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Item Open Access Towards integrating and harmonising information on plant invasions across Australia(Pensoft Publishers, 2024) Martín-Forés, I.; Guerin, G.R.; Lewis, D.; Gallagher, R.V.; Vilà, M.; Catford, J.A.; Pauchard, A.; Sparrow, B.Terminology for the invasion status of alien species has typically relied either on ecological- or policy-based criteria, with the former emphasising species’ ability to overcome ecological barriers and the latter on species’ impacts. There remains no universal consensus about definitions of invasion. Without an agreement on definitions, it is difficult to combine data that comes from a range of sources. In Australia, information on plant invasions is provided by a collection of independent jurisdictions. This has led to inconsistencies in terminology used to describe species invasion status at the national level, impeding efficient management. In this paper, we review and discuss the steps taken to harmonise the different terminologies used across Australia’s states and territories. We identified mismatches in definitions and records of invasion status for vascular plant taxa across different jurisdictions and propose prioritisation procedures to tackle these mismatches and to integrate information into a harmonised workflow at the national scale. This integration has made possible the creation of a standardised dataset at the Australian national scale (the Alien Flora of Australia). In Australia, having an integrated workflow for referring to and monitoring alien flora will aid early warning and prevent species introduction, facilitate decision-making and aid biosecurity measures.Item Open Access Shining a LAMP on the applications of isothermal amplification for monitoring environmental biosecurity(Pensoft Publishers, 2023) Deliveyne, N.; Young, J.M.; Austin, J.J.; Cassey, P.Environmental biosecurity risks associated with the transnational wildlife trade include the loss of biodiversity, threats to public health, and the proliferation of invasive alien species. To assist enforcement agencies in identifying species either intentionally (trafficked) or unintentionally (stowaway) entrained in the trade-chain pathway, rapid forensic techniques are needed to enable their detection from DNA samples when physical identification is not possible. Loop Mediated Isothermal Amplification (LAMP) is an emerging technique, with recent applications in biosecurity and forensic sciences, which has potential to function as a field-based detection tool. Here we provide an overview of current research that applies LAMP to environmental biosecurity, including identification of ornamental wildlife parts, consumer products, and invasive species monitoring and biosecurity detection. We discuss the current scope of LAMP as applied to various wildlife trade scenarios and biosecurity checkpoint monitoring, highlight the specificity, sensitivity, and robustness for these applications, and review the potential utility of LAMP for rapid field-based detection at biosecurity checkpoints. Based on our assessment of the literature we recommend broader interest, research uptake, and investment in LAMP as an appropriate field-based species detection method for a wide range of environmental biosecurity scenarios.Item Open Access Elucidating the morphology and ecology of Eoandromeda octobrachiata from the Ediacaran of South Australia(Wiley, 2023) Botha, T.; Sherratt, E.; Droser, M.; Gehling, J.; Garcia-Bellido, D.Eoandromeda octobrachiata is a poorly understood Ediacaran organism, with spiral- octoradial arms, found in South Australia and South China. The informal Nilpena member of the Rawnsley Quartzite, Flinders Ranges in South Australia preserves more than 200 specimens of Eoandromeda. Here we use the novel application of rotational geometric morphometrics together with palaeoenvironmental information to provide a better insight into their palaeobiology and ecology and to address conflicting hypotheses regarding mode of life and taxonomic affinity. We find that Eoandromeda likely had a radially symmetrical shape in life, was cone-shaped and had a high relief off the microbial mat. Analysis of the symmetric and asymmetric shape components revealed they deform strongly in the direction of palaeocurrent, therefore are thought to be made of a flexible material. Almost all specimens are compressed flat. Specimens that appear to have not fully collapsed support the idea that Eoandromeda was likely cone-shaped and further suggest that they possibly collapsed spirally. Our shape analysis along with observed morphological features support the benthic mode of life hypothesis rather than pelagic. Morphological and ecological inconsistencies such as a lack of biradial symmetry and a benthic mode of life do not support the hypothesis of a Ctenophora taxonomic affinity.Item Open Access Shape and size variation in elapid snake fangs, and the effects of phylogeny and diet(Springer