ABSTRACT In the era of “Anthropocene defaunation,” large species are often no longer detected in habitats where they formerly occurred. However, it is unclear whether this apparent missing, or “dark,” diversity of megafauna results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in human-impacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations.

ABSTRACT Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species. An Integrated Assessment Framework (IAF) was devised to systematically incorporate data across jurisdictions and create a regional synopsis, and amalgamated a suite of data from the Australasian region. Scalloped hammerhead populations are segregated by sex and size, with Australian populations dominated by juveniles and small adult males, while Indonesian and PNG populations included large adult females. The IAF process introduced genetic and tagging data to produce conceptual models of stock structure and movement. Several hypotheses were produced to explain stock structure and movement patterns, but more data are needed to identify the most likely hypothesis. This study demonstrates a process for assessing migratory species connectivity and highlights priority areas for hammerhead management and research.

ABSTRACT 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.

ABSTRACT We present the first mitochondrial genome sequence of the great hammerhead shark, Sphyrna mokarran. This species is of considerable conservation concern throughout its global distribution, and currently listed as Endangered on the IUCN Red List. The mitochondrial genome is 16,719 bp in length with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The gene arrangement is congruent with other shark and most vertebrate species. This S. mokarran mitogenome provides a genomic resource for assisting with population studies and conservation efforts for this highly depleted species.

ABSTRACT A thorough understanding of movement patterns of a species is critical for designing effective conservation and management initiatives. However, generating such information for large marine vertebrates is challenging, as they typically move over long distances, live in concealing environments, are logistically difficult to capture and, as upper-trophic predators, are naturally low in abundance. Large-bodied, broadly distributed tropical shark typically restricted to coastal and shelf habitats, the great hammerhead shark Sphyrna mokarran epitomizes such challenges. Highly valued for its fins (in target and incidental fisheries), it suffers high bycatch mortality coupled with fecundity conservative life history, and as a result, is vulnerable to over-exploitation and population depletion. Although there are very little species-specific data available, the absence of recent catch records give cause to suspect substantial declines across its range. Here, we used biotelemetry techniques (acoustic and satellite), conventional tagging, laser-photogrammetry, and photo-identification to investigate the level of site fidelity/residency for great hammerheads to coastal areas in the Bahamas and U.S., and the extent of movements and connectivity of great hammerheads between the U.S. and Bahamas. Results revealed large-scale return migrations (3030 km), seasonal residency to local areas (some for 5 months), site fidelity (annual return to Bimini and Jupiter for many individuals) and numerous international movements. These findings enhance the understanding of movement ecology in great hammerhead sharks and have potential to contribute to improved conservation and management.

ABSTRACT Animals exhibit various physiological and behavioural strategies for minimizing travel costs. Fins of aquatic animals play key roles in efficient travel and, for sharks, the functions of dorsal and pectoral fins are considered well divided: the former assists propulsion and generates lateral hydrodynamic forces during turns and the latter generates vertical forces that offset sharks' negative buoyancy. Here we show that great hammerhead sharks drastically reconfigure the function of these structures, using an exaggerated dorsal fin to generate lift by swimming rolled on their side. Tagged wild sharks spend up to 90% of time swimming at roll angles between 50° and 75°, and hydrodynamic modelling shows that doing so reduces drag—and in turn, the cost of transport—by around 10% compared with traditional upright swimming. Employment of such a strongly selected feature for such a unique purpose raises interesting questions about evolutionary pathways to hydrodynamic adaptations, and our perception of form and function.

ABSTRACT Aquatic highly migratory species (HMS) are economically and ecologically important, however, their highly migratory nature makes them difficult to study and thus there are knowledge gaps relating to their movement and habitat use patterns. Highly migratory sharks are likely to interact with commercial longline fishing gear and be caught as target or bycatch, which can threaten their populations. Understanding the environmental factors that influence and drive the movements of highly migratory sharks may help researchers better predict their presence and subsequently identify areas where they are vulnerability to fisheries. Here I evaluated the overlap between habitat suitability and gear restricted zones for three co-occurring apex predatory sharks in the Southwest Atlantic Ocean and Gulf of Mexico (great hammerhead Sphyrna mokarran, tiger Galeocerdo cuvier, and bull sharks Carcharhinus leucas) to identify areas in this region where these species are vulnerable to and protected from commercial longline fishing. This research was accomplished in three integrated steps. First, I reviewed and summarized what is known about the environmental drivers of great hammerhead, tiger, and bull shark habitat use and movement patterns. Second, I used the results of this review to parameterize and subsequently generate habitat suitability models for these three species. Third, I used these models to spatially compare where each species’ highly suitable habitat overlaps with longline gear restricted areas within the Southwest Atlantic Ocean and Gulf of Mexico, to identify regions where these species were both vulnerable to and protected from longline fishing gear. The results of this thesis have implications to the management of these species as well as for the conservation of other highly migratory aquatic species.