Developing African mahogany (Khaya senegalensis) germplasm and its management for a sustainable forest plantation industry in northern Australia: Progress and needs.

The demonstrated wide adaptability, substantial yield potential and proven timber quality of African mahogany (Khaya senegalensis) from plantings of the late 1960s and early 1970s in northern Australia have led to a resurgence of interest in this high-value species. New plantations or trials have been established in several regions since the early 1990s -in four regions in north Queensland, two in the Northern Territory and one in Western Australia. Overall, more than 1500 ha had been planted by early 2007, and the national annual planting from 2007-2008 as currently planned will exceed 2400 ha. Proceedings of two workshops have summarised information available on the species in northern Australia, and suggested research and development (R&D) needs and directions. After an unsustained first phase of domestication of K. senegalensis in the late 1960s to the early 1970s, a second phase began in northern Australia in 2001 focused on conservation and tree improvement that is expected to provide improved planting stock by 2010. Work on other aspects of domestication is also described in this paper: the current estate and plans for extension; site suitability, soils and nutrition; silviculture and management; productivity; pests and diseases; and log and wood properties of a sample of superior trees from two mature plantations of unselected material near Darwin. Some constraints on sustainable plantation development in all these fields are identified and R&D needs proposed. A sustained R&D effort will require a strategic coordinated approach, cooperative implementation and extra funding. Large gains in plantation profitability can be expected to flow from such inputs.

Forest health surveillance methodology in hardwood plantations in Queensland, Australia

Forest health surveillance (FHS) of hardwood plantations commenced in Queensland in 1997 as plantations expanded following a state government planting initiative arising from the national 2020 forest policy vision. The estate was initially characterised by a large number of small plantations (10-50 ha), although this has changed more recently with the concentration of larger plantations in the central coast and South Burnett regions. Due to the disparate nature of the resource, drive- and walkthrough surveys of subsets of plantations have been undertaken in preference to aerial surveys. FHS has been effective in detecting a number of new hardwood pests in Queensland including erinose mites (Rhombacus and Acalox spp.), western white gum plate galler (Ophelimus sp.), Creiis psyllid and bronzing bug (Thaumastocoris sp.), in evaluating their potential impact and assisting in focussing future research efforts. Since 2003 there has been an increased emphasis on training operational staff to take a greater role in identifying and reporting on forest health issues. This has increased their awareness of forest health issues, but their limited time to specifically survey and report on pests and diseases, and high rates of staff turnover, necessitate frequent ongoing training. Consequently, common and widespread problems such as quambalaria shoot blight (Quambalaria pitereka), chrysomelid leaf beetles (mainly Paropsis atomaria) and erinose mites may be under-reported or not reported, and absence data may often not be recorded at all. Comment is made on the future directions that FHS may take in hardwood plantations in Queensland.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05-7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

Tree growth relationships and silvicultural tools to assist stand management in private native spotted gum dominant forests in Queensland and northern New South Wales.

Spotted gum dominant forests occur from Cooktown in northern Queensland (Qld) to Orbost in Victoria (Boland et al. 2006) and these forests are commercially very important with spotted gum the most commonly harvested hardwood timber in Qld and one of the most important in New South Wales (NSW). Spotted gum has a wide range of end uses from solid wood products through to power transmission poles and generally has excellent sawing and timber qualities (Hopewell 2004). The private native forest resource in southern Qld and northern NSW is a critical component of the hardwood timber industry (Anon 2005, Timber Qld 2006) and currently half or more of the native forest timber resource harvested in northern NSW and Qld is sourced from private land. However, in many cases productivity on private lands is well below what could be achieved with appropriate silvicultural management. This project provides silvicultural management tools to assist extension staff, land owners and managers in the south east Qld and north eastern NSW regions. The intent was that this would lead to improvement of the productivity of the private estate through implementation of appropriate management. The other intention of this project was to implement a number of silvicultural experiments and demonstration sites to provide data on growth rates of managed and unmanaged forests so that landholders can make informed decisions on the future management of their forests. To assist forest managers and improve the ability to predict forest productivity in the private resource, the project has developed: • A set of spotted gum specific silvicultural guidelines for timber production on private land that cover both silvicultural treatment and harvesting. The guidelines were developed for extension officers and property owners. • A simple decision support tool, referred to as the spotted gum productivity assessment tool (SPAT), that allows an estimation of: 1. Tree growth productivity on specific sites. Estimation is based on the analysis of site and growth data collected from a large number of yield and experimental plots on Crown land across a wide range of spotted gum forest types. Growth algorithms were developed using tree growth and site data and the algorithms were used to formulate basic economic predictors. 2. Pasture development under a range of tree stockings and the expected livestock carrying capacity at nominated tree stockings for a particular area. 3. Above-ground tree biomass and carbon stored in trees. •A series of experiments in spotted gum forests on private lands across the study area to quantify growth and to provide measures of the effect of silvicultural thinning and different agro-forestry regimes. The adoption and use of these tools by farm forestry extension officers and private land holders in both field operations and in training exercises will, over time, improve the commercial management of spotted gum forests for both timber and grazing. Future measurement of the experimental sites at ages five, 10 and 15 years will provide longer term data on the effects of various stocking rates and thinning regimes and facilitate modification and improvement of these silvicultural prescriptions.

