Quantitative methods to measure pigmentation variation in farmed Giant Tiger Prawns, Penaeus monodon, and the effects of different harvest methods on cooked colour

Cooked prawn colour is known to be a driver of market price and a visual indicator of product quality for the consumer. Although there is a general understanding that colour variation exists in farmed prawns, there has been no attempt to quantify this variation or identify where this variation is most prevalent. The objectives of this study were threefold: firstly to compare three different quantitative methods to measure prawn colour or pigmentation, two different colorimeters and colour quantification from digital images. Secondly, to quantify the amount of pigmentation variation that exists in farmed prawns within ponds, across ponds and across farms. Lastly, to assess the effects of ice storage or freeze-thawing of raw product prior to cooking. Each method was able to detect quantitative differences in prawn colour, although conversion of image based quantification of prawn colour from RGB to Lab was unreliable. Considerable colour variation was observed between prawns from different ponds and different farms, and this variation potentially affects product value. Different post-harvest methods prior to cooking were also shown to have a profound detrimental effect on prawn colour. Both long periods of ice storage and freeze thawing of raw product were detrimental to prawn colour. However, ice storage immediately after cooking was shown to be beneficial to prawn colour. Results demonstrated that darker prawn colour was preserved by holding harvested prawns alive in chilled seawater, limiting the time between harvesting and cooking, and avoiding long periods of ice storage or freeze thawing of uncooked product.

Isolation and characterization of 21 polymorphic microsatellite loci in the iconic Australian lungfish, Neoceratodus forsteri, using the Ion Torrent next-generation sequencing platform

We isolated and characterized 21 microsatellite loci in the vulnerable and iconic Australian lungfish, Neoceratodus forsteri. Loci were screened across eight individuals from the Burnett River and 40 individuals from the Pine River. Genetic diversity was low with between one and six alleles per locus within populations and a maximum expected heterozygosity of 0.774. These loci will now be available to assess effective population sizes and genetic structure in N. forsteri across its natural range in South East Queensland, Australia.

Age and growth of two newly established invasive populations of Tilapiamariae in northern Australia

Sagittal otoliths were used to age the samples of Tilapia mariae collected from a coastal river and an impoundment. Validation of sagittae checks was achieved using both quantitative marginal increment analysis and by tetracycline marking of the otoliths of fish kept in tanks and in a farm dam. The annulus pattern on the otoliths was generally clear and their formation appeared to be temperature related and largely completed in the Austral spring around September and October. Male T. mariae grow faster and larger than females and the maximum ages of fish from the coastal river and impoundment was 9+ and 4+ years, respectively. Past fish surveys and the absence of older age classes in the impoundment population would suggest that this population was only very recently established.

Is stocking barramundi (Lates calcarifer) in north-eastern Queensland a threat to aquatic biodiversity?

The stocking of predators can have significant consequences on recipient aquatic ecosystems. We investigated some potential ecological impacts of stocking a predatory fish (Lates calcarifer) into a coastal river and a large impoundment in north-eastern Australia. L. calcarifer was mostly found in slower-moving, larger reaches of the river or in the main body of the impoundment where there was abundant suitable habitat. In the tidally influenced freshwater reaches of the coastal river, L. calcarifer predominately consumed aytid and palaemonid shrimp that were associated with local macrophyte beds or littoral grasses. In this area the diets of juvenile stocked and wild L. calcarifer were similar and stocked fish displayed a high degree of site fidelity. Further upstream in the river, away from tidal influence, and in the impoundment, fish were the main prey item. Cannibalism was uncommon and we suggest that, at the current stocking densities, there was little dietary evidence of predatory impacts from L. calcarifer on species of conservation concern. We caution against introducing novel predatory species such as L. calcarifer in or near areas that are outside their natural range and are known to support rare, threatened or endangered species.

Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes

Despite international protection of white sharks Carcharodon carcharias, important conservation parameters such as abundance, population structure and genetic diversity are largely unknown. The tissue of 97 predominately juvenile white sharks sampled from spatially distant eastern and southwestern Australian coastlines was sequenced for the mitochondrial DNA (mtDNA) control region and genotyped with 6 nuclear-encoded microsatellite loci. MtDNA population structure was found between the eastern and southwestern coasts (F-ST = 0.142, p < 0.0001), implying female reproductive philopatry. This concurs with recent satellite and acoustic tracking findings which suggest the sustained presence of discrete east coast nursery areas. Furthermore, population subdivision was found between the same regions with biparentally inherited micro satellite markers (F-ST = 0.009, p < 0.05), suggesting that males may also exhibit some degree of reproductive philopatry; 5 sharks captured along the east coast had mtDNA haplotypes that resembled western Indian Ocean sharks more closely than Australian/New Zealand sharks, suggesting that transoceanic dispersal, or migration resulting in breeding, may occur sporadically. Our most robust estimate of contemporary genetic effective population size was low and close to thresholds at which adaptive potential may be lost. For a variety of reasons, these contemporary estimates were at least 1, possibly 2, orders of magnitude below our historical effective size estimates. Population decline could expose these genetically isolated populations to detrimental genetic effects. Regional Australian white shark conservation management units should be implemented until genetic population structure, size and diversity can be investigated in more detail.

