Stock assessment of whaler and hammerhead sharks (Carcharhinidae and Sphyrnidae) in Queensland

This stock assessment provides detailed results for the most common sharks encountered by Queensland commercial fishers. These sharks come from the whaler (Carcharhinidae) and hammerhead (Sphyrnidae) families and comprise sharpnose sharks (Rhizoprionodon taylori and R. oligolinx), the milk shark (R. acutus), the creek whaler (Carcharhinus fitzroyensis), the hardnose shark (C. macloti), the spot-tail shark (C. sorrah), the Australian blacktip shark (C. tilstoni), the common blacktip shark (C. limbatus), the spinner shark (C. brevipinna), bull and pigeye sharks (C. leucas and C. amboinensis), the winghead shark (Eusphyra blochii), the scalloped hammerhead (Sphyrna lewini) and the great hammerhead (S. mokarran). Reef sharks were excluded because fishery observer data indicated that they were largely spatially segregated from sharks caught in the inshore net fisheries. The three common species of reef sharks in Queensland, which are all whaler sharks, are the grey reef shark Carcharhinus amblyrhynchos, the blacktip reef shark C. melanopterus and the whitetip reef shark Triaenodon obesus.

Stock assessment of the Queensland-New South Wales tailor fishery (Pomatomus saltatrix)

Data on catch sizes, catch rates, length-frequency and age composition from the Australian east coast tailor fishery are analysed by three different population dynamic models: a surplus production model, an age-structured model, and a model in which the population is structured by both age and length. The population is found to be very heavily exploited, with its ability to reproduce dependent on the fishery’s incomplete selectivity of one-year-old fish. Estimates of recent harvest rates (proportion of fish available to the fishery that are actually caught in a single year) are over 80%. It is estimated that only 30–50% of one-year-old fish are available to the fishery. Results from the age-length-structured model indicate that both exploitable biomass (total mass of fish selected by the fishery) and egg production have fallen to about half the levels that prevailed in the 1970s, and about 40% of virgin levels. Two-year-old fish appear to have become smaller over the history of the fishery. This is assumed to be due to increased fishing pressure combined with non-selectivity of small one-year-old fish, whereby the one-year-old fish that survive fishing are small and grow into small two-year-old fish the following year. An alternative hypothesis is that the stock has undergone a genetic change towards smaller fish; the true explanation is unknown. The instantaneous natural mortality rate of tailor is hypothesised to be higher than previously thought, with values between 0.8 and 1.3 yr–1 consistent with the models. These values apply only to tailor up to about three years of age, and it is possible that a lower value applies to fish older than three. The analysis finds no evidence that fishing pressure has yet affected recruitment. If a recruitment downturn were to occur, however, under current management and fishing pressure there is a strong chance that the fishery would need a complete closure for several years to recover, and even then recovery would be uncertain. Therefore it is highly desirable to better protect the spawning stock. The major recommendations are • An increase in the minimum size limit from 30cm to 40cm in order to allow most one-year-old fish to spawn, and • An experiment on discard mortality to gauge the proportion of fish between 30cm and 40cm that are likely to survive being caught and released by recreational line fishers (the dominant component of the fishery, currently harvesting roughly 1000t p.a. versus about 200t p.a. from the commercial fishery).

Stock assessment report on Queensland east coast red throat emperor (Lethrinus miniatus) fishery

The Red Throat Emperor fishery was assessed using an age-structured model that incorporated all available information on catch, catch per unit effort (CPUE) and age structure and a surplus production model fitted to the catch and CPUE data. The Great Barrier Reef (GBR) was divided into five regions: Townsville, Mackay, Storm Cay, Swain reefs, and Capricorn Bunker. Age structure varied greatly between regions, with fish aged 5-8 years predominating in the Townsville region, 4-7 years in the Mackay, Storm Cay and Swains regions, and 2-3 years in the Capricorn-Bunker region. These differences were explained by different age-dependent vulnerabilities to fishing between the regions. The age-structured model estimated that exploitable biomass fell to about 60% of virgin biomass in the late 1990s, due mainly to years of poor recruitment, but recovered to around 70% by 2004. Further recovery can be expected due to the fishery not meeting its total allowable commercial catch (TACC) of 700 t in recent years. The current TACC of 700 t, combined with a recreational-charter catch of around 450 t, contains little margin for error, especially in view of high year-to-year variability of recruitment of red throat emperor and stresses on the GBR from land clearing, coastal development and climate change. The state of the population needs to be monitored closely. Further data on age structures after 2000 will provide more certainty to this assessment.

