Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus

Information on the spatial ecology of reef sharks is critical to understanding life-history patterns, yet gaps remain in our knowledge of how these species move and occupy space. Previous studies have focused on offshore reefs and atolls with little information available on the movement and space use of sharks utilising reef habitats closer to shore. Cross-shelf differences in physical and biological properties of reefs can alter regional ecosystem processes resulting in different movement patterns for resident sharks. Passive acoustic telemetry was used to examine residency, space use and depth use of 40 blacktip reef sharks, Carcharhinus melanopterus, on an inshore reef in Queensland, Australia, and assess temporal or biological influences. All sharks showed strong site-attachment to inshore reefs with residency highest among adult females. Sharks exhibited a sex-based, seasonal pattern in space use where males moved more, occupied more space and explored new areas during the reproductive season, while females utilised the same amount of space throughout the year, but shifted the location of the space used. A positive relationship was also observed between space use and size. There was evidence of seasonal site fidelity and long-distance movement with the coordinated, annual migration of two adult males to the study site during the mating season. Depth use was segregated with some small sharks occupying shallower depths than adults throughout the day and year, most likely as refuge from predation. Results highlight the importance of inshore reef habitats to blacktip reef sharks and provide evidence of connectivity with offshore reefs, at least for adult males

Prioritising search effort to locate previously unknown populations of endangered marine reptiles

Strategies aimed to conserve and manage rare species are often hindered by the lack of data needed for their effective design. Incomplete and inaccurate data on habitat associations and current species distributions pose a barrier to effective conservation and management for several species of endemic sea snakes in Western Australia that are thought to be in decline. Here we used a correlative modelling approach to understand habitat associations and identify suitable habitats for five of these species (Aipysurus apraefrontalis, A. foliosquama, A. fuscus, A. l. pooleorum and A. tenuis). We modelled species-specific habitat suitability across 804,244 km(2) of coastal waters along the North-west Shelf of Western Australia, to prioritise future survey regions to locate unknown populations of these rare species. Model projections were also used to quantify the effectiveness of current spatial management strategies (Marine Protected Areas) in conserving important habitats for these species. Species-specific models matched well with the records on which they were trained, and identified additional regions of suitability without records. Subsequent field validation of the model projections uncovered a previously unknown locality for A. fuscus within the mid-shelf shoal region, outside its currently recognised global range. Defining accurate geographic distributions for rare species is a vital first step in defining more robust extent of species occurrence and range overlap with threatening processes

Continental-scale animal tracking reveals functional movement classes across marine taxa

Acoustic telemetry is a principle tool for observing aquatic animals, but coverage over large spatial scales remains a challenge. To resolve this, Australia has implemented the Integrated Marine Observing System's Animal Tracking Facility which comprises a continental-scale hydrophone array and coordinated data repository. This national acoustic network connects localized projects, enabling simultaneous monitoring of multiple species over scales ranging from 100 s of meters to 1000 s of kilometers. There is a need to evaluate the utility of this national network in monitoring animal movement ecology, and to identify the spatial scales that the network effectively operates over. Cluster analyses assessed movements and residency of 2181 individuals from 92 species, and identified four functional movement classes apparent only through aggregating data across the entire national network. These functional movement classes described movement metrics of individuals rather than species, and highlighted the plasticity of movement patterns across and within populations and species. Network analyses assessed the utility and redundancy of each component of the national network, revealing multiple spatial scales of connectivity influenced by the geographic positioning of acoustic receivers. We demonstrate the significance of this nationally coordinated network of receivers to better reveal intra-specific differences in movement profiles and discuss implications for effective management

A standardised framework for analysing animal detections from automated tracking arrays