Nineteenth century narratives reveal historic catch rates for Australian snapper (Pagrus auratus)

Snapper (Pagrus auratus) is widely distributed throughout subtropical and temperate southern oceans and forms a significant recreational and commercial fishery in Queensland, Australia. Using data from government reports, media sources, popular publications and a government fisheries survey carried out in 1910, we compiled information on individual snapper fishing trips that took place prior to the commencement of fisherywide organized data collection, from 1871 to 1939. In addition to extracting all available quantitative data, we translated qualitative information into bounded estimates and used multiple imputation to handle missing values, forming 287 records for which catch rate (snapper fisher−1 h−1) could be derived. Uncertainty was handled through a parametric maximum likelihood framework (a transformed trivariate Gaussian), which facilitated statistical comparisons between data sources. No statistically significant differences in catch rates were found among media sources and the government fisheries survey. Catch rates remained stable throughout the time series, averaging 3.75 snapper fisher−1 h−1 (95% confidence interval, 3.42–4.09) as the fishery expanded into new grounds. In comparison, a contemporary (1993–2002) south-east Queensland charter fishery produced an average catch rate of 0.4 snapper fisher−1 h−1 (95% confidence interval, 0.31–0.58). These data illustrate the productivity of a fishery during its earliest years of development and represent the earliest catch rate data globally for this species. By adopting a formalized approach to address issues common to many historical records – missing data, a lack of quantitative information and reporting bias – our analysis demonstrates the potential for historical narratives to contribute to contemporary fisheries management.

Infection and pathology in Queensland grouper, Epinephelus lanceolatus, (Bloch), caused by exposure to Streptococcus agalactiae via different routes

Since 2007, 96 wild Queensland groupers, Epinephelus lanceolatus, (Bloch), have been found dead in NE Australia. In some cases, Streptococcus agalactiae (Group B Streptococcus, GBS) was isolated. At present, a GBS isolate from a wild grouper case was employed in experimental challenge trials in hatchery-reared Queensland grouper by different routes of exposure. Injection resulted in rapid development of clinical signs including bilateral exophthalmia, hyperaemic skin or fins and abnormal swimming. Death occurred in, and GBS was re-isolated from, 98% fish injected and was detected by PCR in brain, head kidney and spleen from all fish, regardless of challenge dose. Challenge by immersion resulted in lower morbidity with a clear dose response. Whilst infection was established via oral challenge by admixture with feed, no mortality occurred. Histology showed pathology consistent with GBS infection in organs examined from all injected fish, from fish challenged with medium and high doses by immersion, and from high-dose oral challenge. These experimental challenges demonstrated that GBS isolated from wild Queensland grouper reproduced disease in experimentally challenged fish and resulted in pathology that was consistent with that seen in wild Queensland grouper infected with S. agalactiae.

A novel method for the age estimation of Saddletail snapper (Lutjanus malabaricus) using Fourier Transform-near infrared (FT-NIR) spectroscopy

Near infrared (NIR) spectroscopy was investigated as a potential rapid method of estimating fish age from whole otoliths of Saddletail snapper (Lutjanus malabaricus). Whole otoliths from 209 Saddletail snapper were extracted and the NIR spectral characteristics were acquired over a spectral range of 800–2780 nm. Partial least-squares models (PLS) were developed from the diffuse reflectance spectra and reference-validated age estimates (based on traditional sectioned otolith increments) to predict age for independent otolith samples. Predictive models developed for a specific season and geographical location performed poorly against a different season and geographical location. However, overall PLS regression statistics for predicting a combined population incorporating both geographic location and season variables were: coefficient of determination (R2) = 0.94, root mean square error of prediction (RMSEP) = 1.54 for age estimation, indicating that Saddletail age could be predicted within 1.5 increment counts. This level of accuracy suggests the method warrants further development for Saddletail snapper and may have potential for other fish species. A rapid method of fish age estimation could have the potential to reduce greatly both costs of time and materials in the assessment and management of commercial fisheries.

