Ryan Johnson’s research while affiliated with Oceans and other places

Human activities in the oceans increase the extinction risk of marine megafauna. Interventions require an understanding of movement patterns and the spatiotemporal overlap with threats. We analysed the movement patterns of 33 white sharks (Carcharodon carcharias) satellite-tagged in South Africa between 2012 and 2014 to investigate the influence of size, sex and season on movement patterns and the spatial and temporal overlap with longline and gillnet fisheries and marine protected areas (MPAs). We used a hidden Markov model to identify ‘resident’ and ‘transient’ movement states and investigate the effect of covariates on the transition probabilities between states. A model with sex, total length and season had the most support. Tagged sharks were more likely to be in a resident state near the coast and a transient state away from the coast, while the probability of finding a shark in the transient state increased with size. White sharks moved across vast areas of the southwest Indian Ocean, emphasising the need for a regional management plan. White sharks overlapped with longline and gillnet fisheries within 25% of South Africa’s Exclusive Economic Zone and spent 15% of their time exposed to these fisheries during the study period. The demersal shark longline fishery had the highest relative spatial and temporal overlap, followed by the pelagic longline fishery and the KwaZulu-Natal (KZN) shark nets and drumlines. However, the KZN shark nets and drumlines reported the highest white shark catches, emphasising the need to combine shark movement and fishing effort with reliable catch records to assess risks to shark populations accurately. White shark exposure to shark nets and drumlines, by movement state, sex and maturity status, corresponded with the catch composition of the fishery, providing support for a meaningful exposure risk estimate. White sharks spent significantly more time in MPAs than expected by chance, likely due to increased prey abundance or less disturbance, suggesting that MPAs can benefit large, mobile marine megafauna. Conservation of white sharks in Southern Africa can be improved by implementing non-lethal solutions to beach safety, increasing the observer coverage in fisheries, and continued monitoring of movement patterns and existing and emerging threats.

106,107 ✉ replying to A. V. Harry & J. M. Braccini Nature https://doi.org/10.1038/s41586-021-03463-w (2021) Our global analysis 1 estimated the overlap and fishing exposure risk (FEI) using the space use of satellite-tracked sharks and longline fishing effort monitored by the automatic identification system (AIS). In the accompanying Comment, Harry and Braccini 2 draw attention to two localized shark-longline vessel overlap hotspots in Australian waters, stating that 47 fishing vessels were misclassified as longline and purse seine vessels in the Global Fishing Watch (GFW) 3 2012-2016 AIS fishing effort data product that we used. This, they propose 2 , results in misi-dentifications that highlight fishing exposure hotspots that are subject to an unexpected level of sensitivity in the analysis and they suggest that misidentifications could broadly affect the calculations of fishing exposure and the central conclusions of our study 1. We acknowledged in our previously published paper 1 that gear reclassifications were likely to occur for a small percentage of the more than 70,000 vessels studied, however, here we demonstrate that even using much larger numbers of vessel reclassifications than those proposed by Harry and Braccini 2 , the central results and conclusions of our paper 1 do not change. In our use of a third-party dataset such as GFW 3 , we stated clearly 1 that the dataset is undergoing continuous refinement to correct for acknowledged contamination of some gear types with others in some regions (for example, drifting longlines with bottom-set longlines off New Zealand 1). The characterization of GFW vessels (gear) is under-taken using two convolutional neural networks that were trained 3 on 45,441 marine vessels (fishing and non-fishing) that identified six Published online: xx xx xxxx Check for updates Q1 Q2 Q3 Q4 Q5 A list of affiliations appears at the end of the paper.

This article is a response to Murua et al.'s Matters Arising article in Nature, "Shark mortality cannot be assessed by fishery overlap alone," which arose from arising from N. Queiroz et al. Nature https://doi.org/10.1038/s41586-019-1444-4 (2019).

The white shark (Carcharodon carcharias) is responsible for 49% of shark-related injuries in South Africa, yet no information currently exists on the composition or antibiotic resistance of bacteria hosted by these apex predators in South African waters. This study aimed to address this gap by sampling the bacteria present in the oral cavities of 28 live C. carcharias along South Africa’s southern coastline. The antibiotic resistance of the range of microbiota was also assessed using antibiotic disc diffusion tests. A total of 51 strains from at least 20 species of bacteria were isolated from the oral cavities of C. carcharias. Of these strains, the most common bacteria present were Serratia spp., Proteus vulgaris and Vibrio alginolyticus. The overall antibiotic resistance was relatively higher in this study than that reported for bacterial microbiota sampled from other shark species. Results indicate that the combination therapy of imipenem (carbapenem antibiotic) and vancomycin (glycopeptide antibiotic) might be the most parsimonious option to effectively treat infections resulting from white shark bites, particularly in South Africa. It is hoped that, in addition to assisting medical professionals to treat shark bite victims, these findings enhance the understanding of the microbial communities present in large coastal predators and their surrounding environments. Significance: • Overall antibiotic resistance of bacteria in the oral cavities of C. carcharias was relatively high. • Combination therapy of imipenem (carbapenem antibiotic) and vancomycin (glycopeptide antibiotic) is recommended for the treatment of white shark bites, particularly in South Africa. • The findings add to understanding of the microbial communities present in large coastal predators and their surrounding environments.

