Recovery of the red-finned blue-eye: An endangered fish from springs of the Great Artesian Basin

The red-finned blue-eye (Scaturiginichthys vermeilipinnis) is endemic to a single complex of springs emanating from the Great Artesian Basin, Australia. The species has been recorded as naturally occurring in eight separate very shallow (generally <20 mm) springs, with a combined wetland area of ~0.3 ha. Since its discovery in 1990, five red-finned blue-eye (RFBE) populations have been lost and subsequent colonisation has occurred in two spring wetlands. Current population size is estimated at <3000 individuals. Artesian bores have reduced aquifer pressure, standing water levels and spring-flows in the district. There is evidence of spatial separation within the spring pools where RFBE and the introduced fish gambusia (Gambusia holbrooki) co-occur, although both species are forced together when seasonal extremes affect spring size and water temperature. Gambusia was present in four of the five springs where RFBE populations have been lost. Four out of the five remaining subpopulations of RFBE are Gambusia free. Circumstantial evidence suggests that gambusia is a major threat to red-finned blue-eyes. The impact of Gambusia is probably exacerbated by domestic stock (cattle and sheep), feral goats and pigs that utilise the springs and can negatively affect water quality and flow patterns. Three attempts to translocate RFBE to apparently suitable springs elsewhere within the complex have failed. Opportunities to mitigate threats are discussed, along with directions for future research to improve management of this extremely threatened fish and habitat.

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).

Recovery of fish and crustacean communities during remediation of tidal wetlands affected by leachate from acid sulfate soils in north-eastern Australia.

In the 1970s, acid sulfate soils (ASS) distributed within about 720 ha of predominantly mangrove and salt pan wetlands at East Trinity in north Queensland were developed after the area was isolated from tidal flooding by a surrounding seawall and the installation of tidal gates on major drainage creeks. Following drainage and oxidation of these estuarine acidic sediments, resultant acid leachate caused considerable, ongoing environmental problems including regular fish kills. A rehabilitation program covering much of these former tidal wetlands commenced in 2000 using a lime-assisted tidal exchange management regime. Changes in the established populations of estuarine fish and crustaceans were monitored in the two creeks (Firewood and Hills Creeks) where tidal flows were reinstated. In Firewood Creek between 2001 and 2005, there was a progressive increase in fish species richness, diversity and abundance. The penaeid prawn Fenneropenaeus merguiensis was a major component of the cast net catches in the lower sections of both Firewood and Hills Creeks but its relative abundance decreased upstream of the tidal gates on the seawall. Well established stocks of predominantly juvenile, male Scylla serrata resident upstream of the tidal gates indicated suitable habitats with acceptable water and sediment quality and adequate availability of food. The regular fish kills that occurred prior to the management regime abated and, overall, the implementation of the rehabilitation program is yielding positive benefits for the local fisheries.

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.

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.

Fishery biology and management of Protonibea diacanthus (Sciaenidae) aggregations in far Northern Cape York Peninsula waters

The sciaenid Protonibea diacanthus is a large, long-lived predatory fish of inshore northern Australian waters, which forms annual aggregations that are fished extensively by traditional (subsistence) and recreational fishers. There are now widespread concerns that the resource is being overexploited. Indigenous fishers of the Cape York Northern Peninsula Area (NPA) relate that large adult fish (up to 1500 mm total length (TL)) made up the bulk of the catch from the sciaenid aggregations until about 1994. In contrast, sexually mature P. diacanthus comprised only a small component (12 fish out of 270=4.4%) examined in a 1999–2000 sampling programme that was biased towards the largest individuals available. At 790 mm TL, the minimum size at first maturity for female P. diacanthus in this study is much smaller than the 920 mm TL reported previously in Queensland waters. Developing ovaries were observed in specimens sampled from sciaenid aggregations which formed in NPA waters between May and September 2000. However, no fish with ripe or spent gonads were found in the study, so the current timing and location of the spawning season for P. diacanthus in the region remain unknown. Food items observed in the analysis of the diet of P. diacanthus from the NPA included a variety of teleosts and invertebrates. The range of animal taxa represented in the prey items support the description of an ‘opportunistic predator’ attributed to the species. In our sampling, the stomach contents of fish caught during the time of the aggregation events did not differ from those observed at other times of the year. A total of 114 P. diacanthus were tagged and released at aggregation sites during the study period, and 3 fish (2.6%) were subsequently recaptured. The low rate of tag returns from the wild stock tagging programme, both in this study (2.6%) and from recreational fisher tag/release programmes for the sciaenid elsewhere in Queensland (6.5%), were not explained by tag loss nor mortality, given the high retention rate of tags and the zero mortality seen in tank trials. In response to the biological findings from this study, indigenous community councils of the NPA imposed a 2-year fishing moratorium for P. diacanthus. Surveys at aggregation sites in 2002 and 2003 established that much larger fish (mean size 103.5 cm TL) were again present on the grounds, albeit in very low numbers. These recent preliminary results highlight the critical need for continued monitoring and management of the P. diacanthus fishery in the NPA, if prospects for resource recovery are to be realised. The NPA initiative has provided a rare opportunity to negotiate a co-management strategy, based on scientific data and traditional knowledge, for the recovery of a cultural and economically significant fished resource.

