencia de las especies y los ecosistemas. Sin embargo, la protección ante otros factores estresantes, como los cambios inducidos por los humanos en los incendios y la hidrología, que causan la pérdida, degradación y fragmentación del hábitat, también son necesarios para asegurar que los esfuerzos de conservación enfocados en el clima no sean afectados por otras amenazas. Por lo tanto, los avances conceptuales y metodológicos para cuantificar los refugios potenciales ante múltiples factores estresantes causados por el humano son importantes para asegurar que los esfuerzos de conservación logren sus objetivos. Diseñamos una nueva estrategia conceptual, los dominios de los refugios, para evaluar la capacidad de refugio de un paisaje donde la exposición a múltiples factores estresantes es baja. En nuestro marco conceptual usamos los patrones de variabilidad ambiental (p. ej.: incremento en la frecuencia de veranos cálidos), los umbrales de resiliencia y la extensión e intensidad de los factores estresantes para identificar las áreas de refugios potenciales a partir de un conjunto de factores antropogénicos persistentes (p. ej.: cambios en el régimen de incendios). Para demostrar su utilidad, aplicamos el marco conceptual a un paisaje del sur de California. Los sitios con una alta capacidad de refugio (sitios de súper-refugios) tuvieron en promedio un 30% menos veranos extremadamente cálidos, 20% menos eventos de incendios y 50% menos senderos recreativos que el paisaje circundante. Nuestros resultados sugieren que los sitios de súper-refugios (∼ 8,200 km从保护的角度来看, 目前对潜在避难能力的量化主要关注的是气候避难所, 它们对于维持物种和生态系统续存至关重要。然而, 为了确保关注气候的保护工作不受其它威胁因素破坏, 还需要考虑针对其它压力因素的保护, 包括人类引起的火灾和水文变化, 因为它们会导致栖息地丧失、退化和破碎化。因此, 在概念和方法上推动量化多种人为压力因素的潜在避难所的研究进展, 对支持保护工作十分重要。本研究设计了一个新的概念性方法 (即避难所领域) 用于评估避难能力, 以识别受多种压力因素影响较小的地区。我们的框架利用环境变异性格局 (如暖夏出现频率增加) 、恢复力阈值, 以及压力因素的范围和强度来识别一系列持续的人为压力因素 (如火灾变化) 影响下的潜在避难所。为了证明该框架的有效性, 我们将其应用于南加州的一处景观之中。结果表明, 与周围景观相比, 具有高避难能力的位点 (超级避难所) 极端暖夏出现的概率平均低 30%, 火灾出现概率平均低 20%, 河道和河岸地区被改变的风险低 10%, 且存在的休闲步道少 50%。我们的结果指出, 一些自然群落的超级避难所 (约 8,200 平方公里) 在现有的保护区网络中的代表性不足, 这一发现可以指导扩大保护区的工作。我们的案例研究还强调了考虑多种压力因素的暴露情况将如何为规划和实践提供信息, 从而在不断变化的世界中保护生物多样性。 【翻译: 胡怡思; 审校: 聂永刚】.

Cetaceans in the Southern California Bight (SCB) are exposed to high levels of halogenated organic contaminants (HOCs), which have previously been linked to impaired reproductive health and immune responses. We used a combination of molecular tools to examine the potential physiological impacts of HOC exposure in two bottlenose dolphin ( Tursiops truncatus) ecotypes in the SCB. We quantified 25 HOCs in the blubber of 22 biopsies collected from males between 2012 and 2016. We then analyzed genome-wide gene expression in skin using RNA-sequencing and measured blubber testosterone to compare HOC exposure with cellular and endocrine biomarkers. We found high levels of HOCs in both ecotypes with significantly higher total polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), tris(4-chlorophenyl)methanol (TCPMOH), and chlordane-related compounds in the coastal ecotype versus the offshore ecotype. We found evidence of PBDE bioaccumulation in both ecotypes, however, the pattern of bioaccumulation or endocrine disruption for other HOCs was different between the ecotypes, suggesting potential endocrine disruption in the coastal ecotype. We also observed correlations between HOCs and gene coexpression networks enriched for xenobiotic metabolism, hormone metabolism, and immune response that could indicate cellular effects from HOC exposure. By integrating measurements of HOC load with both transcriptome profiling and endocrine biomarkers, our approach provides insight into HOC exposure and potential impacts on wild cetacean health in southern California.

