School of BioSciences - Research Publications

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    Defining and evaluating predictions of joint species distribution models
    Wilkinson, DP ; Golding, N ; Guillera-Arroita, G ; Tingley, R ; McCarthy, MA ; Freckleton, R (WILEY, 2021-03)
    Abstract Joint species distribution models (JSDMs) simultaneously model the distributions of multiple species, while accounting for residual co‐occurrence patterns. Despite increasing adoption of JSDMs in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. We define four different JSDM prediction types that correspond to different aspects of species distribution and community assemblage processes. Marginal predictions are environment‐only predictions akin to predictions from single‐species models; joint predictions simultaneously predict entire community assemblages; and conditional marginal and conditional joint predictions are made at the species or assemblage level, conditional on the known occurrence state of one or more species at a site. We define five different classes of metrics that can be used to evaluate these types of predictions: threshold‐dependent, threshold‐independent, community dissimilarity, species richness and likelihood metrics. We illustrate different prediction types and evaluation metrics using a case study in which we fit a JSDM to a frog occurrence dataset collected in Melbourne, Australia. Joint species distribution models present opportunities to investigate the facets of species distribution and community assemblage processes that are not possible to explore with single‐species models. We show that there are a variety of different metrics available to evaluate JSDM predictions, and that choice of prediction type and evaluation metric should closely match the questions being investigated.
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    Alien Smooth Newts (Lissotriton vulgaris) in Australia Are Infected with Batrachochytrium dendrobatidis but Test Negative for Ranaviruses
    Whinfield, J ; Tingley, R ; Tweedie, A ; Hufschmid, J ; Hick, P (WILDLIFE DISEASE ASSOC, INC, 2022-01)
    Smooth newts (Lissotriton vulgaris) established recently in Melbourne, Australia. Previously, the population's disease status was unknown. Samples from 34 adults and 78 larvae, collected 2011-16, were tested for two pathogens driving the global amphibian extinction crisis. The fungus Batrachochytrium dendrobatidis was identified (6.3% quantitative PCR positive); ranaviruses were not detected.
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    virToad: simulating the spatiotemporal population dynamics and management of a global invader
    Pili, AN ; Tingley, R ; Chapple, DG ; Schumaker, NH (SPRINGER, 2022-09)
    Abstract Context The cane toad (Rhinella marina) is one of the most globally significant and well-studied invasive alien species, and the detrimental impacts of its invasions warrant the design and application of decision support tools. While many models have been developed for guiding policies addressing cane toad invasions, none reliably predict the species’ population dynamics at scales relevant to on-the-ground management. Objectives We describe virToad—an individual-based life-history simulator of the cane toad. We then illustrate virToad’s ability to forecast the cane toad’s spatiotemporal population dynamics at local- to landscape-scales, and its potential for improving management responses to cane toad invasions. Methods We designed virToad to make population dynamics an emergent consequence of the cane toad’s fitness-maximising behavioural responses to mechanistic constraints (e.g., water availability, kin selection), and to management actions. We used virToad to simulate cane toad population dynamics in the absence of management, and under alternative management strategies implemented across a spectrum of effort: hand-capturing and trapping of juveniles and adults, fencing waterbodies, and trapping and chemically suppressing tadpoles. Results virToad produced plausible predictions of cane toad population densities, detection probabilities, distributions, and spatial segregation. Simulation experiments indicated that the efficacy of competing management actions varied significantly, and that only moderate to high effort hand-capturing and trapping of juveniles and adults had the potential to suppress invasions. Conclusion virToad is an open-source, rigorous, and extensible decision support platform that will enable researchers and practitioners to defensibly forecast local- to landscape-scale cane toad spatiotemporal population dynamics and management outcomes.
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    Automated assessment reveals that the extinction risk of reptiles is widely underestimated across space and phylogeny.