The performance of broilers offered sorghum - compared to wheat-based diets: a large sacle experiment.

Sufficient evidence tended to indicate that at least four factors can negatively influence broiler performance when offered sorghum-based diets; in particular energy utilisation of sorghum in young birds. It was proposed that mainly CT would further influence sorghum grain AME values when consumed by young chicks (0-7 and 7-14 d old). Overall, birds consuming sorghum-based diets during the starter phase (0-21 d), did not match the performance of birds offered wheat-based diets. The use of phytase enzymes in sorghum-based diets tended to improve bird performance. However, reducing the obtained AME of sorghum grains by -0.8 MJ during the 0-21 d period appears to be a practical solution.

How can warren destruction by ripping control European wild rabbits (Oryctolagus cuniculus) on large properties in the Australian arid zone?

Context: For over 100 years, control efforts have been unable to stop rabbits causing damage to cattle production and native plants and animals on large properties in arid parts of Australia. Warren destruction by ripping has shown promise, but doubts about long-term success and the perceived expense of treating vast areas have led to this technique not being commonly used. Aims: This study measured the long-term reduction in rabbit activity and calculated the potential cost saving associated with treating just the areas where rabbits are believed to survive drought. Wealso considered whether ripping should be used in a full-scale rabbit control program on a property where rabbits have been exceptionally resilient to the influence of biological and other control measures. Methods: Rabbits were counted along spotlight transects before warrens were ripped and during the two years after ripping, in treated and untreated plots. Rabbit activity was recorded to determine the immediate and long-term impact of ripping, up to seven years after treatment. The costs of ripping warrens within different distances from drought refuge areas were calculated. Key results: Destroying rabbit warrens by ripping caused an immediate reduction in rabbit activity and there were still 98% fewer rabbits counted by spotlight in ripped plots five months after ripping. Seven years after ripping no active warrens were found in ripped plots, whereas 57% of warrens in unripped plots showed signs of rabbit activity. The cost of ripping only the areas where rabbits were likely to seek refuge from drought was calculated to be less than 4%of the cost of ripping all warrens on the property. Conclusions: Destroying rabbit warrens by ripping is a very effective way of reducing rabbit numbers on large properties in arid Australia. Ripping should commence in areas used by rabbits to survive drought. It is possible that no further ripping will be required. Implications: Strategic destruction of warrens in drought refuge areas could provide an alternative to biological control for managing rabbits on large properties in the Australian arid zone.

Gear selectivity of large-mesh nets and drumlines used to catch sharks in the Queensland Shark Control Program.

Catches of sharks and bycatch in large-mesh nets and baited drumlines used by the Queensland Shark Control Program were examined to determine the efficacy of both gear types and assess fishing strategies that minimise their impacts. There were few significant differences in the size of both sharks and bycatch in the two gear types, apart from significantly smaller (p < 0.05) tiger sharks Galeocerdo cuvier being taken on drumlines and smaller green turtles Chelonia mydas in nets. Catch per unit effort showed orders of magnitude differences among species, even within the same family. Hammerhead sharks and rays were particularly vulnerable to net capture, whereas higher catch rates of tiger sharks were observed for drumlines. Nets caught more marine mammals, teleost fish and rays, whereas drumlines exhibited higher catch rates of the threatened loggerhead turtle Caretta caretta. Survival of most taxa (particularly obligate ram ventilators) was lower in nets than drumlines. Bycatch species (turtles and marine mammals) were able to swim to the surface to breathe when they were hooked on drumlines, enhancing their survival potential. Fishing strategies that recognise the different selectivity patterns of the gear can be developed to suit local biotic and abiotic conditions, although it is recognised that quantification of both ecological risk and risk to bathers is not a simple task.