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Over the past 15 years, the integration of localised passive telemetry networks into centralised data repositories has greatly enhanced our ability to monitor the presence and movements of highly mobile and migratory species. These large-scale networks are now generating big data, allowing meta-analyses across multiple species, locations, and temporal scales. Broad-scale comparisons of animal movement metrics are constrained by the use of diverse analytical techniques among researchers. Accordingly, there is a need for a tool-set to assist in calculating animal movement metrics that can be easily applied to datasets from local studies to large-scale cooperative networks. Results: We present a standardised framework and an associated analysis tool-set that facilitates the calculation of a range of activity space and movement metrics for passive telemetry datasets. Application of the tool-set is demonstrated using data from the Integrated Marine Observing System continental-scale network of underwater acoustic receivers. We show how the metrics can: (1) be directly compared among multiple species monitored at multiple sites; (2) be compared among multiple species tagged at a single study site; and (3) assess changes in activity space metrics over time. Conclusions: Establishing a framework and tool-set to analyse data from large-scale networks progresses the field of passive telemetry beyond the traditional individual-, species-, or location-centric approaches to facilitate national- or international-scale outputs that better address important questions in the field of movement ecology.Integrated Marine Observing Syste

A Trait‐Based Framework for Assessing the Vulnerability of Marine Species to Human Impacts

Marine species and ecosystems are widely affected by anthropogenic stressors, ranging from pollution and fishing to climate change. Comprehensive assessments of how species and ecosystems are impacted by anthropogenic stressors are critical for guiding conservation and management investments. Previous global risk or vulnerability assessments have focused on marine habitats, or on limited taxa or specific regions. However, information about the susceptibility of marine species across a range of taxa to different stressors everywhere is required to predict how marine biodiversity will respond to human pressures. We present a novel framework that uses life-history traits to assess species’ vulnerability to a stressor, which we compare across more than 44,000 species from 12 taxonomic groups (classes). Using expert elicitation and literature review, we assessed every combination of each of 42 traits and 22 anthropogenic stressors to calculate each species’ or representative species group’s sensitivity and adaptive capacity to stressors, and then used these assessments to derive their overall relative vulnerability. The stressors with the greatest potential impact were related to biomass removal (e.g., fisheries), pollution, and climate change. The taxa with the highest vulnerabilities across the range of stressors were mollusks, corals, and echinoderms, while elasmobranchs had the highest vulnerability to fishing-related stressors. Traits likely to confer vulnerability to climate change stressors were related to the presence of calcium carbonate structures, and whether a species exists across the interface of marine, terrestrial, and atmospheric realms. Traits likely to confer vulnerability to pollution stressors were related to planktonic state, organism size, and respiration. Such a replicable, broadly applicable method is useful for informing ocean conservation and management decisions at a range of scales, and the framework is amenable to further testing and improvement. Our framework for assessing the vulnerability of marine species is the first critical step toward generating cumulative human impact maps based on comprehensive assessments of species, rather than habitats

Data Descriptor: Australia’s continental-scale acoustic tracking database and its automated quality control process

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article.Our ability to predict species responses to environmental changes relies on accurate records of animal movement patterns. Continental-scale acoustic telemetry networks are increasingly being established worldwide, producing large volumes of information-rich geospatial data. During the last decade, the Integrated Marine Observing System’s Animal Tracking Facility (IMOS ATF) established a permanent array of acoustic receivers around Australia. Simultaneously, IMOS developed a centralised national database to foster collaborative research across the user community and quantify individual behaviour across a broad range of taxa. Here we present the database and quality control procedures developed to collate 49.6 million valid detections from 1891 receiving stations. This dataset consists of detections for 3,777 tags deployed on 117 marine species, with distances travelled ranging from a few to thousands of kilometres. Connectivity between regions was only made possible by the joint contribution of IMOS infrastructure and researcher-funded receivers. This dataset constitutes a valuable resource facilitating meta-analysis of animal movement, distributions, and habitat use, and is important for relating species distribution shifts with environmental covariates

Spatial ecology of true sea snakes (Hydrophiinae) in coastal waters of North Queensland

