Individual-based modelling of the efficacy of fumigation tactics to control lesser grain borer (Rhyzopertha dominica) in stored grain

Increasing resistance to phosphine (PH 3) in insect pests, including lesser grain borer (Rhyzopertha dominica) has become a critical issue, and development of effective and sustainable strategies to manage resistance is crucial. In practice, the same grain store may be fumigated multiple times, but usually for the same exposure period and concentration. Simulating a single fumigation allows us to look more closely at the effects of this standard treatment.We used an individual-based, two-locus model to investigate three key questions about the use of phosphine fumigant in relation to the development of PH 3 resistance. First, which is more effective for insect control; long exposure time with a low concentration or short exposure period with a high concentration? Our results showed that extending exposure duration is a much more efficient control tactic than increasing the phosphine concentration. Second, how long should the fumigation period be extended to deal with higher frequencies of resistant insects in the grain? Our results indicated that if the original frequency of resistant insects is increased n times, then the fumigation needs to be extended, at most, n days to achieve the same level of insect control. The third question is how does the presence of varying numbers of insects inside grain storages impact the effectiveness of phosphine fumigation? We found that, for a given fumigation, as the initial population number was increased, the final survival of resistant insects increased proportionally. To control initial populations of insects that were n times larger, it was necessary to increase the fumigation time by about n days. Our results indicate that, in a 2-gene mediated resistance where dilution of resistance gene frequencies through immigration of susceptibles has greater effect, extending fumigation times to reduce survival of homozygous resistant insects will have a significant impact on delaying the development of resistance. © 2012 Elsevier Ltd.

Constructing a new individual-based model of phosphine resistance in lesser grain borer (Rhyzopertha dominica): do we need to include two loci rather than one?

In this article, we describe and compare two individual-based models constructed to investigate how genetic factors influence the development of phosphine resistance in lesser grain borer (R. dominica). One model is based on the simplifying assumption that resistance is conferred by alleles at a single locus, while the other is based on the more realistic assumption that resistance is conferred by alleles at two separate loci. We simulated the population dynamic of R. dominica in the absence of phosphine fumigation, and under high and low dose phosphine treatments, and found important differences between the predictions of the two models in all three cases. In the absence of fumigation, starting from the same initial frequencies of genotypes, the two models tended to different stable frequencies, although both reached Hardy-Weinberg equilibrium. The one-locus model exaggerated the equilibrium proportion of strongly resistant beetles by 3.6 times, compared to the aggregated predictions of the two-locus model. Under a low dose treatment the one-locus model overestimated the proportion of strongly resistant individuals within the population and underestimated the total population numbers compared to the two-locus model. These results show the importance of basing resistance evolution models on realistic genetics and that using oversimplified one-locus models to develop pest control strategies runs the risk of not correctly identifying tactics to minimise the incidence of pest infestation.

A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Growth and species interactions of Eucalyptus pellita in a mixed and monoculture plantation in the humid tropics of north Queensland

This study investigated whether mixed-species designs can increase the growth of a tropical eucalypt when compared to monocultures. Monocultures of Eucalyptus pellita (E) and Acacia peregrina (A) and mixtures in various proportions (75E:25A, 50E:50A, 25E:75A) were planted in a replacement series design on the Atherton Tablelands of north Queensland, Australia. High mortality in the establishment phase due to repeated damage by tropical cyclones altered the trial design. Effects of experimental designs on tree growth were estimated using a linear mixed-effects model with restricted maximum likelihood analysis (REML). Volume growth of individual eucalypt trees were positively affected by the presence of acacia trees at age 5 years and this effect generally increased with time up to age 10 years. However, the stand volume and basal area increased with increasing proportions of E. pellita, due to its larger individual tree size. Conventional analysis did not offer convincing support for mixed-species designs. Preliminary individual-based modelling using a modified Hegyi competition index offered a solution and an equation that indicates acacias have positive ecological interactions (facilitation or competitive reduction) and definitely do not cause competition like a eucalypt. These results suggest that significantly increased in growth rates could be achieved with mixed-species designs. This statistical methodology could enable a better understanding of species interactions in similarly altered experiments, or undesigned mixed-species plantations.