Stock assessment of the Queensland east coast common coral trout (Plectropomus leopardus) fishery

Common coral trout Plectropomus leopardus is an iconic fish of the Great Barrier Reef (GBR) and is the most important fish for the commercial fishery there. Most of the catch is exported live to Asia. This stock assessment was undertaken in response to falls in catch sizes and catch rates in recent years, in order to gauge the status of the stock. It is the first stock assessment ever conducted of coral trout on the GBR, and brings together a multitude of different data sources for the first time. The GBR is very large and was divided into a regional structure based on the Bioregions defined by expert committees appointed by the Great Barrier Reef Marine Park Authority (GBRMPA) as part of the 2004 rezoning of the GBR. The regional structure consists of six Regions, from the Far Northern Region in the north to the Swains and Capricorn–Bunker Regions in the south. Regions also closely follow the boundaries between Bioregions. Two of the northern Regions are split into Subregions on the basis of potential changes in fishing intensity between the Subregions; there are nine Subregions altogether, which include four Regions that are not split. Bioregions are split into Subbioregions along the Subregion boundaries. Finally, each Subbioregion is split into a “blue” population which is open to fishing and a “green” population which is closed to fishing. The fishery is unusual in that catch rates as an indicator of abundance of coral trout are heavily influenced by tropical cyclones. After a major cyclone, catch rates fall for two to three years, and rebound after that. This effect is well correlated with the times of occurrence of cyclones, and usually occurs in the same month that the cyclone strikes. However, statistical analyses correlating catch rates with cyclone wind energy did not provide significantly different catch rate trends. Alternative indicators of cyclone strength may explain more of the catch rate decline, and future work should investigate this. Another feature of catch rates is the phenomenon of social learning in coral trout populations, whereby when a population of coral trout is fished, individuals quickly learn not to take bait. Then the catch rate falls sharply even when the population size is still high. The social learning may take place by fish directly observing their fellows being hooked, or perhaps heeding a chemo-sensory cue emitted by fish that are hooked. As part of the assessment, analysis of data from replenishment closures of Boult Reef in the Capricorn–Bunker Region (closed 1983–86) and Bramble Reef in the Townsville Subregion (closed 1992–95) estimated a strong social learning effect. A major data source for the stock assessment was the large collection of underwater visual survey (UVS) data collected by divers who counted the coral trout that they sighted. This allowed estimation of the density of coral trout in the different Bioregions (expressed as a number of fish per hectare). Combined with mapping data of all the 3000 or so reefs making up the GBR, the UVS results provided direct estimates of the population size in each Subbioregion. A regional population dynamic model was developed to account for the intricacies of coral trout population dynamics and catch rates. Because the statistical analysis of catch rates did not attribute much of the decline to tropical cyclones, (and thereby implied “real” declines in biomass), and because in contrast the UVS data indicate relatively stable population sizes, model outputs were unduly influenced by the unlikely hypothesis that falling catch rates are real. The alternative hypothesis that UVS data are closer to the mark and declining catch rates are an artefact of spurious (e.g., cyclone impact) effects is much more probable. Judging by the population size estimates provided by the UVS data, there is no biological problem with the status of coral trout stocks. The estimate of the total number of Plectropomus leopardus on blue zones on the GBR in the mid-1980s (the time of the major UVS series) was 5.34 million legal-sized fish, or about 8400 t exploitable biomass, with an 2 additional 3350 t in green zones (using the current zoning which was introduced on 1 July 2004). For the offshore regions favoured by commercial fishers, the figure was about 4.90 million legal-sized fish in blue zones, or about 7700 t exploitable biomass. There is, however, an economic problem, as indicated by relatively low catch rates and anecdotal information provided by commercial fishers. The costs of fishing the GBR by hook and line (the only method compatible with the GBR’s high conservation status) are high, and commercial fishers are unable to operate profitably when catch rates are depressed (e.g., from a tropical cyclone). The economic problem is compounded by the effect of social learning in coral trout, whereby catch rates fall rapidly if fishers keep returning to the same fishing locations. In response, commercial fishers tend to spread out over the GBR, including the Far Northern and Swains Regions which are far from port and incur higher travel costs. The economic problem provides some logic to a reduction in the TACC. Such a reduction during good times, such as when the fishery is rebounding after a major tropical cyclone, could provide a net benefit to the fishery, as it would provide a margin of stock safety and make the fishery more economically robust by providing higher catch rates during subsequent periods of depressed catches. During hard times when catch rates are low (e.g., shortly after a major tropical cyclone), a change to the TACC would have little effect as even a reduced TACC would not come close to being filled. Quota adjustments based on catch rates should take account of long-term trends in order to mitigate variability and cyclone effects in data.

