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.

Seasonal resource availability and use by an endangered tropical mycophagous marsupial

This study highlights the importance of considering how seasonality of rainfall affects availability of resources and consequently species distributions within tropical ecosystems. The endangered northern bettong, Bettongia tropica Wakefield is thought to be restricted to habitats where seasonal availability of hypogeous fungi, their principal food resource, remains high. To test this hypothesis fungal abundance was quantified in the early wet, late wet, early dry and late dry seasons within known bettong habitat. A relationship was found between precipitation and fungal availability, with the abundance of hypogeous fungi being significantly lower in the late dry season. Fungal availability correlated strongly with the seasonal rainfall pattern determined from 74-year monthly means. This contrasts with a previous study where mycophagy, measured by faecal analysis, remained high across seasons presumably because of aseasonal rainfall during that study period. Alloteropsis semialata R.Br. (cockatoo grass) use by bettongs increased significantly during the period of low fungal availability. This suggests that the importance of cockatoo grass as an alternative food resource during annual and extended dry periods has previously been underestimated. With the frequency and intensity of drought expected to increase with global climate change, these findings have significant implications for bettong management. The important and possibly equivalent dependence of B. tropica on both hypogeous fungi and A. semialata helps to explain their habitat preference and identifies this species as a true ecotonal specialist.

Queensland Coastal Wetland Resource Investigation of the Bowen Region: Cape Upstart to Gloucester Island

The wetland resources of the Queensland coastline have been mapped as a baseline dataset for Marine Protected Area investigation and particularly Fish Habitat Area (FHA) declaration, Ramsar site nomination and continued monitoring of these important fish habitats. This report summarises the results of the mapping undertaken in the Bowen region from the East Coast of Cape Upstart (Abbot Bay) to Gloucester Island (encompassing Edgecumbe Bay). The study was undertaken in order to: 1. document and map the coastal wetland communities within the Bowen region; 2. document levels of existing disturbance to and protection of the wetlands; 3. examine existing recreational and commercial fisheries in the region; and 4. evaluate the significance of the coastal wetlands in the region. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Leaf trait co-ordination in relation to construction cost, carbon gain and resource-use efficiency in exotic invasive and native woody vine species

Background and Aims: Success of invasive plant species is thought to be linked with their higher leaf carbon fixation strategy, enabling them to capture and utilize resources better than native species, and thus pre-empt and maintain space. However, these traits are not well-defined for invasive woody vines. Methods: In a glass house setting, experiments were conducted to examine how leaf carbon gain strategies differ between non-indigenous invasive and native woody vines of south-eastern Australia, by investigating their biomass gain, leaf structural, nutrient and physiological traits under changing light and moisture regimes. Key Results: Leaf construction cost (CC), calorific value and carbon : nitrogen (C : N) ratio were lower in the invasive group, while ash content, N, maximum photosynthesis, light-use efficiency, photosynthetic energyuse efficiency (PEUE) and specific leaf area (SLA) were higher in this group relative to the native group. Trait plasticity, relative growth rate (RGR), photosynthetic nitrogen-use efficiency and water-use efficiency did not differ significantly between the groups. However, across light resource, regression analyses indicated that at a common (same) leaf CC and PEUE, a higher biomass RGR resulted for the invasive group; also at a common SLA, a lower CC but higher N resulted for the invasive group. Overall, trait co-ordination (using pair-wise correlation analyses) was better in the invasive group. Ordination using 16 leaf traits indicated that the major axis of invasive-native dichotomy is primarily driven by SLA and CC (including its components and/or derivative of PEUE) and was significantly linked with RGR. Conclusions: These results demonstrated that while not all measures of leaf resource traits may differ between the two groups, the higher level of trait correlation and higher revenue returned (RGR) per unit of major resource need (CC) and use (PEUE) in the invasive group is in line with their rapid spread where introduced.

Resource Assessment of the Tidal Wetland Vegetation of Western Cape York Peninsula, North Queensland, Report to Ocean Rescue 2000

A project to allow the resource assessment of tidal wetland vegetation of western Cape York Peninsula, in north Queensland, was undertaken as part of the longterm assessment of the coastal fisheries resources of Queensland. The project incorporated a littoral invertebrate fauna component. Extending from May 1993 to December 1994, fieldwork was undertaken in May 1993, November 1993 and April 1994. The aims of this project were to: • obtain baseline information on the distribution of marine plants of western Cape York Peninsula; • commence a preliminary assessment of the littoral invertebrate fauna and their habitat requirements with a view to extending knowledge of their biogeographic affinities; • perform biogeographic classification of the tidal wetlands at a meso and local scale for marine conservation planning; • evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important/threatened species. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Development of a Gulf community based natural resource monitoring program.

Development of a Gulf community based natural resource monitoring program, with sawfish as an initial focus.

FWPRDC PN06.3016 Resource Characterisation

Linking non-destructive field assessment of wood property and quality traits in slash pine to yield of structural grades of timber. Produce a review of wood quality studies in sub-tropical pines planted in Queensland and northern New South Wales.

Small Log Processing Resource Specification

Sawing studies of mixed species and age plantation hardwoods representing potential early resource flows available to plantation sawlog processing industry. Provide information needed to underpin a business case to invest in small log sawing infrastucture.

