Simple software processes and tests improve the reliability and usefulness of a model.

Models are abstractions of reality that have predetermined limits (often not consciously thought through) on what problem domains the models can be used to explore. These limits are determined by the range of observed data used to construct and validate the model. However, it is important to remember that operating the model beyond these limits, one of the reasons for building the model in the first place, potentially brings unwanted behaviour and thus reduces the usefulness of the model. Our experience with the Agricultural Production Systems Simulator (APSIM), a farming systems model, has led us to adapt techniques from the disciplines of modelling and software development to create a model development process. This process is simple, easy to follow, and brings a much higher level of stability to the development effort, which then delivers a much more useful model. A major part of the process relies on having a range of detailed model tests (unit, simulation, sensibility, validation) that exercise a model at various levels (sub-model, model and simulation). To underline the usefulness of testing, we examine several case studies where simulated output can be compared with simple relationships. For example, output is compared with crop water use efficiency relationships gleaned from the literature to check that the model reproduces the expected function. Similarly, another case study attempts to reproduce generalised hydrological relationships found in the literature. This paper then describes a simple model development process (using version control, automated testing and differencing tools), that will enhance the reliability and usefulness of a model.

Baseline responses of Alphitobius diaperinus (Coleoptera: Tenebrionidae) to spinosad, and susceptibility of broiler populations in eastern and southern Australia

Spinosad was proposed as a potential chemical for control of lesser mealworm, Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae), in Australian broiler houses after the detection of strong cyfluthrin resistance in many beetle populations. In 2004-2006, spinosad susceptibility of 13 beetle populations from eastern and southern Australian broiler houses and a cyfluthrin/fenitrothion-resistant reference population was determined using topical application, and was compared with the susceptibility of an insecticide-susceptible reference population. Comparisons of dose-response curves and baseline data showed that all populations, including the insecticide-susceptible population, were roughly equivalent in their response to spinosad, indicating no preexisting spinosad resistance. Two field populations, including the resistant reference population, which had confirmed cyfluthrin/fenitrothion- resistance, showed no cross-resistance to spinosad. There was no significant correlation between beetle weight and LC99.9. A discriminating concentration of 3% spinosad was set to separate resistant and susceptible individuals. Considering the levels of spinosad resistance that have been recorded in other insect pests, the sustained future usefulness of spinosad as a broiler house treatment will rely on effective integrated beetle management programs combined with carefully planned chemical use strategies.

A collaborative design to adaptively manage for landscape sustainability in north Australia: lessons from a decade of cooperative research

Approaches to manage for the sustainable use of natural and cultural resources in a landscape can have many different designs. One design is adaptive collaborative landscape management (ACLM) where research providers and users work closely together on projects to develop resources while adaptively managing to sustain or maintain landscapes in the long term. We propose that collaborative projects are more useful for achieving outcomes than integrative projects where participants merely join their separate contributions. To foster collaborative research projects to adaptively manage landscapes in northern Australia, a Tropical Savannas Cooperative Research Centre (TSCRC) was established in 1995. The TSCRC is a joint venture of major organizations involved in research and land management. This paper is our perspective on the four most important 'lessons learned' after using a ACLM-type approach for over 10 y. We learnt that collaboration (working in combination) not necessarily integration (combining parts into a whole) achieved sustainable outcomes. We found that integration across culturally diverse perspectives seldom achieved sustainable solutions because it devalued the position of the less empowered participants. In addition, positive outcomes were achieved when participants developed trust and respect for each other by embracing and respecting their differences and by sharing unifying concepts such as savanna health. Another lesson learned was that a collaborative organization must act as an honest broker by resisting advocacy of one view point over another. Finally, we recognized the importance of strongly investing in communication and networking so that people could adaptively learn from one another's experiences, understand each other's challenges and respect each other's choices. Our experience confirms the usefulness of the ACLM approach and highlights its role in the process of sustaining healthy landscapes.

A comparison of plotless density estimators using Monte Carlo simulation on totally enumerated field data sets