Modelling predicts positive and negative interactions between three Australian tropical tree species in monoculture and binary mixture

Computer modelling promises to be an important tool for analysing and predicting interactions between trees within mixed species forest plantations. This study explored the use of an individual-based mechanistic model as a predictive tool for designing mixed species plantations of Australian tropical trees. The `spatially explicit individually based-forest simulator' (SeXI-FS) modelling system was used to describe the spatial interaction of individual tree crowns within a binary mixed-species experiment. The three-dimensional model was developed and verified with field data from three forest tree species grown in tropical Australia. The model predicted the interactions within monocultures and binary mixtures of Flindersia brayleyana, Eucalyptus pellita and Elaeocarpus grandis, accounting for an average of 42% of the growth variation exhibited by species in different treatments. The model requires only structural dimensions and shade tolerance as species parameters. By modelling interactions in existing tree mixtures, the model predicted both increases and reductions in the growth of mixtures (up to +/-50% of stem volume at 7 years) compared to monocultures. This modelling approach may be useful for designing mixed tree plantations.

Predicting dispersal and recruitment of Miconia calvescens (Melastomataceae) in Australian tropical rainforests

Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes.

New efforts at biological control of Mikania micrantha H.B.K. (Asteraceae) in Papua New Guinea and Fiji.

New efforts at biological control of Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes. Mikania micrantha H.B.K. (Asteraceae) in Papua New Guinea and Fiji.

Two sympatric spotted gum species are molecularly homogeneous.

Large fruited spotted gum eucalypt Corymbia henryi occurs sympatrically with small fruited spotted gum Corymbia citriodora subspecies variegata over a large portion of its range on the east coast of Australia. The two taxa are interfertile, have overlapping flowering times and share a common set of insect and vertebrate pollinators. Previous genetic analysis of both taxa from two geographically remote sites suggested that the two were morphotypes rather than genetically distinct species. In this study we further explore this hypothesis of genic species by expanding sampling broadly through their sympatric locations and examine local-scale spatial genetic structure in stands that differ in species and age composition. Delineation of populations at five microsatellite loci, using an individual-based approach and Bayesian modelling, as well as clustering of individuals based on allele frequencies showed the two species to be molecularly homogeneous. Genetic structure aligned largely with geographic areas of origin, and followed an isolation-by-distance model, where proximal populations were generally less differentiated than more distant ones. At the stand level, spotted gums also generally showed little structure consistent with the high levels of gene flow inferred across the species range. Disturbances in the uniformity of structuring were detected, however, and attributed to localised events giving rise to even aged stands, probably due to regeneration from a few individuals following fire.

Dosage consistency is the key factor in avoiding evolution of resistance to phosphine and population increase in stored-grain pests

BACKGROUND Control of pests in stored grain and the evolution of resistance to pesticides are serious problems worldwide. A stochastic individual-based two-locus model was used to investigate the impact of two important issues, the consistency of pesticide dosage through the storage facility and the immigration rate of the adult pest, on overall population control and avoidance of evolution of resistance to the fumigant phosphine in an important pest of stored grain, the lesser grain borer. RESULTS A very consistent dosage maintained good control for all immigration rates, while an inconsistent dosage failed to maintain control in all cases. At intermediate dosage consistency, immigration rate became a critical factor in whether control was maintained or resistance emerged. CONCLUSION Achieving a consistent fumigant dosage is a key factor in avoiding evolution of resistance to phosphine and maintaining control of populations of stored-grain pests; when the dosage achieved is very inconsistent, there is likely to be a problem regardless of immigration rate. © 2012 Society of Chemical Industry

