Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

We examine the structure and phylogeography of the pig-eye shark (Carcharhinus amboinensis) common in shallow coastal environments in northern Australia using two types of genetic markers, two mitochondrial (control region and NADH hydrogenase 4) and two nuclear (microsatellite and Rag 1) DNA. Two populations were defined within northern Australia on the basis of mitochondrial DNA evidence, but this result was not supported by nuclear microsatellite or Rag 1 markers. One possibility for this structure might be sex-specific behaviours such as female philopatry, although we argue it is doubtful that sufficient time has elapsed for any potential signatures from this behaviour to be expressed in nuclear markers. It is more likely that the observed pattern represents ancient populations repeatedly isolated and connected during episodic sea level changes during the Pleistocene epoch, until current day with restricted contemporary gene flow maintaining population genetic structure. Our results show the need for an understanding of both the history and ecology of a species in order to interpret patterns in genetic structure.

Evidence for reproductive philopatry in the bull shark Carcharhinus leucas

Reproductive philopatry in bull sharks Carcharhinus leucas was investigated by comparing mitochondrial (NADH dehydrogenase subunit 4, 797 base pairs and control region genes 837 base pairs) and nuclear (three microsatellite loci) DNA of juveniles sampled from 13 river systems across northern Australia. High mitochondrial and low microsatellite genetic diversity among juveniles sampled from different rivers (mitochondrial fST = 0.0767, P < 0.05; microsatellite FST = -0.0022, P > 0.05) supported female reproductive philopatry. Genetic structure was not further influenced by geographic distance (P > 0.05) or long-shore barriers to movement (P > 0.05). Additionally, results suggest that C. leucas in northern Australia has a long-term effective population size of 11 000-13 000 females and has undergone population bottlenecks and expansions that coincide with the timing of the last ice-ages.

The distribution and abundance of electrosensory pores in two benthic sharks: a comparison of the wobbegong shark, Orectolobus maculatus, and the angel shark, Squatina australis

Electroreception is an ancient sense found in many aquatic animals, including sharks, which may be used in the detection of prey, predators and mates. Wobbegong sharks (Orectolobidae) and angel sharks (Squatinidae) represent two distantly related families that have independently evolved a similar dorso-ventrally compressed body form to complement their benthic ambush feeding strategy. Consequently, these groups represent useful models in which to investigate the specific morphological and physiological adaptations that are driven by the adoption of a benthic lifestyle. In this study, we compared the distribution and abundance of electrosensory pores in the spotted wobbegong shark (Orectolobus maculatus) with the Australian angel shark (Squatina australis) to determine whether both species display a similar pattern of clustering of sub-dermal electroreceptors and to further understand the functional importance of electroreception in the feeding behaviour of these benthic sharks. Orectolobus maculatus has a more complex electrosensory system than S. australis, with a higher abundance of pores and an additional cluster of electroreceptors positioned in the snout (the superficial ophthalmic cluster). Interestingly, both species possess a cluster of pores (the hyoid cluster, positioned slightly posterior to the first gill slit) more commonly found in rays, but which may be present in all benthic elasmobranchs to assist in the detection of approaching predators.

Queensland shark control program non-target statistics by year

Spreadsheet of non-target species (bycatch) numbers in the Shark Control Program by species, date of capture, location, size and sex from 2001 onwards The shark control program (SCP) relies on nets or drumlines, or a combination of both, to minimise the threat of shark attack on humans in particular locations. Following is information on numbers and locations of sharks that have been caught by the SCP. It is important to reduce the inadvertent impacts of the SCP on other marine animals (bycatch) without compromising human safety. Bycatch levels are carefully monitored and research is focused on minimising impacts on non-target species. This dataset contains details of non-target numbers in the Shark Control program by species, date of capture, and location from 2001

Desk Review of Queensland shark stock assessment for Fisheries Queensland

An independent desk review of the document entitled “Stock assessment of whaler and hammerhead sharks (Carcharhinidae and Sphyrnidae) in Queensland” commissioned by the Queensland’s Department of Agriculture and Fisheries was undertaken during January 15-February 12, 2016.

