Population structure and residency patterns of the blacktip reef shark Carcharhinus melanopterus in turbid coastal environments

Genomic insights into the historical and contemporary demographics of the grey reef shark

Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (N_e) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in N_e were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in N_e were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient N_e observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary N_e, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.

Optimal soak times for Baited Remote Underwater Video Station surveys of reef-associated elasmobranchs

Effective sampling of marine communities is essential to provide robust estimates of species richness and abundance. Baited Remote Underwater Video Stations (BRUVS) are a useful tool in assessment of fish assemblages, but research on the optimal sampling period required to record common and rare elasmobranch species is limited. An appropriate ‘soak time’ (time elapsed between settlement of the BRUVS on the seabed and when it is hauled off the seabed) requires consideration, since longer soak times may be required to record species rare in occurrence, or sightings in areas of generally low elasmobranch abundance. We analysed 5352 BRUVS deployments with a range of soak times across 21 countries in the Coral Triangle and Pacific Ocean, to determine the optimal soak time required for sampling reef-associated elasmobranchs, considering species rarity, and community abundance at each site. Species were categorised into 4 ‘rarity’ groups (very rare to common), by their relative occurrence in the dataset, defined simply by the proportion of BRUVS on which they occurred. Individual BRUVS were categorised into 3 ‘abundance’ groups (low to high) by overall relative elasmobranch abundance, defined as total number of all elasmobranchs sighted per unit of sampling effort. The effects of BRUVS soak times, and levels of rarity and abundance groupings, on the time to first sighting (TFS) and time to maximum number of elasmobranchs observed (t_MaxN) were examined. We found that TFS occurred earlier for species groups with high occurrence, and on BRUVS with high elasmobranch abundance, yet longer soak times were not essential to observe rarer species. Our models indicated an optimum of 95% of both sighting event types (TFS, t_MaxN) was recorded within 63–77 minutes, and a soak time of 60 minutes recorded 78–94% of the elasmobranch sighting events recorded (78–94% of TFS events and 82–90% of t_MaxN events), when species rarity and abundance on BRUVS was accounted for. Our study shows that deployments of ~ 77 minutes are optimal for recording all species we observed, although 60 minutes soak time effectively samples the majority of elasmobranch species in shallow coral reef habitats using BRUVS.

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.

Sex biased individual variation in movement patterns of a highly mobile, near-shore marine planktivore, the reef manta ray Mobula alfredi

We examined individual variation and the role of sex on the movements of the reef manta ray Mobula alfredi. Specifically, we analysed several movement metrics using 6 years of nightly observations (1 January 2009-31 December 2014) of 118 individually identifiable manta rays at two discrete but spatially proximate sites, locally known as Manta Heaven and Manta Village, 15 km apart on the west side of the island of Hawaii, USA. Males were slightly more often (33.5%, model fitted mean, P < 0.05) observed than females at Manta Heaven, but females were much more often (156.4%, model fitted mean, P < 0.05) observed at Manta Village. Movement patterns among individuals varied greatly, but the level of variation was similar between sexes. Some animals, mainly females, displayed more resident patterns, whereas other, more mobile, animals moved between sites more frequently and had longer gaps between sightings. We did not detect discrete behavioural groups; rather, individuals varied along a continuous spectrum from many observations and high affinity to few observations and low fidelity to survey locations. These complex and variable movement patterns observed at the individual level, between sexes and between two nearby sites, in Hawaii's manta rays highlight the need for finer scale considerations in conservation and management of highly mobile marine populations.

Size frequency, dispersal distances and variable growth rates of young sharks in a multi-species aggregation

During a mark-recapture survey from November 2014 until April 2017, 333 neonatal and juvenile blacktip reef sharks Carcharhinus melanopterus and 302 neonatal and juvenile sicklefin lemon sharks Negaprion acutidens were tagged and measured at the uninhabited and isolated St. Joseph Atoll (Republic of Seychelles). Both species demonstrated seasonal reproductive synchronicity and relatively large sizes at birth. Despite the extended times at liberty > 2.5 years, the majority of recaptures were found in close proximity to the initial tagging location (< 500 m). Annual growth rates of C. melanopterus (n = 24) and N. acutidens (n = 62) ranged from 6.6 to 31.7 cm year^-1 (mean ± SE; 16.2 ± 1.2 cm year^-1 ) and 0.2 to 32.2 cm year^-1 (11.8 ± 1 cm year^-1 ), respectively and are to date the most variable ever recorded in wild juvenile sharks. High abundances of both species coupled with long-term and repeated recaptures are indicative of a habitat where juveniles can reside for their first years of life. However, large variability in annual growth rates in both species may suggest high intra and interspecific competition induced by a possibly resource limited, isolated habitat.