AG15 (Sustainable Agricultural State-level Investment Program) natural resource management extension in irrigated cotton and grain

Natural Resource Management project developing reources and supporting best practice management for irrigated cotton and grain growers in Queensland.

Resource characterisation of slash pine plantation wood quality.

This review highlights the considerable variation found in wood properties impacting timber stiffness and stability such as wood density, spiral grain and microfibril angle. Variation with age, site quality and environment, as well as amongst species, hybrids and genetic stock is reported and opportunities for product-focused wood quality improvement are identified.

Short-range resource location by Tribolium castaneum Herbst (Coleoptera: Tenebrionidae) demonstrates a strong preference for fungi associated with cotton seed

Tribolium castaneum Herbst (Coleoptera: Tenebrionidae) is a common stored grain pest for which a wide range of suitable resources has been recorded. These beetles are facultatively fungivorous and their resource range may extend to fungi associated with non-grain resources (e.g. cotton seed) and other decaying plant matter. Little is known with respect to fungi in terms of resource location by these beetles in the field. We, therefore, conducted a series of experiments in laboratory arenas, glasshouse cages and the field to determine how beetles respond to grain resources in relation to cotton seed (together with its lint stubble and associated fungal flora). Results from the tests conducted in relatively small arenas and cages in the laboratory and glasshouse reveal that the responses of T. castaneum adults to food resources were twice as strong when walking as when flying (as measured by the proportion of the released beetles that were trapped). Also, a clear preference for linted cotton seeds was evident in walking T. castaneum, especially in small-scale arenas in the laboratory, where at least 60% of beetles released preferred linted cotton seeds over wheat and sorghum. Similarly, in cages (1 m3) they responded five times more strongly to linted cotton seed than to conventional grain resources. However, this pattern was not consistent with those obtained from field trapping over 20 m and the beetles did not show any particular preference to any of the resources tested above. Our results suggest a focus on walking beetles in trapping studies for population estimations and, for developing effective food-based trapping lures, the potential use of active volatiles from the fungi associated with linted cotton seed. © 2012 Elsevier Ltd.

CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

The Rhipicephalus micro plus genome is large and complex in structure, making it difficult to assemble a genome sequence and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8 Gigabase pairs of DNA from gene-enriched regions of the R. micro plus genome. We also have several datasets containing transcript sequences from a number of gene expression experiments conducted by the consortium. A web-based resource was developed to enable the scientific community to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed CattleTickBase. Our consortium has acquired genomic and transcriptomic sequence data at approximately 0.9X coverage of the gene-coding regions of the R. microplus genome. The YABI tool will facilitate access and manipulation of cattle tick genome sequence data as the genome sequencing of R. microplus proceeds. During this process the CattleTickBase resource will continue to be updated. Published by Elsevier Ltd. on behalf of Australian Society for Parasitology Inc.

Estimating Resource Requirements to Staff a Response to a Medium to Large Outbreak of Foot and Mouth Disease in Australia

A recent report to the Australian Government identified concerns relating to Australia's capacity to respond to a medium to large outbreak of FMD. To assess the resources required, the AusSpread disease simulation model was used to develop a plausible outbreak scenario that included 62 infected premises in five different states at the time of detection, 28 days after the disease entered the first property in Victoria. Movements of infected animals and/or contaminated product/equipment led to smaller outbreaks in NSW, Queensland, South Australia and Tasmania. With unlimited staff resources, the outbreak was eradicated in 63 days with 54 infected premises and a 98% chance of eradication within 3 months. This unconstrained response was estimated to involve 2724 personnel. Unlimited personnel was considered unrealistic, and therefore, the course of the outbreak was modelled using three levels of staffing and the probability of achieving eradication within 3 or 6 months of introduction determined. Under the baseline staffing level, there was only a 16% probability that the outbreak would be eradicated within 3 months, and a 60% probability of eradication in 6 months. Deployment of an additional 60 personnel in the first 3 weeks of the response increased the likelihood of eradication in 3 months to 68%, and 100% in 6 months. Deployment of further personnel incrementally increased the likelihood of timely eradication and decreased the duration and size of the outbreak. Targeted use of vaccination in high-risk areas coupled with the baseline personnel resources increased the probability of eradication in 3 months to 74% and to 100% in 6 months. This required 25 vaccination teams commencing 12 days into the control program increasing to 50 vaccination teams 3 weeks later. Deploying an equal number of additional personnel to surveillance and infected premises operations was equally effective in reducing the outbreak size and duration.

Targeting resource investments to achieve sediment reduction and improved Great Barrier Reef health

Concerns about excessive sediment loads entering the Great Barrier Reef (GBR) lagoon in Australia have led to a focus on improving ground cover in grazing lands. Ground cover has been identified as an important factor in reducing sediment loads, but improving ground cover has been difficult for reef stakeholders in major catchments of the GBR. To provide better information an optimising linear programming model based on paddock scale information in conjunction with land type mapping was developed for the Fitzroy, the largest of the GBR catchments. This identifies at a catchment scale which land types allow the most sediment reduction to be achieved at least cost. The results suggest that from the five land types modelled, the lower productivity land types present the cheapest option for sediment reductions. The study allows more informed decision making for natural resource management organisations to target investments. The analysis highlights the importance of efficient allocation of natural resource management funds in achieving sediment reductions through targeted land type investments. © 2012.