Large scale surveys suggest limited mercury availability in tropical north Queensland (Australia)

Little is known about the threat of mercury (Hg) to consumers in food webs of Australia's wet-dry tropics. This is despite high concentrations in similar biomes elsewhere and a recent history of gold mining that could lead to a high degree of exposure for biota. We analysed Hg in water, sediments, invertebrates and fishes in rivers and estuaries of north Queensland, Australia to determine its availability and biomagnification in food webs. Concentrations in water and sediments were low relative to other regions of Hg concern, with only four of 138 water samples and five of 60 sediment samples above detection limits of 0.1 mu g L-1 and 01 mu g g(-1), respectively. Concentrations of Hg in fishes and invertebrates from riverine and wetland food webs were well below international consumption guidelines, including those in piscivorous fishes, likely due to low baseline concentrations and limited rates of biomagnification (average slope of log Hg vs. delta N-15 = 0.08). A large fish species of recreational, commercial, and cultural importance (the barramundi, Lates calcarifer), had low concentrations that were below consumption guidelines. Observed variation in Hg concentrations in this species was primarily explained by age and foraging location (floodplain vs. coastal), with floodplain feeders having higher Hg concentrations than those foraging at sea. These analyses suggest that there is a limited threat of Hg exposure for fish-eating consumers in this region. (C) 2011 Published by Elsevier B.V.

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.

Large-chamber methane and nitrous oxide measurements are comparable to the backward Lagrangian stochastic method

Measurement of individual emission sources (e.g., animals or pen manure) within intensive livestock enterprises is necessary to test emission calculation protocols and to identify targets for decreased emissions. In this study, a vented, fabric-covered large chamber (4.5 × 4.5 m, 1.5 m high; encompassing greater spatial variability than a smaller chamber) in combination with on-line analysis (nitrous oxide [N2O] and methane [CH4] via Fourier Transform Infrared Spectroscopy; 1 analysis min-1) was tested as a means to isolate and measure emissions from beef feedlot pen manure sources. An exponential model relating chamber concentrations to ambient gas concentrations, air exchange (e.g., due to poor sealing with the surface; model linear when ≈ 0 m3 s-1), and chamber dimensions allowed data to be fitted with high confidence. Alternating manure source emission measurements using the large-chamber and the backward Lagrangian stochastic (bLS) technique (5-mo period; bLS validated via tracer gas release, recovery 94-104%) produced comparable N2O and CH4 emission values (no significant difference at P < 0.05). Greater precision of individual measurements was achieved via the large chamber than for the bLS (mean ± standard error of variance components: bLS half-hour measurements, 99.5 ± 325 mg CH4 s-1 and 9.26 ± 20.6 mg N2O s-1; large-chamber measurements, 99.6 ± 64.2 mg CH4 s-1 and 8.18 ± 0.3 mg N2O s-1). The large-chamber design is suitable for measurement of emissions from manure on pen surfaces, isolating these emissions from surrounding emission sources, including enteric emissions. © © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Large-scale characterization of drought pattern: a continent-wide modelling approach applied to the Australian wheatbelt – spatial and temporal trends

* Plant response to drought is complex, so that traits adapted to a specific drought type can confer disadvantage in another drought type. Understanding which type(s) of drought to target is of prime importance for crop improvement. * Modelling was used to quantify seasonal drought patterns for a check variety across the Australian wheatbelt, using 123 yr of weather data for representative locations and managements. Two other genotypes were used to simulate the impact of maturity on drought pattern. * Four major environment types summarized the variability in drought pattern over time and space. Severe stress beginning before flowering was common (44% of occurrences), with (24%) or without (20%) relief during grain filling. High variability occurred from year to year, differing with geographical region. With few exceptions, all four environment types occurred in most seasons, for each location, management system and genotype. * Applications of such environment characterization are proposed to assist breeding and research to focus on germplasm, traits and genes of interest for target environments. The method was applied at a continental scale to highly variable environments and could be extended to other crops, to other drought-prone regions around the world, and to quantify potential changes in drought patterns under future climates.