Resetting predator baselines in coral reef ecosystems

What did coral reef ecosystems look like before human impacts became pervasive? Early efforts to reconstruct baselines resulted in the controversial suggestion that pristine coral reefs have inverted trophic pyramids, with disproportionally large top predator biomass. The validity of the coral reef inverted trophic pyramid has been questioned, but until now, was not resolved empirically. We use data from an eight-year tag-recapture program with spatially explicit, capture-recapture models to re-examine the population size and density of a key top predator at Palmyra atoll, the same location that inspired the idea of inverted trophic biomass pyramids in coral reef ecosystems. Given that animal movement is suspected to have significantly biased early biomass estimates of highly mobile top predators, we focused our reassessment on the most mobile and most abundant predator at Palmyra, the grey reef shark (Carcharhinus amblyrhynchos). We estimated a density of 21.3 (95% CI 17.8, 24.7) grey reef sharks/km², which is an order of magnitude lower than the estimates that suggested an inverted trophic pyramid. Our results indicate that the trophic structure of an unexploited reef fish community is not inverted, and that even healthy top predator populations may be considerably smaller, and more precarious, than previously thought.

Growth and life history variability of the grey reef shark (Carcharhinus amblyrhynchos) across its range

For broadly distributed, often overexploited species such as elasmobranchs (sharks and rays), conservation management would benefit from understanding how life history traits change in response to local environmental and ecological factors. However, fishing obfuscates this objective by causing complex and often mixed effects on the life histories of target species. Disentangling the many drivers of life history variability requires knowledge of elasmobranch populations in the absence of fishing, which is rarely available. Here, we describe the growth, maximum size, sex ratios, size at maturity, and offer a direct estimate of survival of an unfished population of grey reef sharks (Carcharhinus amblyrhynchos) using data from an eight year tag-recapture study. We then synthesized published information on the life history of C. amblyrhynchos from across its geographic range, and for the first time, we attempted to disentangle the contribution of fishing from geographic variation in an elasmobranch species. For Palmyra's unfished C. amblyrhynchos population, the von Bertalanffy growth function (VBGF) growth coefficient k was 0.05 and asymptotic length L∞ was 163.3 cm total length (TL). Maximum size was 175.5 cm TL from a female shark, length at maturity was estimated at 116.7-123.2 cm TL for male sharks, maximum lifespan estimated from VBGF parameters was 18.1 years for both sexes combined, and annual survival was 0.74 year-1. Consistent with findings from studies on other elasmobranch species, we found significant intraspecific variability in reported life history traits of C. amblyrhynchos. However, contrary to what others have reported, we did not find consistent patterns in life history variability as a function of biogeography or fishing. Ultimately, the substantial, but not yet predictable variability in life history traits observed for C. amblyrhynchos across its geographic range suggests that regional management may be necessary to set sustainable harvest targets and to recover this and other shark species globally.

Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives

Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.

Patterns of Occurrence of Sharks in Sydney Harbour, a Large Urbanised Estuary

Information about spatial and temporal variability in the distribution and abundance of shark-populations are required for their conservation, management and to update measures designed to mitigate human-shark interactions. However, because some species of sharks are mobile, migratory and occur in relatively small numbers, estimating their patterns of distribution and abundance can be very difficult. In this study, we used a hierarchical sampling design to examine differences in the composition of species, size- and sex-structures of sharks sampled with bottom-set longlines in three different areas with increasing distance from the entrance of Sydney Harbour, a large urbanised estuary. During two years of sampling, we obtained data for four species of sharks (Port Jackson, Heterodontus portusjacksoni; wobbegong, Orectolobus maculatus; dusky whaler, Carcharhinus obscurus and bull shark, Carcharhinus leucas). Only a few O. maculatus and C. obscurus were caught, all in the area closest to the entrance of the Harbour. O. maculatus were caught in all seasons, except summer, while C. obscurus was only caught in summer. Heterodontus portusjacksoni were the most abundant species, caught in the entrance location mostly between July to November, when water temperature was below 21.5°C. This pattern was consistent across both years. C. leucas, the second most abundant species, were captured in all areas of Sydney Harbour but only in summer and autumn when water temperatures were above 23°C. This study quantified, for this first time, how different species utilise different areas of Sydney Harbour, at different times of the year. This information has implications for the management of human-shark interactions, by enabling creation of education programs to modify human behaviour in times of increased risk of potentially dangerous sharks.

