School of BioSciences - Research Publications
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ItemSubmillimeter diameter rotary-pullback fiber-optic endoscope for narrowband red-green-blue reflectance, optical coherence tomography, and autofluorescence in vivo imaging.(SPIE-Intl Soc Optical Eng, 2019-10)A fiber-based endoscopic imaging system combining narrowband red-green-blue (RGB) reflectance with optical coherence tomography (OCT) and autofluorescence imaging (AFI) has been developed. The system uses a submillimeter diameter rotary-pullback double-clad fiber imaging catheter for sample illumination and detection. The imaging capabilities of each modality are presented and demonstrated with images of a multicolored card, fingerprints, and tongue mucosa. Broadband imaging, which was done to compare with narrowband sources, revealed better contrast but worse color consistency compared with narrowband RGB reflectance. The measured resolution of the endoscopic system is 25 μm in both the rotary direction and the pullback direction. OCT can be performed simultaneously with either narrowband RGB reflectance imaging or AFI.
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ItemThreatened and invasive reptiles are not two sides of the same coin(WILEY, 2016-09)Abstract Aim The ‘two sides of the same coin’ hypothesis posits that biological traits that predispose species to extinction and invasion lie on opposite ends of a continuum. Conversely, anthropogenic factors may have similar effects on extinction and invasion risk. We test these two hypotheses using data on more than 1000 reptile species. Location Global. Methods We used hierarchical Bayesian models to determine whether biological traits and anthropogenic factors were correlated with whether a species was: (1) listed as Threatened versus Least Concern on the IUCN Red List, and (2) successful versus unsuccessful at establishing a viable population once introduced outside of its native geographical range. The ‘two sides of the same coin’ hypothesis predicts that model coefficients for each trait should be opposite in sign between these two models. Results Seventy‐three per cent of model coefficients describing 10 aspects of a species’ life history, ecology, biogeography and environmental niche breadth were opposite in sign between the two groups; however, most effect sizes for variables that showed contrasting relationships were small and/or uncertain. The only exception was body size: larger‐bodied species were more likely to be threatened, whereas smaller‐bodied species were more likely to be invasive. As predicted, human population density across a species’ native geographical range was positively correlated with both threat and invasion probabilities. Other anthropogenic variables did not have strong analogous effects. Main conclusions The assumption that threatened and invasive species lie on opposite ends of a continuum, while consistent with life‐history theory, appears to be an oversimplification. Our results do suggest, however, that anthropogenic variables can be important predictors of a species’ fate, and should be more routinely incorporated in trait‐based analyses of extinction and invasion risk.
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ItemDisparity in the timing of vertebrate diversification events between the northern and southern hemispheres(BMC, 2012-12-15)BACKGROUND: Climatic oscillations throughout the Quaternary had profound effects on temperate biodiversity, but the extent of Quaternary climate change was more severe in temperate regions of the northern hemisphere than in the southern hemisphere. We sought to determine whether this geographic disparity differentially influenced the timing of intraspecific diversification events within ectothermic and endothermic vertebrate species. Using published phylogenetic hypotheses, we gathered data on the oldest intraspecific diversification event within mammal, bird, freshwater fish, amphibian, and reptile species from temperate-zone areas. We then tested whether the timing of diversification events differed between hemispheres. RESULTS: Our analyses provide strong evidence that vertebrates from temperate regions of the northern hemisphere are younger than those from the southern hemisphere. However, we find little evidence to suggest that this relationship differs between endotherms versus ectotherms, or that it varies widely across the five classes of vertebrates that we considered. In addition, we find that on average, endothermic species are much younger than ectothermic species. CONCLUSION: Our findings suggest that geographic variation in the magnitude of climatic oscillations during the Quaternary led to substantial disparity in the timing of intraspecific diversification events between northern and southern hemisphere vertebrates, and that the magnitude of this divergence is largely congruent across vertebrate taxa.
