Sharon A. Appleyard

Population structure of the Patagonian toothfish around Heard, McDonald and Macquarie Islands

Two mitochondrial DNA regions and seven microsatellite loci were examined in Patagonian toothfish from three locations in the Southern Ocean (Macquarie Island, five collections; Heard and McDonald Islands, four collections; Shag Rocks/South Georgia area, one collection). Striking mtDNA heterogeneity was detected between the three fishing locations (FST=0.445, P<0.001), but spatial and temporal collections within the same location were not significantly different. No significant overall microsatellite differentiation between the three locations was apparent (FST=−0.009, P=0.785). However, some individual loci showed small but significant differentiation, which in each case was attributable to between rather than within-location differentiation. Greater differentiation of mtDNA can, in principle, be explained either by female philopatry and male dispersal, or by its greater sensitivity to changes in effective population size. The latter seems more likely as tagging indicates that toothfish is generally a sedentary species. The genetic heterogeneity between the three locations indicates restricted gene flow, with the fish at each location comprising independent units. Depletion in one location is therefore unlikely to be quickly replaced by immigration from another.

Effects of including misidentified sharks in life history analyses: a case study on the grey reef shark Carcharhinus amblyrhynchos from Papua New Guinea

Fisheries observer programs are used around the world to collect crucial information and samples that inform fisheries management. However, observer error may misidentify similar-looking shark species. This raises questions about the level of error that species misidentifications could introduce to estimates of species’ life history parameters. This study addressed these questions using the Grey Reef Shark Carcharhinus amblyrhynchos as a case study. Observer misidentification rates were quantified by validating species identifications using diagnostic photographs taken on board supplemented with DNA barcoding. Length-at-age and maturity ogive analyses were then estimated and compared with and without the misidentified individuals. Vertebrae were retained from a total of 155 sharks identified by observers as C. amblyrhynchos. However, 22 (14%) of these were sharks were misidentified by the observers and were subsequently re-identified based on photographs and/or DNA barcoding. Of the 22 individuals misidentified as C. amblyrhynchos, 16 (73%) were detected using photographs and a further 6 via genetic validation. If misidentified individuals had been included, substantial error would have been introduced to both the length-at-age and the maturity estimates. Thus validating the species identification, increased the accuracy of estimated life history parameters for C. amblyrhynchos. From the corrected sample a multi-model inference approach was used to estimate growth for C. amblyrhynchos using three candidate models. The model averaged length-at-age parameters for C. amblyrhynchos with the sexes combined were L¯∞ = 159 cm TL and L¯0 = 72 cm TL. Females mature at a greater length (l50 = 136 cm TL) and older age (A50 = 9.1 years) than males (l50 = 123 cm TL; A50 = 5.9 years). The inclusion of techniques to reduce misidentification in observer programs will improve the results of life history studies and ultimately improve management through the use of more accurate data for assessments.

Rediscovery of the Threatened River Sharks, Glyphis garricki and G. glyphis, in Papua New Guinea

Recent surveys of the shark and ray catches of artisanal fishers in the Western Province of Papua New Guinea (PNG) resulted in the rediscovery of the threatened river sharks, Glyphis garricki and Glyphis glyphis. These represent the first records of both species in PNG since the 1960s and 1970s and highlight the lack of studies of shark biodiversity in PNG. Two individuals of G. garricki and three individuals of G. glyphis were recorded from coastal marine waters of the Daru region of PNG in October and November 2014. The two G. garricki specimens were small individuals estimated to be 100–105 cm and ~113 cm total length (TL). The three G. glyphis specimens were all mature, one a pregnant female and two adult males. These are the first adults of G. glyphis recorded to date providing a more accurate maximum size for this species, i.e. ~260 cm TL. A single pup which was released from the pregnant female G. glyphis, was estimated to be ~65 cm TL. Anecdotal information from the fishers of pregnant females of G. glyphis containing 6 or 7 pups provides the first estimate of litter size for this species. The jaws of the pregnant female G. glyphis were retained and a detailed description of the dentition is provided, since adult dentition has not been previously documented for this species. Genetic analyses confirmed the two species cluster well within samples from these species collected in northern Australia.

Establishing the evolutionary compatibility of potential sources of colonizers for overfished stocks: a population genomics approach.

Identifying fish stock structure is fundamental to pinpoint stocks that might contribute colonizers to overfished stocks. However, a stocks potential to contribute to rebuilding hinges on demographic connectivity, a challenging parameter to measure. With genomics as a new tool, fisheries managers can detect signatures of natural selection and thus identify fishing areas likely to contribute evolutionarily compatible colonizers to an overfished area (i.e. colonizers that are not at a fitness disadvantage in the overfished area and able to reproduce at optimal rates). Identifying evolutionarily compatible stocks would help narrow the focus on establishing demographic connectivity where it matters. Here, we genotype 4723 SNPs in 616 orange roughy (Hoplostethus atlanticus) across five fishing areas off the Tasmanian coast in Australia. We ask whether these areas form a single genetic unit, and test for signatures of local adaptation. Results from amova, structure, discriminant analysis of principal components, bayesass and isolation by distance suggest that sampled locations are subjected to geneflow amounts that are above what is needed to establish ‘drift connectivity’. However, it remains unclear whether there is a single panmictic population or several highly connected populations. Most importantly, we did not find any evidence of local adaptation, suggesting that the examined orange roughy stocks are evolutionarily compatible. The data have helped test an assumption of the orange roughy management programme and to formulate hypotheses regarding stock demographic connectivity. Overall, our results demonstrate the potential of genomics to inform fisheries management, even when evidence for stock structure is sparse.