Assessment of a data-limited, multi-species shark fishery in the Great Barrier Reef Marine Park and south-east Queensland

The status of five species of commercially exploited sharks within the Great Barrier Reef Marine Park (GBRMP) and south-east Queensland was assessed using a data-limited approach. Annual harvest rate, U, estimated empirically from tagging between 2011 and 2013, was compared with an analytically-derived proxy for optimal equilibrium harvest rate, UMSY Lim. Median estimates of U for three principal retained species, Australian blacktip shark, Carcharhinus tilstoni, spot-tail shark, Carcharhinus sorrah, and spinner shark, Carcharhinus brevipinna, were 0.10, 0.06 and 0.07 year-1, respectively. Median U for two retained, non-target species, pigeye shark, Carcharhinus amboinensis and Australian sharpnose shark, Rhizoprionodon taylori, were 0.27 and 0.01 year-1, respectively. For all species except the Australian blacktip the median ratio of U/UMSY Lim was <1. The high vulnerability of this species to fishing combined with life history characteristics meant UMSY Lim was low (0.04-0.07 year-1) and that U/UMSY Lim was likely to be > 1. Harvest of the Australian blacktip shark above UMSY could place this species at a greater risk of localised depletion in parts of the GBRMP. Results of the study indicated that much higher catches, and presumably higher U, during the early 2000s were likely unsustainable. The unexpectedly high level of U on the pigeye shark indicated that output-based management controls may not have been effective in reducing harvest levels on all species, particularly those caught incidentally by other fishing sectors including the recreational sector. © 2016 Elsevier B.V.

Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

Handling of Two Tropical Australian Sharks to Improve Quality and to Identify the Cause of Tough Texture

Sharks caught in tropical Australian waters occasionally exhibit tough texture. Two species of Carcharinid shark, originally known as the sorrah shark (Carcharinus sorrah) and the black spot shark (Carcharinus tilstoni), compose the majority of the catch. Experiments were conducted to identify the cause of tough texture and to improve the overall quality of the catch. The possibility that a cold shock reaction may occur was investigated by observing the contraction of fillets under a range of temperature conditions before freezing. The effect of on-board handling practices were evaluated using frozen shark fillets, which had been stored prior to freezing in refrigerated seawater at different rigor stages, temperatures and times as trunks. Fillets were analyzed for nucleotides, lactate, thaw pH, sarcomere length and raw and cooked shear force values. The existence of thaw rigor was also investigated. There was little difference in the texture between the individual strips of a fillet exposed to different temperatures but there were significant differences between individual sharks. A cold shock reaction could not be demonstrated in these species. The main influences on texture were of biological origin. The species, sex and size were found to have significant links with texture of fillets. The quality of the fillets deteriorated quicker during the warmer season and were at their worst if the trunks were kept on deck till post-rigor or held in 15 degree C refrigerated seawater before freezing

Toxoplasmosis in Indo-Pacific humpbacked dolphins (Sousa chinensis) from Queensland

Objective: To describe the clinical signs, gross pathology, serology, bacteriology, histopathology, electron microscopy and immunohistochemistry findings associated with toxoplasmosis in four Indo-Pacific humpbacked dolphins (Sousa chinensis) that stranded in Queensland in 2000 and 2001. Design: Clinical assessment, gross necropsy, and laboratory examinations. Procedure: Necropsies were performed on four S chinensis to determine cause of death. Laboratory tests including serology, bacteriology, histopathology and transmission electron microscopy were done on the four dolphins. lmmunohistochemistry was done on the brain, heart, liver, lung, spleen and adrenal gland from various dolphins to detect Toxoplasma gondii antigens. Results: Necropsies showed all of four S chinensis that stranded in Queensland in 2000 and 2001 had evidence of predatory shark attack and three were extremely emaciated. Histopathological examinations showed all four dolphins had toxoplasmosis with tissue cysts resembling T gondii in the brain. Tachyzoite stages of T gondii were detected in the lungs, heart, liver, spleen and adrenal gland, variously of all four dolphins. Electron microscopy studies and immunohistochemistry confirmed the tissues cysts were those of Tgondii. All four dolphins also had intercurrent disease including pneumonia, three had peritonitis and one had pancreatitis. Conclusion: Four S chinensis necropsied in Queensland in 2000 and 2001 were found to be infected with toxoplasmosis. It is uncertain how these dolphins became infected and further studies are needed to determine how S chinensis acquire toxoplasmosis. All four dolphins stranded after periods of heavy rainfall, and coastal freshwater runoff may be a risk factor for T gondii infection in S chinensis. This disease should be of concern to wildlife managers since S chinensis is a rare species and its numbers appear to be declining.

Population genetic structure of the brown tiger prawn, Penaeus esculentus, in tropical northern Australia

Eight polymorphic microsatellite loci were analysed in six population samples from four locations of the Australian endemic brown tiger prawn, Penaeus esculentus. Tests of Hardy-Weinberg equilibrium were generally in accord with expectations, with only one locus, in two samples, showing significant deviations. Three samples were taken in different years from the Exmouth Gulf. These showed no significant heterogeneity, and it was concluded that they were from a single panmictic population. A sample from Shark Bay, also on the west coast of Australia, showed barely detectable differentiation from Exmouth Gulf (F (ST) = 0 to 0.0014). A northeast sample from the Gulf of Carpentaria showed low (F (ST) = 0.008) but significant differentiation from Moreton Bay, on the east coast. However, Exmouth Gulf/Shark Bay samples were well differentiated from the Gulf of Carpentaria/Moreton Bay (F (ST) = 0.047-0.063). The data do not fit a simple isolation by distance model. It is postulated that the east-west differentiation largely reflects the isolation of east and west coast populations that occurred at the last glacial maximum when there was a land bridge between north-eastern Australia and New Guinea.

