From little things big things grow: enhancement of an acoustic telemetry network to monitor broad-scale movements of marine species along Australia's east coast

BACKGROUND

Acoustic telemetry has become a fundamental tool to monitor the movement of aquatic species. Advances in technology, in particular the development of batteries with lives of > 10 years, have increased our ability to track the long-term movement patterns of many species. However, logistics and financial constraints often dictate the locations and deployment duration of acoustic receivers. Consequently, there is often a compromise between optimal array design and affordability. Such constraints can hinder the ability to track marine animals over large spatial and temporal scales. Continental-scale receiver networks have increased the ability to study large-scale movements, but significant gaps in coverage often remain.

METHODS

Since 2007, the Integrated Marine Observing System's Animal Tracking Facility (IMOS ATF) has maintained permanent receiver installations on the eastern Australian seaboard. In this study, we present the recent enhancement of the IMOS ATF acoustic tracking infrastructure in Queensland to collect data on large-scale movements of marine species in the northeast extent of the national array. Securing a relatively small initial investment for expanding receiver deployment and tagging activities in Queensland served as a catalyst, bringing together a diverse group of stakeholders (research institutes, universities, government departments, port corporations, industries, Indigenous ranger groups and tourism operators) to create an extensive collaborative network that could sustain the extended receiver coverage into the future. To fill gaps between existing installations and maximise the monitoring footprint, the new initiative has an atypical design, deploying many single receivers spread across 2,100 km of Queensland waters.

RESULTS

The approach revealed previously unknown broad-scale movements for some species and highlights that clusters of receivers are not always required to enhance data collection. However, array designs using predominantly single receiver deployments are more vulnerable to data gaps when receivers are lost or fail, and therefore "redundancy" is a critical consideration when designing this type of array.

CONCLUSION

Initial results suggest that our array enhancement, if sustained over many years, will uncover a range of previously unknown movements that will assist in addressing ecological, fisheries, and conservation questions for multiple species.

Scaling of Activity Space in Marine Organisms across Latitudinal Gradients

AbstractUnifying models have shown that the amount of space used by animals (e.g., activity space, home range) scales allometrically with body mass for terrestrial taxa; however, such relationships are far less clear for marine species. We compiled movement data from 1,596 individuals across 79 taxa collected using a continental passive acoustic telemetry network of acoustic receivers to assess allometric scaling of activity space. We found that ectothermic marine taxa do exhibit allometric scaling for activity space, with an overall scaling exponent of 0.64. However, body mass alone explained only 35% of the variation, with the remaining variation best explained by trophic position for teleosts and latitude for sharks, rays, and marine reptiles. Taxon-specific allometric relationships highlighted weaker scaling exponents among teleost fish species (0.07) than sharks (0.96), rays (0.55), and marine reptiles (0.57). The allometric scaling relationship and scaling exponents for the marine taxonomic groups examined were lower than those reported from studies that had collated both marine and terrestrial species data derived using various tracking methods. We propose that these disparities arise because previous work integrated summarized data across many studies that used differing methods for collecting and quantifying activity space, introducing considerable uncertainty into slope estimates. Our findings highlight the benefit of using large-scale, coordinated animal biotelemetry networks to address cross-taxa evolutionary and ecological questions.

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements.

Flexibility for fuelling reproduction in a pelagic ray (Mobula eregoodoo) suggested by bioenergetic modelling

This study investigated the measurements of energy density and bioenergetic modelling for a pelagic ray, Mobula eregoodoo, to estimate its relative allocation to various bodily processes and especially reproduction. The data revealed M. eregoodoo uses up to 21.0% and 2.5% of its annual energy budget on growth and reproduction, respectively. During pregnancy, females depleted energy reserves in the liver, which, along with their biennial reproductive cycle, aligns with general theory that ectotherms are capital breeders and thus build energy reserves before reproduction. Nonetheless, the reduction in energy reserves did not account for all reproductive costs, and therefore, gravid females supplement reproductive costs through energy derived from the diet, according to an income-breeding strategy. These characteristics imply that M. eregoodoo exhibits some flexibility in fuelling reproduction depending on energy availability throughout the reproductive cycle, which may be prevalent in other elasmobranchs. The data represent the first estimates of both the metabolic costs of gestation in elasmobranchs and the relative cost of reproduction in rays. Energy costs and plasticity associated with highly variable reproductive strategies in elasmobranchs may influence long-term population viability under a rapidly changing environment.