Background: Plotless density estimators are those that are based on distance measures rather than counts per unit area (quadrats or plots) to estimate the density of some usually stationary event, e.g. burrow openings, damage to plant stems, etc. These estimators typically use distance measures between events and from random points to events to derive an estimate of density. The error and bias of these estimators for the various spatial patterns found in nature have been examined using simulated populations only. In this study we investigated eight plotless density estimators to determine which were robust across a wide range of data sets from fully mapped field sites. They covered a wide range of situations including animal damage to rice and corn, nest locations, active rodent burrows and distribution of plants. Monte Carlo simulations were applied to sample the data sets, and in all cases the error of the estimate (measured as relative root mean square error) was reduced with increasing sample size. The method of calculation and ease of use in the field were also used to judge the usefulness of the estimator. Estimators were evaluated in their original published forms, although the variable area transect (VAT) and ordered distance methods have been the subjects of optimization studies. Results: An estimator that was a compound of three basic distance estimators was found to be robust across all spatial patterns for sample sizes of 25 or greater. The same field methodology can be used either with the basic distance formula or the formula used with the Kendall-Moran estimator in which case a reduction in error may be gained for sample sizes less than 25, however, there is no improvement for larger sample sizes. The variable area transect (VAT) method performed moderately well, is easy to use in the field, and its calculations easy to undertake. Conclusion: Plotless density estimators can provide an estimate of density in situations where it would not be practical to layout a plot or quadrat and can in many cases reduce the workload in the field.

The impact of dry matter, ripeness and internal defects on consumer perceptions of avocado quality and intentions to purchase.

Insights into the relative importance of various aspects of product quality can be provided through quantitative analysis of consumer preference and choice of fruit. In this study, methods previously used to establish taste preferences for kiwifruit (Harker et al., 2008) and conjoint approaches were used to determine the influence of three key aspects of avocado quality on consumer liking and willingness to purchase fruit: dry matter percentage (DM), level of ripeness (firmness) and internal defects (bruising). One hundred and seven consumers tasted avocados with a range of DM levels from ~20% (minimally mature) to nearly 40% (very mature), and at a range of fruit firmness (ripeness) stages (firm-ripe to soft-ripe). Responses to bruising, a common quality defect in fruit obtained from the retail shelf, were examined using a conjoint approach in which consumers were presented with photographs showing fruit affected by damage of varying severity. In terms of DM, consumers showed a progressive increase in liking and intent to buy avocados as the DM increased. In terms of ripeness, liking and purchase intent was higher in avocados that had softened to a firmness of 6.5 N or below (hand-rating 5). For internal defects, conjoint analysis revealed that price, level of bruising and incidence of bruising all significantly lowered consumers' future purchase decision, but the latter two factors had a greater impact than price. These results indicate the usefulness of the methodology, and also provide realistic targets for Hass avocado quality on the retail shelf.

Development of a DNA based aging technique for use in fisheries assessments. Final report, Australian Fisheries Research and Development Corporation Project 2007/033.

The productivity of a fisheries resource can be quantified from estimates of recruitment, individual growth and natural and fisheries-related mortality, assuming the spatial extent of the resource has been quantified and there is minimal immigration or emigration. The sustainability of a fisheries resource is facilitated by management controls such as minimum and maximum size limits and total allowable catch. Minimum size limits are often set to allow individuals the opportunity to reproduce at least once before the chance of capture. Total allowable catches are a proportion of the population biomass, which is estimated based on known reproduction, recruitment, mortality and growth rates. In some fisheries, however, management actions are put in place without quantification of the resource through the stock assessment process. This occurs because species-specific information, for example individual growth, may not be available. In these circumstances, management actions need to be precautionary to protect against future resource collapse, but this often means that the resource is lightly exploited. Consequently, the productivity of the resource is not fully realised. Australia’s most valuable fisheries are invertebrate fisheries (Australian Department of Agriculture Fisheries and Forestry, 2008). For example, Australian fisheries (i.e. excluding aquaculture) production of crustaceans (largely prawns, rock lobster and crab) was 41,000 tonnes in 2006/7, worth $778 million. Production from mollusc (largely abalone, scallops, oysters and squid) fisheries was 39,000 tonnes, worth $502 million. Together, in 2006/7 crustacean and mollusc fisheries represented 58% of the total value of Australian wild fisheries production. Sustainable management of Australia’s invertebrate fisheries is frustrated by the lack of data on species-specific growth rates. This project investigated a new method to estimate age, and hence individual growth rates, in invertebrate fisheries species. The principle behind the new aging method was that telomeres (i.e. DNA end-caps of chromosomes) get shorter as an individual gets older. We studied commercial crustacean and molluscan species. A vertebrate fish species (silver perch, Bidyanus bidyanus) was used as a control to standardise our work against the literature. We found a clear relationship between telomere length and shell size for temperate abalone (Haliotis rubra). Further research is recommended before the method can be implemented to assist management of wildharvested abalone populations. Age needs to be substituted for shell size in the relationship and it needs to be studied for abalone from several regions. This project showed that telomere length declined with increasing age in Sydney rock oysters (Saccostrea glomerata) and was affected by regional variation. A relationship was not apparent between telomere length and age (or size as a surrogate for age) for crustacean species (school prawns, Metapenaeus macleayi; eastern rock lobster, Sagmariasus verreauxi; southern rock lobster, Jasus edwardsii; and spanner crabs, Ranina ranina). For school prawns, there was no difference between telomere length in males and females. Further research is recommended, however, as telomeric DNA from crustaceans was difficult to analyse using the terminal restriction fragment (TRF) assay. Telomere lengths of spanner crabs and lobsters were at the upper limit of resolution of the assay used and results were affected by degradation and possible contamination of telomeric DNA. It is possible that telomere length is an indicator of remaining lifespan in molluscan and crustacean individuals, as suggested for some vertebrate species (e.g. Monaghan, 2010). Among abalone of similar shell size and among lobster pueruli, there was evidence of individuals having significantly longer or shorter telomeres than the group average. At a population level, this may be a surrogate for estimates of future natural mortality, which may have usefulness in the management of those populations. The method used to assay telomere length (terminal restriction fragment assay) performed adequately for most species, but it was too expensive and time-consuming to be considered a useful tool for gathering information for fisheries management. Research on alternative methods is strongly recommended.

