Determination of management units for grey mackerel fisheries in northern Australia.

The requirement for Queensland, Northern Territory and Western Australian jurisdictions to ensure sustainable harvest of fish resources and their optimal use relies on robust information on the resource status. For grey mackerel (Scomberomorus semifasciatus) fisheries, each of these jurisdictions has their own management regime in their corresponding waters. The lack of information on stock structure of grey mackerel, however, means that the appropriate spatial scale of management is not known. As well, fishers require assurance of future sustainability to encourage investment and long-term involvement in a fishery that supplies lucrative overseas markets. These management and fisher-unfriendly circumstances must be viewed in the context of recent 3-fold increases in catches of grey mackerel along the Queensland east coast, combined with significant and increasing catches in other parts of the species' northern Australian range. Establishing the stock structure of grey mackerel would also immensely improve the relevance of resource assessments for fishery management of grey mackerel across northern Australia. This highlighted the urgent need for stock structure information for this species. The impetus for this project came from the strategic recommendations of the FRDC review by Ward and Rogers (2003), "Northern mackerel (Scombridae: Scomberomorus): current and future research needs" (Project No. 2002/096), which promoted the urgency for information on the stock structure of grey mackerel. In following these recommendations this project adopted a multi-technique and phased sampling approach as carried out by Buckworth et al (2007), who examined the stock structure of Spanish mackerel, Scomberomorus commerson, across northern Australia. The project objectives were to determine the stock structure of grey mackerel across their northern Australian range, and use this information to define management units and their appropriate spatial scales. We used multiple techniques concurrently to determine the stock structure of grey mackerel. These techniques were: genetic analyses (mitochondrial DNA and microsatellite DNA), otolith (ear bones) isotope ratios, parasite abundances, and growth parameters. The advantage of using this type of multi-technique approach was that each of the different methods is informative about the fish’s life history at different spatial and temporal scales. Genetics can inform about the evolutionary patterns as well as rates of mixing of fish from adjacent areas, while parasites and otolith microchemistry are directly influenced by the environment and so will inform about the patterns of movement during the fishes lifetime. Growth patterns are influenced by both genetic and environmental factors. Due to these differences the use of these techniques concurrently increases the likelihood of detecting different stocks where they exist. We adopted a phased sampling approach whereby sampling was carried out at broad spatial scales in the first year: east coast, eastern Gulf of Carpentaria (GoC), western GoC, and the NW Northern Territory (NW NT). By comparing the fish samples from each of these locations, and using each of the techniques, we tested the null hypothesis that grey mackerel were comprised of a single homogeneous population across northern Australia. Having rejected the null hypothesis we re-sampled the 1st year locations to test for temporal stability in stock structure, and to assess stock structure at finer spatial scales. This included increased spatial coverage on the east coast, the GoC, and WA. From genetic approaches we determined that there at least four genetic stocks of grey mackerel across northern Australia: WA, NW NT (Timor/Arafura), the GoC and the east Grey mackerel management units in northern Australia ix coast. All markers revealed concordant patterns showing WA and NW NT to be clearly divergent stocks. The mtDNA D-loop fragment appeared to have more power to resolve stock boundaries because it was able to show that the GoC and east coast QLD stocks were genetically differentiated. Patterns of stock structure on a finer scale, or where stock boundaries are located, were less clear. From otolith stable isotope analyses four major groups of S. semifasciatus were identified: WA, NT/GoC, northern east coast and central east coast. Differences in the isotopic composition of whole otoliths indicate that these groups must have spent their life history in different locations. The magnitude of the difference between the groups suggests a prolonged separation period at least equal to the fish’s life span. The parasite abundance analyses, although did not include samples from WA, suggest the existence of at least four stocks of grey mackerel in northern Australia: NW NT, the GoC, northern east coast and central east coast. Grey mackerel parasite fauna on the east coast suggests a separation somewhere between Townsville and Mackay. The NW NT region also appears to comprise a separate stock while within the GoC there exists a high degree of variability in parasite faunas among the regions sampled. This may be due to 1. natural variation within the GoC and there is one grey mackerel stock, or 2. the existence of multiple localised adult sub-stocks (metapopulations) within the GoC. Growth parameter comparisons were only possible from four major locations and identified the NW NT, the GoC, and the east coast as having different population growth characteristics. Through the use of multiple techniques, and by integrating the results from each, we were able to determine that there exist at least five stocks of grey mackerel across northern Australia, with some likelihood of additional stock structuring within the GoC. The major management units determined from this study therefore were Western Australia, NW Northern Territory (Timor/Arafura), the Gulf of Carpentaria, northern east Queensland coast and central east Queensland coast. The management implications of these results indicate the possible need for management of grey mackerel fisheries in Australia to be carried out on regional scales finer than are currently in place. In some regions the spatial scales of management might continue as is currently (e.g. WA), while in other regions, such as the GoC and the east coast, managers should at least monitor fisheries on a more local scale dictated by fishing effort and assess accordingly. Stock assessments should also consider the stock divisions identified, particularly on the east coast and for the GoC, and use life history parameters particular to each stock. We also emphasise that where we have not identified different stocks does not preclude the possibility of the occurrence of further stock division. Further, this study did not, nor did it set out to, assess the status of each of the stocks identified. This we identify as a high priority action for research and development of grey mackerel fisheries, as well as a management strategy evaluation that incorporates the conclusions of this work. Until such time that these priorities are addressed, management of grey mackerel fisheries should be cognisant of these uncertainties, particularly for the GoC and the Queensland east coast.