    Caetano, GHDO ; Chapple, DG ; Grenyer, R ; Raz, T ; Rosenblatt, J ; Tingley, R ; Böhm, M ; Meiri, S ; Roll, U ; Jordano, P (Public Library of Science (PLoS), 2022-05)
    The Red List of Threatened Species, published by the International Union for Conservation of Nature (IUCN), is a crucial tool for conservation decision-making. However, despite substantial effort, numerous species remain unassessed or have insufficient data available to be assigned a Red List extinction risk category. Moreover, the Red Listing process is subject to various sources of uncertainty and bias. The development of robust automated assessment methods could serve as an efficient and highly useful tool to accelerate the assessment process and offer provisional assessments. Here, we aimed to (1) present a machine learning-based automated extinction risk assessment method that can be used on less known species; (2) offer provisional assessments for all reptiles-the only major tetrapod group without a comprehensive Red List assessment; and (3) evaluate potential effects of human decision biases on the outcome of assessments. We use the method presented here to assess 4,369 reptile species that are currently unassessed or classified as Data Deficient by the IUCN. The models used in our predictions were 90% accurate in classifying species as threatened/nonthreatened, and 84% accurate in predicting specific extinction risk categories. Unassessed and Data Deficient reptiles were considerably more likely to be threatened than assessed species, adding to mounting evidence that these species warrant more conservation attention. The overall proportion of threatened species greatly increased when we included our provisional assessments. Assessor identities strongly affected prediction outcomes, suggesting that assessor effects need to be carefully considered in extinction risk assessments. Regions and taxa we identified as likely to be more threatened should be given increased attention in new assessments and conservation planning. Lastly, the method we present here can be easily implemented to help bridge the assessment gap for other less known taxa.
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    Correlates of extinction risk in Australian squamate reptiles
    Senior, AF ; Böhm, M ; Johnstone, CP ; McGee, MD ; Meiri, S ; Chapple, DG ; Tingley, R (Wiley, 2021-09-01)
    Abstract Aim Identification of particular traits that predispose species to elevated extinction risk is an important component of proactive conservation. We capitalise on a recent strategic extinction risk assessment of all Australian squamate reptiles to identify intrinsic life history traits and extrinsic threats that correlate with extinction risk. We further assess whether extinction risk correlates differ between species impacted by different threatening processes (habitat loss vs. invasive species). Location Australia. Taxon Squamate reptiles. Methods We used the IUCN Red List data for Australian squamates, and publicly available datasets for 14 intrinsic and extrinsic traits. We used phylogenetically controlled Bayesian inference to test hypotheses regarding relationships between extinction risk and species traits, environment, and threat measures. Results We found that intrinsic characteristics (habitat specialisation, small range size and large body size), as well as extrinsic factors (high human footprint, accessibility from human population centres, cold temperatures and high rainfall), predispose a species to extinction. Similar predictors were important in threat‐specific analyses, although relationships were generally more uncertain. Conclusions Our results largely accord with those of global and regional studies of extinction risk in reptiles and of terrestrial vertebrates more broadly. Our findings illustrate that there is no single pathway to extinction among Australian squamates.
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    Environmental correlates of morphological diversity in Australian geckos
    Norris, J ; Tingley, R ; Meiri, S ; Chapple, DG ; Sandel, B (Wiley, 2021-05-01)
    Abstract Aim Climatic variation has long been regarded as a primary source of morphological variation. However, there is mixed support for the adherence of reptiles to ecogeographical hypotheses, such as Bergmann’s rule (body size decreases with temperature) and Allen’s rule (limb length increases with temperature). We quantified body and limb morphology among the diverse Australian gecko fauna (4 families, 30 genera, 226 of the 231 described species) to investigate environmental correlates of morphological variation in this radiation. Location Australia. Major taxa studied Geckos (Squamata: Gekkota; the families Gekkonidae, Carphodactylidae, Diplodactylidae and Pygopodidae). Methods We measured 20 external features of ethanol‐preserved museum specimens. We investigated whether principal component axes of morphology were correlated with three key environmental variables, and the microhabitat occupied by each species. Results Morphology varied greatly among Australian gecko families and genera, although there was a strong phylogenetic signal in morphology. After accounting for phylogeny, morphology was correlated with a species’ microhabitat use. Saxicolous species and species with variable microhabitat requirements (i.e., generalists) had larger body dimensions than terrestrial species. Saxicolous species also had longer proportional forelimbs and hindlimbs than terrestrial species. Main conclusions Our results highlight the importance of phylogeny and microhabitat use in shaping the morphology of Australian geckos. We find little evidence that Australian geckos adhere to Bergmann’s rule or Allen’s rule, suggesting that these ecogeographical hypotheses provide limited insight into the adaptive potential of lizard species to altered environmental conditions.
