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Understanding the efficacy of marine protected areas (MPAs) for wide-ranging predators is essential to designing effective management and conservation approaches. The use of acoustic monitoring and network analysis can improve our understanding of the spatial ecology and functional connectivity of reef-associated species, providing a useful approach for reef-based conservation planning. This study compared and contrasted the movement and connectivity of sharks with different degrees of reef association. We examined the residency, dispersal, degree of reef connectivity, and MPA use of grey reef ( Carcharhinus amblyrhynchos ), silvertip ( C. albimarginatus ), and bull ( C. leucas ) sharks monitored in the central Great Barrier Reef (GBR). An array of 56 acoustic receivers was used to monitor shark movements on 17 semi-isolated reefs. Carcharhinus amblyrhynchos and C. albimarginatus were detected most days at or near their tagging reef. However, while C. amblyrhynchos spent 80% of monitoring days in the array, C. albimarginatus was only detected 50% of the time. Despite both species moving similar distances (<50 km), a large portion of the population of C. albimarginatus (71%) was detected on multiple reefs and moved more frequently between reefs and management zones than C. amblyrhynchos . Carcharhinus leucas was detected less than 20% of the time within the tagging array, and 42% of the population undertook long-range migrations to other arrays in the GBR. Networks derived for C. leucas were larger and more complex than those for C. amblyrhynchos and C. albimarginatus . Our findings suggest that protecting specific reefs based on prior knowledge (e.g., healthier reefs with high fish biomass) and increasing the level of protection to include nearby, closely spaced reef habitats (<20 km) may perform better for species like C. albimarginatus than having either a single or a network of isolated MPAs. This design would also provide protection for larger male C. amblyrhynchos , which tend to disperse more and use larger areas than females. For wide-ranging sharks like C. leucas , a combination of spatial planning and other alternative measures is critical. Our findings demonstrate that acoustic monitoring can serve as a useful platform for designing more effective MPA networks for reef predators displaying a range of movement patterns.

Understanding the environmental drivers of movement of potentially dangerous shark species can help inform mitigation strategies. Bull sharks are known to undertake seasonal migrations from tropical to temperate waters along the east coast of Australia. However, the environmental drivers of their movements from sub-tropical to temperate waters are unknown. Using multi-year (2010–2016) acoustic telemetry data from 68 bull sharks and generalised additive models, we evaluate the (1) temporal and (2) environmental variables that drive shark abundance, presence/absence and residency along the south-eastern coast of Australia. Bull sharks were detected in sub-tropical waters (∼28°S) almost year-round but were most abundant in the southern latitudes in the austral summer and autumn. Abundance, presence and residency were all highest around the latitudes that sharks were tagged, indicating a bias to tagging location, and at estuary mouths and mid-shelf (20–60 m water depth) habitats. Bull sharks were present when sea surface temperature (SST) was 20–26°C, with peak abundance at 24°C, and low chlorophyll a (chl a). There was a higher abundance of sharks in months when SST was higher than the long-term average. Residency duration was longest when SST was <22°C or >24°C, and in areas of low SST slope (<3°C) and chl a slope. Although no sex bias in residency time was detected, sharks <200 cm TL had the longest residency times. These results provide the power to predict when and where bull shark abundance may be higher, which can help management authorities deploy mitigation strategies for bull shark interactions along eastern Australia.

Particle filters and smoothers are sequential Monte Carlo algorithms used to fit non‐linear, non‐Gaussian state‐space models. These algorithms are well placed to fit process‐oriented models to animal‐tracking data, especially in receiver arrays, but to date they have received limited attention in the ecological literature. We introduce a Bayesian filtering–smoothing algorithm that reconstructs individual movements and patterns of space use from animal‐tracking data, with a focus on passive acoustic telemetry systems. Within a sound probabilistic framework, the methodology integrates the movement process and the observation processes of disparate datasets, while correctly representing uncertainty. In a simulation‐based analysis, we compare the performance of our algorithm to the prevailing heuristic methods used to study movements and space use in passive acoustic telemetry systems and analyse algorithm sensitivity. We find the particle smoothing methodology outperforms heuristic methods across the board. Particle‐based maps represent simulated movements more accurately, even in dense receiver arrays, and are better suited to analyses of home ranges, residency and habitat preferences. This study sets a new state‐of‐the‐art for movement modelling in receiver arrays. Particle algorithms provide a robust, flexible and intuitive modelling framework with potential applications in many ecological settings.

