School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemNo Preview Availablemixchar: An R Package for the Deconvolution of Thermal Decay Curves(Ubiquity Press, Ltd., 2021-01-01)
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ItemAusTraits, a curated plant trait database for the Australian flora(NATURE PORTFOLIO, 2021-09-30)We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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ItemPredicting reliability through structured expert elicitation with repliCATS (Collaborative Assessments for Trustworthy Science)(Early Release, 2021-02-22)
Replication is a hallmark of scientific research. As replications of individual studies are resource intensive, techniques for predicting the replicability are required. We introduce a new technique to evaluating replicability, the repliCATS (Collaborative Assessments for Trustworthy Science) process, a structured expert elicitation approach based on the IDEA protocol. The repliCATS process is delivered through an underpinning online platform and applied to the evaluation of research claims in social and behavioural sciences. This process can be deployed for both rapid assessment of small numbers of claims, and assessment of high volumes of claims over an extended period. Pilot data suggests that the accuracy of the repliCATS process meets or exceeds that of other techniques used to predict replicability. An important advantage of the repliCATS process is that it collects qualitative data that has the potential to assist with problems like understanding the limits of generalizability of scientific claims. The repliCATS process has potential applications in alternative peer review and in the allocation of effort for replication studies.
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ItemPHENOTYPIC PLASTICITY MASKS RANGE-WIDE GENETIC DIFFERENTIATION FOR VEGETATIVE BUT NOT REPRODUCTIVE TRAITS IN A SHORT-LIVED PLANT(WILEY, 2021-11)Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with observational field data throughout the range of a widespread short-lived herb, Plantago lanceolata, we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait-environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field-observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness.
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ItemEliciting group judgements about replicability: A technical implementation of the IDEA Protocol(Hawaii International Conference on System Sciences, 2021-01-01)In recent years there has been increased interest in replicating prior research. One of the biggest challenges to assessing replicability is the cost in resources and time that it takes to repeat studies. Thus there is an impetus to develop rapid elicitation protocols that can, in a practical manner, estimate the likelihood that research findings will successfully replicate. We employ a novel implementation of the IDEA ('Investigate', 'Discuss', 'Estimate' and 'Aggregate) protocol, realised through the repliCATS platform. The repliCATS platform is designed to scalably elicit expert opinion about replicability of social and behavioural science research. The IDEA protocol provides a structured methodology for eliciting judgements and reasoning from groups. This paper describes the repliCATS platform as a multi-user cloud-based software platform featuring (1) a technical implementation of the IDEA protocol for eliciting expert opinion on research replicability, (2) capture of consent and demographic data, (3) on-line training on replication concepts, and (4) exporting of completed judgements. The platform has, to date, evaluated 3432 social and behavioural science research claims from 637 participants.
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ItemPredicting species and community responses to global change using structured expert judgement: An Australian mountain ecosystems case study(WILEY, 2021-09)Conservation managers are under increasing pressure to make decisions about the allocation of finite resources to protect biodiversity under a changing climate. However, the impacts of climate and global change drivers on species are outpacing our capacity to collect the empirical data necessary to inform these decisions. This is particularly the case in the Australian Alps which have already undergone recent changes in climate and experienced more frequent large-scale bushfires. In lieu of empirical data, we use a structured expert elicitation method (the IDEA protocol) to estimate the change in abundance and distribution of nine vegetation groups and 89 Australian alpine and subalpine species by the year 2050. Experts predicted that most alpine vegetation communities would decline in extent by 2050; only woodlands and heathlands are predicted to increase in extent. Predicted species-level responses for alpine plants and animals were highly variable and uncertain. In general, alpine plants spanned the range of possible responses, with some expected to increase, decrease or not change in cover. By contrast, almost all animal species are predicted to decline or not change in abundance or elevation range; more species with water-centric life-cycles are expected to decline in abundance than other species. While long-term ecological data will always be the gold standard for informing the future of biodiversity, the method and outcomes outlined here provide a pragmatic and coherent basis upon which to start informing conservation policy and management in the face of rapid change and a paucity of data.
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ItemTraits explain invasion of alien plants into tropical rainforests(WILEY, 2021-05)1. The establishment of new botanic gardens in tropical regions highlights a need for weed risk assessment tools suitable for tropical ecosystems. The relevance of plant traits for invasion into tropical rainforests has not been well studied.2. Working in and around four botanic gardens in Indonesia where 590 alien species have been planted, we estimated the effect of four plant traits, plus time since species introduction, on: (a) the naturalization probability and (b) abundance (density) of naturalized species in adjacent native tropical rainforests; and (c) the distance that naturalized alien plants have spread from the botanic gardens.3. We found that specific leaf area (SLA) strongly differentiated 23 naturalized from 78 non-naturalized alien species (randomly selected from 577 non-naturalized species) in our study. These trends may indicate that aliens with high SLA, which had a higher probability of naturalization, benefit from at least two factors when establishing in tropical forests: high growth rates and occupation of forest gaps. Naturalized aliens had high SLA and tended to be short. However, plant height was not significantly related to species' naturalization probability when considered alongside other traits.4. Alien species that were present in the gardens for over 30 years and those with small seeds also had higher probabilities of becoming naturalized, indicating that garden plants can invade the understorey of closed canopy tropical rainforests, especially when invading species are shade tolerant and have sufficient time to establish.5. On average, alien species that were not animal dispersed spread 78 m further into the forests and were more likely to naturalize than animal-dispersed species. We did not detect relationships between the measured traits and estimated density of naturalized aliens in the adjacent forests.6. Synthesis: Traits were able to differentiate alien species from botanic gardens that naturalized in native forest from those that did not; this is promising for developing trait-based risk assessment in the tropics. To limit the risk of invasion and spread into adjacent native forests, we suggest tropical botanic gardens avoid planting alien species with fast carbon capture strategies and those that are shade tolerant.