Reef manta rays forage on tidally driven, high density zooplankton patches in Hanifaru Bay, Maldives

Manta rays forage for zooplankton in tropical and subtropical marine environments, which are generally nutrient-poor. Feeding often occurs at predictable locations where these large, mobile cartilaginous fishes congregate to exploit ephemeral productivity hotspots. Investigating the zooplankton dynamics that lead to such feeding aggregations remains a key question for understanding their movement ecology. The aim of this study is to investigate the feeding environment at the largest known aggregation for reef manta rays Mobula alfredi in the world. We sampled zooplankton throughout the tidal cycle, and recorded M. alfredi activity and behaviour, alongside environmental variables at Hanifaru Bay, Maldives. We constructed generalised linear models to investigate possible relationships between zooplankton dynamics, environmental parameters, and how they influenced M. alfredi abundance, behaviour, and foraging strategies. Zooplankton biomass changed rapidly throughout the tidal cycle, and M. alfredi feeding events were significantly related to high zooplankton biomass. Mobula alfredi switched from non-feeding to feeding behaviour at a prey density threshold of 53.7 mg dry mass m⁻³; more than double the calculated density estimates needed to theoretically meet their metabolic requirements. The highest numbers of M. alfredi observed in Hanifaru Bay corresponded to when they were engaged in feeding behaviour. The community composition of zooplankton was different when M. alfredi was feeding (dominated by copepods and crustaceans) compared to when present but not feeding (more gelatinous species present than in feeding samples). The dominant zooplankton species recorded was Undinula vulgaris. This is a large-bodied calanoid copepod species that blooms in oceanic waters, suggesting offshore influences at the site. Here, we have characterised aspects of the feeding environment for M. alfredi in Hanifaru Bay and identified some of the conditions that may result in large aggregations of this threatened planktivore, and this information can help inform management of this economically important marine protected area.

Age and growth of the tropical oviparous shark, Chiloscyllium punctatum in Indonesian waters

The brown-banded bamboo shark, Chiloscyllium punctatum, is the most common shark caught in coastal commercial fisheries throughout Southeast Asia, yet there is a lack of the life-history information necessary for reliable stock assessments. The authors estimated growth rates and age at maturity using analysis of growth bands in vertebral centra. They trialled four different techniques to enhance the visibility and improve identification of the putative annual growth bands necessary for age estimation. The authors found that the burn method on whole vertebral centra provided the most readable and consistent results for age analysis. The logistic model was chosen as the best-fit growth model for age estimation of 330 individual C. punctatum from Indonesia. Several age verification methods, including marginal increment ratio and length-frequency analysis, were performed with the support of age validation through the use of calcein-labelled vertebrae from two sharks maintained in captivity. This study found that C. punctatum from Indonesian waters is a fast-growing species that can grow up to 18 cm year^-1 , reach an estimated maximum total length of 1 m, mature at c. 6.5 years and live for up to 14 years.

Delimiting cryptic species within the brown-banded bamboo shark, Chiloscyllium punctatum in the Indo-Australian region with mitochondrial DNA and genome-wide SNP approaches

Background

Delimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove problematic for further studies and for implementing conservation management. In this study, we examined mitochondrial DNA and genome-wide nuclear single nucleotide polymorphisms (SNPs) in the brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential cryptic species and the species-population boundary in the group.

Results

Both mtDNA and SNP analyses showed potential delimitation within C. punctatum from the Indo-Australian region and consisted of four operational taxonomic units (OTUs), i.e. those from Indo-Malay region, the west coast of Sumatra, Lesser Sunda region, and the Australian region. Each OTU can be interpreted differently depending on available supporting information, either based on biological, ecological or geographical data. We found that SNP data provided more robust results than mtDNA data in determining the boundary between population and cryptic species.

Conclusion

To split a cryptic species complex and erect new species based purely on the results of genetic analyses is not recommended. The designation of new species needs supportive diagnostic morphological characters that allow for species recognition, as an inability to recognise individuals in the field creates difficulties for future research, management for conservation and fisheries purposes. Moreover, we recommend that future studies use a comprehensive sampling regime that encompasses the full range of a species complex. This approach would increase the likelihood of identification of operational taxonomic units rather than resulting in an incorrect designation of new species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01852-3.

