Evolutionary relationships between bat coronaviruses and their hosts

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

Microbial ecology of the equine hindgut during oligofructose-induced laminitis

Alimentary carbohydrate overload is a significant cause of laminitis in horses and is correlated with drastic shifts in the composition of hindgut microbiota. Equine hindgut streptococcal species (EHSS), predominantly Streptococcus lutetiensis, have been shown to be the most common microorganisms culturable from the equine caecum prior to the onset of laminitis. However, the inherent biases of culture-based methods are estimated to preclude up to 70% of the normal caecal microbiota. The objective of this study was to evaluate bacterial population shifts occurring in the equine caecum throughout the course of oligofructose-induced laminitis using several culture-independent techniques and to correlate these with caecal lactate, volatile fatty acid and degrees of polymerization 3-7 fructo-oligosaccharide concentrations. Our data conclusively show that of the total microbiota present in the equine hindgut, the EHSS S. lutetiensis is the predominant microorganism that proliferates prior to the onset of laminitis, utilizing oligofructose to produce large quantities of lactate. Population shifts in lactobacilli and Escherichia coli subpopulations occur secondarily to the EHSS population shifts, thus confirming that lactobacilli and coliforms have no role in laminitis. A large, curved, Gram-negative rod previously observed during the early phases of laminitis induction was most closely related to the Anaerovibrio genus and most likely represents a new, yet to be cultured, genus and species. Correlation of fluorescence in situ hybridization and quantitative real-time PCR results provide evidence supporting the hypothesis that laminitis is associated with the death en masse and rapid cell lysis of EHSS. If EHSS are lysed, liberated cellular components may initiate laminitis.

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

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

Detecting quantitative trait loci affecting beef tenderness on bovine chromosome 7 near calpastatin and lysyl oxidase

From a study of 3 large half-sib families of cattle, we describe linkage between DNA polymorphisms on bovine chromosome 7 and meat tenderness. Quantitative trait loci (QTL) for Longissimus lumborum peak force (LLPF) and Semitendonosis adhesion (STADH) were located to this map of DNA markers, which includes the calpastatin ( CAST) and lysyl oxidase (LOX) genes. The LLPF QTL has a maximum lodscore of 4.9 and allele substitution of approximately 0.80 of a phenotypic standard deviation, and the peak is located over the CAST gene. The STADH QTL has a maximum lodscore of 3.5 and an allele substitution of approximately 0.37 of a phenotypic standard deviation, and the peak is located over the LOX gene. This suggests 2 separate likelihood peaks on the chromosome. Further analyses of meat tenderness measures in the Longissimus lumborum, LLPF and LL compression (LLC), in which outlier individuals or kill groups are removed, demonstrate large shifts in the location of LLPF QTL, as well as confirming that there are indeed 2 QTL on bovine chromosome 7. We found that both QTL are reflected in both LLPF and LLC measurements, suggesting that both these components of tenderness, myofibrillar and connective tissue, are detected by both measurements in this muscle.

The limit to wheat water-use efficiency in eastern Australia. I. Gradients in the radiation environment and atmospheric demand

In the wheatbelt of eastern Australia, rainfall shifts from winter dominated in the south (South Australia, Victoria) to summer dominated in the north (northern New South Wales, southern Queensland). The seasonality of rainfall, together with frost risk, drives the choice of cultivar and sowing date, resulting in a flowering time between October in the south and August in the north. In eastern Australia, crops are therefore exposed to contrasting climatic conditions during the critical period around flowering, which may affect yield potential, and the efficiency in the use of water (WUE) and radiation (RUE). In this work we analysed empirical and simulated data, to identify key climatic drivers of potential water- and radiation-use efficiency, derive a simple climatic index of environmental potentiality, and provide an example of how a simple climatic index could be used to quantify the spatial and temporal variability in resource-use efficiency and potential yield in eastern Australia. Around anthesis, from Horsham to Emerald, median vapour pressure deficit (VPD) increased from 0.92 to 1.28 kPa, average temperature increased from 12.9 to 15.2°C, and the fraction of diffuse radiation (FDR) decreased from 0.61 to 0.41. These spatial gradients in climatic drivers accounted for significant gradients in modelled efficiencies: median transpiration WUE (WUEB/T) increased southwards at a rate of 2.6% per degree latitude and median RUE increased southwards at a rate of 1.1% per degree latitude. Modelled and empirical data confirmed previously established relationships between WUEB/T and VPD, and between RUE and photosynthetically active radiation (PAR) and FDR. Our analysis also revealed a non-causal inverse relationship between VPD and radiation-use efficiency, and a previously unnoticed causal positive relationship between FDR and water-use efficiency. Grain yield (range 1-7 t/ha) measured in field experiments across South Australia, New South Wales, and Queensland (n = 55) was unrelated to the photothermal quotient (Pq = PAR/T) around anthesis, but was significantly associated (r2 = 0.41, P < 0.0001) with newly developed climatic index: a normalised photothermal quotient (NPq = Pq . FDR/VPD). This highlights the importance of diffuse radiation and vapour pressure deficit as sources of variation in yield in eastern Australia. Specific experiments designed to uncouple VPD and FDR and more mechanistic crop models might be required to further disentangle the relationships between efficiencies and climate drivers.