Improving management of summer weeds in dryland cropping systems with Cotton

In 2001 a scoping study (phase I) was commissioned to determine and prioritise the weed issues of cropping systems with dryland cotton. The main findings were that the weed flora was diverse, cropping systems complex, and weeds had a major financial and economical impact. Phase II 'Best weed management strategies for dryland cropping systems with cotton' focused on improved management of the key weeds, bladder ketmia, sowthistle, fleabane, barnyard grass and liverseed grass.In Phase III 'Improving management of summer weeds in dryland cropping systems with cotton', more information on the seed-bank dynamics of key weeds was gained in six pot and field studies. The studies found that these characteristics differed between species, and even climate in the case of bladder ketmia. Species such as sowthistle, fleabane and barnyard grass emerged predominately from the surface soil. Sweet summer grass was also in this category but also had a significant proportion emerging from 5 cm depth. Bladder ketmia in central Queensland emerged mainly from the top 2 cm, whereas in southern Queensland it emerged mainly from 5 cm. Liverseed grass had its highest emergence from 5 cm below the surface. In all cases the persistence of seed increased with increasing soil depth. Fleabane was also found to be sensitive to soil type with no seedlings emerging in the self-mulching black vertisol soil. A strategic tillage trial showed that burial of fleabane seed, using a disc or chisel plough, to a depth of greater than 2 cm can significantly reduce subsequent fleabane emergence. In contrast, tillage increased barnyard grass emergence and tended to decrease persistence. This research showed that weed management plans can not be blanketed across all weed species, rather they need to be targeted for each main weed species.This project has also resulted in an increased knowledge of how to manage fleabane from the eight experiments; one in wheat, two in sorghum, one in cotton and three in fallow on double knock. For summer crops, the best option is to apply a highly effective fallow treatment prior to sowing the crops. For winter crops, the strategy is the integration of competitive crops, residual herbicide followed by a knockdown to control survivors. This project explored further the usefulness of the double knock tactic for weed control and preventing seed set. Two field and one pot experiments have shown that this tactic was highly effective for fleabane control. Paraquat products provided good control when followed by glyphosate. When 2, 4-D was added in a tank mix with glyphosate and followed by paraquat products, 99-100% control was achieved in all cases. The ideal follow-up times for paraquat products after glyphosate were 5-7 days. The preferred follow-up times for 2, 4-D after glyphosate were on the same day and one day later. The pot trial, which compared a population from a cropping field with previous glyphosate exposure and a population from a non-cropping area with no previous glyphosate herbicide exposure, showed that the pervious herbicide exposure affected the response of fleabane to herbicidal control measures. The web-based brochure on managing fleabane has been updated.Knowledge on management of summer grasses and safe use of residual herbicides was derived from eight field and pot experiments. Residual grass and broadleaf weed control was excellent with atrazine pre-plant and at-planting treatments, provided rain was received within a short interval after application. Highly effective fallow treatments (cultivation and double knock), not only gave excellent grass control in the fallow, also gave very good control in the following cotton. In the five re-cropping experiments, there were no adverse impacts on cotton from atrazine, metolachlor, metsulfuron and chlorsulfuron residues following use in previous sorghum, wheat and fallows. However, imazapic residues did reduce cotton growth.The development of strategies to reduce the heavy reliance on glyphosate in our cropping systems, and therefore minimise the risk of glyphosate resistance development, was a key factor in the research undertaken. This work included identifying suitable tactics for summer grass control, such as double knock with glyphosate followed by paraquat and tillage. Research on fleabane also concentrated on minimising emergence through tillage, and applying the double knock tactic. Our studies have shown that these strategies can be used to prevent seed set with the goal of driving down the seed bank. Utilisation of the strategies will also reduce the reliance on glyphosate, and therefore reduce the risk of glyphosate resistance developing in our cropping systems.Information from this research, including ecological and management data were collected from an additional eight paddock monitoring sites, was also incorporated into the Weeds CRC seed bank model "Weed Seed Wizard", which will be able to predict the impact of different management options on weed populations in cotton and grain farming systems. Extensive communication activities were undertaken throughout this project to ensure adoption of the new strategies for improved weed management and reduced risk for glyphosate resistance.