Domestication and the storage starch biosynthesis pathway: Signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Sex change strategy and the aromatase genes

5′ flanking regions of CYP19A1/A2 genes are reported for three sex changing fish.

Recovery and succession in a multi-species tropical seagrass meadow following experimental disturbance: the role of sexual and asexual reproduction

Recolonisation and succession in a multi-species tropical seagrass meadow was examined by creating gaps (50×50 cm) in the meadow and manipulating the supply of sexual and asexual propagules. Measurements of leaf shoot density and estimates of above-ground biomass were conducted monthly to measure recovery of gaps between September 1995 and November 1997. Measurements of the seeds stored in the sediment (seed bank) and horizontal rhizome growth of colonising species were also conducted to determine their role in the recovery process. Asexual colonisation through horizontal rhizome growth from the surrounding meadow was the main mechanism for colonisation of gaps created in the meadow. The seed bank played no role in recolonisation of cleared plots. Total shoot density and above-ground biomass (all species pooled) of cleared plots recovered asexually to the level of the undisturbed controls in 10 and 7 months, respectively. There was some sexual recruitment into cleared plots where asexual colonisation was prevented but seagrass abundance (shoot density and biomass) did not reach the level of unmanipulated controls. Seagrass species did not appear to form seed banks despite some species being capable of producing long-lived seeds. The species composition of cleared plots remained different to the undisturbed controls throughout the 26-month experiment. Syringodium isoetifolium was a rapid asexual coloniser of disturbed plots and remained at higher abundances than in the control treatments for the duration of the study. S. isoetifolium had the fastest horizontal rhizome growth of species asexually colonising cleared plots (6.9 mm day−1). Halophila ovalis was the most successful sexual coloniser but was displaced by asexually colonising species. H. ovalis was the only species observed to produce fruits during the study. Small disturbances in the meadow led to long-term (>2 years) changes in community composition. This study demonstrated that succession in tropical seagrass communities was not a deterministic process. Variations in recovery observed for different tropical seagrass communities highlighted the importance of understanding life history characteristics of species within individual communities to effectively predict their response to disturbance. A reproductive strategy involving clonal growth and production of long-lived, locally dispersed seeds is suggested which may provide an evolutionary advantage to plants growing in tropical environments subject to temporally unpredictable major disturbances such as cyclones

Exploring profit - Sustainability trade-offs in cropping systems using evolutionary algorithms

Models that implement the bio-physical components of agro-ecosystems are ideally suited for exploring sustainability issues in cropping systems. Sustainability may be represented as a number of objectives to be maximised or minimised. However, the full decision space of these objectives is usually very large and simplifications are necessary to safeguard computational feasibility. Different optimisation approaches have been proposed in the literature, usually based on mathematical programming techniques. Here, we present a search approach based on a multiobjective evaluation technique within an evolutionary algorithm (EA), linked to the APSIM cropping systems model. A simple case study addressing crop choice and sowing rules in North-East Australian cropping systems is used to illustrate the methodology. Sustainability of these systems is evaluated in terms of economic performance and resource use. Due to the limited size of this sample problem, the quality of the EA optimisation can be assessed by comparison to the full problem domain. Results demonstrate that the EA procedure, parameterised with generic parameters from the literature, converges to a useable solution set within a reasonable amount of time. Frontier ‘‘peels’’ or Pareto-optimal solutions as described by the multiobjective evaluation procedure provide useful information for discussion on trade-offs between conflicting objectives.