Weed management in wide-row cropping systems: a review of current practices and risks for Australian farming systems.

Growing agricultural crops in wide row spacings has been widely adopted to conserve water, to control pests and diseases, and to minimise problems associated with sowing into stubble. The development of herbicide resistance combined with the advent of precision agriculture has resulted in a further reason for wide row spacings to be adopted: weed control. Increased row spacing enables two different methods of weed control to be implemented with non-selective chemical and physical control methods utilised in the wide inter-row zone, with or without selective chemicals used on the on-row only. However, continual application of herbicides and tillage on the inter-row zone brings risks of herbicide resistance, species shifts and/or changes in species dominance, crop damage, increased costs, yield losses, and more expensive weed management technology.

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.

Variation in ecophysiology and carbon economy of invasive and native woody vines of riparian zones in south-eastern Queensland

Exotic and invasive woody vines are major environmental weeds of riparian areas, rainforest communities and remnant natural vegetation in coastal eastern Australia, where they smother standing vegetation, including large trees, and cause canopy collapse. We investigated, through glasshouse resource manipulative experiments, the ecophysiological traits that might facilitate faster growth, better resource acquisition and/or utilization and thus dominance of four exotic and invasive vines of South East Queensland, Australia, compared with their native counterparts. Relative growth rate was not significantly different between the two groups but water use efficiency (WUE) was higher in the native species while the converse was observed for light use efficiency (quantum efficiency, AQE) and maximum photosynthesis on a mass basis (Amax mass). The invasive species, as a group, also exhibited higher respiration load, higher light compensation point and higher specific leaf area. There were stronger correlations of leaf traits and greater structural (but not physiological) plasticity in invasive species than in their native counterparts. The scaling coefficients of resource use efficiencies (WUE, AQE and respiration efficiency) as well as those of fitness (biomass accumulated) versus many of the performance traits examined did not differ between the two species-origin groups, but there were indications of significant shifts in elevation (intercept values) and shifts along common slopes in many of these relationships – signalling differences in carbon economy (revenue returned per unit energy invested) and/or resource usage. Using ordination and based on 14 ecophysiological attributes, a fair level of separation between the two groups was achieved (51.5% explanatory power), with AQE, light compensation point, respiration load, WUE, specific leaf area and leaf area ratio, in decreasing order, being the main drivers. This study suggests similarity in trait plasticity, especially for physiological traits, but there appear to be fundamental differences in carbon economy and resource conservation between native and invasive vine species.

Native and exotic pests of Eucalyptus: A worldwide perspective.

Eucalyptus species, native to Australia, Indonesia, the Philippines, and New Guinea, are the most widely planted hardwood timber species in the world. The trees, moved around the globe as seeds, escaped the diverse community of herbivores found in their native range. However, a number of herbivore species from the native range of eucalypts have invaded many Eucalyptus-growing regions in North America, Europe, Africa, Asia, and South America in the last 30 years. In addition, there have been shifts of native species, particularly in Africa, Asia, and South America, onto Eucalyptus. There are risks that these species as well as generalist herbivores from other parts of the world will invade Australia and threaten the trees in their native range. The risk to Eucalyptus plantations in Australia is further compounded by planting commercially important species outside their endemic range and shifting of local herbivore populations onto new host trees. Understanding the mechanisms underlying host specificity of Australian insects can provide insight into patterns of host range expansion of both native and exotic insects.

Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (FST = 0· 09 − 0· 49; P < 0· 05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

Spatial subdivision among assemblages of Spanish mackerel, Scomberomorus commerson (Pisces: Scombridae) across northern Australia: implications for fisheries management

Aim: This study investigated the use of stable δ13C and δ18O isotopes in the sagittal otolith carbonate of narrow-barred Spanish mackerel, Scomberomorus commerson, as indicators of population structure across Australia. Location: Samples were collected from 25 locations extending from the lower west coast of Western Australia (30°), across northern Australian waters, and to the east coast of Australia (18°) covering a coastline length of approximately 9500 km, including samples from Indonesia. Methods: The stable δ13C and δ18O isotopes in the sagittal otolith carbonate of S. commerson were analysed using standard mass spectrometric techniques. The isotope ratios across northern Australian subregions were subjected to an agglomerative hierarchical cluster analysis to define subregions. Isotope ratios within each of the subregions were compared to assess population structure across Australia. Results: Cluster analysis separated samples into four subregions: central Western Australia, north Western Australia, northern Australia and the Gulf of Carpentaria and eastern Australia. Isotope signatures for fish from a number of sampling sites from across Australia and Indonesia were significantly different, indicating population separation. No significant differences were found in otolith isotope ratios between sampling times (no temporal variation). Main conclusions: Significant differences in the isotopic signatures of S. commerson demonstrate that there is unlikely to be any substantial movement of fish among these spatially discrete adult assemblages. The lack of temporal variation among otolith isotope ratios indicates that S. commerson populations do not undergo longshore spatial shifts in distribution during their life history. The temporal persistence of spatially explicit stable isotopic signatures indicates that, at these spatial scales, the population units sampled comprise functionally distinct management units or separate ‘stocks’ for many of the purposes of fisheries management. The spatial subdivision evident among populations of S. commerson across northern and western Australia indicates that it may be advantageous to consider S. commerson population dynamics and fisheries management from a metapopulation perspective (at least at the regional level).

Wastewater remediation options for prawn farms - Aquaculture Industry Development Initiative 2002-04.

There are many potential bioremediation approaches that may be suitable for prawn farms in Queensland. Although most share generally accepted bioremediation principles, advocacy for different methods tends to vary widely. This diversity of approach is particularly driven by the availability and knowledge of functional species at different localities around the world. In Australia, little is known about the abilities of many native species in this regard, and translocation and biosecurity issues prevent the use of exotic species that have shown potential in other countries. Species selected must be tolerant of eutrophic conditions and ecological shifts, because prawn pond nutrient levels and pathways can vary with different assemblages of autotrophic and heterotrophic organisms. Generally, they would be included in a constructed ecosystem because of their functional contributions to nutrient cycling and uptake, and to create nutrient sinks in forms of harvestable biomass. Wide salinity, temperature and water quality tolerances are also valuable attributes for selected species due to the sometimes-pronounced effects of environmental extremes, and to provide over-wintering options and adequate safety margins in avoiding mass mortalities. To practically achieve these bioremediation polycultures on a large scale, and in concert with the operations of a prawn farm, methods involving seed production, stock management, and a range of other farm engineering and product handling systems need to be reliably achievable and economically viable. Research funding provided by the Queensland Government through the Aquaculture Industry Development Initiative (AIDI) 2002-04 has enabled a number of technical studies into biological systems to treat prawn farm effluent for recirculation and improved environmental sustainability. AIDI bioremediation research in southern Queensland was based at the Bribie Island Aquaculture Research Centre (BIARC), and was conducted in conjunction with AIDI genetics and selection research, and a Natural Heritage Trust (NHT) funded program (Coast and Clean Seas Project No.717757). This report compilation provides a summary of some of the work conducted within these programs.

Managing the grass-legume balance in Stylosanthes scabra cv. Seca pastures in central Queensland

The impacts of 4 grazing strategies (year-long grazing, summer grazing, winter grazing and winter grazing plus spring burning) on the grass:legume balance were studied between 2000 and 2006 in a pasture oversown with Stylosanthes scabra cv. Seca (Seca stylo) in central Queensland. Seasonal rainfall throughout the study was generally below average. Total pasture yields in autumn were higher in the 2 winter grazing than the 2 summer grazing treatments, largely reflecting the sampling time relative to when grazing occurred. There were few differences in Seca composition in autumn, although there was a clear trend for Seca composition to be reduced by winter grazing plus burning. Both the frequency of occurrence and plant density of Seca were higher under the 2 summer grazing treatments and there was also a trend for the density of juvenile plants (<5 cm height) to be higher in the 2 summer grazing treatments. Seca soil seed banks were generally low and were reduced in the winter grazing plus burning treatment in spring 2002. The frequency of the palatable perennial grass Pennisetum ciliaris (Biloela buffel grass) was reduced while that of the 'increaser' species Bothriochloa pertusa (Indian couch grass) and Stachytarpheta jamaicensis (snake weed) increased in the 2 summer grazing treatments compared with the 2 winter grazing treatments. Burning in spring increased soil loss in treatments grazed in winter. Differences in Seca frequency and density but not composition were explained by the 2 summer grazing treatments promoting 'gaps' in the pasture which were then colonised by Seca plants and other 'increaser' species. It was reasoned that, with time, mature Seca plants in the 2 winter grazing treatments would die so that Seca composition would eventually become higher under summer grazing regimes than under winter grazing. It was concluded that limiting grazing to particular seasons can alter legume:grass balance and that a time-frame of 5-8 years with average to good rainfall would be necessary to achieve large shifts in composition.

