Planning, Managing and Evaluating Group Housing Systems for Gestating Sows

This project will examine infrastructure changes required to existing gestation stall accommodation including performance and economics.

Climate information needs of Gascoyne-Murchison pastoralists: a representative study of the Western Australian grazing industry

The Gascoyne-Murchison region of Western Australia experiences an arid to semi-arid climate with a highly variable temporal and spatial rainfall distribution. The region has around 39.2 million hectares available for pastoral lease and supports predominantly catle and sheep grazing leases. In recent years a number of climate forecasting systems have been available offering rainfall probabilities with different lead times and a forecast period; however, the extent to which these systems are capable of fulfilling the requirements of the local pastoralists is still ambiguous. Issues can range from ensuring forecasts are issued with sufficient lead time to enable key planning or decisions to be revoked or altered, to ensuring forecast language is simple and clear, to negate possible misunderstandings in interpretation. A climate research project sought to provide an objective method to determine which available forecasting systems had the greatest forecasting skill at times of the year relevant to local property management. To aid this climate research project, the study reported here was undertaken with an overall objective of exploring local pastoralists' climate information needs. We also explored how well they understand common climate forecast terms such as 'mean', median' and 'probability', and how they interpret and apply forecast information to decisions. A stratified, proportional random sampling was used for the purpose of deriving the representative sample based on rainfall-enterprise combinations. In order to provide more time for decision-making than existing operational forecasts that are issued with zero lead time, pastoralists requested that forecasts be issued for May-July and January-March with lead times counting down from 4 to 0 months. We found forecasts of between 20 and 50 mm break-of-season or follow-up rainfall were likely to influence decisions. Eighty percent of pastoralists demonstrated in a test question that they had a poor technical understanding of how to interpret the standard wording of a probabilistic median rainfall forecast. this is worthy of further research to investigate whether inappropriate management decisions are being made because the forecasts are being misunderstood. We found more than half the respondents regularly access and use weather and climate forecasts or outlook information from a range of sources and almost three-quarters considered climate information or tools useful, with preferred methods for accessing this information by email, faxback service, internet and the Department of Agriculture Western Australia's Pastoral Memo. Despite differences in enterprise types and rainfall seasonality across the region we found seasonal climate forecasting needs were relatively consistent. It became clear that providing basic training and working with pastoralists to help them understand regional climatic drivers, climate terminology and jargon, and the best ways to apply the forecasts to enhance decision-making are important to improve their use of information. Consideration could also be given to engaging a range of producers to write the climate forecasts themselves in the language they use and understand, in consultation with the scientists who prepare the forecasts.

Optimal management of agricultural systems

To remain competitive, many agricultural systems are now being run along business lines. Systems methodologies are being incorporated, and here evolutionary computation is a valuable tool for identifying more profitable or sustainable solutions. However, agricultural models typically pose some of the more challenging problems for optimisation. This chapter outlines these problems, and then presents a series of three case studies demonstrating how they can be overcome in practice. Firstly, increasingly complex models of Australian livestock enterprises show that evolutionary computation is the only viable optimisation method for these large and difficult problems. On-going research is taking a notably efficient and robust variant, differential evolution, out into real-world systems. Next, models of cropping systems in Australia demonstrate the challenge of dealing with competing objectives, namely maximising farm profit whilst minimising resource degradation. Pareto methods are used to illustrate this trade-off, and these results have proved to be most useful for farm managers in this industry. Finally, land-use planning in the Netherlands demonstrates the size and spatial complexity of real-world problems. Here, GIS-based optimisation techniques are integrated with Pareto methods, producing better solutions which were acceptable to the competing organizations. These three studies all show that evolutionary computation remains the only feasible method for the optimisation of large, complex agricultural problems. An extra benefit is that the resultant population of candidate solutions illustrates trade-offs, and this leads to more informed discussions and better education of the industry decision-makers.

A method for mapping the distribution and density of rabbits and other vertebrate pests in Australia

