School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemOn assessing some of the net effects of IPM(Australian Agricultural and Resource Economics Society, 1996)The potential costs and benefits, private and external, of a shift to Integrated Pest Management (IPM) are considered. A method is developed to estimate the private net returns of IPM in particular farm situations. This method is then applied to compare the financial characteristics of IPM and conventional systems in apple and grain legume production in Victoria. A key finding is that in a 'typical year' of a 'typical operation' the annual net returns of a shift to IPM, in both crops, could be positive. Externalities associated with IPM may be positive or negative depending on the circumstances.
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ItemAn economic evaluation of alternative pest management strategies in Northern Victorian peach orchards(Australian Agricultural Economics Society, 1994)
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ItemThe tax Australia has to have(Australian Agricultural Economics Society, 1994)
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ItemThe decision to invest in lime for acid soils(Australian Agricultural Economics Society, 1994)This study is about how to make long-term farm management decisions effectively when the amount of information available is extremely limited. Long-term decisions rely on judgements of input responses and outcomes which are uncertain or unknown. This is the reality of farm management decision-making. Complex decisions have to be based, in part, on some very ‘soft’ data. Therefore, good decision-making relies on good judgement. Judgement derives from lessons from experience (old information), and from the assimilation of new information generated by analysis of all the available information. In this study, information about liming acid soils in north-eastern Victoria is used, along with farm management information, to generate further information, and thus facilitate the making of some judgements about the economic merit of investing in lime on a particular farm. Soil acidity is a physical phenomenon which has the potential to lower agricultural production and reduce farm profitability. The potential of soil acidity to lower agricultural production has led to it being described as a serious problem for agricultural activities in south-eastern Australia (Coventry 1985; Coventry et. al. 1987a; Cregan 1980; Ellington 1984b; Evans 1991; Helyar et. al. 1990; Reeves and Ellington 1985; and Williams 1980). Making long-term farm management decisions with the limited information which is available requires finding a way to analyse and assimilate the available and new information, and then presenting it in such a way that sound judgements can be made about the likelihood of the possible outcomes actually eventuating. In this study, the standard farm management investment technique discounted cash flow analysis is used. To facilitate making sound judgements about the likelihood of outcomes, a break-even method is developed and applied to the major unknown parameter. The break-even level of the critical factor in the investment provides the decision-maker, who is looking ahead in a world of very uncertain input responses and outcomes, with something concrete on which to focus. Judgements can be formed about the likelihood of this critical level of the critical variable being achieved. The analysis of liming as an investment provides information on the yields required for an investment in lime on the case study farm to break-even, that is, to cover all costs, including the opportunity cost of capital. The judgement made as to whether such yields are achievable will determine whether liming is a worthwhile investment on the case study farm and, implicitly, whether soil acidity is a problem requiring action by the case study farmer at this stage.
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ItemNo Preview AvailableBootstrapping of gene-expression data improves and controls the false discovery rate of differentially expressed genes(E D P SCIENCES, 2004)The ordinary-, penalized-, and bootstrap t-test, least squares and best linear unbiased prediction were compared for their false discovery rates (FDR), i.e. the fraction of falsely discovered genes, which was empirically estimated in a duplicate of the data set. The bootstrap-t-test yielded up to 80% lower FDRs than the alternative statistics, and its FDR was always as good as or better than any of the alternatives. Generally, the predicted FDR from the bootstrapped P-values agreed well with their empirical estimates, except when the number of mRNA samples is smaller than 16. In a cancer data set, the bootstrap-t-test discovered 200 differentially regulated genes at a FDR of 2.6%, and in a knock-out gene expression experiment 10 genes were discovered at a FDR of 3.2%. It is argued that, in the case of microarray data, control of the FDR takes sufficient account of the multiple testing, whilst being less stringent than Bonferoni-type multiple testing corrections. Extensions of the bootstrap simulations to more complicated test-statistics are discussed.
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ItemNo Preview AvailableMapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data(BMC, 2004)A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD) information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC) methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.