The intrinsic plasticity of farm businesses and their resilience to change. An Australian example.

This paper examines the idea that plasticity in farm management introduces resilience to change and allows farm businesses to perform when operating in highly variable environments. We also argue for the need to develop and apply more integrative assessments of farm performance that combine the use of modelling tools with deliberative processes involving farmers and researchers in a co-learning process, to more effectively identify and implement more productive and resilient farm businesses. In a plastic farming system, farm management is highly contingent on environmental conditions. In plastic farming systems farm managers constantly vary crops and inputs based on the availability of limited and variable resources (e.g. land, water, finances, labour, machinery, etc.), and signals from its operating environment (e.g. climate, markets), with the objective of maximising a number of, often competing, objectives (e.g. maximise profits, minimise risks, etc.). In contrast in more rigid farming systems farm management is more calendar driven and relatively fixed sequences of crops are regularly followed over time and across the farm. Here we describe the application of a whole farm simulation model to (i) compare, in silico, the sensitivity of two farming systems designs of contrasting levels of plasticity, operating in two contrasting environments, when exposed to a stressor in the form of climate change scenarios;(ii) investigate the presence of interactions and feedbacks at the field and farm levels capable of modifying the intensity and direction of the responses to climate signals; and (iii) discuss the need for the development and application of more integrative assessments in the analysis of impacts and adaptation options to climate change. In both environments, the more plastic farm management strategy had higher median profits and was less risky for the baseline and less intensive climate change scenarios (2030). However, for the more severe climate change scenarios (2070), the benefit of plastic strategies tended to disappear. These results suggest that, to a point, farming systems having higher levels of plasticity would enable farmers to more effectively respond to climate shifts, thus ensuring the economic viability of the farm business. Though, as the intensity of the stress increases (e.g. 2070 climate change scenario) more significant changes in the farming system might be required to adapt. We also found that in the case studies analysed here, most of the impacts from the climate change scenarios on farm profit and economic risk originated from important reductions in cropping intensity and changes in crop mix rather than from changes in the yields of individual crops. Changes in cropping intensity and crop mix were explained by the combination of reductions in the number of sowing opportunities around critical times in the cropping calendar, and to operational constraints at the whole farm level i.e. limited work capacity in an environment having fewer and more concentrated sowing opportunities. This indicates that indirect impacts from shifts in climate on farm operations can be more important than direct impacts from climate on the yield of individual crops. The results suggest that due to the complexity of farm businesses, impact assessments and opportunities for adaptation to climate change might also need to be pursued at higher integration levels than the crop or the field. We conclude that plasticity can be a desirable characteristic in farming systems operating in highly variable environments, and that integrated whole farm systems analyses of impacts and adaptation to climate change are required to identify important interactions between farm management decision rules, availability of resources, and farmer's preference.

A multi-faceted approach for quantifying the estuarine-nearshore transition in the life cycle of the bull shark, Carcharhinus leucas.

Understanding the ontogenetic habitat linkages of sharks is important for conservation and managing human interactions. We used acoustic telemetry, catch data, elemental and stable isotope signatures and dietary analyses to investigate ontogenetic habitat use in south-east Queensland, Australia, by the bull shark Carcharhinus leucas, a IUCN 'near-threatened' species that is implicated in many shark attacks on humans in urban estuaries. Sequential analyses for delta(15)N and delta(13)C of vertebrae from five adult C. leucas and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) for elemental composition from 23 C. leucas, including a pregnant female, were also used to trace ontogenetic habitat dependence. Acoustic telemetry indicated large juvenile and subadult C. leucas remained in estuarine habitats. delta(15)N values across shark vertebrae showed an ontogenetic shift in diet with total length (TL), confirmed by stomach contents. LA-ICPMS data reflected the ontogenetic movements of C. leucas from natal habitats. Differences among adults were gender related. Shifts in habitat use by subadults were correlated with a sigmoidal delta(13)C relationship with TL. C. leucas have a multipartite, stage-specific dependency in their transition between habitats along the freshwater-estuarine-marine continuum, making them particularly susceptible to the habitat alteration that is occurring globally.