Gene expression evidence for off-target effects caused by RNA interference-mediated gene silencing of Ubiquitin-63E in the cattle tick Rhipicephalus microplus.

Knowledge of cattle tick (Rhipicephalus (Boophilus) microplus; Acari: Ixodidae) molecular and cellular pathways has been hampered by the lack of an annotated genome. In addition, most of the tick expressed sequence tags (ESTs) available to date consist of similar to 50% unassigned sequences without predicted functions. The most common approach to address this has been the application of RNA interference (RNAi) methods to investigate genes and their pathways. This approach has been widely adopted in tick research despite minimal knowledge of the tick RNAi pathway and double-stranded RNA (dsRNA) uptake mechanisms. A strong knockdown phenotype of adult female ticks had previously been observed using a 594 bp dsRNA targeting the cattle tick homologue for the Drosophila Ubiquitin-63E gene leading to nil or deformed eggs. A NimbleGen cattle tick custom microarray based on the BmiGI.V2 database of R. microplus ESTs was used to evaluate the expression of mRNAs harvested from ticks treated with the tick Ubiquitin-63E 594 bp dsRNA compared with controls. A total of 144 ESTs including TC6372 (Ubiquitin-63E) were down-regulated with 136 ESTs up-regulated following treatment. The results obtained substantiated the knockdown phenotype with ESTs identified as being associated with ubiquitin proteolysis as well as oogenesis, embryogenesis, fatty acid synthesis and stress responses. A bioinformatics analysis was undertaken to predict off-target effects (OTE) resulting from the in silico dicing of the 594 bp Ubiquitin-63E dsRNA which identified 10 down-regulated ESTs (including TC6372) within the list of differentially expressed probes on the microarrays. Subsequent knockdown experiments utilising 196 and 109 bp dsRNAs, and a cocktail of short hairpin RNAs (shRNA) targeting Ubiquitin-63E, demonstrated similar phenotypes for the dsRNAs but nil effect following shRNA treatment. Quantitative reverse transcriptase PCR analysis confirmed differential expression of TC6372 and selected ESTs. Our study demonstrated the minimisation of predicted OTEs in the shorter dsRNA treatments (similar to 100-200 bp) and the usefulness of microarrays to study knockdown phenotypes.

Pericarps retained in the tree canopy and stomatal abundance are components of resistance to husk spot caused by Pseudocercospora macadamiae in macadamia

Pseudocercospora macadamiae Beilharz, Mayers and Pascoe infects macadamia fruit via stomata causing husk spot disease. Information on the variability of fruit stomatal abundance, its association with diseased fruit pericarps (sticktights) that are retained in the tree canopy, and its influence on the husk spot intensity (incidence, severity and lesion number) among macadamia genotypes is lacking. We examined a total of 230 macadamia trees comprising 19 cultivars, 56 wild germplasm accessions and 40 breeding progeny, for the prevalence of sticktights and husk spot intensity over three production seasons. We observed a strong association between the prevalence of sticktights and disease intensity indicating its usefulness as a predictor of husk spot and as a useful phenotypic trait for husk spot resistance selection in breeding programmes. Similarly, stomatal abundance varied among macadamia genotypes, and a significant linear relationship (P < 0.001; 93%) was observed between fruit stomatal abundance and husk spot for all the macadamia genotypes analysed, confirming the utility of that trait for disease resistance screening. The genotypes were grouped into disease resistance groups. Correlations between fruit stomatal abundance, disease intensity and prevalence of sticktights revealed that the numbers of sticktights, and relative stomatal abundance were the main factors influencing the intensity of husk spot among macadamia genotypes. This is the first comprehensive study of natural variation of stomatal abundance in Macadamia species that reveals genetic variation, and provides relevant relationships with disease intensity and the prevalence of sticktights. The phenotypic plant traits indentified in this study may serve as selection tools for disease resistance screening in macadamia breeding programmes.

