Flying-Fox Species Density-A Spatial Risk Factor for Hendra Virus Infection in Horses in Eastern Australia

Hendra virus causes sporadic but typically fatal infection in horses and humans in eastern Australia. Fruit-bats of the genus Pteropus (commonly known as flying-foxes) are the natural host of the virus, and the putative source of infection in horses; infected horses are the source of human infection. Effective treatment is lacking in both horses and humans, and notwithstanding the recent availability of a vaccine for horses, exposure risk mitigation remains an important infection control strategy. This study sought to inform risk mitigation by identifying spatial and environmental risk factors for equine infection using multiple analytical approaches to investigate the relationship between plausible variables and reported Hendra virus infection in horses. Spatial autocorrelation (Global Moran’s I) showed significant clustering of equine cases at a distance of 40 km, a distance consistent with the foraging ‘footprint’ of a flying-fox roost, suggesting the latter as a biologically plausible basis for the clustering. Getis-Ord Gi* analysis identified multiple equine infection hot spots along the eastern Australia coast from far north Queensland to central New South Wales, with the largest extending for nearly 300 km from southern Queensland to northern New South Wales. Geographically weighted regression (GWR) showed the density of P. alecto and P. conspicillatus to have the strongest positive correlation with equine case locations, suggesting these species are more likely a source of infection of Hendra virus for horses than P. poliocephalus or P. scapulatus. The density of horses, climate variables and vegetation variables were not found to be a significant risk factors, but the residuals from the GWR suggest that additional unidentified risk factors exist at the property level. Further investigations and comparisons between case and control properties are needed to identify these local risk factors.

Temporal and Spatial Patterns in Recruitment of Three Penaeid Prawns in Moreton Bay, Queensland, Australia

The size at recruitment, temporal and spatial distribution, and abiotic factors influencing abundance of three commercially important species of penaeid prawns in the sublittoral trawl grounds of Moreton Bay (Queensland, Australia) were compared. Metapenaeus bennettae and Penaeus plebejus recruit to the trawl grounds at sizes which are relatively small (14-15 mm carapace length, CL) and below that at which prawns are selected for, and retained, in the fleet's cod-ends. In contrast, Penaeus esculenlus recruit at the relatively large size of 27 mm CL from February to May, well above the size ranges selected for. Recruitment of M. bennettae extends over several months, September-October and February March, and was thus likely to be bi-annual, while the recruitment period of P. plebejus was distinct, peaking in October-November each year. Size classes of M . bennettae were the most spatially stratified of the three species. Catch rates of recruits were negatively correlated with depth for all three species, and were also negatively correlated with salinity for M. bennettae.

Correlation of plasma IGF-I concentrations and growth rate in aquacultured finfish: a tool for assessing the potential of new diets

A recently developed radioimmunoassay (RIA) for measuring insulin-like growth factor (IGF-I) in a variety of fish species was used to investigate the correlation between growth rate and circulating IGF-I concentrations of barramundi (Lates calcarifer), Atlantic salmon (Salmo salar) and Southern Bluefin tuna (Thunnus maccoyii). Plasma IGF-I concentration significantly increased with increasing ration size in barramundi and IGF-I concentration was positively correlated to growth rates obtained in Atlantic salmon (r2=0.67) and barramundi (r2=0.65) when fed a variety of diet formulations. IGF-I was also positively correlated to protein concentration (r2=0.59). This evidence suggested that measuring IGF-I concentration may provide a useful tool for monitoring fish growth rate and also as a method to rapidly assess different aquaculture diets. However, no such correlation was demonstrated in the tuna study probably due to seasonal cooling of sea surface temperature shortly before blood was sampled. Thus, some recommendations for the design and sampling strategy of nutritional trials where IGF-I concentrations are measured are discussed

Assessing the relationship between shire winter crop yield and seasonal variability of the MODIS NDVI and EVI images

Australian researchers have been developing robust yield estimation models, based mainly on the crop growth response to water availability during the crop season. However, knowledge of spatial distribution of yields within and across the production regions can be improved by the use of remote sensing techniques. Images of Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices, available since 1999, have the potential to contribute to crop yield estimation. The objective of this study was to analyse the relationship between winter crop yields and the spectral information available in MODIS vegetation index images at the shire level. The study was carried out in the Jondaryan and Pittsworth shires, Queensland , Australia . Five years (2000 to 2004) of 250m resolution, 16-day composite of MODIS Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) images were used during the winter crop season (April to November). Seasonal variability of the profiles of the vegetation index images for each crop season using different regions of interest (cropping mask) were displayed and analysed. Correlation analysis between wheat and barley yield data and MODIS image values were also conducted. The results showed high seasonal variability in the NDVI and EVI profiles, and the EVI values were consistently lower than those of the NDVI. The highest image values were observed in 2003 (in contrast to 2004), and were associated with rainfall amount and distribution. The seasonal variability of the profiles was similar in both shires, with minimum values in June and maximum values at the end of August. NDVI and EVI images showed sensitivity to seasonal variability of the vegetation and exhibited good association (e.g. r = 0.84, r = 0.77) with winter crop yields.