Aquatic snakes are a diverse group that represent multiple evolutionary transitions from a terrestrial to an aquatic mode of life. Current systematics of aquatic snakes identifies four independent lineages (file snakes, Acrochordidae; homalopsid snakes, Homalopsidae; sea kraits: Laticaudinae and 'true' sea snakes, Hydrophiinae), species of which are represented on almost every continent. Despite their widespread distributions, this group of snakes is under−represented in the scientific literature with many fundamental questions about their ecology and biology still unanswered. In Chapter 2 of this thesis, I review the current scientific literature on the spatial ecology of aquatic and semi−aquatic snakes and assess both the horizontal (i.e. geographic movements) and vertical (i.e. dive patterns) patterns in their movement. I also assess what is currently known about the intrinsic (e.g. food, predator avoidance, reproductive state, ontogenetic shifts, philopatry and homing) and extrinsic (e.g. temperature, salinity, lunar and tidal cycles) factors that drive movement and space use in this group of snakes and identify key knowledge gaps. Chapter 2 also reviews the current knowledge on natural and anthropogenic threats these animals face and how movement affects their susceptibility to these threats. Incidental trawl capture represents a major threat to sea snake populations throughout their global distribution where they often represent a large proportion of bycatch in artisanal and commercial trawl fisheries. Recent global assessments have highlighted the need for data regarding the distribution patterns and spatial ecology of sea snakes to better understand their interactions with trawl fisheries throughout their range. This dissertation focuses on 'true' sea snakes, which are found in tropical waters of South East Asia, Australia and the Pacific Islands. Data obtained using multiple techniques were used to define the distribution patterns, spatial ecology and physiology of true sea snakes within the Great Barrier Reef Marine Park (GBRMP), Australia. These data were used to explore and better understand how sea snakes are distributed and utilise space throughout the GBRMP over multiple spatial (i.e., geographic to regional) and temporal (i.e., diel to seasonal) scales. In Chapter 3, data from baited remote underwater video stations (BRUVS) were used to estimate geographic−scale distribution patterns of three species of sea snake (Aipysurus laevis, Hydrophis curtus and H. ocellatus) over 14˚ of latitude within the GBRMP. A total of 2471 deployments of BRUVS were made in a range of locations, in sites open and closed to trawl fishing. Sightings of sea snakes were analysed alongside six spatial factors [depth, relative distance across (longitude) and along (latitude) the GBRMP, proximity to land, proximity to the nearest reef and habitat complexity] to determine the factors that most strongly influenced the distribution and abundance of sea snakes. The results showed a strong latitudinal effect on the distribution of all three species, with the highest densities and diversities occurring in central and southern GBRMP locations, while the northern Great Barrier Reef (GBR) was relatively depauperate in terms of both occurrence and diversity. Shallow inshore areas were identified as key habitats for A. laevis and H. curtus, whereas deeper offshore habitats were most important for H. ocellatus. No significant difference was found in the mean number of snakes sighted per hour between sites open and closed to trawling. Overall, sea snakes displayed 'patchy' geographic distribution patterns in the GBRMP. Inshore waters of the central GBR were one area that all three species had high abundances, indicating that this area is particularly favourable for sea snake populations on the GBR. In Chapter 4, the movement patterns and three−dimensional home ranges of two species of sea snake (Hydrophis curtus and H. elegans) were examined at multiple temporal scales using passive acoustic telemetry. Over a diel period, monitored snakes exhibited a clear diel pattern in their use of space, with individuals displaying restricted movements at greater depths during the day, and larger movements on the surface at night. Hydrophis curtus generally occupied space in deep water within the bay, while H. elegans were restricted to mud flats in inundated inter−tidal habitats. The overlap in space used between day and night showed that individuals used different core areas; however, the extent of areas used was similar. The space use patterns of monitored sea snakes were also evaluated alongside environmental parameters to determine what factors influenced the spatial ecology of sea snakes in nearshore habitats. Presence, movement