Passive acoustic telemetry is a powerful tool for tracking aquatic animals, yet the data derived from acoustic tags have important limitations. For example, inferences about habitat associations rely on statistical correlations, where frequent observations within a given habitat are interpreted as habitat preference. However, tagging data are not measures of movement per se, or even behavior more generally; rather, tagging data are representations of locations in space and time and can reflect limitations in the sampling technology as much as animal behavior. This interaction between sampling technology and resulting data means it is necessary to have some null expectation in order to evaluate a hypothesis predicting a habitat association. Here, we developed a null model for animal movement based on random walk simulations and examined our ability to distinguish random from intentioned movements when using passive acoustics. By comparing simulations to telemetry observations, we provide guidance for both data interpretation and future study design. We found that (1) real-world telemetry observations cannot be distinguished from random walks during initial portions of sampling and (2) researchers must account for the interaction between study duration and the ratio of organismal step size relative to detection radius when calculating site fidelity. To assist in the interpretation of passive acoustic data, we provide an analytical solution to forecast when real-world observations are reliably distinguishable from simple random walks.

State‐space models are a powerful modelling framework in movement ecology that represents individual movements and the processes connecting movements to observations. However, fitting state‐space models to animal‐tracking data can be difficult and computationally expensive. Here, we introduce patter, a package that provides particle filtering and smoothing algorithms that fit Bayesian state‐space models to tracking data, with a focus on data from aquatic animals in receiver arrays. patter is written in R, with a performant Julia backend. Package functionality supports data simulation, preparation, filtering, smoothing and mapping. In two examples, we demonstrate how to implement patter to reconstruct the movements of a tagged animal in an acoustic telemetry system from acoustic detections and ancillary observations. With perfect information, the particle filter reconstructs the true (unobserved) movement path (Example One). More generally, particle algorithms represent an individual's possible location probabilistically as a weighted series of samples (‘particles’). In our illustration, we resolve an individual's (unobserved) location every 2 min during 1 month and use particles to visualise movements, map space use and quantify residency (Example Two). patter facilitates robust, flexible and efficient analyses of animal‐tracking data. The methods are widely applicable and enable refined analyses of space use, home ranges and residency.

Offshore oil and gas platforms in the northern Gulf of Mexico are known aggregation sites for red snapper Lutjanus campechanus. To examine habitat use and potential mortality from explosive platform removals, fine-scale movements of red snapper were estimated based on acoustic telemetry from March 2017 to July 2018. Study sites in the northern Gulf of Mexico, USA, included one platform off coastal Alabama (30.09° N, 87.88° W) and 2 platforms off Louisiana (28.81° N, 91.97°W; 28.92° N, 93.15° W). Red snapper (n = 59) showed a high affinity for platforms, with most (94%) positions being recorded within 95 m of the platforms. Home range areas were correlated with water temperature and inversely correlated with dissolved oxygen concentrations. During summer and fall, red snapper used larger areas and many fish (54%) emigrated from their platforms but most (83%) returned in ≤3 d. Site fidelity for red snapper was 31% yr−1 and residency time was 7 mo, but the probability-of-presence at platforms was 70% after 1 yr, indicating the importance of platforms for this species. Overall fishing mortality was high for platforms (F = 0.86, 95% CL = 0.47−1.40), but since the stock is managed on a quota basis this high mortality should have little effect on total stock abundance. Thus, platforms can still provide an important habitat for red snapper, and consideration of area use patterns, fishing mortality and environmental factors can reduce red snapper mortality when scheduling explosive platform removals. As such, the present study indicates that an optimum time for explosive removal would be in late summer after the red snapper fishing season is completed.

Maintaining hydrological connectivity is important for sustaining freshwater fish populations as the high habitat connectivity supports large-scale fish movements, enabling individuals to express their natural behaviours and spatial ecology. Northern pike Esox lucius is a freshwater apex predator that requires access to a wide range of functional habitats across its lifecycle, including spatially discrete foraging and spawning areas. Here, pike movement ecology was assessed using acoustic telemetry and stable isotope analysis in the River Bure wetland system, eastern England, comprising of the Bure mainstem, the River Ant and Thurne tributaries, plus laterally connected lentic habitats, and a system of dykes and ditches. Of 44 tagged pike, 30 were tracked for over 100 days, with the majority of detections being in the laterally connected lentic habitats and dykes and ditches, but with similar numbers of pike detected across all macrohabitats. The movement metrics of these pike indicated high individual variability, with total ranges to over 26 km, total movements to over 1182 km and mean daily movements to over 2.9 km. Pike in the Thurne tributary were more vagile than those in the Ant and Bure, and with larger Thurne pike also having relatively high proportions of large-bodied and highly vagile common bream Abramis brama in their diet, suggesting the pike movements were potentially related to bream movements. These results indicate the high individual variability in pike movements, which was facilitated here by their access to a wide range of connected macrohabitats due to high hydrological connectivity.