Time-dependent instantaneous mortality rates from multiple tagging experiments with exact times of release and recovery

Instantaneous natural mortality rates and a nonparametric hunting mortality function are estimated from a multiple-year tagging experiment with arbitrary, time-dependent fishing or hunting mortality. Our theory allows animals to be tagged over a range of times in each year, and to take time to mix into the population. Animals are recovered by hunting or fishing, and death events from natural causes occur but are not observed. We combine a long-standing approach based on yearly totals, described by Brownie et al. (1985, Statistical Inference from Band Recovery Data: A Handbook, Second edition, United States Fish and Wildlife Service, Washington, Resource Publication, 156), with an exact-time-of-recovery approach originated by Hearn, Sandland and Hampton (1987, Journal du Conseil International pour l'Exploration de la Mer, 43, 107-117), who modeled times at liberty without regard to time of tagging. Our model allows for exact times of release and recovery, incomplete reporting of recoveries, and potential tag shedding. We apply our methods to data on the heavily exploited southern bluefin tuna (Thunnus maccoyii).

The stock structure of grey mackerel Scomberomorus semifasciatus in Australia as inferred from its parasite fauna

The scombrid Scomberomorus semifasciatus is an important component of inshore fisheries in tropical Australia. Data on the parasite fauna of 593 fish from areas off northern and eastern Australia were examined for evidence of discrete fish populations. The parasites used were juveniles of Pterobothrium pearsoni, Callitetrarhynchus gracilis, Anisakis simplex (sensu latu) and Terranova sp. Tukey Kramer pairwise comparisons gave significant differences in the abundances of two or more parasites between fish from the east coast, the eastern Gulf of Carpentaria and the remainder of northern Australia. Multivariate analysis gave further evidence of differences and the results suggest that at least 4 populations or stocks of grey mackerel occur along the northern and eastern coastline of Australia.

Stock structure of Grey Mackerel, Scomberomorus semifasciatus (Pisces: Scombridae) across northern Australia, based on otolith stable isotope chemistry

The stable isotopes of delta O-18 and delta C-13 in sagittal otolith carbonates were used to determine the stock structure of Grey Mackerel, Scomberomorus semifasciatus. Otoliths were collected from Grey Mackerel at ten locations representing much of their distributional and fisheries range across northern Australia from 2005 to 2007. Across this broad range (similar to 6500 km), fish from four broad locations-Western Australia (S1), Northern Territory and Gulf of Carpentaria (S2, S3, S4, S5, S6, S7), Queensland east coast mid and north sites (S8, S9) and Queensland east coast south site (S10)-had stable isotope values that were significantly different indicating stock separation. Otolith stable isotopes differed more between locations than among years within a location, indicating temporal stability across years. The spatial separation of these populations indicates a complex stock structure across northern Australia. Stocks of S. semifasciatus appear to be associated with large coastal embayments. These results indicate that optimal fisheries management may require a review of the current spatial arrangements, particularly in relation to the evidence of shared stocks in the Gulf of Carpentaria. Furthermore, as the population of S. semifasciatus in Western Australia exhibited high spatial separation from those at all the other locations examined, further research activities should focus on investigating additional locations within Western Australia for an enhanced determination of stock delineation. From the issue entitled "Proceedings of the 4th International Otolith Symposium, 24-28 August 2009, Monterey, California"

Stock structure of the blue threadfin (Eleutheronema tetradactylum) across northern Australia derived from life-history characteristics

Life history characteristics were used to determine the stock structure of the polynemid Eleutheronema tetradactylum across northern Australia. Growth, estimated from back-calculated length-at-age from sagittal otoliths, and length at sex change were estimated from samples collected from 12 different locations across western, northern and eastern Australia between 2007 and 2009. Comparison of back-calculated length-at-age, growth and length at sex change between locations revealed significant variation in the life-history characteristics of E. tetradactylum across northern Australia, with significant differences detected in 43 of 45 location comparisons. Differences in otolith size relative to fish length also existed amongst locations. No differences in other morphometric relationships were detected. The results of this study provide evidence for a high degree of spatial population subdivision for E. tetradactylum across northern Australia, the finding of which has implications for E. tetradactylum fisheries throughout its range, and provides a biological basis for spatial management of the species in Australia. (C) 2012 Elsevier B.V. All rights reserved.

