Assessing the impacts of grazing levels on bird density in woodland habitat: a Bayesian approach using expert opinion

Many studies on birds focus on the collection of data through an experimental design, suitable for investigation in a classical analysis of variance (ANOVA) framework. Although many findings are confirmed by one or more experts, expert information is rarely used in conjunction with the survey data to enhance the explanatory and predictive power of the model. We explore this neglected aspect of ecological modelling through a study on Australian woodland birds, focusing on the potential impact of different intensities of commercial cattle grazing on bird density in woodland habitat. We examine a number of Bayesian hierarchical random effects models, which cater for overdispersion and a high frequency of zeros in the data using WinBUGS and explore the variation between and within different grazing regimes and species. The impact and value of expert information is investigated through the inclusion of priors that reflect the experience of 20 experts in the field of bird responses to disturbance. Results indicate that expert information moderates the survey data, especially in situations where there are little or no data. When experts agreed, credible intervals for predictions were tightened considerably. When experts failed to agree, results were similar to those evaluated in the absence of expert information. Overall, we found that without expert opinion our knowledge was quite weak. The fact that the survey data is quite consistent, in general, with expert opinion shows that we do know something about birds and grazing and we could learn a lot faster if we used this approach more in ecology, where data are scarce. Copyright (c) 2005 John Wiley & Sons, Ltd.

Modelling pre-clearing vegetation distribution using GIS-integrated statistical, ecological and data models: A case study from the wet tropics of Northeastern Australia

Traditional vegetation mapping methods use high cost, labour-intensive aerial photography interpretation. This approach can be subjective and is limited by factors such as the extent of remnant vegetation, and the differing scale and quality of aerial photography over time. An alternative approach is proposed which integrates a data model, a statistical model and an ecological model using sophisticated Geographic Information Systems (GIS) techniques and rule-based systems to support fine-scale vegetation community modelling. This approach is based on a more realistic representation of vegetation patterns with transitional gradients from one vegetation community to another. Arbitrary, though often unrealistic, sharp boundaries can be imposed on the model by the application of statistical methods. This GIS-integrated multivariate approach is applied to the problem of vegetation mapping in the complex vegetation communities of the Innisfail Lowlands in the Wet Tropics bioregion of Northeastern Australia. The paper presents the full cycle of this vegetation modelling approach including sampling sites, variable selection, model selection, model implementation, internal model assessment, model prediction assessments, models integration of discrete vegetation community models to generate a composite pre-clearing vegetation map, independent data set model validation and model prediction's scale assessments. An accurate pre-clearing vegetation map of the Innisfail Lowlands was generated (0.83r(2)) through GIS integration of 28 separate statistical models. This modelling approach has good potential for wider application, including provision of. vital information for conservation planning and management; a scientific basis for rehabilitation of disturbed and cleared areas; a viable method for the production of adequate vegetation maps for conservation and forestry planning of poorly-studied areas. (c) 2006 Elsevier B.V. All rights reserved.

Guideline to reference gene selection for quantitative real-time PCR

Today, quantitative real-time PCR is the method of choice for rapid and reliable quantification of mRNA transcription. However, for an exact comparison of mRNA transcription in different samples or tissues it is crucial to choose the appropriate reference gene. Recently glyceraldehyde 3-phosphate dehydrogenase and P-actin have been used for that purpose. However, it has been reported that these genes as well as alternatives, like rRNA genes, are unsuitable references, because their transcription is significantly regulated in various experimental settings and variable in different tissues. Therefore, quantitative real-time PCR was used to determine the mRNA transcription profiles of 13 putative reference genes, comparing their transcription in 16 different tissues and in CCRF-HSB-2 cells stimulated with 12-O-tetradecanoylphorbol-13-acetate and ionomycin. Our results show that Classical reference genes are indeed unsuitable, whereas the RNA polymerase II gene was the gene with the most constant expression in different tissues and following stimulation in CCRF-HSB-2 cells. (C) 2003 Elsevier Inc. All rights reserved.

Gene-flow between populations of cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is highly variable between years

Both large and small scale migrations of Helicoverpa armigera Hübner in Australia were investigated using AMOVA analysis and genetic assignment tests. Five microsatellite loci were screened across 3142 individuals from 16 localities in eight major cotton and grain growing regions within Australia, over a 38-month period (November 1999 to January 2003). From November 1999 to March 2001 relatively low levels of migration were characterized between growing regions. Substantially higher than average gene-flow rates and limited differentiation between cropping regions characterized the period from April 2001 to March 2002. A reduced migration rate in the year from April 2002 to March 2003 resulted in significant genetic structuring between cropping regions. This differentiation was established within two or three generations. Genetic drift alone is unlikely to drive genetic differentiation over such a small number of generations, unless it is accompanied by extreme bottlenecks and/or selection. Helicoverpa armigera in Australia demonstrated isolation by distance, so immigration into cropping regions is more likely to come from nearby regions than from afar. This effect was most pronounced in years with limited migration. However, there is evidence of long distance dispersal events in periods of high migration (April 2001-March 2002). The implications of highly variable migration patterns for resistance management are considered.