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.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Production of microalgal concentrates by flocculation and their assessment as aquaculture feeds

A novel technique was developed for the flocculation of marine microalgae commonly used in aquaculture. The process entailed an adjustment of pH of culture to between 10 and 10.6 using NaOH, followed by addition of a non-ionic polymer Magnafloc LT-25 to a final concentration of 0.5 mg L-1. The ensuing flocculate was harvested, and neutralised giving a final concentration factor of between 200- and 800-fold. This process was successfully applied to harvest cells of Chaetoceros calcitrans, C. muelleri, Thalassiosira pseudonana, Attheya septentrionalis, Nitzschia closterium, Skeletonema sp., Tetraselmis suecica and Rhodomonas salina, with efficiencies >=80%. The process was rapid, simple and inexpensive, and relatively cost neutral with increasing volume (cf. concentration by centrifugation). Harvested material was readily disaggregated to single cell suspensions by dilution in seawater and mild agitation. Microscopic examination of the cells showed them to be indistinguishable from corresponding non-flocculated cells. Chlorophyll analysis of concentrates prepared from cultures of Concentrates of T. pseudonana prepared using pH-induced flocculation gave better growth of juvenile Pacific oysters (Crassostrea gigas) than concentrates prepared by ferric flocculation, or centrifuged concentrates using a cream separator or laboratory centrifuge. In follow up experiments, concentrates prepared from 1000 L Chaetoceros muelleri cultures were effective as supplementary diets to improve the growth of juvenile C. gigas and the scallop Pecten fumatus reared under commercial conditions, though not as effective as the corresponding live algae. The experiments demonstrated a proof-of-concept for a commercial application of concentrates prepared by flocculation, especially for use at a remote nursery without on-site mass-algal culture facilities.

Water use studies and implications for management of subtropical C4 turfgrasses in dryland and irrigated urban open space

A 2000-03 study to improve irrigation efficiency of grassed urban public areas in northern Australia found it would be difficult to grow most species in dry areas without supplementary watering. Sporoboulus virginicus and sand couch, Zoysia macrantha, were relatively drought-tolerant. Managers of sporting fields, parks and gardens could more than halve their current water use by irrigating over a long cycle, irrigating according to seasonal conditions and using grasses with low water use and sound soil management practices that encourage deep rooting. The use of effluent water provides irrigation and fertiliser cost savings and reduced nitrogen and phosphorus discharge to local waterways. Projected savings are $8000/ha/year in water costs for a typical sporting field.

MOE and MOR assessment technologies for improving graded recovery of exotic pines in Australia.