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ItemIndigenous plants promote insect biodiversity in urban greenspaces(WILEY, 2021-06)The contribution of urban greenspaces to support biodiversity and provide benefits for people is increasingly recognized. However, ongoing management practices favor vegetation oversimplification, often limiting greenspaces to lawns and tree canopy rather than multi-layered vegetation that includes under- and midstorey, and the use of nonnative species. These practices hinder the potential of greenspaces to sustain indigenous biodiversity, particularly for taxa like insects that rely on plants for food and habitat. Yet, little is known about which plant species may maximize positive outcomes for taxonomically and functionally diverse insect communities in greenspaces. Additionally, while cities are expected to experience high rates of introductions, quantitative assessments of the relative occupancy of indigenous vs. introduced insect species in greenspace are rare, hindering understanding of how management may promote indigenous biodiversity while limiting the establishment of introduced insects. Using a hierarchically replicated study design across 15 public parks, we recorded occurrence data from 552 insect species on 133 plant species, differing in planting design element (lawn, midstorey, and tree canopy), midstorey growth form (forbs, lilioids, graminoids, and shrubs) and origin (nonnative, native, and indigenous), to assess (1) the relative contributions of indigenous and introduced insect species and (2) which plant species sustained the highest number of indigenous insects. We found that the insect community was overwhelmingly composed of indigenous rather than introduced species. Our findings further highlight the core role of multi-layered vegetation in sustaining high insect biodiversity in urban areas, with indigenous midstorey and canopy representing key elements to maintain rich and functionally diverse indigenous insect communities. Intriguingly, graminoids supported the highest indigenous insect richness across all studied growth forms by plant origin groups. Our work highlights the opportunity presented by indigenous understory and midstorey plants, particularly indigenous graminoids, in our study area to promote indigenous insect biodiversity in urban greenspaces. Our study provides a blueprint and stimulus for architects, engineers, developers, designers, and planners to incorporate into their practice plant species palettes that foster a larger presence of indigenous over regionally native or nonnative plant species, while incorporating a broader mixture of midstorey growth forms.
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ItemAssessing the accuracy of density-independent demographic models for predicting species ranges(WILEY, 2021-03)Accurately predicting species ranges is a primary goal of ecology. Demographic distribution models (DDMs), which correlate underlying vital rates (e.g. survival and reproduction) with environmental conditions, can potentially predict species ranges through time and space. However, tests of DDM accuracy across wide ranges of species' life histories are surprisingly lacking. Using simulations of 1.5 million hypothetical species' range dynamics, we evaluated when DDMs accurately predicted future ranges, to provide clear guidelines for the use of this emerging approach. We limited our study to deterministic demographic models ignoring density dependence, since these models are the most commonly used in the literature. We found that density‐independent DDMs overpredicted extinction if populations were near carrying capacity in the locations where demographic data were available. However, DDMs accurately predicted species ranges if demographic data were limited to sites with mean initial abundance less than one half of carrying capacity. Additionally, the DDMs required demographic data from at least 25 sites, over a short time‐interval (< 10 time‐steps), as populations initially below carrying capacity can saturate in long‐term studies. For species with demographic data from many low density sites, DDMs predicted occurrence more accurately than correlative species distribution models (SDMs) in locations where the species eventually persisted, but not where the species went extinct. These results were insensitive to differences in simulated dispersal, levels of environmental stochasticity, the effects of the environmental variables and the functional forms of density dependence. Our findings suggest that deterministic, density‐independent DDMs are appropriate for applications where locating all possible sites the species might occur in is prioritized over reducing false presence predictions in absent sites. This makes DDMs a promising tool for mapping invasion risk. However, demographic data are often collected at sites where a species is abundant. Density‐independent DDMs are inappropriate in this case.
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ItemTransferability of trait-based species distribution models(WILEY, 2021-01)The need for reliable prediction of species distributions dependent upon traits has been hindered by a lack of model transferability testing. We tested the predictive capacity of trait‐SDMs by fitting hierarchical generalised linear models with three trait and four environmental predictors for 20 eucalypt taxa in a reference region. We used these models to predict occurrence for a much larger set of taxa and target areas (82 taxa across 18 target regions) in south‐eastern Australia. Median predictive performance for new species in target regions was 0.65 (area under receiver operating curve) and 1.24 times random (area under precision recall curve). Prediction in target regions did not worsen with increasing geographic, environmental or community compositional distance from the reference region, and was improved with reliable trait–environment relationships. Transfer testing also identified trait–environment relationships that did not transfer. These results give confidence that traits and transfer testing can assist in the hard problem of predicting environmental responses for new species, environmental conditions and regions.