School of BioSciences - Research Publications

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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)
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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)
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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, 2021-04-20)
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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, 2022-05-10)
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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, 2021-06-01)
    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.
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    Niche shifts and environmental non-equilibrium undermine the usefulness of ecological niche models for invasion risk assessments.
    Pili, AN ; Tingley, R ; Sy, EY ; Diesmos, MLL ; Diesmos, AC (Springer Science and Business Media LLC, 2020-05-14)
    Niche shifts and environmental non-equilibrium in invading alien species undermine niche-based predictions of alien species' potential distributions and, consequently, their usefulness for invasion risk assessments. Here, we compared the realized climatic niches of four alien amphibian species (Hylarana erythraea, Rhinella marina, Hoplobatrachus rugulosus, and Kaloula pulchra) in their native and Philippine-invaded ranges to investigate niche changes that have unfolded during their invasion and, with this, assessed the extent of niche conservatism and environmental equilibrium. We investigated how niche changes affected reciprocal transferability of ecological niche models (ENMs) calibrated using data from the species' native and Philippine-invaded ranges, and both ranges combined. We found varying levels of niche change across the species' realized climatic niches in the Philippines: climatic niche shift for H. rugulosus; niche conservatism for R. marina and K. pulchra; environmental non-equilibrium in the Philippine-invaded range for all species; and environmental non-equilibrium in the native range or adaptive changes post-introduction for all species except H. erythraea. Niche changes undermined the reciprocal transferability of ENMs calibrated using native and Philippine-invaded range data. Our paper highlights the difficulty of predicting potential distributions given niche shifts and environmental non-equilibrium; we suggest calibrating ENMs with data from species' combined native and invaded ranges, and to regularly reassess niche changes and recalibrate ENMs as species' invasions progress.
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    Rapid assessment of the biodiversity impacts of the 2019-2020 Australian megafires to guide urgent management intervention and recovery and lessons for other regions
    Legge, S ; Woinarski, JCZ ; Scheele, BC ; Garnett, ST ; Lintermans, M ; Nimmo, DG ; Whiterod, NS ; Southwell, DM ; Ehmke, G ; Buchan, A ; Gray, J ; Metcalfe, DJ ; Page, M ; Rumpff, L ; van Leeuwen, S ; Williams, D ; Ahyong, ST ; Chapple, DG ; Cowan, M ; Hossain, MA ; Kennard, M ; Macdonald, S ; Moore, H ; Marsh, J ; McCormack, RB ; Michael, D ; Mitchell, N ; Newell, D ; Raadik, TA ; Tingley, R ; Boer, M (WILEY, 2021-10-21)
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    Threatened and invasive reptiles are not two sides of the same coin
    Tingley, R ; Mahoney, PJ ; Durso, AM ; Tallian, AG ; Moran-Ordonez, A ; Beard, KH (WILEY, 2016-09-01)