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.

CIMMYT-selected derived synthetic bread wheats for rainfed environments: Yield evaluation in Mexico and Australia.

Synthetic backcrossed-derived bread wheats (SBWs) from CIMMYT were grown in the Northwest of Mexico at Centro de Investigaciones Agrícolas del Noroeste (CIANO) and sites across Australia during three seasons. During three consecutive years Australia received “shipments” of different SBWs from CIMMYT for evaluation. A different set of lines was evaluated each season, as new materials became available from the CIMMYT crop enhancement program. These consisted of approximately 100 advanced lines (F7) per year. SBWs had been top and backcrossed to CIMMYT cultivars in the first two shipments and to Australian wheat cultivars in the third one. At CIANO, the SBWs were trialled under receding soil moisture conditions. We evaluated both the performance of each line across all environments and the genotype-by-environment interaction using an analysis that fits a multiplicative mixed model, adjusted for spatial field trends. Data were organised in three groups of multienvironment trials (MET) containing germplasm from shipment 1 (METShip1), 2 (METShip2), and 3 (METShip3), respectively. Large components of variance for the genotype × environment interaction were found for each MET analysis, due to the diversity of environments included and the limited replication over years (only in METShip2, lines were tested over 2 years). The average percentage of genetic variance explained by the factor analytic models with two factors was 50.3% for METShip1, 46.7% for METShip2, and 48.7% for METShip3. Yield comparison focused only on lines that were present in all locations within a METShip, or “core” SBWs. A number of core SBWs, crossed to both Australian and CIMMYT backgrounds, outperformed the local benchmark checks at sites from the northern end of the Australian wheat belt, with reduced success at more southern locations. In general, lines that succeeded in the north were different from those in the south. The moderate positive genetic correlation between CIANO and locations in the northern wheat growing region likely reflects similarities in average temperature during flowering, high evaporative demand, and a short flowering interval. We are currently studying attributes of this germplasm that may contribute to adaptation, with the aim of improving the selection process in both Mexico and Australia.

Spatial requirements of animals: Allometry and beyond

Space allowance is a major factor influencing animal welfare. For livestock, at least, it plays a critical role in profitability, yet there is little information on the amount of space that animals require. The amount of space an animal occupies as a consequence of its shape and size can be estimated using allometry; linear dimensions (L) can be expressed as L = kW1/3 and surface area (S) as S = kW2/3, where k = a constant and W = the weight of the animal. Such equations have been used to determine the amount of space needed by standing (area [m2] = 0.019W0.66) and lying (area [m2] = 0.027W0.67) animals. Limited studies on the lying down and standing up behaviors of pigs and cattle suggest that the amount of space required can be estimated by area (m2) = 0.047W0.66. Linear space required per animal for behaviors such as feeding or drinking from a trough can be estimated from 0.064W0.33, but in groups this requirement will be affected by social interactions among group members and the amount of competition for the resource. Determining the amount of space for groups of animals is complex, as the amount of useable space can vary with group size and by how group members share space in time. Some studies have been conducted on the way in which groups of domestic fowl use space, but overall, we know very little about the ways in which livestock time-share space, synchronicity in the performance of behaviors, and the effects of spatial restrictions on behavior and welfare.

Spatial patterns of sub-tidal seagrasses and their tissue nutrients in the Torres Strait, northern Australia: Implications for management

The distribution and nutritional profiles of sub-tidal seagrasses from the Torres Strait were surveyed and mapped across an area of 31,000 km2. Benthic sediment composition, water depth, seagrass species type and nutrients were sampled at 168 points selected in a stratified representative pattern. Eleven species of seagrass were present at 56 (33.3%) of the sample points. Halophila spinulosa, Halophila ovalis, Cymodocea serrulata and Syringodium isoetifolium were the most common species and these were nutrient profiled. Sub-tidal seagrass distribution (and associated seagrass nutrient concentrations) was generally confined to northern-central and south-western regions of the survey area (spatial and nutritional information can be used by local agencies to manage and to protect the ecological, economic and cultural values of the sub-tidal seagrass ecosystems and associated fisheries of the Torres Strait.