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ItemSmart Moves: Effects of Relative Brain Size on Establishment Success of Invasive Amphibians and Reptiles(PUBLIC LIBRARY SCIENCE, 2011-04-06)Brain size relative to body size varies considerably among animals, but the ecological consequences of that variation remain poorly understood. Plausibly, larger brains confer increased behavioural flexibility, and an ability to respond to novel challenges. In keeping with that hypothesis, successful invasive species of birds and mammals that flourish after translocation to a new area tend to have larger brains than do unsuccessful invaders. We found the same pattern in ectothermic terrestrial vertebrates. Brain size relative to body size was larger in species of amphibians and reptiles reported to be successful invaders, compared to species that failed to thrive after translocation to new sites. This pattern was found in six of seven global biogeographic realms; the exception (where relatively larger brains did not facilitate invasion success) was Australasia. Establishment success was also higher in amphibian and reptile families with larger relative brain sizes. Future work could usefully explore whether invasion success is differentially associated with enlargement of specific parts of the brain (as predicted by the functional role of the forebrain in promoting behavioural flexibility), or with a general size increase (suggesting that invasion success is facilitated by enhanced perceptual and motor skills, as well as cognitive ability).
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ItemDesiccation Risk Drives the Spatial Ecology of an Invasive Anuran (Rhinella marina) in the Australian Semi-Desert(PUBLIC LIBRARY SCIENCE, 2011-10-17)Some invasive species flourish in places that impose challenges very different from those faced in their native geographic ranges. Cane toads (Rhinella marina) are native to tropical and subtropical habitats of South and Central America, but have colonised extremely arid regions over the course of their Australian invasion. We radio-tracked 44 adult cane toads at a semi-arid invasion front to investigate how this invasive anuran has managed to expand its geographic range into arid areas that lie outside of its native climatic niche. As predicted from their low physiological control over rates of evaporative water loss, toads selected diurnal shelter sites that were consistently cooler and damper (and thus, conferred lower water loss rates) than nearby random sites. Desiccation risk also had a profound influence on rates of daily movement. Under wet conditions, toads that were far from water moved further between shelter sites than did conspecifics that remained close to water, presumably in an attempt to reach permanent water sources. However, this relationship was reversed under dry conditions, such that only toads that were close to permanent water bodies made substantial daily movements. Toads that were far from water bodies also travelled along straighter paths than did conspecifics that generally remained close to water. Thus, behavioural flexibility--in particular, an ability to exploit spatial and temporal heterogeneity in the availability of moist conditions--has allowed this invasive anuran to successfully colonize arid habitats in Australia. This finding illustrates that risk assessment protocols need to recognise that under some circumstances an introduced species may be able to thrive in conditions far removed from any that it experiences in its native range.
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ItemA comparison of joint species distribution models for presence-absence data(WILEY, 2019-02-01)1. Joint species distribution models (JSDMs) account for biotic interactions and missing environmental predictors in correlative species distribution models. Several different JSDMs have been proposed in the literature, but the use of different or conflicting nomenclature and statistical notation potentially obscures similarities and differences among them. Furthermore, new JSDM implementations have been illustrated with different case studies, preventing direct comparisons of computational and statistical performance. 2. We aim to resolve these outstanding issues by (a) highlighting similarities among seven presence–absence JSDMs using a clearly defined, singular notation; and (b) evaluating the computational and statistical performance of each JSDM using six datasets that vary widely in numbers of sites, species, and environmental covariates considered. 3. Our singular notation shows that many of the JSDMs are very similar, and in turn parameter estimates of different JSDMs are moderate to strongly, positively correlated. In contrast, the different JSDMs clearly differ in computational efficiency and memory limitations. 4. Our framework will allow ecologists to make educated decisions about the JSDM that best suits their objective, and enable wider uptake of JSDM methods among the ecological community.
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ItemStatistical approaches to account for false-positive errors in environmental DNA samples(WILEY, 2016-05)Environmental DNA (eDNA) sampling is prone to both false-positive and false-negative errors. We review statistical methods to account for such errors in the analysis of eDNA data and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false-positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability and false-positive rates. We advocate alternative approaches to account for false-positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false-positive errors. We illustrate the advantages of these approaches over ad hoc classifications of detections and provide practical advice and code for fitting these models in maximum likelihood and Bayesian frameworks. Given the severe bias induced by false-negative and false-positive errors, the methods presented here should be more routinely adopted in eDNA studies.