Integrated Taxonomy Reveals Hidden Diversity in Northern Australian Fishes: A New Species of Seamoth (Genus Pegasus)

Fishes are one of the most intensively studied marine taxonomic groups yet cryptic species are still being discovered. An integrated taxonomic approach is used herein to delineate and describe a new cryptic seamoth (genus Pegasus) from what was previously a wide-ranging species. Preliminary mitochondrial DNA barcoding indicated possible speciation in Pegasus volitans specimens collected in surveys of the Torres Strait and Great Barrier Reef off Queensland in Australia. Morphological and meristic investigations found key differences in a number of characters between P. volitans and the new species, P. tetrabelos. Further mt DNA barcoding of both the COI and the slower mutating 16S genes of additional specimens provided strong support for two separate species. Pegasus tetrabelos and P. volitans are sympatric in northern Australia and were frequently caught together in trawls at the same depths.

Genetic structure of Patagonian toothfish populations from otolith DNA

Abstract The Patagonian toothfish, Dissostichus eleginoides, is a valuable fishery species and has a discontinuous distribution across the Southern Ocean. Identification of the genetic stock structure of toothfish would allow evaluation of the suitability of the spatial scale at which fisheries management operates. Genetic subdivision seems likely given the species distribution. Population genetics studies of this species have been performed; however, they have been limited by sample size, spatial coverage and/or the type of markers investigated. As a potential solution, we developed methods for extracting toothfish DNA from otoliths that are available in large numbers from collections held at several research institutes. Genetic differentiation between the three oceanic sectors was investigated. Four mitochondrial and four nuclear markers with multiple single nucleotide polymorphisms were sequenced by high throughput sequencing for samples from six locations. Genetic differentiation was found between three sectors with nuclear markers. However, only the Pacific sector was differentiated from other sectors with mitochondrial markers. This study demonstrates the usefulness of otolith DNA as a means of increasing sample sizes for population genetics research of fish. Additionally, the combination of nuclear and mitochondrial markers may allow insight into how the observed differences in movements between male and female toothfish impact population structure.

Artisanal shark fishing in Milne Bay Province, Papua New Guinea: biomass estimation from genetically identified shark and ray fins

Our study is the first detailed examination of species composition using DNA COI barcoding of elasmobranchs from an artisanal fishery of Papua New Guinea. The study is the first in the region to provide biomass estimates based on species confirmation following examination of dried fins. Over 20 species of elasmobranchs were identified from 623 fins from the artisanal fishery in Milne Bay Province of PNG, with Carcharhinus amblyrhynchos and Carcharhinus melanopterus the most abundant species in the catches. Of concern, 21% of fins examined were from IUCN listed threatened species (Vulnerable or Endangered) with 8% of fins from the Endangered scalloped hammerhead (Sphyrna lewini). Following species identifications and use of species-specific length and weight extrapolations, we estimated over 9 t of elasmobranchs contributed to the fin batch. Importantly, the vast majority of the elasmobranchs in this batch were from immature animals. Genetic identification has an important role to play in the ongoing sustainable management of elasmobranchs in artisanal fisheries in PNG and more widely. However in the absence of ongoing genetic testing, recording the species (if known) at the time of catch is more achievable and would provide more robust data for fisheries managers in PNG over the longer term.

Variability in multiple paternity rates for grey reef sharks ( Carcharhinus amblyrhynchos ) and scalloped hammerheads ( Sphyrna lewini )

This study assessed the presence and prevalence of multiple paternity (MP) in litters of grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini) opportunistically caught in Papua New Guinea (PNG). Litter size between species were significantly different with an average of 3.3 pups for grey reef sharks and 17.2 pups for scalloped hammerhead. Using 14 and 10 microsatellite loci respectively, we identified MP in 66% of grey reef sharks (4 out of 6 litters) and 100% MP in scalloped hammerheads (5 litters). We found high paternal skew (the uneven contribution of sires per litter) and a positive correlation between female adult size and litter size in scalloped hammerheads but not in grey reef sharks. Differences in the frequency of MP between species and the identification of paternal skew may be linked with mating strategies and post-copulatory mechanisms. Multiple paternity is thought to benefit populations by enhancing genetic diversity therefore increasing the population’s genetic resilience to extrinsic pressures. The identification of MP in two shark species reported here, further elucidates the complex breeding strategies elasmobranchs undertake.

Novel polymorphic microsatellite loci for the eastern king prawn, Penaeus (Melicertus) plebejus

Eastern king prawn, Penaeus (Melicertus) plebejus, is an endemic Australian species which is heavily exploited both commercially and recreationally in estuaries and in offshore trawl fisheries across several jurisdictions. P. plebejus shows extensive movement throughout the known distribution range during various life history stages (Montgomery et al. in Fish Res 80:80–87, 2007). It is currently unknown whether there is a full migration throughout the species range, or step-wise migration, and identifying the origins of important spawning populations remains as a challenge. We report 20 high resolution microsatellite markers, to address such questions and assist conservation planning for long-term sustainability.