Spatial model of site index based on Y-ray spectrometry and a digital elevation model for two Pinus species in Tuan Toolara State Forest, Queensland, Australia

Site index prediction models are an important aid for forest management and planning activities. This paper introduces a multiple regression model for spatially mapping and comparing site indices for two Pinus species (Pinus elliottii Engelm. and Queensland hybrid, a P. elliottii x Pinus caribaea Morelet hybrid) based on independent variables derived from two major sources: g-ray spectrometry (potassium (K), thorium (Th), and uranium (U)) and a digital elevation model (elevation, slope, curvature, hillshade, flow accumulation, and distance to streams). In addition, interpolated rainfall was tested. Species were coded as a dichotomous dummy variable; interaction effects between species and the g-ray spectrometric and geomorphologic variables were considered. The model explained up to 60% of the variance of site index and the standard error of estimate was 1.9 m. Uranium, elevation, distance to streams, thorium, and flow accumulation significantly correlate to the spatial variation of the site index of both species, and hillshade, curvature, elevation and slope accounted for the extra variability of one species over the other. The predicted site indices varied between 20.0 and 27.3 m for P. elliottii, and between 23.1 and 33.1 m for Queensland hybrid; the advantage of Queensland hybrid over P. elliottii ranged from 1.8 to 6.8 m, with the mean at 4.0 m. This compartment-based prediction and comparison study provides not only an overview of forest productivity of the whole plantation area studied but also a management tool at compartment scale.

Spatial and temporal variation and effects of changes in management in discard rates from the commercial reef line fishery of the Great Barrier Reef, Australia

Discarding in commercially exploited fisheries has received considerable attention in the last decade, though only more recently in Australia. The Reef Line fishery (RLF) of the Great Barrier Reef (GBR) in Australia is a large-scale multi-sector, multi-species, highly regulated hook and line fishery with the potential for high levels of discarding. We used a range of data sources to estimate discard rates and discard quantities for the two main target groups of the RLF, the coral trout, Plectropomus spp, and the red throat emperor, Lethrinus miniatus, and investigated possible effects on discarding of recent changes in management of the fishery. Fleet-wide estimates of total annual quantities discarded from 1989 to 2003 were 292-622 t and 33-95 t for coral trout and red throat emperor, respectively. Hypothetical scenarios of high-grading after the introduction of a total allowable commercial catch for coral trout resulted in increases in discard quantities up to 3895 t, while no high-grading still meant 421 t were discarded. Increasing the minimum size limit of red throat emperor from 35 to 38 cm also increased discards to an estimated 103 t. We provide spatially and temporally explicit estimates of discarding for the two most important species in the GBR RLF of Australia to demonstrate the importance of accounting for regional variation in quantification of discarding. Effects of management changes on discarding are also highlighted. This study provides a template for exploring discarding levels for other species in the RLF and elsewhere.

A spatial assessment of the risk to a mobile marine mammal from bycatch

Several species of marine mammals are at risk of extinction from being captured as bycatch in commercial fisheries. Various approaches have been developed and implemented to address this bycatch problem, including devices and gear changes, time and area closures and fisheries moratoria. Most of these solutions are difficult to implement effectively, especially for artisanal fisheries in developing countries and remote regions. Re-zoning of the Great Barrier Reef World Heritage Area (GBRWHA) in 2004 closed 33% of the region to extractive activities, including commercial fishing. However, the impact of re-zoning and the associated industry restructuring on a threatened marine mammal, the dugong (Dugong dugon), is difficult to quantify. Accurate information on dugong bycatch in commercial nets is unavailable because of the large geographic extent of the GBRWHA, the remoteness of the region adjacent to the Cape York Peninsula where most dugongs occur and the artisanal nature of the fishery. In the face of this uncertainty, a spatial risk-assessment approach was used to evaluate the re-zoning and associated industry restructuring for their ability to reduce the risk of dugong bycatch from commercial fisheries netting. The new zoning arrangements appreciably reduced the risk of dugong bycatch by reducing the total area where commercial netting is permitted. Netting is currently not permitted in 67% of dugong habitats of high conservation value, a 56% improvement over the former arrangements. Re-zoning and industry restructuring also contributed to a 22% decline in the spatial extent of conducted netting. Spatial risk assessment approaches that evaluate the risk of mobile marine mammals from bycatch are applicable to other situations where there is limited information on the location and intensity of bycatch, including remote regions and developing countries where resources are limited.