The European wild rabbit has been considered Australia’s worst vertebrate pest and yet little effort appears to have gone into producing maps of rabbit distribution and density. Mapping the distribution and density of pests is an important step in effective management. A map is essential for estimating the extent of damage caused and for efficiently planning and monitoring the success of pest control operations. This paper describes the use of soil type and point data to prepare a map showing the distribution and density of rabbits in Australia. The potential for the method to be used for mapping other vertebrate pests is explored. The approach used to prepare the map is based on that used for rabbits in Queensland (Berman et al. 1998). An index of rabbit density was determined using the number of Spanish rabbit fleas released per square kilometre for each Soil Map Unit (Atlas of Australian Soils). Spanish rabbit fleas were released into active rabbit warrens at 1606 sites in the early 1990s as an additional vector for myxoma virus and the locations of the releases were recorded using a Global Positioning System (GPS). Releases were predominantly in arid areas but some fleas were released in south east Queensland and the New England Tablelands of New South Wales. The map produced appears to reflect well the distribution and density of rabbits, at least in the areas where Spanish fleas were released. Rabbit pellet counts conducted in 2007 at 54 sites across an area of south east South Australia, south eastern Queensland, and parts of New South Wales (New England Tablelands and south west) in soil Map Units where Spanish fleas were released, provided a preliminary means to ground truth the map. There was a good relationship between mean pellet count score and the index of abundance for soil Map Units. Rabbit pellet counts may allow extension of the map into other parts of Australia where there were no Spanish rabbit fleas released and where there may be no other consistent information on rabbit location and density. The recent Equine Influenza outbreak provided a further test of the value of this mapping method. The distribution and density of domestic horses were mapped to provide estimates of the number of horses in various regions. These estimates were close to the actual numbers of horses subsequently determined from vaccination records and registrations. The soil Map Units are not simply soil types they contain information on landuse and vegetation and the soil classification is relatively localised. These properties make this mapping method useful, not only for rabbits, but also for other species that are not so dependent on soil type for survival.

Predicting risk and benefit a priori in biological control of invasive plant species: a systems modelling approach

While the method using specialist herbivores in managing invasive plants (classical biological control) is regarded as relatively safe and cost-effective in comparison to other methods of management, the rarity of strict monophagy among insect herbivores illustrates that, like any management option, biological control is not risk-free. The challenge for classical biological control is therefore to predict risks and benefits a priori. In this study we develop a simulation model that may aid in this process. We use this model to predict the risks and benefits of introducing the chrysomelid beetle Charidotis auroguttata to manage the invasive liana Macfadyena unguis-cati in Australia. Preliminary host-specificity testing of this herbivore indicated that there was limited feeding on a non-target plant, although the non-target was only able to sustain some transitions of the life cycle of the herbivore. The model includes herbivore, target and non-target life history and incorporates spillover dynamics of populations of this herbivore from the target to the non-target under a variety of scenarios. Data from studies of this herbivore in the native range and under quarantine were used to parameterize the model and predict the relative risks and benefits of this herbivore when the target and non-target plants co-occur. Key model outputs include population dynamics on target (apparent benefit) and non-target (apparent risk) and fitness consequences to the target (actual benefit) and non-target plant (actual risk) of herbivore damage. The model predicted that risk to the non-target became unacceptable (i.e. significant negative effects on fitness) when the ratio of target to non-target in a given patch ranged from 1:1 to 3:2. By comparing the current known distribution of the non-target and the predicted distribution of the target we were able to identify regions in Australia where the agent may be pose an unacceptable risk. By considering risk and benefit simultaneously, we highlight how such a simulation modelling approach can assist scientists and regulators in making more objective decisions a priori, on the value of releasing specialist herbivores as biological control agents.

Northern Grazing Systems Project Development

Control of grazing distribution, management of stocking rate, wet season spelling and fire