Host-delivered RNAi: An effective strategy to silence genes in plant parasitic nematodes

Root-knot nematodes (Meloidogyne spp.) are obligate, sedentary endoparasites that infect many plant species causing large economic losses worldwide. Available nematicides are being banned due to their toxicity or ozone-depleting properties and alternative control strategies are urgently required. We have produced transgenic tobacco (Nicotiana tabacum) plants expressing different dsRNA hairpin structures targeting a root-knot nematode (Meloidogyne javanica) putative transcription factor, MjTis11. We provide evidence that MjTis11 was consistently silenced in nematodes feeding on the roots of transgenic plants. The observed silencing was specific for MjTis11, with other sequence-unrelated genes being unaffected in the nematodes. Those transgenic plants able to induce silencing of MjTis11, also showed the presence of small interfering RNAs. Even though down-regulation of MjTis11 did not result in a lethal phenotype, this study demonstrates the feasibility of silencing root-knot nematode genes by expressing dsRNA in the host plant. Host-delivered RNA interference-triggered (HD-RNAi) silencing of parasite genes provides a novel disease resistance strategy with wide biotechnological applications. The potential of HD-RNAi is not restricted to parasitic nematodes but could be adapted to control other plant-feeding pests.

Development of a stable isotope index to assess decadal-scale vegetation change and application to woodlands of the Burdekin catchment, Australia

Forty-four study sites were established in remnant woodland in the Burdekin River catchment in tropical north-east Queensland, Australia, to assess recent (decadal) vegetation change. The aim of this study was further to evaluate whether wide-scale vegetation 'thickening' (proliferation of woody plants in formerly more open woodlands) had occurred during the last century, coinciding with significant changes in land management. Soil samples from several depth intervals were size separated into different soil organic carbon (SOC) fractions, which differed from one another by chemical composition and turnover times. Tropical (C4) grasses dominate in the Burdekin catchment, and thus δ13C analyses of SOC fractions with different turnover times can be used to assess whether the relative proportion of trees (C3) and grasses (C4) had changed over time. However, a method was required to permit standardized assessment of the δ13C data for the individual sites within the 13 Mha catchment, which varied in soil and vegetation characteristics. Thus, an index was developed using data from three detailed study sites and global literature to standardize individual isotopic data from different soil depths and SOC fractions to reflect only the changed proportion of trees (C3) to grasses (C3) over decadal timescales. When applied to the 44 individual sites distributed throughout the Burdekin catchment, 64% of the sites were shown to have experienced decadal vegetation thickening, while 29% had remained stable and the remaining 7% had thinned. Thus, the development of this index enabled regional scale assessment and comparison of decadal vegetation patterns without having to rely on prior knowledge of vegetation changes or aerial photography.

Improved Approach for Analyzing Bromophenols in Seafood Using Stable Isotope Dilution Analysis in Combination with SPME

An analytical method for the measurement of five naturally occurring bromophenols of sensory relevance in seafood (barramundi and prawns) is presented. The method combines simultaneous distillation−extraction followed by alkaline back extraction of a hexane extract and subsequent acetylation of the bromophenols. Analysis of the bromophenol acetates was accomplished by headspace solid phase microextraction and gas chromatography−mass spectrometry using selected ion monitoring. The addition of 13C6 bromophenol stable isotope internal standards for each of the five congeners studied permitted the accurate quantitation of 2-bromophenol, 4-bromophenol, 2,6-dibromophenol, 2,4-dibromophenol, and 2,4,6-tribromophenol down to a limit of quantification of 0.05 ng/g of fish flesh. The method indicated acceptable precision and repeatability and excellent linearity over the typical concentration range of these compounds in seafood (0.5−50 ng/g). The analytical method was applied to determine the concentration of bromophenols in a range of farmed and wild barramundi and prawns and was also used to monitor bromophenol uptake in a pilot feeding trial.

Evolutionary relationships between bat coronaviruses and their hosts

Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002-2003. We examined the evolutionary relationships between bat CoVs and their hosts by using sequence data of the virus RNA-dependent RNA polymerase gene and the bat cytochrome b gene. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. These shifts may be due to either virus biologic traits or host behavioral traits. This finding has implications for the emergence of SARS and for the potential future emergence of SARS-CoVs or related viruses.