Characterization of disease resistance gene candidates of the nucleotide binding site (NBS) type from banana and correlation of a transcriptional polymorphism with resistance to Fusarium oxysporum f.sp. cubense race 4

Most plant disease resistance (R) genes encode proteins with a nucleotide binding site and leucine-rich repeat structure (NBS-LRR). In this study, degenerate primers were used to amplify genomic NBS-type sequences from wild banana (Musa acuminata ssp. malaccensis) plants resistant to the fungal pathogen Fusarium oxysporum formae specialis (f. sp.) cubense (FOC) race 4. Five different classes of NBS-type sequences were identified and designated as resistance gene candidates (RGCs). The deduced amino acid sequences of the RGCs revealed the presence of motifs characteristic of the majority of known plant NBS-LRR resistance genes. Structural and phylogenetic analyses grouped the banana RGCs within the non-TIR (homology to Toll/interleukin-1 receptors) subclass of NBS sequences. Southern hybridization showed that each banana RGC is present in low copy number. The expression of the RGCs was assessed by RT-PCR in leaf and root tissues of plants resistant or susceptible to FOC race 4. RGC1, 3 and 5 showed a constitutive expression profile in both resistant and susceptible plants whereas no expression was detected for RGC4. Interestingly, RGC2 expression was found to be associated only to FOC race 4 resistant lines. This finding could assist in the identification of a FOC race 4 resistance gene.

Odour emissions from anaerobic piggery ponds. 2: Improving estimates of emission rate through recognition of spatial variability

Odour emission rates were measured for seven different anaerobic ponds treating piggery wastes at six to nine discrete locations across the surface of each pond on each sampling occasion over a thirteen month period. Significant variability in emission rates were observed for each pond. Measurement of a number of water quality variables in pond liquor samples collected at the same time and from the same locations as the odour samples indicated that the composition of the pond liquor was also variable. The results indicated that spatial variability was a real phenomenon and could have a significant impact on odour assessment practices. Considerably more odour samples would be required to characterise pond emissions than currently recommended by most practitioners, or regulatory agencies.

Spatial and temporal patterns of feral pig diggings in rainforests of north Queensland

Feral pigs (Sus scrofa) are believed to have a severe negative impact on the ecological values of tropical rainforests in north Queensland, Australia. Most perceptions of the environmental impacts of feral pigs focus on their disturbance of the soil or surface material (diggings). Spatial and temporal patterns of feral pig diggings were identified in this study: most diggings occurred in the early dry season and predominantly in moist soil (swamp and creek) microhabitats, with only minimal pig diggings found elsewhere through the general forest floor. The overall mean daily pig diggings were 0.09% of the rainforest floor. Most diggings occurred 3-4 months after the month of maximum rainfall. Most pig diggings were recorded in highland swamps, with over 80% of the swamp areas dug by pigs at some time during the 18-month study period. These results suggest that management of feral pig impacts should focus on protecting swamp and creek microhabitats in the rainforest, which are preferred by pigs for digging and which have a high environmental significance.

Reassessing spatial and temporal dynamics of kangaroo populations

Long-running datasets from aerial surveys of kangaroos (Macropus giganteus, Macropus [uliginosus, Macropus robustus and Macropus rufus) across Queensland, New South Wales and South Australia have been analysed, seeking better predictors of rates of increase which would allow aerial surveys to be undertaken less frequently than annually. Early models of changes in kangaroo numbers in response to rainfall had shown great promise, but much variability. We used normalised difference vegetation index (NDVI) instead, reasoning that changes in pasture condition would provide a better predictor than rainfall. However, except at a fine scale, NDVI proved no better; although two linked periods of rainfall proved useful predictors of rates of increase, this was only in some areas for some species. The good correlations reported in earlier studies were a consequence of data dominated by large droughtinduced adult mortality, whereas over a longer time frame and where changes between years are less dramatic, juvenile survival has the strongest influence on dynamics. Further, harvesting, density dependence and competition with domestic stock are additional and important influences and it is now clear that kangaroo movement has a greater influence on population dynamics than had been assumed. Accordingly, previous conclusions about kangaroo populations as simple systems driven by rainfall need to be reassessed. Examination of this large dataset has permitted descriptions of shifts in distribution of three species across eastern Australia, changes in dispersion in response to rainfall, and an evaluation of using harvest statistics as an index of density and harvest rate. These results have been combined into a risk assessment and decision theory framework to identify optimal monitoring strategies.