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.

Hazard Function Models to Estimate Mortality Rates Affecting Fish Populations with Application to the Sea Mullet (Mugil cephalus) Fishery on the Queensland Coast (Australia)

Fisheries management agencies around the world collect age data for the purpose of assessing the status of natural resources in their jurisdiction. Estimates of mortality rates represent a key information to assess the sustainability of fish stocks exploitation. Contrary to medical research or manufacturing where survival analysis is routinely applied to estimate failure rates, survival analysis has seldom been applied in fisheries stock assessment despite similar purposes between these fields of applied statistics. In this paper, we developed hazard functions to model the dynamic of an exploited fish population. These functions were used to estimate all parameters necessary for stock assessment (including natural and fishing mortality rates as well as gear selectivity) by maximum likelihood using age data from a sample of catch. This novel application of survival analysis to fisheries stock assessment was tested by Monte Carlo simulations to assert that it provided unbiased estimations of relevant quantities. The method was applied to the data from the Queensland (Australia) sea mullet (Mugil cephalus) commercial fishery collected between 2007 and 2014. It provided, for the first time, an estimate of natural mortality affecting this stock: 0.22±0.08 year −1 .

Multijurisdictional fisheries performance reporting: How Australia’s nationally standardised approach to assessing stock status compares

Australian marine wild-capture fisheries are managed by eight separate jurisdictions. Traditionally, fishery status reports have been produced separately by most of these jurisdictions, assessing the fish stocks they manage, and reporting on the effectiveness of their fisheries management. However, the format, the type of stock status assessments, the thresholds and terminology used to describe stock status and the classification frameworks have varied over time and among jurisdictions. These differences complicate efforts to understand stock status on a national scale. They also create potential misunderstanding among the wider community about how to interpret information on the status of fish stocks, and the fisheries management and science processes more generally. This is especially true when considering stocks that are shared across two or more jurisdictional boundaries. A standardised approach was developed in 2011 leading to production of the first national Status of key Australian fish stocks reports in 2012, followed by a second edition in 2014 (www.fish.gov.au). Production of these reports was the first step towards a broader national approach to reporting on the performance of Australian fisheries for target species and for wider ecosystem and socioeconomic consequences. This paper outlines the challenges associated with moving towards national performance reporting for target fish stocks and Australia’s successes so far. It also outlines the challenges ahead, in particular those relating to reporting more broadly on the status of entire fisheries. Comparisons are drawn between Australia and New Zealand and more broadly between Australia and other countries.

Multijurisdictional fisheries performance reporting: How Australia’s nationally standardised approach to assessing stock status compares

Australian marine wild-capture fisheries are managed by eight separate jurisdictions. Traditionally, fishery status reports have been produced separately by most of these jurisdictions, assessing the fish stocks they manage, and reporting on the effectiveness of their fisheries management. However, the format, the type of stock status assessments, the thresholds and terminology used to describe stock status and the classification frameworks have varied over time and among jurisdictions. These differences complicate efforts to understand stock status on a national scale. They also create potential misunderstanding among the wider community about how to interpret information on the status of fish stocks, and the fisheries management and science processes more generally. This is especially true when considering stocks that are shared across two or more jurisdictional boundaries. A standardised approach was developed in 2011 leading to production of the first national Status of key Australian fish stocks reports in 2012, followed by a second edition in 2014 (www.fish.gov.au). Production of these reports was the first step towards a broader national approach to reporting on the performance of Australian fisheries for target species and for wider ecosystem and socioeconomic consequences. This paper outlines the challenges associated with moving towards national performance reporting for target fish stocks and Australia’s successes so far. It also outlines the challenges ahead, in particular those relating to reporting more broadly on the status of entire fisheries. Comparisons are drawn between Australia and New Zealand and more broadly between Australia and other countries.

Effects of Low Dose Irradiation on the K-Value and Hypoxanthine Concentration of Fish Fillets

Fillets of five fish species were irradiated at 0, 1 and 3kGy to investigate whether the K-value test of freshness can be applied to irradiated fish. Following irradiation, the fillets were stored on ice and sampled regularly for K-value analysis. Hypoxanthine (Hx) and total nucleotide content were also determined on fillets of two species. K-values of irradiated fillets were generally lower than those of unirradiated controls. Hypoxanthine levels paralleled the K-value changes. These results indicated that quality standards based on K-values or Hx levels that have been set for unirradiated species cannot be directly applied to fish that has been irradiated. Total nucleotide content did not appear to be affected by irradiation.