Mutualism promotes site selection in a large marine planktivore

Mutualism is a form of symbiosis whereby both parties benefit from the relationship. An example is cleaning symbiosis, which has been observed in terrestrial and marine environments. The most recognized form of marine cleaning symbiosis is that of cleaner fishes and their clients.Cleaner species set up cleaning stations on the reef, and other species seek out their services. However, it is not well understood how the presence of cleaning stations influence movements of large highly mobile species. We examined the role of cleaning stations as a driver of movement and habitat use in a mobile client species.Here, we used a combination of passive acoustic telemetry and in-water surveys to investigate cleaning station attendance by the reef manta ray Mobula alfredi. We employed a novel approach in the form of a fine-scale acoustic receiver array set up around a known cleaning area and tagged 42 rays. Within the array, we mapped structural features, surveyed the distribution of cleaner wrasse, and observed the habitat use of the rays.We found manta ray space use was significantly associated with blue-streak cleaner wrasse Labroides dimidiatus distribution and hard coral substrate. Cleaning interactions dominated their habitat use at this site, taking precedence over other life history traits such as feeding and courtship.This study has demonstrated that cleaning symbiosis is a driver for highly mobile, and otherwise pelagic, species to visit inshore reef environments. We suggest that targeted and long-term use of specific cleaning stations reflects manta rays having a long-term memory and cognitive map of some shallow reef environments where quality cleaning is provided. We hypothesize that animals prefer cleaning sites in proximity to productive foraging regions.

The geographic distribution of reef and oceanic manta rays (Mobula alfredi and Mobula birostris) in Australian coastal waters

The known distribution of manta rays in Australian waters is patchy, with records primarily centred around tourism hotspots. We collated 11,614 records of Mobula alfredi from photo-ID databases (n = 10,715), aerial surveys (n = 378) and online reports (n = 521). The study confirms an uninterrupted coastal distribution from north of 26°S and 31°S on the west and east coasts, respectively. More southerly M. alfredi records relate to warm-water events with a southernmost extent at 34°S. Coastal sightings of Mobula birostris were rare (n = 32), likely reflecting a preference for offshore waters, but encompass a wider latitudinal extent than M. alfredi of 10-40°S.

Rapid wound healing in a reef manta ray masks the extent of vessel strike

Increasing vessel traffic in the marine environment due to commercial and recreational activities has amplified the number of conflicts with marine animals. However, there are limited multi-year observations of the healing rate of marine animals following vessel strike. Here we document the healing rate of a reef manta ray Mobula alfredi, following lacerations caused by a propeller along the pectoral fin. We demonstrate a high healing capacity, with wound length following a negative exponential curve over time. Lacerations healed to 5% of the initial wound length (i.e. 95% closure) within 295 days. The wounds appeared to stabilise at this point as observed more than three years following the incident and resulted in a distinctive scarring pattern. Examination of an extensive photo-identification catalogue of manta rays from the Ningaloo Coast World Heritage Area showed that the scarring pattern occurs more frequently than previously recognised, as the wounds had been previously attributed to failed predation attempts. This study provides baseline information for wound healing from vessel strike in reef manta rays and indirect evidence for increased vessel strikes on manta rays within the Ningaloo Coast World Heritage Area. We discuss the implication for spatial and behavioural management of vessels around manta rays.

Development and characterization of 17 polymorphic microsatellite markers for the reef manta ray (Mobula alfredi)

Objective

Limited sample sizes are often a problem for species of conservation concern when using genetic tools to make population assessments. Lack of analytical power from small sample sizes can be compensated for by use of a large marker set. Here we report on development and characterization of 17 novel microsatellite markers for the reef manta ray (Mobula alfredi).

Results

Loci were screened on 60 reef manta rays (M. alfredi) sampled from the east coast of Australia. The number of alleles per locus varied from 2 to 13 with observed heterozygosities ranging between 0.300 and 0.917. The development of these 17 additional markers increases the total number of microsatellite markers available for this species to 27.

Can estimates of genetic effective population size contribute to fisheries stock assessments?

Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (N_e ). Recent studies of elasmobranch species have shown correspondence between N_e and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of N_e /N ratios across species may be more restricted than previously thought, and also show that declines in N_e track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data-poor fisheries or species of conservation interest.