Immune function plays an important role in an animal's defense against infectious disease. In reptiles, immune responses may be complex and counterintuitive, and diagnostic tools used to identify infection, such as induced antibody responses are limited. Recent studies using gene transcription profiling in tortoises have proven useful in identifying immune responses to various intrinsic and extrinsic stressors. As part of a larger experiment with Mojave desert tortoises (Gopherus agassizii), we facilitated the transmission of the pathogenic bacteria, Mycoplasma agassizii (Myag), to naïve adults and measured innate and induced immune reactions over time. Specifically, we evaluated clinical condition, presence of Myag in the nasal/oral cavity, induced antibody responses specific to Myag, and measured molecular reactions (gene transcript profiles) in 15 captive tortoises classified as naïve, exposed, or infected and 14 wild tortoises for comparison. Myag was confirmed inside the nasal/oral cavity in exposed tortoises within 30–60 days of introduction to infected animals, yet we did not detect Myag specific induced antibody responses in these individuals until 420–595 days post exposure. Surprisingly, we found no overall differences in the gene transcript profiles between our experimental treatment groups throughout this study. This work highlights the complexities in assessing immune function and diagnosing pathogen related infections in tortoises and other reptiles.

BackgroundTranscriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations.ResultsWe generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata),loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance.ConclusionsObtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

Human activities influence the environment on a planetary scale and have led to an overall trend of global warming worldwide. Power generating plants have emerged as unlikely candidates to study the effects of temperature change on aquatic organisms, like sea turtles. Industrial power plants that utilize once-through cooling (OTC) systems discharge thermal effluent into freshwater and/or marine environments, and the heated discharge often significantly affects the local habitat, creating an unnatural thermal ecology. These types of power plants are common around the world, and their effects on local ecosystems are comparable making them opportune study sites. This chapter discusses the effects of thermal effluent on thermoregulation of aquatic reptiles like the sea turtles, with focus on the green turtles in San Diego Bay.

Methylmercury concentrations vary widely across geographic space and among habitat types, with marine and aquatic-feeding organisms typically exhibiting higher mercury concentrations than terrestrial-feeding organisms. However, there are few model organisms to directly compare mercury concentrations as a result of foraging in marine, estuarine, or terrestrial food webs. The ecological impacts of differential foraging may be especially important for generalist species that exhibit high plasticity in foraging habitats, locations, or diet. Here, we investigate whether foraging habitat, sex, or fidelity to a foraging area impact blood mercury concentrations in western gulls (Larus occidentalis) from three colonies on the US west coast. Cluster analyses showed that nearly 70% of western gulls foraged primarily in ocean or coastal habitats, whereas the remaining gulls foraged in terrestrial and freshwater habitats. Gulls that foraged in ocean or coastal habitats for half or more of their foraging locations had 55% higher mercury concentrations than gulls that forage in freshwater and terrestrial habitats. Ocean-foraging gulls also had lower fidelity to a specific foraging area than freshwater and terrestrial-foraging gulls, but fidelity and sex were unrelated to gull blood mercury concentrations in all models. These findings support existing research that has described elevated mercury levels in species using aquatic habitats. Our analyses also demonstrate that gulls can be used to detect differences in contaminant exposure over broad geographic scales and across coarse habitat types, a factor that may influence gull health and persistence of other populations that forage across the land-sea gradient.

Compound specific nitrogen isotope analysis of amino acids (AA CSIA) has been used to study the trophic ecology of many marine organisms because of its ability to characterize the δ15N value at the base of a food web while simultaneously providing trophic position information from a single tissue sample of a consumer. Although application of this method is becoming more widely used in trophic studies, critical assumptions such as amino acid designation and trophic discrimination factors remain unresolved for many taxa and tissue types. In this study, we used captive green turtles (Chelonia mydas) in a controlled feeding study to determine and evaluate individual amino acid isotope fractionation patterns and trophic discrimination factors (TDFs) for skin and plasma. Our data build on findings from previous studies that show that the traditional paradigm of using glutamic acid and phenylalanine as trophic and source amino acids, respectively, for trophic position estimation is consistent for green turtles; we also provide evidence to support the potential utility of other combinations of amino acids for trophic position calculations. Green turtle TDFs for glutamic acid and phenylalanine were 4.0 ± 0.5 ‰ and 6.6 ± 0.7 ‰ for skin and plasma, respectively. We found serine to have the largest Δδ15N (turtle-diet discrimination) value of all amino acids in both skin and plasma, while lysine Δδ15N values were consistent for use as a source amino acid in skin and plasma tissue. We evaluated our TDFs by estimating trophic position of four sea turtle species using previously published amino acid isotope data. These results indicate that for green turtles, the traditional use of glutamic acid and phenylalanine along with a combination of trophic amino acids paired with lysine can provide robust trophic position estimates. Moreover, we highlight the taxa and tissue-specific nature of amino acid nitrogen isotope fractionation patterns in green turtle tissues and underscore that well-approximated TDFs can refine trophic position estimates for sea turtles.

Preserving landscape connectivity is one of the most frequently recommended strategies to address the synergistic threats of climate change, habitat fragmentation, and intensifying disturbances. Although assessments to develop plans for linked and connected landscapes in response to climate and land-use change have been increasingly employed in the last decade, efforts to operationalize and implement these plans have been limited. Here, we present a framework using existing, available biological data to design an implementable, comprehensive multispecies connectivity plan. This framework uses a scenario-based approach to consider how ecosystems, habitats, and species may need to adapt to future conditions with an ensemble of connectivity models. We use the south coast ecoregion of California as an example to evaluate and prioritize linkages by combining linked metapopulation models and key landscape features (e.g., conservation planning status and implementation feasibility) to identify and prioritize a multispecies linkage network. Our analyses identified approximately 30,000 km2 of land, roughly one-fifth of our study area, where actions to preserve or enhance connectivity may support climate adaptation, nearly half of which is already conserved. By developing and implementing a dynamic connectivity assessment with an eye towards projected changes, our analysis demonstrates how dynamic connectivity can be integrated into feasible regional conservation and management plans that account for demographic as well as landscape change. We observed overlap across multiple models, reinforcing the importance of areas that appeared across methods. We also identified unique areas important for connectivity captured by our complementary models. By integrating multiple approaches, the resultant linkage network is robust, building on the strengths of a variety of methods to identify model consensus and reduce uncertainty. By linking quantitative connectivity metrics with prioritized areas for conservation, our approach supports transparent and robust decision-making for landscape planning, despite uncertainties of climate and land-use change.

Recent warnings from scientists suggest there is limited time to enact policies to avert wide‐ranging ecological and social damage from climate change. In the United States, discussions about comprehensive national policies to avert climate change have begun, with “Green New Deal” proposals and climate plans put forth by members of Congress and presidential candidates. Oceans are largely absent or separate from these nascent policy proposals. Here, we highlight a policy framework to develop terrestrial and ocean‐integrated policies that can complement and enhance terrestrial‐focused initiatives focused on four specific sectors: 1) energy; 2) transportation; 3) food security; and 4) habitat restoration. Given political friction and constrained budgets, an integrated policy framework offers greater potential to achieve a portfolio of mitigation and adaptation goals in a cost‐effective manner, beyond what could be realized with marine or terrestrial policy solutions alone.

Fisheries bycatch has been identified as the greatest threat to marine mammals worldwide. Characterizing the impacts of bycatch on marine mammals is challenging because it is difficult to both observe and quantify, particularly in small-scale fisheries where data on fishing effort and marine mammal abundance and distribution are often limited. The lack of risk frameworks that can integrate and visualize existing data have hindered the ability to describe and quantify bycatch risk. Here, we describe the design of a new geographic information systems tool built specifically for the analysis of bycatch in small-scale fisheries, called Bycatch Risk Assessment (ByRA). Using marine mammals in Malaysia and Vietnam as a test case, we applied ByRA to assess the risks posed to Irrawaddy dolphins (Orcaella brevirostris) and dugongs (Dugong dugon) by five small-scale fishing gear types (hook and line, nets, longlines, pots and traps, and trawls). ByRA leverages existing data on animal distributions, fisheries effort, and estimates of interaction rates by combining expert knowledge and spatial analyses of existing data to visualize and characterize bycatch risk. By identifying areas of bycatch concern while accounting for uncertainty using graphics, maps and summary tables, we demonstrate the importance of integrating available geospatial data in an accessible format that taps into local knowledge and can be corroborated by and communicated to stakeholders of data-limited fisheries. Our methodological approach aims to meet a critical need of fisheries managers: to identify emergent interaction patterns between fishing gears and marine mammals and support the development of management actions that can lead to sustainable fisheries and mitigate bycatch risk for species of conservation concern.

Dynamic management (DM) is a novel approach to spatial management that aligns scales of environmental variability, animal movement and human uses. While static approaches to spatial management rely on one‐time assessments of biological, environmental, economic, and/or social conditions, dynamic approaches repeatedly assess conditions to produce regularly updated management recommendations. Owing to this complexity, particularly regarding operational challenges, examples of applied DM are rare. To implement DM, scientific methodologies are operationalized into tools, i.e., self‐contained workflows that run automatically at a prescribed temporal frequency (e.g., daily, weekly, monthly). Here we present a start‐to‐finish framework for operationalizing DM tools, consisting of four stages: Acquisition, Prediction, Dissemination, and Automation. We illustrate this operationalization framework using an applied DM tool as a case study. Our DM tool operates in near real‐time and was designed to maximize target catch and minimize bycatch of non‐target and protected species in a US‐based commercial fishery. It is important to quantify the sensitivity of DM tools to missing data, because dissemination streams for observed (i.e., remotely sensed or directly sampled) data can experience delays or gaps. To address this issue, we perform a detailed example sensitivity analysis using our case study tool. Synthesis and applications. Dynamic management (DM) tools are emerging as viable management solutions to accommodate the biological, environmental, economic, and social variability in our fundamentally dynamic world. Our four‐stage operationalization framework and case study can facilitate the implementation of DM tools for a wide array of resource and disturbance management objectives.

Genetic analyses of nuclear DNA (e.g., microsatellites) are a primary tool for investigating mating systems in reptiles, particularly marine turtles. Whereas studies over the past two decades have demonstrated that polyandry (i.e., females mating with multiple males) is common in marine turtles, polygyny (i.e., males mating with multiple females) has rarely been reported. In this study we investigated the mating structure of Critically Endangered hawksbill turtles (Eretmochelys imbricata) at Bahia de Jiquilisco in El Salvador, one of the largest rookeries in the eastern Pacific Ocean. We collected genetic samples from 34 nesting females and hatchlings from 41 clutches during the 2015 nesting season, including one nest from each of 27 females and two nests from seven additional females. Using six highly polymorphic microsatellite loci, we reconstructed the paternal genotypes for 22 known male turtles and discovered that seven (31.8%) sired nests from multiple females, which represents the highest polygyny level reported to date for marine turtles and suggests that this is a common mating structure for this population. We also detected multiple paternity in four (11.8%) clutches from the 34 females analyzed, confirming polyandrous mating strategies are also employed. The high level of polygyny we documented suggests there may be a limited number of sexually mature males at Bahia de Jiquilisco; a scenario supported by multiple lines of empirical evidence. Our findings highlight key management uncertainties, including whether polygynous mating strategies can compensate for potential ongoing feminization and the low number of adult males found for this and possibly other marine turtle populations.

Incidental catch of nontarget species (bycatch) is a major barrier to ecological and economic sustainability in marine capture fisheries. Key to mitigating bycatch is an understanding of the habitat requirements of target and nontarget species and the influence of heterogeneity and variability in the dynamic marine environment. While patterns of overlap among marine capture fisheries and habitats of a taxonomically diverse range of marine vertebrates have been reported, a mechanistic understanding of the real-time physical drivers of bycatch events is lacking. Moving from describing patterns toward understanding processes, we apply a Lagrangian analysis to a high-resolution ocean model output to elucidate the fundamental mechanisms that drive fisheries interactions. We find that the likelihood of marine megafauna bycatch is intensified in attracting Lagrangian coherent structures associated with submesoscale and mesoscale filaments, fronts, and eddies. These results highlight how the real-time tracking of dynamic structures in the oceans can support fisheries sustainability and advance ecosystem-based management.

Healthy fisheries can reduce bycatch Bycatch of marine mammals, turtles, and birds during commercial fishing is a considerable threat. Activities intended to reduce bycatch are often thought to conflict with commercial fishing. However, Burgess et al. show that in the majority of cases, managing fishery stocks to best promote long-term sustainability would also reduce bycatch. Rebuilding fish stocks will naturally promote lower bycatch, and these factors together will facilitate sustainable profit generation from fish harvest. Science , this issue p. 1255

While environmental pollutants have been associated with changes in endocrine health in cetaceans, efforts to link contaminant exposure with hormones have largely been limited to a list of known, targeted contaminants, overlooking minimally characterized or unknown compounds of emerging concern. To address this gap, we analyzed a suite of potential endocrine disrupting halogenated organic compounds (HOCs) in blubber from 16 male short-beaked common dolphins ( Delphinus delphis) with known maturity status collected from fishery bycatch in the Southern California Bight. We employed a suspect screening mass spectrometry-based method to investigate a wide range of HOCs that were previously observed in cetaceans from the same region. Potential endocrine effects were assessed through the measurement of blubber testosterone. We detected 167 HOCs, including 81 with known anthropogenic sources, 49 of unknown origin, and 37 with known natural sources. The sum of 11 anthropogenic and 4 unknown HOC classes were negatively correlated with blubber testosterone. Evidence suggests that elevated anthropogenic HOC load contributes to impaired testosterone production in mature male D. delphis. The application of this integrative analytical approach to cetacean contaminant analysis allows for inference of the biological consequences of accumulation of HOCs and prioritization of compounds for future environmental toxicology research.

The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing ecoinformatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 years (1990-2014) of NOAA fisheries’ observer data from the California drift gillnet fishery, we model relative probability of occurrence (presence-absence) and catchability (total catch) of broadbill swordfish Xiphias gladius in the California Current System (CCS). Using freely-available environmental datasets and open source software, we explore the physical drivers of regional swordfish distribution. Comparing models built upon remotely-sensed datasets with those built upon a data-assimilative configuration of the Regional Ocean Modelling System (ROMS), we explore trade-offs in model construction and address how physical data can affect predictive performance and operational capacity. Swordfish catchability was found to be highest in deeper waters (>1500m) with surface temperatures in the 14-20°C range, isothermal layer depth (ILD) of 20-40m, positive sea surface height anomalies and during the new moon (

AIM: Animal tracking can provide unique insights into the ecology and conservation of marine species, such as the partitioning of habitat, including differences between life history stages or sexes, and can inform fisheries stock assessments, bycatch reduction and spatial management such as dynamic management. LOCATION: Northeast Pacific Ocean. METHODS: We used satellite tracking data from 47 blue sharks (Prionace glauca) from the Northeast Pacific to determine movements and home range along the west coast of North America, and sex–size class (immature females, mature males) specific habitat preferences using boosted regression trees. Using a suite of static and dynamic environmental variables, we determined distribution and habitat preferences across summer and fall for each sex–size class. RESULTS: We found that there was spatial segregation between sex–size classes particularly in the summer months with immature females found largely north of 33°N, and males south of 35°N. In fall, females travelled south, resulting in an overlap in distributions south of 37°N. Sea surface temperature (SST), latitude and longitude were top predictors. However, immature females and adult males demonstrated unique habitat preferences including SST, with immature females preferring cooler temperatures (SST

Horswill and Manica (1) provide a useful extension to Scales et al. (2), quantifying the relative risk of bycatch for each swordfish caught at several values of backward-in-time Finite-Time Lyapunov Exponent (FTLEb), a parameter derived from ocean surface velocity that identifies aggregative features known as Lagrangian coherent structures (LCS). We concur that the catch ratio of target to nontarget species with respect to the location of these structures is a useful measure for guiding spatial bycatch mitigation strategies in marine fisheries, but we want to highlight some aspects of Horswill and Manica’s response that require clarification. First, Horswill and Manica (1) combine all nontarget species … [↵][1]1To whom correspondence should be addressed. Email: kscales{at}usc.edu.au. [1]: #xref-corresp-1-1

Natural resource policies enacted to protect environmental integrity play an important role in promoting sustainability. However, when resources are shared ecologically, economically, or through a common, global interest, policies implemented to protect resource sustainability in one domain can displace, and in some cases magnify, environmental degradation to other domains. Although such displacement has been recognized as a fundamental challenge to environmental and conservation policy within some resource sectors, there has been little cross‐disciplinary and cross‐sectoral integration to address the problem. This suggests that siloed knowledge may be impeding widespread recognition of the ubiquity of displacement and the need for mitigation. Here, we connect research across multiple disciplines to promote a broader discussion and recognition of the processes and pathways that can lead to displaced impacts that countermand or undermine resource policy and outline a number of approaches that can mitigate displacement.