This project was designed to provide the structural softwood processing industry with the basis for improved green and dry grading to allow maximise MGP grade yields, consistent product performance and reduced processing costs. To achieve this, advanced statistical techniques were used in conjunction with state-of-the-art property measurement systems. Specifically, the project aimed to make two significant steps forward for the Australian structural softwood industry: • assessment of technologies, both existing and novel, that may lead to selection of a consistent, reliable and accurate device for the log yard and green mill. The purpose is to more accurately identify and reject material that will not make a minimum grade of MGP10 downstream; • improved correlation of grading MOE and MOR parameters in the dry mill using new analytical methods and a combination of devices. The three populations tested were stiffness-limited radiata pine, strength-limited radiata pine and Caribbean pine. Resonance tests were conducted on logs prior to sawmilling, and on boards. Raw data from existing in-line systems were captured for the green and dry boards. The dataset was analysed using classical and advanced statistical tools to provide correlations between data sets and to develop efficient strength and stiffness prediction equations. Stiffness and strength prediction algorithms were developed from raw and combined parameters. Parameters were analysed for comparison of prediction capabilities using in-line parameters, off-line parameters and a combination of in-line and off-line parameters. The results show that acoustic resonance techniques have potential for log assessment, to sort for low stiffness and/or low strength, depending on the resource. From the log measurements, a strong correlation was found between the average static MOE of the dried boards within a log and the predicted value. These results have application in segregating logs into structural and non-structural uses. Some commercial technologies are already available for this application such as Hitman LG640. For green boards it was found that in-line and laboratory acoustic devices can provide a good prediction of dry static MOE and moderate prediction for MOR.There is high potential for segregating boards at this stage of processing. Grading after the log breakdown can improve significantly the effectiveness of the mill. Subsequently, reductions in non-structural volumes can be achieved. Depending on the resource it can be expected that a 5 to 8 % reduction in non structural boards won’t be dried with an associated saving of $70 to 85/m3. For dry boards, vibration and a standard Metriguard CLT/HCLT provided a similar level of prediction on stiffness limited resource. However, Metriguard provides a better strength prediction in strength limited resources (due to this equipment’s ability to measure local characteristics). The combination of grading equipment specifically for stiffness related predictors (Metriguard or vibration) with defect detection systems (optical or X-ray scanner) provides a higher level of prediction, especially for MOR. Several commercial technologies are already available for acoustic grading on board such those from Microtec, Luxscan, Falcon engineering or Dynalyse AB for example. Differing combinations of equipment, and their strategic location within the processing chain, can dramatically improve the efficiency of the mill, the level of which will vary depending of the resource. For example, an initial acoustic sorting on green boards combined with an optical scanner associated with an acoustic system for grading dry board can result in a large reduction of the proportion of low value low non-structural produced. The application of classical MLR on several predictors proved to be effective, in particular for MOR predictions. However, the usage of a modern statistics approach(chemometrics tools) such as PLS proved to be more efficient for improving the level of prediction. Compared to existing technologies, the results of the project indicate a good improvement potential for grading in the green mill, ahead of kiln drying and subsequent cost-adding processes. The next stage is the development and refinement of systems for this purpose.

Northern Grazing Systems Bioeconomic analysis and regional assessment

This project is part of the Northern Grazing Systems (NGS) projects which aim to increase adoption of innovative best-practice grazing management by beef producers throughout Queensland, Northern Territory and the Kimberley and Pilbara regions of Western Australia.

Strength and stiffness assessment technologies for improving grading effectiveness of radiata pine wood.

This work was designed to provide the Australian structural radiata pine processing industry with some indications for improving stress grading methods and/or technologies to give an increase in structural grade yields, and significantly reduce processing costs without compromising product quality. To achieve this, advanced statistical techniques were used in conjunction with state-of-the-art property measurement systems applied to the same sample of sawn timber. Acoustic vibration analyses were conducted on green and dry boards. Raw data from existing in-line systems was captured on the same boards. The Metriguard HCLT stress rating system was used as the "reference" machine grading because of its current common use in the industry. A WoodEye optical scanning system and an X-ray LHG scanner were also able to provide relevant information on knots. The data set was analyzed using classical and advanced statistical tools to provide correlations between data sets, and to develop efficient strength and stiffness prediction equations. Reductions in non-structural dry volumes can be achieved..

Potential Distribution and Risk Assessment of an Invasive Plant Species: A Case Study of Hymenachne amplexicaulis in Australia

Given the limited resources available for weed management, a strategic approach is required to give the best bang for your buck. The current study incorporates: (1) a model ensemble approach to identify areas of uncertainty and commonality regarding a species invasive potential, (2) current distribution of the invaded species, and (3) connectivity of systems to identify target regions and focus efforts for more effective management. Uncertainty in the prediction of suitable habitat for H. amplexicaulis (study species) in Australia was addressed in an ensemble-forecasting approach to compare distributional scenarios from four models (CLIMATCH; CLIMEX; boosted regression trees [BRT]; maximum entropy [Maxent]). Models were built using subsets of occurrence and environmental data. Catchment risk was determined through incorporating habitat suitability, the current abundance and distribution of H. amplexicaulis, and catchment connectivity. Our results indicate geographic differences between predictions of different approaches. Despite these differences a number of catchments in northern, central, and southern Australia were identified as high risk of invasion or further spread by all models suggesting they should be given priority for the management of H. amplexicaulis. The study also highlighted the utility of ensemble approaches in indentifying areas of uncertainty and commonality regarding the species invasive potential.

A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.