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    Conservation status of the world's skinks (Scincidae): Taxonomic and geographic patterns in extinction risk
    Chapple, DG ; Roll, U ; Boehm, M ; Aguilar, R ; Amey, AP ; Austin, CC ; Baling, M ; Barley, AJ ; Bates, MF ; Bauer, AM ; Blackburn, DG ; Bowles, P ; Brown, RM ; Chandramouli, SR ; Chirio, L ; Cogger, H ; Colli, GR ; Conradie, W ; Couper, PJ ; Cowan, MA ; Craig, MD ; Das, I ; Datta-Roy, A ; Dickman, CR ; Ellis, RJ ; Fenner, AL ; Ford, S ; Ganesh, SR ; Gardner, MG ; Geissler, P ; Gillespie, GR ; Glaw, F ; Greenlees, MJ ; Griffith, OW ; Grismer, LL ; Haines, ML ; Harris, DJ ; Hedges, SB ; Hitchmough, RA ; Hoskin, CJ ; Hutchinson, MN ; Ineich, I ; Janssen, J ; Johnston, GR ; Karin, BR ; Keogh, JS ; Kraus, F ; LeBreton, M ; Lymberakis, P ; Masroor, R ; McDonald, PJ ; Mecke, S ; Melville, J ; Melzer, S ; Michael, DR ; Miralles, A ; Mitchell, NJ ; Nelson, NJ ; Nguyen, TQ ; Nogueira, CDC ; Ota, H ; Pafilis, P ; Pauwels, OSG ; Perera, A ; Pincheira-Donoso, D ; Reed, RN ; Ribeiro-Junior, MA ; Riley, JL ; Rocha, S ; Rutherford, PL ; Sadlier, RA ; Shacham, B ; Shea, GM ; Shine, R ; Slavenko, A ; Stow, A ; Sumner, J ; Tallowin, OJS ; Teale, R ; Torres-Carvajal, O ; Trape, J-F ; Uetz, P ; Ukuwela, KDB ; Valentine, L ; Dyke, JUV ; van Winkel, D ; Vasconcelos, R ; Vences, M ; Wagner, P ; Wapstra, E ; While, GM ; Whiting, MJ ; Whittington, CM ; Wilson, S ; Ziegler, T ; Tingley, R ; Meiri, S (ELSEVIER SCI LTD, 2021-05)
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    A demographic framework for understanding fire-driven reptile declines in the 'land of the lizards'
    Santos, JL ; Sitters, H ; Keith, DA ; Geary, WL ; Tingley, R ; Kelly, LT (WILEY, 2022-10-01)
    Background: Fire creates habitats for many animals but changes in fire activity threaten species worldwide. While conservation assessments routinely identify fire as a threat to lizards and snakes, the processes underlying fire-driven population declines have received less attention. Assessing the effects of fire on demographic processes – survival, reproduction and movement – provides a means to identify mechanisms of population declines and forecast population changes. Here, we synthesize how inappropriate fire regimes contribute to declines of animal populations, using threatened Australian squamates as a case study. Methods: We applied a demographic framework in a systematic review to identify fire characteristics and interacting threats associated with population declines in imperilled Australian squamates (n = 88). We reviewed primary literature and conservation assessments on these species and classified fire-related threats according to seven key mechanisms of population decline, five fire-regime characteristics, and eight interacting threats. Results: Inappropriate fire regimes threaten 43% of Australian squamates of conservation concern, including geckos, skinks and snakes. Our analysis indicates that high fire intensity and severity, high fire frequency, and large fires are the main causes of fire-related population declines, particularly via their impacts on survival. Low fire frequency also contributes to declines of some species through reduced survival or reproductive success. Weed invasion and predation are observed or predicted to interact with fire to amplify reptile declines. Our results also reveal a dearth of robust empirical studies on squamates of conservation concern. Main conclusions: The demographic framework applied here will help forecast population changes in a new era of fire. By focusing on processes that are relevant to squamate populations globally, we anticipate that the framework will help diagnose causes of population declines in ecosystems that experience fire, and quantify the consequences of alternative management actions, including urgent conservation interventions after megafires.
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    Submillimeter diameter rotary-pullback fiber-optic endoscope for narrowband red-green-blue reflectance, optical coherence tomography, and autofluorescence in vivo imaging.
    Buenconsejo, AL ; Hohert, G ; Manning, M ; Abouei, E ; Tingley, R ; Janzen, I ; McAlpine, J ; Miller, D ; Lee, A ; Lane, P ; MacAulay, C (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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    A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis
    Melville, J ; Chapple, DG ; Keogh, JS ; Sumner, J ; Amey, A ; Bowles, P ; Brennan, IG ; Couper, P ; Donnellan, SC ; Doughty, P ; Edwards, DL ; Ellis, RJ ; Esquerre, D ; Fenker, J ; Gardner, MG ; Georges, A ; Haines, ML ; Hoskin, CJ ; Hutchinson, M ; Moritz, C ; Nankivell, J ; Oliver, P ; Pavon-Vazquez, CJ ; Pepper, M ; Rabosky, DL ; Sanders, K ; Shea, G ; Singhal, S ; Wilmer, JW ; Tingley, R ; Dobson, AP (PUBLIC LIBRARY SCIENCE, 2021-06)
    Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.