and three−dimensional home range metrics calculated from monitoring data were tested against environmental (water temperature, atmospheric pressure, wind speed, accumulated rainfall and tidal range) and biological (snout−vent length) factors on daily and monthly temporal scales to identify key environmental drivers of movement and the use of space. A generalised linear mixed model (GLMM) framework using Akaike information criterion (AIC) indicated that tidal reach and atmospheric pressure strongly influenced the daily presence and movements of tagged individuals, respectively. Accumulated rainfall significantly influenced the volume of space used on a monthly timescale. In Chapter 5, the data obtained from passive acoustic telemetry was used to determine how sea snakes select habitats based on habitat type, depth and proximity to sources of freshwater within a nearshore environment. A hierarchical Bayesian model was used to estimate if individuals were selecting habitats significantly more or less than random on a population− and individual−level. Composition of diet was also assessed using regurgitate from captured individuals. Selection of habitats by the two species differed with H. elegans displaying an affinity for mudflat and seagrass habitats less than 4 km from sources of freshwater and depths less than 3 m. Hydrophis curtus selected for slightly deeper seagrass habitats (1 – 4 m) further from freshwater sources (2 – 5 km). Data from regurgitate showed H. curtus displayed some level of intraspecific predation. Both species prominently selected seagrass areas indicating these habitats provide key resources for sea snakes within nearshore environments. Any degradation or loss of these habitats may have significant consequences for local sea snake populations. Understanding the habitat requirements of sea snakes is essential to defining how natural and anthropogenic disturbances may affect populations and is necessary to inform targeted management and conservation practices. This thesis also explored the physiological basis of movement patterns in sea snakes and examined how environmental factors may affect their susceptibility to trawl fishing. In Chapter 6, laboratory observations showed that sea snakes displayed shorter dive durations and surfaced more frequently as water temperature increased. Animal−borne accelerometers were used to provide the first estimates of movement−associated energy expenditure in free−roaming sea snakes and explore diel and seasonal patterns in metabolic rates. The energy requirements of sea snakes estimated in the field showed a doubling of metabolic rate from the cooler dry season to the warmer wet season, which potentially increases their susceptibility to fishing activities that occur in summer months. In bimodally respiring animals like sea snakes, the up−regulation in cutaneous respiration is an important mechanism that can potentially prolong dive durations during periods of stress. This mechanism is important and can potentially allow sea snakes to prolong their dive durations when caught in trawl nets and increase their chances of survival. Results of this thesis showed that sea snakes may not have much control over the amount of oxygen they uptake cutaneously, which may impede their chances of survival once caught in fishing gear. The use of spatial closures (e.g. Marine Protected Areas; MPAs) is effective in reducing the exposure of bycatch species to fishing activities in the GBRMP, and may be useful in managing fishing−related mortality in sea snakes. However, identifying important habitats for sea snakes is critical to ensure that MPAs function effectively. In Chapter 7, I examined the importance of protected, shallow coastal habitats as possible refuge sites for sea snakes in the GBRMP. Extensive boat−based surveys were conducted to investigate the assemblage and abundance of sea snakes within a protected, shallow coastal bay adjacent to trawl fishing grounds. Hydrophis curtus and H. elegans were the most commonly encountered species within the bay. Based on the age structure of these two species the bay was primarily used by juveniles. Temporal trends in age structure showed that H. curtus may use Cleveland Bay as a nursery ground with gravid females entering the bay in summer months to give birth. In contrast, H. elegans appears to use the bay more consistently through the year with approximately 30% of individuals being adult. This chapter also showed that shallow tidal habitats, which are too risky to undertake trawl fishing, are regularly used by sea snakes and may provide refugia for vulnerable life stages of sea snakes. The identification and protection of such habitats may further mitigate risks to sea snake populations from trawl fishing

