Joanna Sumner

Reptiles on the brink: identifying the Australian terrestrial snake and lizard species most at risk of extinction

Publisher: CSIRO Publishing

Date: 2021

DOI: 10.1071/PC20033

Abstract: Australia hosts approximately 10% of the world’s reptile species, the largest number of any country. Despite this and evidence of widespread decline, the first comprehensive assessment of the conservation status of Australian terrestrial squamates (snakes and lizards) was undertaken only recently. Here we apply structured expert elicitation to the 60 species assessed to be in the highest IUCN threat categories to estimate their probability of extinction by 2040. We also assessed the probability of successful reintroduction for two Extinct in the Wild (EW) Christmas Island species with trial reintroductions underway. Collation and analysis of expert opinion indicated that six species are at high risk (& %) of becoming extinct within the next 20 years, and up to 11 species could be lost within this timeframe unless management improves. The consensus among experts was that neither of the EW species were likely to persist outside of small fenced areas without a significant increase in resources for intense threat management. The 20 most imperilled species are all restricted in range, with three occurring only on islands. The others are endemic to a single state, with 55% occurring in Queensland. Invasive species (notably weeds and introduced predators) were the most prevalent threats, followed by agriculture, natural system modifications (primarily fire) and climate change. Increased resourcing and management intervention are urgently needed to avert the impending extinction of Australia’s imperilled terrestrial reptiles.

Integrating phylogeography and high-resolution X-ray CT reveals five new cryptic species and multiple hybrid zones among Australian earless dragons

Publisher: The Royal Society

Date: 12-2019

DOI: 10.1098/RSOS.191166

Abstract: Cryptic lineages, comprising species complexes with deep genetic structuring across the landscape but without distinct morphological differences, impose substantial difficulties for systematists and taxonomists in determining true species ersity. Here, we present an integrative approach that combines data from phylogeography and geometric morphometric analyses of three-dimensional cranial models to revisit the uncertain taxonomy of earless dragons from southern and central Australia that at one time or another have been included under the name Tympanocryptis lineata . Our approach finds strong support for seven previously described species, and more importantly, five undescribed Tympanocryptis taxa for which we provide a taxonomic treatment. We also find evidence of introgression and hybridization in three discrete contact zones between lineages, supported by mitochondrial and nuclear genes, as well as morphological analyses. With a s ling design that includes at least five in iduals for each genetic lineage with corresponding X-ray microcomputed tomography scans, we perform comparative evolutionary analyses to show that there is a significant phylogenetic signal in Tympanocryptis cranial shape. Our results demonstrate the importance of using multiple specimens in each genetic lineage, particularly in cases of potential hybridization, and that geometric morphometrics, when used in an integrative framework, is a powerful tool in species delimitation across cryptic lineages. Our results lay the groundwork for future evolutionary studies in this widespread group across multiple environmental types and identify several species of immediate conservation concern with a focus on T. petersi sp. nov. We suggest that this species has undergone significant population declines and warrants a full conservation assessment.

Morphological and molecular evidence of population divergence in a widespread shorebird across its southern mainland Australian distribution

Publisher: Springer Science and Business Media LLC

Date: 19-06-2020

DOI: 10.1007/S10592-020-01286-2

Three new species of north-eastern Australian earless dragons (Agamidae: Tympanocryptis)

Publisher: Atlas of Living Australia

Date: 10-08-2023

DOI: 10.54102/AJT.VN9BW

Abstract: Earless dragons (Tympanocryptis spp.) are found in most open dry environments across the Australian continent, with the 23 currently described species inhabiting a variety of ecological niches, from stony desert to tropical woodland or cracking clay savannahs. Recent species delimitation research using genetics (mtDNA, nDNA, SNPs) and geometric morphometric analyses of CT scans identified three genetic lineages of earless dragons that are yet to be described in Queensland, supporting the need for a taxonomic revision. Focussing on this geographic region, we use supporting evidence from a mitochondrial DNA (ND2) phylogeny, along with external morphological assessment, to undertake a taxonomic revision of Queensland earless dragons. Based on these data, we describe three new species of Tympanocryptis from the cracking clay grasslands of the Darling Riverine Basin, the Queensland Central Highlands, and the stony open eucalypt woodlands on the Einasleigh Uplands. The revision of these north-eastern Australian earless dragon species provides further taxonomic clarity within the Tympanocryptis genus.

Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional‐scale disturbance

Publisher: Wiley

Date: 03-2022

DOI: 10.1002/ECE3.8627

Abstract: Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific isions to be factored into conservation planning—subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic ersity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 in iduals) covering the distribution of the Australian eastern three‐lined skink, Bassiana duperreyi , to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well‐supported diagnosable operational taxonomic units (OTUs) existed within B . duperreyi . Low levels of ergence of B . duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait ( ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re‐evaluation of this species complex and the need for bio ersity assessment to include an examination of cryptic species and/or cryptic ersity below the level of species. Such information on lineage ersity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.