Maximising profitability with limited water in cotton farming systems

Diminishing water supply, changing weather patterns and pressure to enhance environmental flows are making it imperative to optimise water use efficiency (WUE) on cotton/grain farming systems. Growers are looking for better strategies to make the best use of limited water, but it is still not clear how to best use the available water at farm and field scale. This research project investigated the impact of management strategies to deal with limited water supplies on the yield and quality of irrigated cotton and wheat. The objectives were: (1) to develop irrigation management guidelines for the main irrigated crops on the Darling Downs for full- and deficitirrigation scenarios, taking into account the critical factors that affect irrigation decisions at the local level, (2) to quantify the evapotranspiration (ET) of Bollgard II cotton and wheat and its relationship to yield and quality under full- and deficit-irrigation scenarios, and (3) to increase industry awareness and education of farming systems practises for optimised economic water use efficiency.Objective (1) was addressed by (A) collaborating with ASPRU to develop the APSFarm model within APSIM to be able to perform multi-paddock simulations. APSFarm was then tested by conducting a case study at a farm near Dalby, and (B) conducting semi-structured interviews with individual farmers and crop consultants on the Darling Downs to document the strategies they are using to deal with limited water. Objective (2) was addressed by (A) building and installing 12 large (1 m x 1m x 1.5 m) weighing lysimeters to measure crop evapotranspiration. The lysimeters were installed at the Agri-Science Queensland research station at Kingsthorpe in November 2008, (B) conducting field experiments to measure crop evapotranspiration and crop development under four irrigation treatments, including dryland, deficit-irrigation, and full irrigation. Field experiments were conducted with cotton in 2007-08 and 2008-09, and with wheat in 2008 and 2009, and (C) collaborating with USQ on a PhD thesis to quantify the impact of crop stress on crop evapotranspiration and canopy temperature. Glasshouse experiments were conducted with wheat in 2008 and with cotton in 2008-09. Objective (3) was addressed by (A) conducting a field day at Kingsthorpe in 2009, which was attended by 80 participants, (B) presenting information in conferences in Australia and overseas, (D) presenting information at farmers meeting, (E) making presentations to crop consultants, and (F) preparing extension publications.As part of this project we contributed to the development of APSfarm, which has been successfully applied to evaluate the feasibility of practices at the whole-farm scale. From growers and crop consultants interviews we learned that there is a great variety of strategies, at different scales, that they are using to deal with limited water situation. These strategies will be summarised in the "e;Limited Water Guidelines for the Darling Downs"e; that we are currently preparing. As a result of this project, we now have a state-of-the-art lysimeter research facility (23 large weighing lysimeters) to be able to conduct replicated experiments to investigate daily water use of a variety of crops under different irrigation regimes and under different environments. Under this project, a series of field and glasshouse experiments were conducted with cotton and wheat, investigating aspects like: (A) quantification of daily and seasonal crop water use under nonstressed and stressed conditions, (B) impact of row configuration on crop water use, (C) impact of water stress on yield, evapotranspiration, crop vegetative and reproductive development, soil water extraction pattern, yield and yield quality. The information obtained from this project is now being used to develop web-based tools to help growers make planning and day-to-day irrigation decisions.

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Sensory Systems in Sawfishes. 2. The Lateral Line.

The lateral line system allows elasmobranchs to detect hydrodynamic movements in their close surroundings. We examined the distribution of pit organs and lateral line canals in 4 species of sawfish (Anoxypristis cuspidata, Pristis microdon, P. clavata and P. zijsron). Pit organs could only be located in A. cuspidata, which possesses elongated pits that are lined by dermal denticles. In all 4 pristid species, the lateral line canals are well developed and were separated into regions of pored and non-pored canals. In all species the tubules that extend from pored canals form extensive networks. In A. cuspidata, P. microdon and P. clavata, the lateral line canals on both the dorsal and ventral surfaces of the rostrum possess extensively branched and pored tubules. Based on this morphological observation, we hypothesized that these 3 species do not use their rostrum to search in the substrate for prey as previously assumed. Other batoids that possess lateral line canals adapted to perceive stimuli produced by infaunal prey possess non-pored lateral line canals, which also prevent the intrusion of substrate particles. However, this hypothesis remains to be tested behaviourally in pristids. Lateral line canals located between the mouth and the nostrils are non-pored in all 4 species of sawfish. Thus this region is hypothesized to perceive stimuli caused by direct contact with prey before ingestion. Lateral line canals that contain neuromasts are longest in P. microdon, but canals containing neuromasts along the rostrum are longest in A. cuspidata.

Sensory Systems in Sawfishes. 1. The Ampullae of Lorenzini

The distribution and density of the ampullary electroreceptors in the skin of elasmobranchs are influenced by the phylogeny and ecology of a species. Sensory maps were created for 4 species of pristid sawfish. Their ampullary pores were separated into pore fields based on their innervation and cluster formation. Ventrally, ampullary pores are located in 6 areas (5 in Pristis microdon), covering the rostrum and head to the gills. Dorsally, pores are located in 4 areas (3 in P. microdon), which cover the rostrum, head and may extend slightly onto the pectoral fins. In all species, the highest number of pores is found on the dorsal and ventral sides of the rostrum. The high densities of pores along the rostrum combined with the low densities around the mouth could indicate that sawfish use their rostrum to stun their prey before ingesting it, but this hypothesis remains to be tested. The directions of ampullary canals on the ventral side of the rostrum are species specific. P. microdon possesses the highest number of ampullary pores, which indicates that amongst the study species this species is an electroreception specialist. As such, juvenile P. microdon inhabit low-visibility freshwater habitats.

Grazing for Healthy Coastal Wetlands: Guidelines for managing coastal wetlands in grazing systems.