Characteristics of the shark fisheries of Fiji

Limited information is available on artisanal and subsistence shark fisheries across the Pacific. The aim of this study was to investigate Fiji’s inshore fisheries which catch sharks. In January and February 2013, 253 semi-directive interviews were conducted in 117 villages and at local harbours on Viti Levu, Vanua Levu, Taveuni, Ovalau and a number of islands of the Mamanuca and Yasawa archipelagos. Of the 253 interviewees, 81.4% reported to presently catch sharks, and 17.4% declared that they did not presently catch any sharks. Of the 206 fishers that reported to catch sharks, 18.4% targeted sharks and 81.6% caught sharks as bycatch. When targeted, primary use of sharks was for consumption or for sale. Sharks caught as bycatch were frequently released (69.6%), consumed (64.9%) or shared amongst the community (26.8%). Fishers’ identification based on an identification poster and DNA barcoding revealed that at least 12 species of elasmobranchs, 11 shark and one ray species (Rhynchobatus australiae) were caught. This study, which is the first focused exploration of the shark catch in Fiji’s inshore fisheries, suggests that the country’s artisanal shark fisheries are small but have the potential to develop into larger and possibly more targeted fisheries.

Reef sharks: recent advances in ecological understanding to inform conservation

Sharks are increasingly being recognized as important members of coral-reef communities, but their overall conservation status remains uncertain. Nine of the 29 reef-shark species are designated as data deficient in the IUCN Red List, and three-fourths of reef sharks had unknown population trends at the time of their assessment. Fortunately, reef-shark research is on the rise. This new body of research demonstrates reef sharks' high site restriction, fidelity and residency on coral reefs, their broad trophic roles connecting reef communities and their high population genetic structure, all information that should be useful for their management and conservation. Importantly, recent studies on the abundance and population trends of the three classic carcharhinid reef sharks (grey reef shark Carcharhinus amblyrhynchos, blacktip reef shark Carcharhinus melanopterus and whitetip reef shark Triaenodon obesus) may contribute to reassessments identifying them as more vulnerable than currently realized. Because over half of the research effort has focused on only these three reef sharks and the nurse shark Ginglymostoma cirratum in only a few locales, there remain large taxonomic and geographic gaps in reef-shark knowledge. As such, a large portion of reef-shark biodiversity remains uncharacterized despite needs for targeted research identified in their red list assessments. A research agenda for the future should integrate abundance, life history, trophic ecology, genetics, habitat use and movement studies, and expand the breadth of such research to understudied species and localities, in order to better understand the conservation requirements of these species and to motivate effective conservation solutions.

Blacktip reef sharks (Carcharhinus melanopterus) show high capacity for wound healing and recovery following injury

Wound healing is important for sharks from the earliest life stages, for example, as the 'umbilical scar' in viviparous species heals, and throughout adulthood, when sharks can incur a range of external injuries from natural and anthropogenic sources. Despite anecdotal accounts of rapid healing in elasmobranchs, data regarding recovery and survival of individuals from different wound or injury types has not been systematically collected. The present study documented: (i) 'umbilical scar' healing in wild-caught, neonatal blacktip reef sharks while being reared for 30 days in flow-through laboratory aquaria in French Polynesia; (ii) survival and recovery of free-swimming blacktip reef sharks in Australia and French Polynesia following a range of injuries; and (iii) long-term survival following suspected shark-finning activities. Laboratory monitoring, tag-recapture records, telemetry data and photo-identification records suggest that blacktip reef sharks have a high capacity to survive and recover from small or even large and severe wounds. Healing rates, recovery and survival are important factors to consider when assessing impacts of habitat degradation and fishing stress on shark populations. The present study suggests that individual survival may depend more on handling practices and physiological stress rather than the extent of physical injury. These observations also contribute to discussions regarding the ethics of tagging practices used in elasmobranch research and provide baseline healing rates that may increase the accuracy in estimating reproductive timing inferred from mating scars and birth dates for neonatal sharks based on umbilical scar healing status.

There and back again: a review of residency and return migrations in sharks, with implications for population structure and management

The overexploitation of sharks has become a global environmental issue in need of a comprehensive and multifaceted management response. Tracking studies are beginning to elucidate how shark movements shape the internal dynamics and structure of populations, which determine the most appropriate scale of these management efforts. Tracked sharks frequently either remain in a restricted geographic area for an extended period of time (residency) or return to a previously resided-in area after making long-distance movements (site fidelity). Genetic studies have shown that some individuals of certain species preferentially return to their exact birthplaces (natal philopatry) or birth regions (regional philopatry) for either parturition or mating, even though they make long-distance movements that would allow them to breed elsewhere. More than 80 peer-reviewed articles, constituting the majority of published shark tracking and population genetic studies, provide evidence of at least one of these behaviors in a combined 31 shark species from six of the eight extant orders. Residency, site fidelity, and philopatry can alone or in combination structure many coastal shark populations on finer geographic scales than expected based on their potential for dispersal. This information should therefore be used to scale and inform assessment, management, and conservation activities intended to restore depleted shark populations.

Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range

For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia.