A spatially explicit multi-competitor coexistence model of penaeid (shrimp) distribution on the Australian Great Barrier Reef

A spatially explicit multi-competitor coexistence model was developed for meta-populations of prawns (shrimp) occupying habitat patches across the Great Barrier Reef, where dispersal was localised and dispersal rates varied between species. Prawns were modelled as individuals moving to and from patches or cells according to pre-set decision rules. The landscape was simulated as a matrix of cells with each cell having a spatially explicit survival index for each species. Mixed species prawn assemblages moved over this simplified spatially explicit landscape. A low level of chronic random environmental disturbance was assumed (cyclone and tropical storm damage) with additional acute spatially confined disturbance due to commercial trawling, modelled as an increase in mortality affecting inter-specific competition. The general form of the results was for increased disturbance to favour good-colonising "generalist" species at the expense of good-competitor "specialists". Increasing fishing mortality (local patch extinctions) combined with poor colonising ability resulted in low equilibrium abundance for even the best competitor, while in the same circumstances the poorest competitor but best coloniser could have the highest equilibrium abundance. This mimics the switch from high-value prawn species to lower-value prawn species as trawl effort increases, reflected in historic catch and effort logbook data and reported anecdotaly from the north Queensland trawl fleet. To match the observed distribution and behaviour of prawn assemblages, a combination inter-species competition, a spatially explicit landscape, and a defined pattern of disturbance (trawling) was required. Modelling this combination could simulate not only general trends in spatial distribution of each of prawn species but also localised concentrations observed in the survey data

A multi-field bio-economic model of irrigated grain-cotton farming systems.

We present a participatory modelling framework that integrates information from interviews and discussions with farmers and consultants, with dynamic bio-economic models to answer complex questions on the allocation of limited resources at the farm business level. Interviews and discussions with farmers were used to: describe the farm business; identify relevant research questions; identify potential solutions; and discuss and learn from the whole-farm simulations. The simulations are done using a whole-farm, multi-field configuration of APSIM (APSFarm). APSFarm results were validated against farmers' experience. Once the model was accepted by the participating farmers as a fair representation of their farm business, the model was used to explore changes in the tactical or strategic management of the farm and results were then discussed to identify feasible options for improvement. Here we describe the modelling framework and present an example of the application of integrative whole farm system tools to answer relevant questions from an irrigated farm business case study near Dalby (151.27E - 27.17S), Queensland, Australia. Results indicated that even though cotton crops generates more farm income per hectare a more diversified rotation with less cotton would be relatively more profitable, with no increase in risk, as a more cotton dominated traditional rotation. Results are discussed in terms of the benefits and constraints from developing and applying more integrative approaches to represent farm businesses and their management in participatory research projects with the aim of designing more profitable and sustainable irrigated farming systems.

Tree species diversity and ecosystem function: Can tropical multi-species plantations generate greater productivity?

Results from the humid tropics of Australia demonstrate that diverse plantations can achieve greater productivity than monocultures. We found that increases in both the observed species number and the effective species richness were significantly related to increased levels of productivity as measured by stand basal area or mean individual tree basal area. Four of five plantation species were more productive in mixtures with other species than in monocultures, offering on average, a 55% increase in mean tree basal area. A general linear model suggests that species richness had a significant effect on mean individual tree basal area when environmental variables were included in the model. As monoculture plantations are currently the preferred reforestation method throughout the tropics these results suggest that significant productivity and ecological gains could be made if multi-species plantations are more broadly pursued.

The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials

Modeling of cultivar x trial effects for multienvironment trials (METs) within a mixed model framework is now common practice in many plant breeding programs. The factor analytic (FA) model is a parsimonious form used to approximate the fully unstructured form of the genetic variance-covariance matrix in the model for MET data. In this study, we demonstrate that the FA model is generally the model of best fit across a range of data sets taken from early generation trials in a breeding program. In addition, we demonstrate the superiority of the FA model in achieving the most common aim of METs, namely the selection of superior genotypes. Selection is achieved using best linear unbiased predictions (BLUPs) of cultivar effects at each environment, considered either individually or as a weighted average across environments. In practice, empirical BLUPs (E-BLUPs) of cultivar effects must be used instead of BLUPs since variance parameters in the model must be estimated rather than assumed known. While the optimal properties of minimum mean squared error of prediction (MSEP) and maximum correlation between true and predicted effects possessed by BLUPs do not hold for E-BLUPs, a simulation study shows that E-BLUPs perform well in terms of MSEP.

Estimation in a multiplicative mixed model involving a genetic relationship matrix.

Genetic models partitioning additive and non-additive genetic effects for populations tested in replicated multi-environment trials (METs) in a plant breeding program have recently been presented in the literature. For these data, the variance model involves the direct product of a large numerator relationship matrix A, and a complex structure for the genotype by environment interaction effects, generally of a factor analytic (FA) form. With MET data, we expect a high correlation in genotype rankings between environments, leading to non-positive definite covariance matrices. Estimation methods for reduced rank models have been derived for the FA formulation with independent genotypes, and we employ these estimation methods for the more complex case involving the numerator relationship matrix. We examine the performance of differing genetic models for MET data with an embedded pedigree structure, and consider the magnitude of the non-additive variance. The capacity of existing software packages to fit these complex models is largely due to the use of the sparse matrix methodology and the average information algorithm. Here, we present an extension to the standard formulation necessary for estimation with a factor analytic structure across multiple environments.

The Ethics of a Co-regulatory Model for Farm Animal Welfare Research

Standards for farm animal welfare are variously managed at a national level by government-led regulatory control, by consumer-led welfare economics and co-regulated control in a partnership between industry and government. In the latter case the control of research to support animal welfare standards by the relevant industry body may lead to a conflict of interest on the part of researchers, who are dependent on industry for continued research funding. We examine this dilemma by reviewing two case studies of research published under an Australian co-regulated control system. Evidence of unsupported conclusions that are favourable to industry is provided, suggesting that researchers do experience a conflict of interest that may influence the integrity of the research. Alternative models for the management of research are discussed, including the establishment of an independent research management body for animal welfare because of its public good status and the use of public money derived from taxation, with representation from government, industry, consumers, and advocacy groups.

An improved simulation model to predict pre-harvest aflatoxin risk in maize

Aflatoxin is a potent carcinogen produced by Aspergillus flavus, which frequently contaminates maize (Zea mays L.) in the field between 40° north and 40° south latitudes. A mechanistic model to predict risk of pre-harvest contamination could assist in management of this very harmful mycotoxin. In this study we describe an aflatoxin risk prediction model which is integrated with the Agricultural Production Systems Simulator (APSIM) modelling framework. The model computes a temperature function for A. flavus growth and aflatoxin production using a set of three cardinal temperatures determined in the laboratory using culture medium and intact grains. These cardinal temperatures were 11.5 °C as base, 32.5 °C as optimum and 42.5 °C as maximum. The model used a low (≤0.2) crop water supply to demand ratio—an index of drought during the grain filling stage to simulate maize crop's susceptibility to A. flavus growth and aflatoxin production. When this low threshold of the index was reached the model converted the temperature function into an aflatoxin risk index (ARI) to represent the risk of aflatoxin contamination. The model was applied to simulate ARI for two commercial maize hybrids, H513 and H614D, grown in five multi-location field trials in Kenya using site specific agronomy, weather and soil parameters. The observed mean aflatoxin contamination in these trials varied from <1 to 7143 ppb. ARI simulated by the model explained 99% of the variation (p ≤ 0.001) in a linear relationship with the mean observed aflatoxin contamination. The strong relationship between ARI and aflatoxin contamination suggests that the model could be applied to map risk prone areas and to monitor in-season risk for genotypes and soils parameterized for APSIM.

An improved simulation model to predict pre-harvest aflatoxin risk in maize

Aflatoxin is a potent carcinogen produced by Aspergillus flavus, which frequently contaminates maize (Zea mays L.) in the field between 40° north and 40° south latitudes. A mechanistic model to predict risk of pre-harvest contamination could assist in management of this very harmful mycotoxin. In this study we describe an aflatoxin risk prediction model which is integrated with the Agricultural Production Systems Simulator (APSIM) modelling framework. The model computes a temperature function for A. flavus growth and aflatoxin production using a set of three cardinal temperatures determined in the laboratory using culture medium and intact grains. These cardinal temperatures were 11.5 °C as base, 32.5 °C as optimum and 42.5 °C as maximum. The model used a low (≤0.2) crop water supply to demand ratio—an index of drought during the grain filling stage to simulate maize crop's susceptibility to A. flavus growth and aflatoxin production. When this low threshold of the index was reached the model converted the temperature function into an aflatoxin risk index (ARI) to represent the risk of aflatoxin contamination. The model was applied to simulate ARI for two commercial maize hybrids, H513 and H614D, grown in five multi-location field trials in Kenya using site specific agronomy, weather and soil parameters. The observed mean aflatoxin contamination in these trials varied from <1 to 7143 ppb. ARI simulated by the model explained 99% of the variation (p ≤ 0.001) in a linear relationship with the mean observed aflatoxin contamination. The strong relationship between ARI and aflatoxin contamination suggests that the model could be applied to map risk prone areas and to monitor in-season risk for genotypes and soils parameterized for APSIM.

Statistical methods for analysis of multi-harvest data from perennial pasture variety selection trials

Variety selection in perennial pasture crops involves identifying best varieties from data collected from multiple harvest times in field trials. For accurate selection, the statistical methods for analysing such data need to account for the spatial and temporal correlation typically present. This paper provides an approach for analysing multi-harvest data from variety selection trials in which there may be a large number of harvest times. Methods are presented for modelling the variety by harvest effects while accounting for the spatial and temporal correlation between observations. These methods provide an improvement in model fit compared to separate analyses for each harvest, and provide insight into variety by harvest interactions. The approach is illustrated using two traits from a lucerne variety selection trial. The proposed method provides variety predictions allowing for the natural sources of variation and correlation in multi-harvest data.