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ItemNo Preview AvailableTesting the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome(EDP SCIENCES S A, 2006)Despite growing evidence of rapid evolution in protein coding genes, the contribution of positive selection to intra- and interspecific differences in protein coding regions of the genome is unclear. We attempted to see if genes coding for secreted proteins and genes with narrow expression, specifically those preferentially expressed in the mammary gland, have diverged at a faster rate between domestic cattle (Bos taurus) and humans (Homo sapiens) than other genes and whether positive selection is responsible. Using a large data set, we identified groups of genes based on secretion and expression patterns and compared them for the rate of nonsynonymous (dN) and synonymous (dS) substitutions per site and the number of radical (Dr) and conservative (Dc) amino acid substitutions. We found evidence of rapid evolution in genes with narrow expression, especially for those expressed in the liver and mammary gland and for genes coding for secreted proteins. We compared common human polymorphism data with human-cattle divergence and found that genes with high evolutionary rates in human-cattle divergence also had a large number of common human polymorphisms. This argues against positive selection causing rapid divergence in these groups of genes. In most cases dN/dS ratios were lower in human-cattle divergence than in common human polymorphism presumably due to differences in the effectiveness of purifying selection between long-term divergence and short-term polymorphism.
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ItemNo Preview AvailableThe distribution of the effects of genes affecting quantitative traits in livestock(E D P SCIENCES, 2001)Meta-analysis of information from quantitative trait loci (QTL) mapping experiments was used to derive distributions of the effects of genes affecting quantitative traits. The two limitations of such information, that QTL effects as reported include experimental error, and that mapping experiments can only detect QTL above a certain size, were accounted for. Data from pig and dairy mapping experiments were used. Gamma distributions of QTL effects were fitted with maximum likelihood. The derived distributions were moderately leptokurtic, consistent with many genes of small effect and few of large effect. Seventeen percent and 35% of the leading QTL explained 90% of the genetic variance for the dairy and pig distributions respectively. The number of segregating genes affecting a quantitative trait in dairy populations was predicted assuming genes affecting a quantitative trait were neutral with respect to fitness. Between 50 and 100 genes were predicted, depending on the effective population size assumed. As data for the analysis included no QTL of small effect, the ability to estimate the number of QTL of small effect must inevitably be weak. It may be that there are more QTL of small effect than predicted by our gamma distributions. Nevertheless, the distributions have important implications for QTL mapping experiments and Marker Assisted Selection (MAS). Powerful mapping experiments, able to detect QTL of 0.1sigma(p), will be required to detect enough QTL to explain 90% the genetic variance for a quantitative trait.
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ItemNo Preview AvailablePrediction of identity by descent probabilities from marker-haplotypes(BIOMED CENTRAL LTD, 2001)The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (i.e. all information came from the marker genotypes), and the situation where, say T, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.
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ItemNo Preview AvailableRiparian tree water use by eucalyptus coolabah in the Lake Eyre Basin(Conference Organising Committee, 2006)The Lake Eyre Basin (LEB) is characterised by enormous stream flow variability, low rainfall, saline groundwater and at times saline surface water; conditions that demand flexible tree water use strategies in the riparian zone. In the lower reaches of the Diamantina River, the water sources and extraction patterns of Eucalyptus coolabah were examined using isotope data from xylem, soil water, groundwater and surface water. Additionally, soil chloride and matric potential data were used to infer zones of water availability for root uptake. It was found that despite their elevated salinity, groundwater and soil water formed a large proportion of the transpiration flux, with little contribution from standing pools of surface water. At two sites located on the dry floodplain, the data indicated E. coolabah relied substantially on groundwater with a salinity exceeding 30,000 mgL-1Cl. However, some dilution with fresher soil water was evident at most sites, highlighting the importance of flooding in replenishing soil water. Water extraction primarily occurred in the unsaturated zone where a compromise between salinity and source reliability was required. However, E. coolabah was found to have higher salinity tolerances than previously reported for Eucalyptus species.