The rph2 Gene Is Responsible for High Level Resistance to Phosphine in Independent Field Strains of Rhyzopertha dominica

The lesser grain borer Rhyzopertha dominica (F.) is one of the most destructive insect pests of stored grain. This pest has been controlled successfully by fumigation with phosphine for the last several decades, though strong resistance to phosphine in many countries has raised concern about the long term usefulness of this control method. Previous genetic analysis of strongly resistant (SR) R. dominica from three widely geographically dispersed regions of Australia, Queensland (SRQLD), New South Wales (SRNSW) and South Australia (SRSA), revealed a resistance allele in the rph1 gene in all three strains. The present study confirms that the rph1 gene contributes to resistance in a fourth strongly resistant strain, SR2(QLD), also from Queensland. The previously described rph2 gene, which interacts synergistically with rph1 gene, confers strong resistance on SRQLD and SRNSW. We now provide strong circumstantial evidence that weak alleles of rph2, together with rph1, contribute to the strong resistance phenotypes of SRSA and SR2(QLD). To test the notion that rph1 and rph2 are solely responsible for the strong resistance phenotype of all resistant R. dominica, we created a strain derived by hybridising the four strongly resistant lines. Following repeated selection for survival at extreme rates of phosphine exposure, we found only slightly enhanced resistance. This suggests that a single sequence of genetic changes was responsible for the development of resistance in these insects.

Combining ability, genetic diversity and heterosis in relation to F1 performance of tropically adapted shrunken (sh2) sweet corn lines

With 6 tables Abstract The objectives of this study were to evaluate the importance of heterosis for agronomic and quality traits in shrunken (sh2) sweet corn, assess the usefulness of combining ability to predict the value of parents and their crosses for further genetic improvement and examine whether genetic divergence can predict heterosis or F1 performance. Ten genetically diverse shrunken (sh2) sweet corn inbred lines were used to generate 45 F1s. F1s and parents were evaluated for agronomic and quality traits across environments. Heterosis was more important for yield-related traits than it was for ear aspects and eating quality. Heterosis for most traits was mostly dependent on dominance genetic effects of parental lines. Parents and F1per se performance were highly correlated with general combining ability effects and mid-parent values, respectively, for most traits. Hybrid performance for flavour and plant height was significantly but weakly related to simple sequence repeat (SSR)-based genetic distance (GD). Phenotypic distance (PD), estimated from phenotypic traits was correlated with heterosis for total soluble solids, ear length and flavour. © 2012 State of Queensland.

Managing glyphosate resistance in Australian cotton farming: modelling shows how to delay evolution and maintain long-term population control

Glyphosate resistance is a rapidly developing threat to profitability in Australian cotton farming. Resistance causes an immediate reduction in the effectiveness of in-crop weed control in glyphosate-resistant transgenic cotton and summer fallows. Although strategies for delaying glyphosate resistance and those for managing resistant populations are qualitatively similar, the longer resistance can be delayed, the longer cotton growers will have choice over which tactics to apply and when to apply them. Effective strategies to avoid, delay, and manage resistance are thus of substantial value. We used a model of glyphosate resistance dynamics to perform simulations of resistance evolution in Sonchus oleraceus (common sowthistle) and Echinochloa colona (awnless barnyard grass) under a range of resistance prevention, delaying, and management strategies. From these simulations, we identified several elements that could contribute to effective glyphosate resistance prevention and management strategies. (i) Controlling glyphosate survivors is the most robust approach to delaying or preventing resistance. High-efficacy, high-frequency survivor control almost doubled the useful lifespan of glyphosate from 13 to 25 years even with glyphosate alone used in summer fallows. (ii) Two non-glyphosate tactics in-crop plus two in-summer fallows is the minimum intervention required for long-term delays in resistance evolution. (iii) Pre-emergence herbicides are important, but should be backed up with non-glyphosate knockdowns and strategic tillage; replacing a late-season, pre-emergence herbicide with inter-row tillage was predicted to delay glyphosate resistance by 4 years in awnless barnyard grass. (iv) Weed species' ecological characteristics, particularly seed bank dynamics, have an impact on the effectiveness of resistance strategies; S. oleraceus, because of its propensity to emerge year-round, was less exposed to selection with glyphosate than E. colona, resulting in an extra 5 years of glyphosate usefulness (18 v. 13 years) even in the most rapid cases of resistance evolution. Delaying tactics are thus available that can provide some or many years of continued glyphosate efficacy. If glyphosate-resistant cotton cropping is to remain profitable in Australian farming systems in the long-term, however, growers must adapt to the probability that they will have to deal with summer weeds that are no longer susceptible to glyphosate. Robust resistance management systems will need to include a diversity of weed control options, used appropriately.