Arthur Rylah Institute for Environmental Research

About: Arthur Rylah Institute for Environmental Research is a government organization based out in Melbourne, Victoria, Australia. It is known for research contribution in the topics: Population & Threatened species. The organization has 244 authors who have published 775 publications receiving 25858 citations. The organization is also known as: ARI.

Selecting thresholds for the prediction of species occurrence with presence‐only data

Abstract: Aim Species distribution models have been widely used to tackle ecological, evolutionary and conservation problems. Most species distribution modelling techniques produce continuous suitability predictions, but many real applications (e.g. reserve design, species invasion and climate change impact assessment) and model evaluations require binary outputs, and thresholds are needed for these transformations. Although there are many threshold selection methods for presence/absence data, it is unclear whether these are suitable for presence-only data. In this paper, we investigate mathematically and empirically which of the existing threshold selection methods can be used confidently with presence-only data. Location We used real spatially explicit environmental data derived from the western part of the state of Victoria, south-eastern Australia, and simulated species distributions within this area. Methods Thirteen existing threshold selection methods were investigated mathematically to see whether the same threshold can be produced using either presence/absence data or presence-only data. We further adopted a simulation approach, created many virtual species with differing prevalences in a real landscape in south-eastern Australia, generated data sets with different proportions of pseudo-absences, built eight types of models with four modelling techniques, and investigated the behaviours of four threshold selection methods in these situations. Results Three threshold selection methods were not affected by pseudo-absences, including max SSS (which is based on maximizing the sum of sensitivity and specificity), the prevalence of model training data and the mean predicted value of a set of random points. Max SSS produced higher sensitivity in most cases and higher true skill statistic and kappa in many cases than the other methods. The other methods produced different thresholds from presence-only data to those determined from presence/absence data. Main conclusions Max SSS is a promising method for threshold selection when only presence data are available.

Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation

Abstract: Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Para. Catchments retaining more than 69–80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil’s Forest Code, resulted in a 39–54% loss of conservation value: 96–171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Para, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Para’s strictly protected areas is equivalent to the loss of 92,000–139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.

Assessing functional diversity in the field - methodology matters!

Abstract: 1. Interpreting the functional diversity of vegetation is important in unravelling the relationship between environmental change, community composition and ecosystem processes. Functional diversity is the range and distribution of functional trait values in a community. It can be described, among other indicators, by community-level weighted means of trait values (CWM) and functional divergence. Standard methods exist for trait measurements but not for assessments of CWM and functional divergence in the field. No research has addressed the effects of different methods of estimating relative abundances, nor the need to estimate traits at individual, population or species level, or whether methods could be used that bypass taxonomy all together. 2. This study reviews and evaluates plot-level assessment methods of functional diversity in herbaceous vegetation. We asked: (i) Should the objective of the study influence the method for estimating relative abundance? (ii) What are the strengths and limitations of intensive vs. ‘rapid’ approaches, and when should either be applied? (iii) Are taxon-free methods robust in comparison to taxon-explicit methods of trait measurement? Under what circumstances might they be applied? 3. Our review of published studies that have measured functional diversity in the field showed that the choice of metric has not generally taken into account the link between the metric and the functions of interest, and that vegetation cover has been most widely used, regardless of study purpose. 4. We compared quantitatively in subalpine grasslands three methods for quantification of species abundances plus one taxon-free method. We found that: (i) data base trait values were robust across years for a diverse set of dominant species; (ii) CWM have little sensitivity to method for estimating relative abundances; this sensitivity also depends on traits, for example, seed mass results were less stable than leaf traits and heights; (iii) robust estimates of CWM were obtained from visual estimates of species ranks and biomass using a dry-weight ranking method (BOTANAL), whereas functional divergence was more sensitive to method; and (iv) the taxon-free method should be treated with more caution and performed particularly poorly for estimates of functional divergence. 5. We conclude that methodology can affect estimates of functional diversity. Although care should be taken in the choice of method and interpretation of results, rapid methods often offer promising avenues for sampling larger areas and/or repeated measures.

High-quality male field crickets invest heavily in sexual display but die young

Abstract: Only high-quality males can bear the costs of an extreme sexual display. As a consequence, such males are not only more attractive, but they often live longer than average. Recent theory predicts, however, that high-quality males should sometimes invest so heavily in sexual displays that they die sooner than lower quality males. We manipulated the phenotypic quality of field crickets, Teleogryllus commodus, by altering the protein content of their diet. Here we show that nymphs and adult females reared on a high-protein diet lived longer than those on a low-protein diet. In contrast, adult males reared on a high-protein diet died sooner than those on low-protein diets because they invested more energy in calling during early adulthood. Our findings uphold the theoretical prediction that the relationship between longevity and sexual advertisement may be dynamic (that is, either positive or negative), depending on local conditions such as resource availability. Moreover, they caution the use of longevity as a proxy for fitness in sexual selection studies, and suggest avenues for future research on the relationship between sexual attractiveness and ageing.

Assessing the quality of native vegetation: The 'habitat hectares' approach

Abstract: Summary Assessments of the ‘quality’, condition or status of stands of native vegetation or habitat are now commonplace and are often an essential component of ecological studies and planning processes. Even when soundly based upon ecological principles, these assessments are usually highly subjective and involve implicit value judgements. The present paper describes a novel approach to vegetation or habitat quality assessment (habitat hectares approach) that can be used in almost all types of terrestrial vegetation. It is based on explicit comparisons between existing vegetation features and those of ‘benchmarks’ representing the average characteristics of mature stands of native vegetation of the same community type in a ‘natural’ or ‘undisturbed’ condition. Components of the index incorporate vegetation physiognomy and critical aspects of viability (e.g. degree of regeneration, impact of weeds) and spatial considerations (e.g. area, distribution and connectivity of remnant vegetation in the broader landscape). The approach has been developed to assist in making more objective and explicit decisions about where scarce conservation resources are allocated. Although the approach does not require an intimate botanical knowledge, it is believed to be ecologically valid and useful in many contexts. Importantly, the index does not provide a definitive statement on conservation status nor habitat suitability for individual species. It purposefully takes a ‘broad-brush’ approach and is primarily intended for use by people involved with making environmentally sensitive planning and management decisions, but may be useful within environmental research programmes. The ‘habitat hectares’ approach is subject to further research and ongoing refinement and constructive feedback is sought from practitioners.