Rapid evaluation of COVID-19 vaccine effectiveness against symptomatic infection with SARS-CoV-2 variants by analysis of genetic distance

Publisher: Springer Science and Business Media LLC

Date: 16-06-2022

DOI: 10.1038/S41591-022-01877-1

Abstract: Timely evaluation of the protective effects of Coronavirus Disease 2019 (COVID-19) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is urgently needed to inform pandemic control planning. Based on 78 vaccine efficacy or effectiveness (VE) data from 49 studies and 1,984,241 SARS-CoV-2 sequences collected from 31 regions, we analyzed the relationship between genetic distance (GD) of circulating viruses against the vaccine strain and VE against symptomatic infection. We found that the GD of the receptor-binding domain of the SARS-CoV-2 spike protein is highly predictive of vaccine protection and accounted for 86.3% ( P = 0.038) of the VE change in a vaccine platform-based mixed-effects model and 87.9% ( P = 0.006) in a manufacturer-based model. We applied the VE-GD model to predict protection mediated by existing vaccines against new genetic variants and validated the results by published real-world and clinical trial data, finding high concordance of predicted VE with observed VE. We estimated the VE against the Delta variant to be 82.8% (95% prediction interval: 68.7–96.0) using the mRNA vaccine platform, closely matching the reported VE of 83.0% from an observational study. Among the four sublineages of Omicron, the predicted VE varied between 11.9% and 33.3%, with the highest VE predicted against BA.1 and the lowest against BA.2, using the mRNA vaccine platform. The VE-GD framework enables predictions of vaccine protection in real time and offers a rapid evaluation method against novel variants that may inform vaccine deployment and public health responses.

Speciation in the mountains and dispersal by rivers: Molecular phylogeny of Eulamprus water skinks and the biogeography of Eastern Australia

Publisher: Wiley

Date: 02-07-2018

DOI: 10.1111/JBI.13385

The Unusual Metalloprotease-Rich Venom Proteome of the Australian Elapid Snake Hoplocephalus stephensii

Publisher: MDPI AG

Date: 28-04-2022

DOI: 10.3390/TOXINS14050314

Abstract: The Australasian region is home to the most erse elapid snake radiation on the planet (Hydrophiinae). Many of these snakes have evolved into unique ecomorphs compared to elapids on other continents however, their venom compositions are poorly known. The Australian elapid Hoplocephalus stephensii (Stephen’s banded snake) is an arboreal snake with a unique morphology. Human envenoming results in venom-induced consumption coagulopathy, without neurotoxicity. Using transcriptomics and a multi-step fractionation method involving reverse-phase high-performance liquid chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis and bottom-up proteomics, we characterized the venom proteome of H. stephensii. 92% of the total protein component of the venom by weight was characterized, and included all dominant protein families and 4 secondary protein families. Eighteen toxins made up 76% of the venom, four previously characterized and 14 new toxins. The four dominant protein families made up 77% of the venom, including snake venom metalloprotease (SVMP 36.7% three identified toxins), phospholipase A2 (PLA2 24.0% five identified toxins), three-finger toxin (3FTx 10.2% two toxins) and snake venom serine protease (SVSP 5.9% one toxin Hopsarin). Secondary protein families included L-amino acid oxidase (LAAO 10.8% one toxin), natriuretic peptide (NP 0.8% two toxins), cysteine-rich secretory protein (CRiSP 1.7% two toxins), c-type lectin (CTL 1.1% one toxin), and one minor protein family, nerve growth factor (NGF 0.8% one toxin). The venom composition of H. stephensii differs to other elapids, with a large proportion of SVMP and LAAO, and a relatively small amount of 3FTx. H. stephensii venom appeared to have less toxin ersity than other elapids, with only 18 toxins making up three-quarters of the venom.

A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis

Publisher: Public Library of Science (PLoS)

Date: 06-2021

DOI: 10.1371/JOURNAL.PBIO.3001210

Abstract: Global bio ersity loss is a profound consequence of human activity. Disturbingly, bio ersity 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 bio ersity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly erse 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.

University Of Queensland

Location: Australia

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Chinese University Of Hong Kong

Location: China

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Museums Victoria

Location: Australia

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University Of Sydney

Location: Australia

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Discovery Projects - Grant ID: DP0663875

Start Date: 02-2006

End Date: 12-2008

Amount: $318,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP170100012

Start Date: 10-2018

End Date: 09-2022

Amount: $300,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP210101883

Start Date: 08-2021

End Date: 12-2024

Amount: $549,841.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP160100189

Start Date: 01-2017

End Date: 06-2021

Amount: $164,000.00

Funder: Australian Research Council