Nature, 2023) Palci, A.; Lee, M.S.Y.; Crowe-Riddell, J.; Sherratt, E.Recent studies have found correlations between the shape of snake teeth/fangs and diet. These studies were done at a very broad phylogenetic scale, making it desirable to test if correlations are still detectable at a narrower evolutionary scale, specifically within the family Elapidae. To this end, we studied fang shape in a dense selection of elapids representing most genera worldwide (74%). We used three-dimensional geometric morphometrics to analyse fang diversity and evaluate possible correlations between fang shape, fang size, and diet. We detected only weak phylogenetic signal in our dataset for both shape and size, and no significant evolutionary allometry when correcting for phylogeny. Overall, the distribution of elapid fangs in morphospace was found to be surprisingly conservative, with only a few outliers. The only two dietary categories that were found to have a significant effect on fang shape are fish and snakes, while mammals have a significant effect on absolute but not relative fang size. Our results show that there are disparate patterns in fang-diet relationships at different evolutionary scales. Across all venomous snakes, previous work found that fangs are strongly influenced by diet, but within elapids our study shows these same associations are weaker and often non-significant. This could result from limitations in these types of studies, or could reflect the fact that elapids are a relatively young clade, where recent extensive divergences in diet have yet to be mirrored in fang shape, suggesting a lag between changes in ecology and dental morphology.Item Open Access Evolutionary transition from surface to subterranean living in Australian water beetles (Coleoptera, Dytiscidae) through adaptive and relaxed selection(Oxford University Press (OUP), 2024) Zhao, Y.; Guzik, M.; Humphreys, W.; Watts, C.; Cooper, S.; Sherratt, E.Over the last 5 million years, numerous species of Australian stygobiotic (subterranean and aquatic) beetles have evolved underground following independent colonisation of aquifers by surface ancestors, providing a set of repeated evolutionary transitions from surface to subterranean life. We used this system as an ‘evolutionary experiment’ to investigate whether relaxed selection has provided a source of variability for adaptive radiations into ecosystems containing open niches and whether this variability underpins phenotypic evolution in cave animals. Linear and landmark-based measurements were used to quantify the morphology of subterranean species from different aquifers, compared to interstitial and closely related aquatic surface species. Subterranean dytiscids were observed to be morphologically distinct, suggesting they have a different lifestyle compared to their surface relatives. However, the variation in the measured traits was much greater in the subterranean species, and unstructured, showing no evidence of clustering that would indicate adaptation to specific niches. Furthermore, a previously identified pattern of repeated non-overlapping size variation in beetles across aquifers was not correlated with repeated body shape evolution. The observed variability across body shape and limb traits provides support for the hypothesis that relaxed selection and neutral evolution underlie the phenotypic evolution in these species.Item Open Access Hibbertia fulva (Dilleniaceae), a new species from the Northern Territory in the H. banksii species group(State Herbarium of South Australia, 2023) Hammer, T.The new species Hibbertia fulva T.Hammer is recognised from specimens collected from Frances Creek mine lease, north of Pine Creek, Northern Territory. The differences between it and its closest relatives are discussed.Item Metadata only Reproducibility crisis and gravitation towards a consensus in ocean acidification research(Springer Nature, 2023) Connell, S.D.; Leung, J.Y.S.Reproducibility is a persistent concern in science and recently attracts considerable attention in assessing biological responses to ocean acidification. Here we track the reproducibility of the harmful effects of ocean acidification on calcification of shell-building organisms by conducting a meta-analysis of 373 studies across 24 years. The pioneering studies tended to report large negative effects, but as other researchers assimilated this research into understanding their biological systems, the size of negative effects declined. Such declines represent a scientific process by which discoveries are initially assimilated and their limitations are subsequently explored. We suggest that scientific novelties can polarize a discipline where researchers fail to distinguish between different motivations for testing a phenomenon, that is, its existence (theory proposal) versus its influence within ever-widening contexts (theory development). Where context dependency is high, the lack of reproducibility may not represent a crisis but a part of theory development and eventual gravitation towards a consensus position.Item Metadata only Quaternary plant macrofossils from Robertson Cave, Naracoorte, South Australia: reproductive structures(Taylor & Francis, 2023) Atkins, R.; Hill, R.; Hill, K.; Munroe, S.; Reed, E.The World Heritage Naracoorte Caves in southeastern South Australia are important palaeontological sites known primarily for their diverse vertebrate fossils. Some of the caves also contain well-pre- served Quaternary plant macrofossils, but little palaeobotanical research has been undertaken to date. Here, we describe the angiosperm plant taxa represented by macrofossils of reproductive struc- tures that have been extracted from the Robertson Cave sediment deposit; this has an age range of 820–24,230 years BP. We identified 29 angiosperm taxa representing 20 families. These represent some of the plant species that grew in the Naracoorte region during the Quaternary, and form a database for future plant identification and palaeovegetation reconstructions.Item Open Access A conserved tooth resorption mechanism in modern and fossil snakes.(Springer Science and Business Media LLC, 2023) LeBlanc, A.R.H.; Palci, A.; Anthwal, N.; Tucker, A.S.; Araújo, R.; Pereira, M.F.C.; Caldwell, M.W.Whether snakes evolved their elongated, limbless bodies or their specialized skulls and teeth first is a central question in squamate evolution. Identifying features shared between extant and fossil snakes is therefore key to unraveling the early evolution of this iconic reptile group. One promising candidate is their unusual mode of tooth replacement, whereby teeth are replaced without signs of external tooth resorption. We reveal through histological analysis that the lack of resorption pits in snakes is due to the unusual action of odontoclasts, which resorb dentine from within the pulp of the tooth. Internal tooth resorption is widespread in extant snakes, differs from replacement in other reptiles, and is even detectable via non-destructive μCT scanning, providing a method for identifying fossil snakes. We then detected internal tooth resorption in the fossil snake Yurlunggur, and one of the oldest snake fossils, Portugalophis, suggesting that it is one of the earliest innovations in Pan-Serpentes, likely preceding limb loss.Item Metadata only Two new species of Atopobathynella (Parabathynellidae, Bathynellacea) from the Pilbara region, Australia(Taylor and Francis Online, 2023) Perina, G.; Camacho, A.I.; Danks, M.; White, N.; Guzik, M.T.Fifteen species of the Gondwanan genus Atopobathynella have been described so far from four countries. The position of the genus within the family Parabathynellidae and its species relationships are controversial due to the different characters and species considered by different authors, however most of the phylogenetic reconstructions are based solely on morphological characters. In the past few decades, the arid zones of Western Australia, including the Pilbara region, have been recognized as a hotspot for subterranean fauna. Material is constantly collected to produce Environmental Impact Assessments to protect and manage the subterranean environment. In 2009 the Cleaverville Iron Formation, in the Pilbara region, northern Western Australia, was proposed to be mined, therefore subterranean fauna sampling was conducted as per legislation. Preliminary molecular studies of stygofauna identified two distinct Parabathynellidae lineages from two ridges, however no morphological descriptions were carried out at that time. In this study, we describe two new species from Yarrie and Callawa ridges, respectively: Atopobathynella yarriensis sp. nov. and A. degreyensis sp. nov.. The new species show differences in male antennal organ, ventral tooth of mandible, number of teeth on distal endite of maxillula, absence or presence of epipod of thoracopod I, number of setae on article 4 of thoracopod II, length of distal external seta of exopod of all thoracopods, outer lobe of male thoracopod VIII, number of spines on uropodal sympod and furcal rami, length of the external dorsal plumose seta of the furcal rami. Additionally, we integrated the morphological data with sequences of three genetic loci, Cytochrome Oxidase c Subunit I (COI), 12S rRNA (12S), and nuclear 18S rRNA (18S), calculating p-distances and constructing a multigene molecular phylogeny to support morphology, and explore the monophyletic status of the genus and the relationship amongst its species. The two new species were well supported in our phylogeny, however they appear distantly related.Item Open Access Ecological Considerations When Designing Mitigation Translocations: An Australian Reptile Case Study(MDPI AG, 2023) Bradley, H.S.; Craig, M.D.; Tomlinson, S.; Cross, A.T.; Bamford, M.J.; Bateman, P.W.Translocation science has made considerable progress over the last two decades; however, reptile translocations still frequently fail around the world. Major knowledge gaps surround the basic ecology of reptile species, including basic factors such as habitat preference, which have a critical influence on translocation success. The western spiny-tailed skink (Egernia stokesii badia) is used here as a case study to exemplify how empirical research can directly inform on-ground management and future translocation planning. A combination of studies, including LiDAR scanning of microhabitat structures, camera trapping, plasticine replica model experiments and unbounded point count surveys to assess predation risk, and visual and DNA analysis of dietary requirements, were all used to better understand the ecological requirements of E. s. badia. We found that the skinks have specific log pile requirements, both native and non-native predator management requirements, and a largely herbivorous, broad diet, which all influence translocation site selection and management planning. The use of E. s. badia as an Australian case study provides a clear strategic framework for the targeted research of meaningful ecological factors that influence translocation decision-making. Similar approaches applied to other reptile species are likely to fundamentally increase the capacity for effective management, and the likelihood of future successful translocations.Item Metadata only Cardiac ARIA Index: Measuring the accessibility to cardiovascular services in rural and remote Australia via applied geographic spatial technology(Queensland University of Technology, 2012) Clark, R.A.; Coffee, N.; Turner, D.; Eckert, K.; Bamford, E.; van Gaans, D.; Astles, P.; Milligan, M.; Smail, T.; Stewart, S.; Coombe, D.; Sutcliff, C.; Wilkinson, D.; Tonkin, A.; The Cardiac ARIA projectItem Open Access Improving ecological function of polluted coasts under a tide of plastic waste(Wiley, 2023) McAfee, D.; Leung, J.Y.S.; Connell, S.D.Unprecedented levels of plastics are entering coastal seas, which are already subject to another insidious pollutant: excess nitrogen. Both pollutants were created to enhance human well-being on land but once in the sea they impair the function of filter-feeding organisms that help maintain coastal water quality. We conceptualized evidence to show that oysters (Ostrea spp), the reefs of which can provide a biological solution for managing water quality, can effectively reduce the threat of algal blooms caused by excess nitrogen pollution, even when exposed to moderate microplastic pollution. Yet the functional collapse of this ecosystem service (filter-feeding by oysters) is at risk if current trends in plastic pollution continue, and pollution thresholds that predict functional collapse have already been exceeded in the world’s most polluted rivers. Nevertheless, although the plastic problem is daunting, growing social and political awareness of the need to reduce plastic waste provides hope that a sustainable material society can be attained.Item Open Access Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families(Elsevier, 2023) Thacker, C.E.; Tyler McCraney, W.; Harrington, R.C.; Near, T.J.; Shelley, J.J.; Adams, M.; Hammer, M.P.; Unmack, P.J.Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.Item Open Access Hibbertia radians (Dilleniaceae), a new combination from South Australia(State Herbarium of South Australia, 2023) Hammer, T.Hibbertia empetrifolia (DC.) Hoogland currently comprises subsp. empetrifolia from New South Wales, Tasmania and Victoria and subsp. radians Toelken from South Australia. These subspecies are critically re-evaluated. Evidence is presented to support the recognition of H. empetrifolia subsp. radians as a distinct species, for which the new combination Hibbertia radians (Toelken) T.Hammer is formally made. Descriptions and illustrations are provided for both species.Item Open Access Two new Western Australian species related to Hibbertia priceana (Dilleniaceae)(Atlas of Living Australia, 2023) Hammer, T.; Thiele, K.Hibbertia priceana is a rare species found in two localised areas in southern south-western Western Australia, near Ongerup and in the vicinity of Wickepin and Harrismith. Two new species that are morphologically similar to H. priceana but are disjunct and distinct from it are described in this paper. Hibbertia hapalophylla is a new, potentially geographically restricted and rare species first collected during botanical surveys for a mining project near Mount Holland in the Western Australian Goldfields. It was initially collected from, and only known from, disturbed areas on an active mine site, but larger populations were subsequently discovered on a nearby sandplain, from where is was likely introduced to the mine site on sand transported for construction purposes. The second new species, Hibbertia remanens, appears to be restricted to small areas of remnant vegetation near Cunderdin and Kellerberrin in the Western Australian wheatbelt. The three species differ mainly in their leaf shapes in section, with H. priceana having flat leaves with the abaxial lamina fully exposed, H. remanens having recurved leaf margins with the abaxial shallowly grooved either side of the midrib, and H. hapalophylla having strongly revolute margins with the abaxial lamina surface concealed within lacunae formed between the margins and midrib.Item Open Access Sedimentation from landscape clearance-induced soil erosion threatens waterhole persistence in a semi-arid river system, southern Queensland, Australia(CSIRO Publishing, 2023) Tibby, J.; Marshall, J.C.; Lobegeiger, J.S.; Amos, K.J.; Pickering, G.; Myburgh, T.; Unmack, P.Context: In arid and semi-arid river systems, waterholes are often the only refugia for aquatic organisms during no-flow spells. Sediment accumulation in waterholes reduces their persistence. Aims: To assess this threat, we surveyed the depth of, and dated, waterhole sediments from John Tibby Geography, Environment and Population, the Moonie River, a northern tributary of Australia’s largest river system, the Murray–Darling Basin. Methods: Fine-sediment depth was determined in three of the deepest waterholes in Australia 2010 and 2011 before, and after, the largest flood in over a century. The rate of sediment build up in two waterholes was also determined. Key results: In the deepest sections (>75th percentile depth), there was between 0.7 and 2 m of fine sediment in 2010. Following flooding, sediment depth reduced by 24–54%, with the largest proportional reductions in sediment occurring in the shallowest waterhole. However, net sediment accumulation is still 1.4–2.0 cm year–1 since the 1950s. Conclusions: Sedimentation has reduced the persistence of the deepest waterholes by over 200 days, representing an up to 30% reduction. During the longest droughts known in the Moonie River, this would dry many otherwise permanent waterholes. Implications: Sedimentation is a marked threat to waterhole persistence even following large floods.Item Metadata only Notes from the taxonomic disaster zone: Evolutionary drivers of intractable species boundaries in an Australian lizard clade (Scincidae: Ctenotus)(Wiley, 2024) Prates, I.; Hutchinson, M.N.; Singhal, S.; Moritz, C.; Rabosky, D.L.Genomic-scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst-case” scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation-by-distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that “taxonomic disaster zones” like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization.Item Metadata only Beyond ecology: ecosystem restoration as a process for social-ecological transformation(Elsevier BV, 2023) Tedesco, A.M.; López-Cubillos, S.; Chazdon, R.; Rhodes, J.R.; Archibald, C.L.; Pérez-Hämmerle, K.V.; Brancalion, P.H.S.; Wilson, K.A.; Oliveira, M.; Correa, D.F.; Ota, L.; Morrison, T.H.; Possingham, H.P.; Mills, M.; Santos, F.C.; Dean, A.J.Ecosystem restoration conventionally focuses on ecological targets. However, while ecological targets are crucial to mobilizing political, social, and financial capital, they do not encapsulate the need to: integrate social, economic, and ecological dimensions and systems approaches; reconcile global targets and local objectives; and measure the rate of progress toward multiple and synergistic goals. Restoration is better conceived as an inclusive social-ecological process that integrates diverse values, practices, knowledge, and restoration objectives across temporal and spatial scales and stakeholder groups. Taking a more process-based approach will ultimately enable greater social-ecological transformation, greater restoration effectiveness, and more long-lasting benefits to people and nature across time and place.Item Metadata only A giant armoured skink from Australia expands lizard morphospace and the scope of the Pleistocene extinctions(The Royal Society Publishing, 2023) Thorn, K.M.; Fusco, D.A.; Hutchinson, M.N.; Gardner, M.G.; Clayton, J.L.; Prideaux, G.J.; Lee, M.S.Y.There are more species of lizards and snakes (squamates) alive today than any other order of land vertebrates, yet their fossil record has been poorly documented compared with other groups. Here, we describe a gigantic Pleistocene skink from Australia based on extensive material that includes much of the skull and postcranial skeleton, and spans ontogenetic stages from neonate to adult. Tiliqua frangens substantially expands the known ecomorphological diversity of squamates. At approximately 2.4 kg, it was more than double the mass of any living skink, with an exceptionally broad, deep skull, squat limbs and heavy, ornamented body armour. It probably filled the armoured herbivore niche that land tortoises (testudinids), absent from Australia, occupy on other continents. Tiliqua frangens and other giant Plio-Pleistocene skinks suggest that small-bodied groups that dominate vertebrate biodiversity might have lost their largest and often most morphologically extreme representatives in the Late Pleistocene, expanding the scope of these extinctions.