Integrating acoustic telemetry into mark-recapture models to improve the precision of apparent survival and abundance estimates

Capture-mark-recapture models are useful tools for estimating demographic parameters but often result in low precision when recapture rates are low. Low recapture rates are typical in many study systems including fishing-based studies. Incorporating auxiliary data into the models can improve precision and in some cases enable parameter estimation. Here, we present a novel application of acoustic telemetry for the estimation of apparent survival and abundance within capture-mark-recapture analysis using open population models. Our case study is based on simultaneously collecting longline fishing and acoustic telemetry data for a large mobile apex predator, the broadnose sevengill shark (Notorhynchus cepedianus), at a coastal site in Tasmania, Australia. Cormack-Jolly-Seber models showed that longline data alone had very low recapture rates while acoustic telemetry data for the same time period resulted in at least tenfold higher recapture rates. The apparent survival estimates were similar for the two datasets but the acoustic telemetry data showed much greater precision and enabled apparent survival parameter estimation for one dataset, which was inestimable using fishing data alone. Combined acoustic telemetry and longline data were incorporated into Jolly-Seber models using a Monte Carlo simulation approach. Abundance estimates were comparable to those with longline data only; however, the inclusion of acoustic telemetry data increased precision in the estimates. We conclude that acoustic telemetry is a useful tool for incorporating in capture-mark-recapture studies in the marine environment. Future studies should consider the application of acoustic telemetry within this framework when setting up the study design and sampling program.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.

IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific

The Indo-West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum, is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: 'Least Concern' and 'Vulnerable'. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric F(ST) analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.

Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: Introgressive hybridisation or ancestral polymorphisms

Inter-specific genetic relationships among regional populations of two species of grouper (Plectropomus maculatus and Plectropomus leopardus) were examined using mitochondrial and nuclear markers. mtDNA revealed contrasting regional inter-specific patterns whilst nuclear markers revealed contrasting patterns among markers, irrespective of region. In eastern Australia (EA) the species form a single mtDNA lineage, but the two species are reciprocally monophyletic in Western Australia (WA). This supports previous evidence for hybridisation between these species on the east coast. WA P. leopardus forms a sister relationship with the EA P. leopardus-maculatus clade while WA P. maculatus is more basal and sister to the P. leopardus lineages, indicating mtDNA does not suffer from incomplete lineage sorting for these species. In contrast, one of three nuclear markers (locus 7-90TG) differentiated the species into two reciprocally monophyletic clades, with no evidence of hybridisation or ancestral polymorphism. The remaining two nuclear markers (2-22 and ETS-2) did not separate these two species, while distinguishing other plectropomid species, suggesting incomplete lineage sorting at these nuclear loci. These results together with coalescence analyses suggest that P. leopardus females have hybridised historically with P. maculatus males and that P. maculatus mitochondria were displaced through introgressive hybridisation and fixation in the P. maculatus founder population on the Great Barrier Reef. The contrasting regional patterns of mtDNA structure may be attributed to Quaternary sea-level changes and shelf width differences driving different reef configurations on each coast. These reef configurations have provided opportunities for local scale interaction and reproduction among species on the narrower EA continental shelves, but not on the broader WA continental shelves.

Evidence for sympatric speciation by host shift in the sea

The genetic divergence and evolution of new species within the geographic range of a single population (sympatric speciation) contrasts with the well-established doctrine that speciation occurs when populations become geographically isolated (allopatric speciation). Although there is considerable theoretical support for sympatric speciation, this mode of diversification remains controversial, at least in part because there are few well-supported examples. We use a combination of molecular, ecological, and biogeographical data to build a case for sympatric speciation by host shift in a new species of coral-dwelling fish (genus Gobiodon). We propose that competition for preferred coral habitats drives host shifts in Gobiodon and that the high diversity of corals provides the source of novel, unoccupied habitats. Disruptive selection in conjunction with strong host fidelity could promote rapid reproductive isolation and ultimately lead to species divergence. Our hypothesis is analogous to sympatric speciation by host shift in phytophagous insects except that we propose a primary role for intraspecific competition in the process of speciation. The fundamental similarity between these fishes and insects is a specialized and intimate relationship with their hosts that makes them ideal candidates for speciation by host shift.