Research on fisheries bycatch and discards frequently involves the assessment of reflex impairment,injury, or blood physiology as means of quantifying vitality and predicting post-release mortality, but exceptionally few studies have used all three metrics concurrently. We conducted an experimental purse seine fishery for Pacific salmon in the Juan de Fuca Strait, with a focus on understanding the relationships between different sublethal indicators and whether mortality could be predicted in coho salmon ( Oncorhynchus kisutch ) bycatch. We monitored mortality using a ~24-h net pen experiment ( N = 118) and acoustic telemetry ( N = 50), two approaches commonly used to assess bycatch mortality that have rarely been directly compared. Short-term mortality was 21% in the net pen experiment (~24 h) and estimated at 20% for telemetry-tagged fish (~48-96 h). Mortality was predicted by injury and reflex impairment, but only in the net pen experiment. Higher reflex impairment was mirrored by perturbations to plasma ions and lactate, supporting the notion that reflex impairment can be used as a proxy for departure from physiological homeostasis. Reflex impairment also significantly correlated with injury scores, while injury scores were significantly correlated with plasma ion concentrations. The higher time-specific mortality rate in the net pen and the fact that reflexes and injury corresponded with mortality in that experiment, but not in the telemetry-tagged fish released into the wild could be explained partly by confinement stress. While holding experiments offer the potential to provide insights into the underlying causes of mortality, chronic confinement stress can complicate the interpretation of patterns and ultimately affect mortality rates. Collectively, these results help refine our understanding of the different sublethal metrics used to assess bycatch and the mechanisms that can lead to mortality.

A blend of introductory material and advanced signal processing and communication techniques, of critical importance to underwater system and network development This book, which is the first to describe the processing techniques central to underwater OFDM, is arranged into four distinct sections: First, it describes the characteristics of underwater acoustic channels, and stresses the difference from wireless radio channels. Then it goes over the basics of OFDM and channel coding. The second part starts with an overview of the OFDM receiver, and develops various modules for the receiver design in systems with single or multiple transmitters. This is the main body of the book. Extensive experimental data sets are used to verify the receiver performance. In the third part, the authors discuss applications of the OFDM receiver in i) deep water channels, which may contain very long separated multipath clusters, ii) interference-rich environments, where an unintentional interference such as Sonar will be present, and iii) a network with multiple users where both non-cooperative and cooperative underwater communications are developed. Lastly, it describes the development of a positioning system with OFDM waveforms, and the progress on the OFDM modem development. Closely related industries include the development and manufacturing of autonomous underwater vehicles (AUVs) and scientific sensory equipment. AUVs and sensors in the future could integrate modems, based on the OFDM technology described in this book. Contents includes: Underwater acoustic channel characteristics/OFDM basics/Peak-to-average-ratio control/Detection and Doppler estimation (Doppler scale and CFO)/Channel estimation and noise estimation/A block-by-block progressive receiver and performance results/Extensions to multi-input multi-output OFDM/Receiver designs for multiple users/Cooperative underwater OFDM (Physical layer network coding and dynamic coded cooperation)/Localization with OFDM waveforms/Modem developments A valuable resource for Graduate and postgraduate students on electrical engineering or physics courses; electrical engineers, underwater acousticians, communications engineers

Spawning site selection and reproductive timing affect stock productivity and structure in marine fishes but are poorly understood. Traditionally, stock assessments measure reproductive potential as spawning stock biomass or egg production and do not include other aspects of reproductive behavior. Red drum make an excellent case study to assess these other aspects, as (1) they are highly fecund, pelagic spawners, like most exploited marine fishes; (2) their life cycle is delineated between nursery (estuarine) and adult (coastal and offshore) habitat; and (3) they are managed at these two spatial scales. This study was conducted from August 2012 to December 2013 and integrates data from multiple methods and spatial scales. Aerial surveys were used for large-scale monitoring of aggregations off two known estuarine nursery areas, Tampa Bay and Charlotte Harbor, Florida, USA. Capture-based sampling in Tampa Bay coastal (n = 2581) and estuarine waters (n = 158) was used to assess reproductive state and to confirm coastal spawning. To assess spatial dynamics, we acoustically tagged two population components in the Tampa Bay system, subadults from the estuary (n = 20) and adults from the coastal spawning site (n = 60). Behavioral plasticity was seen in subadult recruitment to coastal habitat, with some subadults maturing and recruiting before or during the spawning season and others (14 of 20 acoustically tagged fish) recruiting at the end of the 2012 spawning season. Both adults and recruited subadults (n = 29) were consequently detected in the Charlotte Harbor array, 132 km to the south. Spawning-site fidelity to the Tampa Bay spawning site occurred at both the population and individual scales. Aggregations consistently occurred in Tampa Bay coastal waters during the spawning season, and approximately two-thirds of tagged adults returned in the 2013 spawning season. A similar proportion of subadults returned to the Tampa Bay spawning site, exhibiting natal homing. However, these first-time spawners arrived later than repeat spawners and were detected over shorter time periods. This study, and others like it, demonstrates how integrating data from individuals tracked over space and time with more traditional population-based sampling is changing our understanding of ecological processes that affect marine fish productivity and our ability to manage for sustainablity.