Cannibalism contributes significantly to the diet of cultured sand crabs, Portunus pelagicus (L.): A dual stable isotope study

The significance of cannibalism in the diet of juvenile pond-cultured blue swimmer crabs (Portunus pelagicus (L.)) was investigated using dual stable isotope analysis of carbon and nitrogen. In a laboratory feeding experiment, δ15N demonstrated a constant trophic shift (Δδ15N ≈+ 1.6‰), and therefore seemed to be a reliable indicator for assessing trophic position for P. pelagicus. This agrees with previously reported trends. Difference in growth rate did not seem to influence δ15N values. In contrast, δ13C did not display consistent shifts between trophic levels (range of Δδ13C: + 1 to + 1.7‰). The results from the pond experiment showed that larger individuals had a more enriched δ15N than smaller individuals, which, when compared to the results from the laboratory experiment, indicates that larger individuals were at a higher trophic level. This is most likely due to cannibalism prevailing in the pond rather than a direct result of faster growth rate. Cannibalistic behaviour might further increase growth, resulting in the observed positive correlation between size and δ15N.

Managing for rainfall variability: effect of grazing strategy on cattle production in a dry tropical savanna

Rainfall variability is a challenge to sustainable and pro. table cattle production in northern Australia. Strategies recommended to manage for rainfall variability, like light or variable stocking, are not widely adopted. This is due partly to the perception that sustainability and profitability are incompatible. A large, long-term grazing trial was initiated in 1997 in north Queensland, Australia, to test the effect of different grazing strategies on cattle production. These strategies are: (i) constant light stocking (LSR) at long-term carrying capacity (LTCC); (ii) constant heavy stocking (HSR) at twice LTCC; (iii) rotational wet-season spelling (R/Spell) at 1.5 LTCC; (iv) variable stocking (VAR), with stocking rates adjusted in May based on available pasture; and (v) a Southern Oscillation Index (SOI) variable strategy, with stocking rates adjusted in November, based on available pasture and SOI seasonal forecasts. Animal performance varied markedly over the 10 years for which data is presented, due to pronounced differences in rainfall and pasture availability. Nonetheless, lighter stocking at or about LTCC consistently gave the best individual liveweight gain (LWG), condition score and skeletal growth; mean LWG per annum was thus highest in the LSR (113 kg), intermediate in the R/Spell (104 kg) and lowest in the HSR(86 kg). MeanLWGwas 106 kg in the VAR and 103 kg in the SOI but, in all years, the relative performance of these strategies was dependent upon the stocking rate applied. After 2 years on the trial, steers from lightly stocked strategies were 60-100 kg heavier and received appreciable carcass price premiums at the meatworks compared to those under heavy stocking. In contrast, LWG per unit area was greatest at stocking rates of about twice LTCC; mean LWG/ha was thus greatest in the HSR (21 kg/ha), but this strategy required drought feeding in four of the 10 years and was unsustainable. Although LWG/ha was lower in the LSR (mean 14 kg/ha), or in strategies that reduced stocking rates in dry years like the VAR(mean 18 kg/ha) and SOI (mean 17 kg/ha), these strategies did not require drought feeding and appeared sustainable. The R/Spell strategy (mean 16 kg/ha) was compromised by an ill-timed fire, but also performed satisfactorily. The present results provide important evidence challenging the assumption that sustainable management in a variable environment is unprofitable. Further research is required to fully quantify the long-term effects of these strategies on land condition and profitability and to extrapolate the results to breeder performance at the property level.

Marine Vegetation of Cape York Peninsula. Cape York Peninsula Land Use Strategy, Office of Co-ordinator General of Queensland, Brisbane, Department of the Environment, Sport and Territories, Canberra

The Cape York Peninsula Land Use Strategy (CYPLUS) is a joint Queensland/Commonwealth initiative to provide a framework for making decisions about how to use and manage the natural resources of Cape York Peninsula in ways that will be ecologically sustainable. As part of the Natural Resources Analysis Program (NRAP) of CYPLUS, the Fisheries Division of the Queensland Department of Primary Industries has mapped the marine vegetation (mangroves and seagrasses) for Cape York Peninsula. The project ran from July 1992 to June 1994. Field work was undertaken in November 1992, May 1993, and April 1994. Final report on project: NRO6 – Marine Plan (Seagrass/Mangrove) Distribution. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

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"

Your fish. Your future. Queensland Fisheries Strategy 2009-2014

The Queensland Fisheries Strategy 2009-2014 sets the direction for the future of fisheries and aims to address some of the challenges impacting Queensland's fisheries both from within Australia and abroad. Every year in Queensland almost a million people fish for a living, for recreation, or for traditional and customary purposes. Countless others rely on sustainable fisheries as the focus of tourism and other businesses - but there are major challenges for the fishing sector. Fisheries resources are finite and under significant stress. Fisheries face challenges including the potential for over-exploitation by all fishing sectors, increasing consumer demand, a rising population, coastal development, the effects of climate change, biosecurity risks, import competition and rising production costs.