Spatial ecology of true sea snakes (Hydrophiinae) in coastal waters of North Queensland

Aquatic snakes are a diverse group that represent multiple evolutionary transitions from a terrestrial to an aquatic mode of life. Current systematics of aquatic snakes identifies four independent lineages (file snakes, Acrochordidae; homalopsid snakes, Homalopsidae; sea kraits: Laticaudinae and 'true' sea snakes, Hydrophiinae), species of which are represented on almost every continent. Despite their widespread distributions, this group of snakes is under−represented in the scientific literature with many fundamental questions about their ecology and biology still unanswered. In Chapter 2 of this thesis, I review the current scientific literature on the spatial ecology of aquatic and semi−aquatic snakes and assess both the horizontal (i.e. geographic movements) and vertical (i.e. dive patterns) patterns in their movement. I also assess what is currently known about the intrinsic (e.g. food, predator avoidance, reproductive state, ontogenetic shifts, philopatry and homing) and extrinsic (e.g. temperature, salinity, lunar and tidal cycles) factors that drive movement and space use in this group of snakes and identify key knowledge gaps. Chapter 2 also reviews the current knowledge on natural and anthropogenic threats these animals face and how movement affects their susceptibility to these threats. Incidental trawl capture represents a major threat to sea snake populations throughout their global distribution where they often represent a large proportion of bycatch in artisanal and commercial trawl fisheries. Recent global assessments have highlighted the need for data regarding the distribution patterns and spatial ecology of sea snakes to better understand their interactions with trawl fisheries throughout their range. This dissertation focuses on 'true' sea snakes, which are found in tropical waters of South East Asia, Australia and the Pacific Islands. Data obtained using multiple techniques were used to define the distribution patterns, spatial ecology and physiology of true sea snakes within the Great Barrier Reef Marine Park (GBRMP), Australia. These data were used to explore and better understand how sea snakes are distributed and utilise space throughout the GBRMP over multiple spatial (i.e., geographic to regional) and temporal (i.e., diel to seasonal) scales. In Chapter 3, data from baited remote underwater video stations (BRUVS) were used to estimate geographic−scale distribution patterns of three species of sea snake (Aipysurus laevis, Hydrophis curtus and H. ocellatus) over 14˚ of latitude within the GBRMP. A total of 2471 deployments of BRUVS were made in a range of locations, in sites open and closed to trawl fishing. Sightings of sea snakes were analysed alongside six spatial factors [depth, relative distance across (longitude) and along (latitude) the GBRMP, proximity to land, proximity to the nearest reef and habitat complexity] to determine the factors that most strongly influenced the distribution and abundance of sea snakes. The results showed a strong latitudinal effect on the distribution of all three species, with the highest densities and diversities occurring in central and southern GBRMP locations, while the northern Great Barrier Reef (GBR) was relatively depauperate in terms of both occurrence and diversity. Shallow inshore areas were identified as key habitats for A. laevis and H. curtus, whereas deeper offshore habitats were most important for H. ocellatus. No significant difference was found in the mean number of snakes sighted per hour between sites open and closed to trawling. Overall, sea snakes displayed 'patchy' geographic distribution patterns in the GBRMP. Inshore waters of the central GBR were one area that all three species had high abundances, indicating that this area is particularly favourable for sea snake populations on the GBR. In Chapter 4, the movement patterns and three−dimensional home ranges of two species of sea snake (Hydrophis curtus and H. elegans) were examined at multiple temporal scales using passive acoustic telemetry. Over a diel period, monitored snakes exhibited a clear diel pattern in their use of space, with individuals displaying restricted movements at greater depths during the day, and larger movements on the surface at night. Hydrophis curtus generally occupied space in deep water within the bay, while H. elegans were restricted to mud flats in inundated inter−tidal habitats. The overlap in space used between day and night showed that individuals used different core areas; however, the extent of areas used was similar. The space use patterns of monitored sea snakes were also evaluated alongside environmental parameters to determine what factors influenced the spatial ecology of sea snakes in nearshore habitats. Presence, movement and three−dimensional home range metrics calculated from monitoring data