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.

The utility of near infrared spectroscopy for age estimation of deepwater sharks

Reliable age information is vital for effective fisheries management, yet age determinations are absent for many deepwater sharks as they cannot be aged using traditional methods of growth bands counts. An alternative approach to ageing using near infrared spectroscopy (NIRS) was investigated using dorsal fin spines, vertebrae and fin clips of three species of deepwater sharks. Ages were successfully estimated for the two dogfish, Squalus megalops and Squalus montalbani, and NIRS spectra were correlated with body size in the catshark, Asymbolus pallidus. Correlations between estimated-ages of the dogfish dorsal fin spines and their NIRS spectra were good, with S. megalops R2=0.82 and S. montalbani R2=0.73. NIRS spectra from S. megalops vertebrae and fin clips that have no visible growth bands were correlated with estimated-ages, with R2=0.89 and 0.76, respectively. NIRS has the capacity to non-lethally estimate ages from fin spines and fin clips, and thus could significantly reduce the numbers of sharks that need to be lethally sampled for ageing studies. The detection of ageing materials by NIRS in poorly calcified deepwater shark vertebrae could potentially enable ageing of this group of sharks that are vulnerable to exploitation.

Satisfaction with fishing and the desire to leave

Predicting who may leave a fishery is an important consideration when designing capacity reduction programs to enhance both ecological and economic sustainability. In this paper, the relationship between satisfaction and the desire to exit a fishery is examined for the Queensland East Coast Trawl fishery. Income from fishing, and changes in income over the last 5 years, were key factors affecting overall satisfaction. Relative income per se was not a significant factor, counter to most satisfaction studies. Continuing a family tradition of fishing and, for one group, pride in being a fisher was found to be significant. Satisfaction with fishing overall and the challenge of fishing were found to be the primary drivers of the desire to stay or leave the fishery. Surprisingly, public perceptions of fishing, trust in management and perceptions of equity in resource allocation did not significantly affect overall satisfaction or the desire to exit the fishery.

Integrating different approaches in the definition of biological stocks: A northern Australian multi-jurisdictional fisheries example using grey mackerel, Scomberomorus semifasciatus

A holistic approach to stock structure studies utilises multiple different techniques on the same individuals sampled from selected populations and combines results across spatial and temporal scales to produce a weight of evidence conclusion. It is the most powerful and reliable source of information to use in formulating resource management and monitoring plans. Few examples of the use of a holistic approach in stock structure studies exist, although more recently this is changing. Using such an approach makes integration of results from each technique challenging. An integrated stock definition (ISD) approach for holistic stock structure studies was developed in this study to aid in the appropriate interpretation of stock structure results to guide the determination of fishery management units. The ISD approach is applied herein to a study of the northern Australian endemic grey mackerel, Scomberomorus semifasciatus (Scombridae). Analyses of genetic (mitochondrial DNA and microsatellites), parasite, otolith stable isotope, and growth data are synthesised to determine the stock structure of S. semifasciatus across northern Australia. Integration of the results from all techniques identified at least six S. semifasciatus stocks for management purposes. Further, the use of the ISD approach provided a simple basis for integrating multiple techniques and for their interpretation. The use of this holistic approach was a powerful tool in providing greater certainty about the appropriate management units for S. semifasciatus. Future stock structure studies investigating spatial management questions in the fisheries context should adopt a holistic approach and apply the ISD approach for a more accurate definition of biological stocks to improve fisheries management.

Selecting and assessing social objectives for Australian fisheries management

This paper details Australian research that developed tools to assist fisheries managers and government agencies in engaging with the social dimension of industry and community welfare in fisheries management. These tools are in the form of objectives and indicators. These highlight the social dimensions and the effects of management plans and policy implementation on fishing industries and associated communities, while also taking into account the primacy of ecological imperatives. The deployment of these objectives and indicators initially provides a benchmark and, over the life of a management plan, can subsequently be used to identify trends in effects on a variety of social and economic elements that may be objectives in the management of a fishery. It is acknowledged that the degree to which factors can be monitored will be dependent upon resources of management agencies, however these frameworks provide a method for effectively monitoring and measuring change in the social dimension of fisheries management.Essentially, the work discussed in this paper provides fisheries management with the means to both track and begin to understand the effects of government policy and management plans on the social dimension of the fishing industry and its associated communities. Such tools allow the consideration of these elements, within an evidence base, into policy arrangements, and consequently provide an invaluable contribution to the ability to address resilience and sustainability of fishing industries and associated communities.