Grazing for Healthy Coastal Wetlands has been developed to provide graziers, landowners and extension officers with information on managing grazing in and around Queensland’s coastal wetlands to maintain healthy coastal wetlands and productive grazing enterprises. It provides practical advice on how grazing and associated land management practices can be implemented to support the long-term health of coastal wetlands whilst maintaining production. The guidelines have been compiled from published literature, grazier knowledge, wetlands managers and the experience of extension and natural resource management professionals. They reflect the current knowledge of suitable management practices for coastal wetlands. They are designed to complement and be considered in conjunction with existing information resources including the EDGEnetwork Grazing Land Management series and best management practice guidelines from regional Natural Resource Management (NRM) groups. While the recommendations apply broadly to Queensland’s coastal wetlands, regional, catchment and landscape-scale variations in wetland characteristics and the objectives of the individual grazing enterprise should be taken into account in planning and deciding management actions for wetlands. An individual grazing property may even have a range of wetland types with different management needs and objectives which should be identified during whole of property planning. Specific land and wetland management advice should also be sought from local grazing extension officers and NRM professionals.

Mikania micrantha Kunth (Asteraceae) (Mile-a-Minute): Its Distribution and Physical and Socioeconomic Impacts in Papua New Guinea

Mikania micrantha or mile-a-minute is regarded as a major invasive weed in Papua New Guinea (PNG) and is now the target of a biological control program. As part of the program, distribution and physical and socioeconomic impacts of M. micrantha were studied to obtain baseline data and to assist with field release of biological control agents. Through public awareness campaigns and dedicated surveys, M. micrantha has been reported in all 15 lowland provinces. It is particularly widespread in East New Britain, as well as in West New Britain and New Ireland. A CLIMEX model suggests that M. micrantha has the potential to continue to spread throughout all lowland areas in PNG. The weed was found in a wide range of land uses, impacting on plantations and food gardens and smothering papaya, young cocoa, banana, taro, young oil palms, and ornamental plants. In socioeconomic surveys, M. micrantha was found to have severe impacts on crop production and income generated through reduced yields and high weeding costs, particularly in subsistence mixed cropping systems. About 89% of all respondents had M. micrantha on their land, and 71% of respondents had to weed monthly. Approximately 96% of respondents in subsistence mixed cropping systems used only physical means of control compared with 68% of respondents in other farming systems. About 45% of all respondents estimated that M. micrantha causes yield losses in excess of 30%. These studies suggest that there would be substantial benefits to landholders if biological control of M. micrantha were to be successful.

The Distribution of Henipaviruses in Southeast Asia and Australasia: Is Wallace's Line a Barrier to Nipah Virus?

Nipah virus (NiV) (Genus Henipavirus) is a recently emerged zoonotic virus that causes severe disease in humans and has been found in bats of the genus Pteropus. Whilst NiV has not been detected in Australia, evidence for NiV-infection has been found in pteropid bats in some of Australia's closest neighbours. The aim of this study was to determine the occurrence of henipaviruses in fruit bat (Family Pteropodidae) populations to the north of Australia. In particular we tested the hypothesis that Nipah virus is restricted to west of Wallace's Line. Fruit bats from Australia, Papua New Guinea, East Timor and Indonesia were tested for the presence of antibodies to Hendra virus (HeV) and Nipah virus, and tested for the presence of HeV, NiV or henipavirus RNA by PCR. Evidence was found for the presence of Nipah virus in both Pteropus vampyrus and Rousettus amplexicaudatus populations from East Timor. Serology and PCR also suggested the presence of a henipavirus that was neither HeV nor NiV in Pteropus alecto and Acerodon celebensis. The results demonstrate the presence of NiV in the fruit bat populations on the eastern side of Wallace's Line and within 500 km of Australia. They indicate the presence of non-NiV, non-HeV henipaviruses in fruit bat populations of Sulawesi and Sumba and possibly in Papua New Guinea. It appears that NiV is present where P. vampyrus occurs, such as in the fruit bat populations of Timor, but where this bat species is absent other henipaviruses may be present, as on Sulawesi and Sumba. Evidence was obtained for the presence henipaviruses in the non-Pteropid species R. amplexicaudatus and in A. celebensis. The findings of this work fill some gaps in knowledge in geographical and species distribution of henipaviruses in Australasia which will contribute to planning of risk management and surveillance activities.

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

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

Harvest weed seed control: is there a role in northern region farming systems?

Harvest weed seed control (HWSC) is a new approach which targets weed seed removal and/or destruction during the crop harvest operation. The success of HWSC is dependant upon weed seed retention at harvest. To identify and define the potential value of HWSC in northern farming systems, we conducted a field survey. In total 1400 transects across 70 paddocks assessed weed distribution, density and seed production at harvest time in wheat, chickpea and sorghum crops. Seventy weed species were identified, of which many had large seed numbers retained at crop harvest. The most prevalent included common sowthistle, flaxleaf fleabane, awnless barnyard grass, wild oat, and African turnip weed. Our field survey has shown there is a role for HWSC in the northern farming system. Therefore the efficacy of specific HWSC systems on problematic weeds should be evaluated in the northern region.