were tested against environmental (water temperature, atmospheric pressure, wind speed, accumulated rainfall and tidal range) and biological (snout−vent length) factors on daily and monthly temporal scales to identify key environmental drivers of movement and the use of space. A generalised linear mixed model (GLMM) framework using Akaike information criterion (AIC) indicated that tidal reach and atmospheric pressure strongly influenced the daily presence and movements of tagged individuals, respectively. Accumulated rainfall significantly influenced the volume of space used on a monthly timescale. In Chapter 5, the data obtained from passive acoustic telemetry was used to determine how sea snakes select habitats based on habitat type, depth and proximity to sources of freshwater within a nearshore environment. A hierarchical Bayesian model was used to estimate if individuals were selecting habitats significantly more or less than random on a population− and individual−level. Composition of diet was also assessed using regurgitate from captured individuals. Selection of habitats by the two species differed with H. elegans displaying an affinity for mudflat and seagrass habitats less than 4 km from sources of freshwater and depths less than 3 m. Hydrophis curtus selected for slightly deeper seagrass habitats (1 – 4 m) further from freshwater sources (2 – 5 km). Data from regurgitate showed H. curtus displayed some level of intraspecific predation. Both species prominently selected seagrass areas indicating these habitats provide key resources for sea snakes within nearshore environments. Any degradation or loss of these habitats may have significant consequences for local sea snake populations. Understanding the habitat requirements of sea snakes is essential to defining how natural and anthropogenic disturbances may affect populations and is necessary to inform targeted management and conservation practices. This thesis also explored the physiological basis of movement patterns in sea snakes and examined how environmental factors may affect their susceptibility to trawl fishing. In Chapter 6, laboratory observations showed that sea snakes displayed shorter dive durations and surfaced more frequently as water temperature increased. Animal−borne accelerometers were used to provide the first estimates of movement−associated energy expenditure in free−roaming sea snakes and explore diel and seasonal patterns in metabolic rates. The energy requirements of sea snakes estimated in the field showed a doubling of metabolic rate from the cooler dry season to the warmer wet season, which potentially increases their susceptibility to fishing activities that occur in summer months. In bimodally respiring animals like sea snakes, the up−regulation in cutaneous respiration is an important mechanism that can potentially prolong dive durations during periods of stress. This mechanism is important and can potentially allow sea snakes to prolong their dive durations when caught in trawl nets and increase their chances of survival. Results of this thesis showed that sea snakes may not have much control over the amount of oxygen they uptake cutaneously, which may impede their chances of survival once caught in fishing gear. The use of spatial closures (e.g. Marine Protected Areas; MPAs) is effective in reducing the exposure of bycatch species to fishing activities in the GBRMP, and may be useful in managing fishing−related mortality in sea snakes. However, identifying important habitats for sea snakes is critical to ensure that MPAs function effectively. In Chapter 7, I examined the importance of protected, shallow coastal habitats as possible refuge sites for sea snakes in the GBRMP. Extensive boat−based surveys were conducted to investigate the assemblage and abundance of sea snakes within a protected, shallow coastal bay adjacent to trawl fishing grounds. Hydrophis curtus and H. elegans were the most commonly encountered species within the bay. Based on the age structure of these two species the bay was primarily used by juveniles. Temporal trends in age structure showed that H. curtus may use Cleveland Bay as a nursery ground with gravid females entering the bay in summer months to give birth. In contrast, H. elegans appears to use the bay more consistently through the year with approximately 30% of individuals being adult. This chapter also showed that shallow tidal habitats, which are too risky to undertake trawl fishing, are regularly used by sea snakes and may provide refugia for vulnerable life stages of sea snakes. The identification and protection of such habitats may further mitigate risks to sea snake populations from trawl fishing

Peaceful coexistence between people and deadly wildlife: Why are recreational users of the ocean so rarely bitten by sea snakes?

International audienc

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Mitochondrial cytochrome b alignmen