Effect of changes in hook pattern and size on catch rate, hooking location, injury and bleeding for a number of tropical reef fish species

The Queensland Great Barrier Reef line fishery in Australia is regulated via a range of input and output controls including minimum size limits, daily catch limits and commercial catch quotas. As a result of these measures a substantial proportion of the catch is released or discarded. The fate of these released fish is uncertain, but hook-related mortality can potentially be decreased by using hooks that reduce the rates of injury, bleeding and deep hooking. There is also the potential to reduce the capture of non-target species though gear selectivity. A total of 1053 individual fish representing five target species and three non-target species were caught using six hook types including three hook patterns (non-offset circle, J and offset circle), each in two sizes (small 4/0 or 5/0 and large 8/0). Catch rates for each of the hook patterns and sizes varied between species with no consistent results for target or non-target species. When data for all of the fish species were aggregated there was a trend for larger hooks, J hooks and offset circle hooks to cause a greater number of injuries. Using larger hooks was more likely to result in bleeding, although this trend was not statistically significant. Larger hooks were also more likely to foul-hook fish or hook fish in the eye. There was a reduction in the rates of injuries and bleeding for both target and non-target species when using the smaller hook sizes. For a number of species included in our study the incidence of deep hooking decreased when using non-offset circle hooks, however, these results were not consistent for all species. Our results highlight the variability in hook performance across a range of tropical demersal finfish species. The most obvious conservation benefits for both target and non-target species arise from using smaller sized hooks and non-offset circle hooks. Fishers should be encouraged to use these hook configurations to reduce the potential for post-release mortality of released fish.

Mitochondrial DNA supports the identification of two endangered river sharks (Glyphis glyphis and Glyphis garricki) across northern Australia

The river sharks (genus Glyphis) are a small group of poorly known sharks occurring in tropical rivers and estuarine waters across northern Australia, south-east Asia and the subcontinent. The taxonomy of the genus has long been unclear due to very few individuals having been caught and examined, resulting in a paucity of data regarding their distribution, biology and ecology. Only recently has attention focussed on the two Australian species, G. glyphis and G. garricki. This study is a result of a rare opportunity to collate the few samples that have been collected from these species and the bull shark Carcharhinus leucas, which shares an overlapping range. These samples were analysed using the DNA barcoding approach (cox1 mitochondrial gene), compared with six other species of carcharhinids and evaluated in light of the current taxonomic classification. Nine species-specific nucleotide differences were found between G. glyphis and G. garricki and no intra-specific variation provides strong support for the separation into distinct species. Significant differences were also observed at the inter-generic level, with Glyphis forming a distinct clade from Carcharhinus. This study provides the basis for future molecular studies required to better address conservation issues confronting G. glyphis and G. garricki in Australia.

Scalloped Hammerhead microsatellite genotypes (eight loci) representing five regions on Australia's east coast and one location in central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Milkshark (Rhizoprionodon acutus) microsatellite genotype data (six loci) from samples collected from five locations in eastern Australia and central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Observations on the reproductive biology of three catsharks (Carcharhiniformes: Scyliorhinidae: Asymbolus and Figaro) from the continental shelf of southern Queensland, Australia.

Three species of Australian endemic catsharks (grey spotted catshark Asymbolus analis, orange spotted catshark A. rubiginosus and Australian sawtail shark Figaro boardmani) were collected from the trawl grounds of a highly seasonal commercial fishery off southern Queensland, Australia. Specimens were collected on the mid to outer continental shelf at depths between 78 and 168 m. This study provides the first information on the reproductive biology of these three poorly-known species. Mature female and male A. analis were observed from 455 mm total length (TL), mature female A. rubiginosus from 410 mm TL, mature male A. rubiginosus from 405 mm TL, mature female F. boardmani from 402 mm TL and mature male F. boardmani from 398 mm TL (although a lack of immature specimens precluded more accurate assessments of size at maturity). The reproductive mode of all species was confirmed as single oviparous (carrying only one egg case in each uterus at a time). Ovarian fecundity (the number of vitellogenic follicles) ranged from 7-20 in A. analis, 5-23 in A. rubiginosus and 9-13 in F. boardmani. Several indicators suggest that Asymbolus catsharks off southern Queensland are reproductively active year-round. The proportion of female A. rubiginosus carrying egg cases was highest in spring (60%), intermediate in autumn (50%) and lowest in winter (44%).