First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region

The first complete genome sequence of capsicum chlorosis virus (CaCV) from Australia was determined using a combination of Illumina HiSeq RNA and Sanger sequencing technologies. Australian CaCV had a tripartite genome structure like other CaCV isolates. The large (L) RNA was 8913 nucleotides (nt) in length and contained a single open reading frame (ORF) of 8634 nt encoding a predicted RNA-dependent RNA polymerase (RdRp) in the viral-complementary (vc) sense. The medium (M) and small (S) RNA segments were 4846 and 3944 nt in length, respectively, each containing two non-overlapping ORFs in ambisense orientation, separated by intergenic regions (IGR). The M segment contained ORFs encoding the predicted non-structural movement protein (NSm; 927 nt) and precursor of glycoproteins (GP; 3366 nt) in the viral sense (v) and vc strand, respectively, separated by a 449-nt IGR. The S segment coded for the predicted nucleocapsid (N) protein (828 nt) and non-structural suppressor of silencing protein (NSs; 1320 nt) in the vc and v strand, respectively. The S RNA contained an IGR of 1663 nt, being the largest IGR of all CaCV isolates sequenced so far. Comparison of the Australian CaCV genome with complete CaCV genome sequences from other geographic regions showed highest sequence identity with a Taiwanese isolate. Genome sequence comparisons and phylogeny of all available CaCV isolates provided evidence for at least two highly diverged groups of CaCV isolates that may warrant re-classification of AIT-Thailand and CP-China isolates as unique tospoviruses, separate from CaCV.

The insecticidal spider toxin SFI1 is a knottin peptide that blocks the pore of insect voltage-gated sodium channels via a large β-hairpin loop

Spider venoms contain a plethora of insecticidal peptides that act on neuronal ion channels and receptors. Because of their high specificity, potency and stability, these peptides have attracted much attention as potential environmentally friendly insecticides. Although many insecticidal spider venom peptides have been isolated, the molecular target, mode of action and structure of only a small minority have been explored. Sf1a, a 46-residue peptide isolated from the venom of the tube-web spider Segesteria florentina, is insecticidal to a wide range of insects, but nontoxic to vertebrates. In order to investigate its structure and mode of action, we developed an efficient bacterial expression system for the production of Sf1a. We determined a high-resolution solution structure of Sf1a using multidimensional 3D/4D NMR spectroscopy. This revealed that Sf1a is a knottin peptide with an unusually large β-hairpin loop that accounts for a third of the peptide length. This loop is delimited by a fourth disulfide bond that is not commonly found in knottin peptides. We showed, through mutagenesis, that this large loop is functionally critical for insecticidal activity. Sf1a was further shown to be a selective inhibitor of insect voltage-gated sodium channels, consistent with its 'depressant' paralytic phenotype in insects. However, in contrast to the majority of spider-derived sodium channel toxins that function as gating modifiers via interaction with one or more of the voltage-sensor domains, Sf1a appears to act as a pore blocker.

Large-scale expansion of no-take closures within the Great Barrier Reef has not enhanced fishery production

A rare opportunity to test hypotheses about potential fishery benefits of large-scale closures was initiated in July 2004 when an additional 28.4% of the 348 000 km2 Great Barrier Reef (GBR) region of Queensland, Australia was closed to all fishing. Advice to the Australian and Queensland governments that supported this initiative predicted these additional closures would generate minimal (10%) initial reductions in both catch and landed value within the GBR area, with recovery of catches becoming apparent after three years. To test these predictions, commercial fisheries data from the GBR area and from the two adjacent (non-GBR) areas of Queensland were compared for the periods immediately before and after the closures were implemented. The observed means for total annual catch and value within the GBR declined from pre-closure (2000–2003) levels of 12 780 Mg and Australian $160 million, to initial post-closure (2005–2008) levels of 8143 Mg and $102 million; decreases of 35% and 36% respectively. Because the reference areas in the non-GBR had minimal changes in catch and value, the beyond-BACI (before, after, control, impact) analyses estimated initial net reductions within the GBR of 35% for both total catch and value. There was no evidence of recovery in total catch levels or any comparative improvement in catch rates within the GBR nine years after implementation. These results are not consistent with the advice to governments that the closures would have minimal initial impacts and rapidly generate benefits to fisheries in the GBR through increased juvenile recruitment and adult spillovers. Instead, the absence of evidence of recovery in catches to date currently supports an alternative hypothesis that where there is already effective fisheries management, the closing of areas to all fishing will generate reductions in overall catches similar to the percentage of the fished area that is closed.