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ItemCost and feasibility of a barrier to halt the spread of invasive cane toads in arid Australia: incorporating expert knowledge into model-based decision-making(Wiley, 2017-02-01)Summary 1. Active engagement with practitioners is a crucial component of model‐based decision‐making in conservation management; it can assist with data acquisition, improve models and help narrow the ‘knowing–doing’ gap. 2. We worked with practitioners of one of the worst invasive species in Australia, the cane toad Rhinella marina, to revise a model that estimates the effectiveness of landscape barriers to contain spread. The original model predicted that the invasion could be contained by managing artificial watering points on pastoral properties, but was initially met with scepticism by practitioners, in part due to a lack of engagement during model development. 3. We held a workshop with practitioners and experts in cane toad biology. Using structured decision‐making, we elicited concerns about the original model, revised its structure, updated relevant input data, added an economic component and found the most cost‐effective location for a barrier across a range of fixed budgets and management scenarios. We then conducted scenario analyses to test the sensitivity of management decisions to model revisions. 4. We found that toad spread could be contained for all of the scenarios tested. Our modelling suggests a barrier could cost $4·5 M (2015 AUD) over 50 years for the most likely landscape scenario. The incorporation of practitioner knowledge into the model was crucial. As well as improving engagement, when we incorporated practitioner concerns (particularly regarding the effects of irrigation and dwellings on toad spread), we found a different location for the optimal barrier compared to a previously published study (Tingley et al. 2013). 5. Synthesis and applications. Through engagement with practitioners, we turned an academic modelling exercise into a decision‐support tool that integrated local information, and considered more realistic scenarios and constraints. Active engagement with practitioners led to productive revisions of a model that estimates the effectiveness of a landscape barrier to contain spread of the invasive cane toad R. marina. Benefits also include greater confidence in model predictions, improving our assessment of the cost and feasibility of containing the spread of toads.
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ItemIntegrating transport pressure data and species distribution models to estimate invasion risk for alien stowaways(WILEY, 2018-04)The number of alien species transported as stowaways is steadily increasing and new approaches are urgently needed to tackle this emerging invasion pathway. We introduce a general framework for identifying high‐risk transport pathways and receiving sites for alien species that are unintentionally transported via goods and services. This approach combines the probability of species arrival at transport hubs with the likelihood that the environment in the new region can sustain populations of that species. We illustrate our approach using a case study of the Asian black‐spined toad Duttaphrynus melanostictus in Australia, a species that is of significant biosecurity concern in Australasia, Indonesia, and Madagascar. A correlative model fitted to occurrence data from the native geographic range of D. melanostictus predicted high environmental suitability at locations where the species has established alien populations globally. Applying the model to Australia revealed that transport hubs with the highest numbers of border interceptions and on‐shore detections of D. melanostictus were environmentally similar to locations within the species’ native range. Numbers of D. melanostictus interceptions and detections in Australia increased over time, but were unrelated to indices of air and maritime trade volume. Instead, numbers of interceptions and detections were determined by the country of origin of airplanes (Thailand) and ships (Indonesia). Thus, the common assumption that transport pressure is correlated with invasion risk does not hold in all cases. Our work builds on previous efforts to integrate transport pressure data and species distribution models, by jointly modelling the number of intercepted and detected stowaways, while incorporating imperfect detection and the environmental suitability of receiving hubs. The approach presented here can be applied to any system for which historical biosecurity data are available, and provides an efficient means to allocate quarantine and surveillance efforts to reduce the probability of alien species establishment.
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ItemPatterns of niche filling and expansion across the invaded ranges of an Australian lizard(WILEY, 2016-03)Studies of realized niche shifts in alien species typically ignore the potential effects of intraspecific niche variation and different invaded‐range environments on niche lability. We incorporate our detailed knowledge of the native‐range source populations and global introduction history of the delicate skink Lampropholis delicata to examine intraspecific variation in realized niche expansion and unfilling, and investigate how alternative niche modelling approaches are affected by that variation. We analyzed the realized niche dynamics of L. delicata using an ordination method, ecological niche models (ENMs), and occurrence records from 1) Australia (native range), 2) New Zealand, 3) Hawaii, 4) the two distinct native‐range clades that were the sources for the New Zealand and Hawaii introductions, and 5) the species’ global range (including Lord Howe Island, Australia). We found a gradient of realized niche change across the invaded ranges of L. delicata: niche stasis on Lord Howe Island, niche unfilling in New Zealand (16%), and niche unfilling (87%) and expansion (14%) in Hawaii. ENMs fitted to native‐range data generally identified suitable climatic conditions at sites where the species has established non‐native populations, whereas ENMs based on native‐range source clades and non‐native populations had lower spatial transferability. Our results suggest that the extent to which realized niches are maintained during invasion does not depend on species‐level traits. When realized niche shifts are predominately due to niche unfilling, fully capturing species’ responses along climatic gradients by basing ENMs on native distributions may be more important for accurate invasion forecasts than incorporating phylogenetic differentiation, or integrating niche changes in the invaded range.