Effective ocean management and the conservation of highly migratory species depend on resolving the overlap between animal movements and distributions, and fishing effort. However, this information is lacking at a global scale. Here we show, using a big-data approach that combines satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space-use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively), and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of fishing effort in marine areas beyond national jurisdictions (the high seas). Our results demonstrate an urgent need for conservation and management measures at high-seas hotspots of shark space use, and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real-time, dynamic management.

Acoustic tracking is a commonly used method to study the movement ecology of marine species. The characteristics of the data collected are not simply functions of the location of the tagged animal as they are also influenced by the method of data collection and its sampling frequency. In particular, since the data are acoustically driven, the significance of any result hinges not only on the accuracy of the equipment but also on the reliability of the information received. While passive acoustic telemetry requires an evaluation of the detection efficiency of receivers moored in different habitats (or sites) to obtain reliable data, active acoustic telemetry requires more field-related information on how to best track tagged animals without impacting on their natural behaviour. This study aimed to evaluate the reliability of active acoustic telemetry data in a temperate coastal environment. This was achieved by conducting a series of field experiments to assess (i) the use of signal strength-to-infer distance to the tracked animal under different tracking conditions, (ii) what signal strength threshold can be used to obtain reliable bio-telemetered data, (iii) whether the behaviour of a tracked animal would be a main concern in terms of data reliability, and (iv) the best filtering option to reduce the data to be analysed. The findings yielded a signal strength-to-distance relationship to improve the accuracy of the positional fixes of actively tracked animals, which can be used as a practical reference for future tracking studies on pelagic species in temperate coastal environments.

Previous work on white sharks indicate the species show seasonally limited movement patters, at certain aggregation sites small areas may play vital roles in the life history of a large amount of the population. Acoustic telemetry was used to estimate habitat use of white sharks, Carcharodon carcharias, while aggregating at Mossel Bay, South Africa. Total range of all shark tracks combined accumulated 782 h and covered an area of 93.5 km2 however, within this range, sharks were found to highly utilise a core habitat (50 % Kernel, K50) of just 1.05 km2 over a reef system adjacent to a river mouth. Individual tracks revealed additional core habitats, some of which were previously undocumented and one adjacent to a commercial harbor. Much was found to be dependent on the size of the shark, with larger sharks (>400 cm) occupying smaller activity areas than subadult (300–399 cm) and juvenile (<300 cm) conspecifics, while Index of Reuse (IOR) and Index of Shared Space (IOSS) were both found to increase with shark size. Such results provide evidence that larger white sharks are more selective in habitat use, which indicates they have greater experience within aggregation sites. Furthermore, the focused nature of foraging means spatially restricted management strategies would offer a powerful tool to aid enforcement of current protective legislation for the white shark in similar environments of limited resources and capacity.

Determining the residency of an aquatic species is important but challenging and it remains unclear what is the best sampling methodology. Photo-identification has been used extensively to estimate patterns of animals' residency and is arguably the most common approach, but it may not be the most effective approach in marine environments. To examine this, in 2005, we deployed acoustic transmitters on 22 white sharks (Carcharodon carcharias) in Mossel Bay, South Africa to quantify the probability of detecting these tagged sharks by photo-identification and different deployment strategies of acoustic telemetry equipment. Using the data collected by the different sampling approaches (detections from an acoustic listening station deployed under a chumming vessel versus those from visual sightings and photo-identification), we quantified the methodologies' probability of detection and determined if the sampling approaches, also including an acoustic telemetry array, produce comparable results for patterns of residency. Photo-identification had the lowest probability of detection and underestimated residency. The underestimation is driven by various factors primarily that acoustic telemetry monitors a large area and this reduces the occurrence of false negatives. Therefore, we propose that researchers need to use acoustic telemetry and also continue to develop new sampling approaches as photo-identification techniques are inadequate to determine residency. Using the methods presented in this paper will allow researchers to further refine sampling approaches that enable them to collect more accurate data that will result in better research and more informed management efforts and policy decisions.