Herbicide resistance modelling: Past, present and future

Computer simulation modelling is an essential aid in building an integrated understanding of how different factors interact to affect the evolutionary and population dynamics of herbicide resistance, and thus in helping to predict and manage how agricultural systems will be affected. In this review, we first discuss why computer simulation modelling is such an important tool and framework for dealing with herbicide resistance. We then explain what questions related to herbicide resistance have been addressed to date using simulation modelling, and discuss the modelling approaches that have been used, focusing first on the earlier, more general approaches, and then on some newer, more innovative approaches. We then consider how these approaches could be further developed in the future, by drawing on modelling techniques that are already employed in other areas, such as individual-based and spatially explicit modelling approaches, as well as the possibility of better representing genetics, competition and economics, and finally the questions and issues of importance to herbicide resistance research and management that could be addressed using these new approaches are discussed. We conclude that it is necessary to proceed with caution when increasing the complexity of models by adding new details, but, with appropriate care, more detailed models will make it possible to integrate more current knowledge in order better to understand, predict and ultimately manage the evolution of herbicide resistance. © 2014 Society of Chemical Industry.

Variability in Voluntary Intake of a Molasses-based Supplement by Cows and Calves

Supplements are often fed to ruminants in extensive grazing situations to provide minerals and nitrogen likely to be deficient in pasture. However a large proportion of animals offered such supplements may not consume any supplement, while among consumer animals the variability in supplement intake may be high (Wheeler et al., 1980; Dixon et al., 1998). An experiment examined the distribution of intake of a molasses-based supplement containing phosphorus and urea in a breeder herd. A herd of mixed-age breeder cows, calves, heifers and bulls were offered ad libitum a molasses-based supplement containing 13% urea and 17% phosphoric acid. After 2 weeks lithium-labelled supplement (2 mg Li/kg LW) was offered on one day to measure individual intakes of supplement. The molasses was offered in three 560 mm diameter feeders placed together near the water point.

Process studies of odour emissions from effluent ponds using machine-based odour measurement

Replicable experimental studies using a novel experimental facility and a machine-based odour quantification technique were conducted to demonstrate the relationship between odour emission rates and pond loading rates. The odour quantification technique consisted of an electronic nose, AromaScan A32S, and an artificial neural network. Odour concentrations determined by olfactometry were used along with the AromaScan responses to train the artificial neural network. The trained network was able to predict the odour emission rates for the test data with a correlation coefficient of 0.98. Time averaged odour emission rates predicted by the machine-based odour quantification technique, were strongly correlated with volatile solids loading rate, demonstrating the increased magnitude of emissions from a heavily loaded effluent pond. However, it was not possible to obtain the same relationship between volatile solids loading rates and odour emission rates from the individual data. It is concluded that taking a limited number of odour samples over a short period is unlikely to provide a representative rate of odour emissions from an effluent pond. A continuous odour monitoring instrument will be required for that more demanding task.

The development of an improved PCR-based marker system for Sw-5, an important TSWV resistance gene of tomato

Sw-5 is an important disease resistance gene of tomato, providing broad resistance to Tomato spotted wilt virus (TSWV). A cleaved amplified polymorphic sequence (CAPS) marker, closely linked to the gene, has been reported. Although the Sw-5 locus has been characterised, a gene-specific marker has not been developed. This paper presents a PCR-based marker-system that consists of the co-amplification of a dominant marker representing the Sw-5 gene sequence, and the modified CAPS marker as a positive control and indicator of genotype.

DNA-based identification of Quambalaria pitereka causing severe leaf blight of Corymbia citriodora in China

Quambalaria spp. include serious plant pathogens, causing leaf and shoot blight of Corymbia and Eucalyptus spp. In this study, a disease resembling Quambalaria leaf blight was observed on young Corymbia citriodora trees in a plantation in the Guangdong Province of China. Comparisons of rDNA sequence data showed that the causal agent of the disease is Q. pitereka. This study provides the first report of Quambalaria leaf blight from China, and it is also the first time that this pathogen has been found on trees outside the native range of Eucalypts.