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Pesticide active ingredients (PAIs) are regularly detected in the rivers, creeks, wetlands, and inshore waterways that discharge to the Great Barrier Reef (GBR) lagoon. Pesticide active ingredients detected above ecologically protective concentrations may pose a hazard and risk to aquatic species. The ability to assess this hazard and risk is reliant on the availability of water quality guidelines, which are only available for a limited number of PAIs detected in GBR catchment waterways. Unendorsed guideline values, known as ecotoxicity threshold values (ETVs) were developed in part one of this study for active ingredients in two fungicides (4-hydroxychlorothalonil (fungicide degradate) and carbendazim) and two insecticides (dimethoate and methoxyfenozide) that are commonly detected in GBR catchment waterways. In the current study, the hazard and risk posed by these PAIs was assessed by comparing the ETVs to environmental monitoring data from the Great Barrier Reef Catchment Loads Monitoring Program. Exceedances of the concentrations that should protect 99 % of aquatic species (i.e., PC99) were observed for all four pesticides. Detected concentrations of 4-hydroxychlorothalonil, carbendazim and methoxyfenozide exceeded the PC95 ETV, however no exceedances of the PC95 were observed for dimethoate. The hazard quotient (HQ) method was used to identify high hazard sites across the GBR catchment area. In total, six sites were identified as having concentrations that exceeded the PC95 ETVs. For 4-hydroxychlorothalonil, the risk to aquatic species based on the 95th percentile concentrations ranged from 3 to 13 %, 1 to 8 % for carbendazim and 2 to 8 % for methoxyfenozide. Detected concentrations of carbendazim were two orders of magnitude higher than concentrations that are reported to induce behavioural effects in some fish species. Considering that detected concentrations of three of the four PAIs individually pose a potential risk to aquatic species, their contributions to pesticide mixture toxicity should be further assessed., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype-environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range-wide genomic diversity and genomic vulnerability in the migratory and fisheries-important golden perch (Macquaria ambigua) from Australia's expansive Murray-Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range-wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross-validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity., (© 2024 John Wiley & Sons Ltd.)

Environmental offsetting has been developed as a mechanism to facilitate the benefits from economic development while avoiding or minimizing environmental harm. This is achieved by compensating for environmental impacts at one location by generating equivalent environmental improvements elsewhere. However, experience with biodiversity and carbon offsetting indicates it can be difficult to ensure the integrity of offsets. Under recent legislation in the catchments of the Great Barrier Reef (GBR), Australia, it is mandatory for water quality emissions from new or expanded point source development to be offset by reducing pollution elsewhere, frequently through reducing non-point source pollution (NPSP). Therefore, informed by experience with biodiversity and carbon offsetting, we summarised sources of uncertainty in NPSP reduction that would influence water quality offset integrity; estimated the maximum potential demand for water quality offsets from sewage treatment plants, the largest point source emitter of total nitrogen (TN) in the GBR catchments, between 2018 and 2050; and discussed the implications of both on the ability of offsetting to counterbalance the impact of economic development in catchments where nitrogen loads have a large influence on the health of important GBR ecosystems. The catchments surrounding the population centres of Cairns and Mackay had both a potentially high future demand for nitrogen water quality offsets and nitrogen loads with a strong influence on the health of the GBR. Consequently, any low integrity water quality offsets in these catchments could jeopardise progress toward the water quality improvements needed to ensure the continued health of the GBR. Water quality offsetting has numerous strengths as a policy instrument however substantial uncertainties remain related to environmental outcomes. Until further research can reduce these uncertainties, water quality offsets that are implemented near increased point source emissions and have a high certainty of effectiveness may provide a balance between scientific rigour and policy workability., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

With large wildfires becoming more frequent 1,2 , we must rapidly learn how megafires impact biodiversity to prioritize mitigation and improve policy. A key challenge is to discover how interactions among fire-regime components, drought and land tenure shape wildfire impacts. The globally unprecedented 3,4 2019-2020 Australian megafires burnt more than 10 million hectares 5 , prompting major investment in biodiversity monitoring. Collated data include responses of more than 2,000 taxa, providing an unparalleled opportunity to quantify how megafires affect biodiversity. We reveal that the largest effects on plants and animals were in areas with frequent or recent past fires and within extensively burnt areas. Areas burnt at high severity, outside protected areas or under extreme drought also had larger effects. The effects included declines and increases after fire, with the largest responses in rainforests and by mammals. Our results implicate species interactions, dispersal and extent of in situ survival as mechanisms underlying fire responses. Building wildfire resilience into these ecosystems depends on reducing fire recurrence, including with rapid wildfire suppression in areas frequently burnt. Defending wet ecosystems, expanding protected areas and considering localized drought could also contribute. While these countermeasures can help mitigate the impacts of more frequent megafires, reversing anthropogenic climate change remains the urgent broad-scale solution., Competing Interests: Competing interests: The authors declare that some of them work for government agencies involved in forestry and implementing planned burns (Supplementary Table 8). The lead author declares that, despite the potential for government agencies to impose policy positions on staff communications (see ref. 51), scientific independence and integrity has been maintained throughout this project., (© 2024. The Author(s).)

Three species in the ectobiid genus Shelfordina are highlighted with two described as new. The Orchid Cockroach, S. orchidae (Asahina) is included because of its occurrence in living orchid collections. A key to the known Australian species is included.

Pesticide active ingredients are frequently detected in the rivers, creeks, wetlands, estuaries, and marine waters of the Great Barrier Reef (GBR) region and are one of the main contributors to poor water quality. Pesticide concentrations detected in the environment through water quality monitoring programs can be compared against estimates of ecologically "safe" concentrations (i.e., water quality guidelines) to assess the potential hazard and risk posed to aquatic ecosystems. Water quality guidelines are also required to estimate the aquatic risk posed by pesticide mixtures, which is used for the Reef 2050 Water Quality Improvement Plan pesticide target. Seventy-four pesticide active ingredients and their degradates are frequently detected in GBR catchment waterways, however many do not have water quality guidelines in the Australian and New Zealand Guidelines for Fresh and Marine Water Quality. The current study derives ecotoxicity threshold values (ETVs) as unendorsed guideline values for active ingredients in two fungicides (4-hydroxychlorothalonil (fungicide degradate) and carbendazim) and two insecticides (dimethoate and methoxyfenozide) that are commonly detected in GBR catchment waterways. The proposed ETVs have been derived using species sensitivity distributions, as recommended in the Australian and New Zealand nationally endorsed method for deriving water quality guidelines for aquatic ecosystem protection. Four ETVs were derived for each chemical with values that should theoretically protect 99, 95, 90 and 80 % of species (i.e., PC99, PC95, PC90, PC80, respectively). The PC99 and PC95 values for 4-hydroxychlorothalonil, carbendazim, dimethoate and methoxyfenozide were 0.49 μg/L and 4 μg/L, 0.029 μg/L and 0.45 μg/L, 0.11 μg/L and 5.8 μg/L and 0.19 μg/L and 2 μg/L, respectively. The ETVs will be used in an ecological hazard and risk assessment across GBR waterways in part two of this study. The ETVs can also be used to assess potential risk across Australia and internationally where monitoring data are available., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier B.V. All rights reserved.)

Over the last 6 million years, the arid Australian Eremaean Zone (EZ) has remained as dry as it is today. A widely accepted hypothesis suggests that the flora and fauna of arid regions were more broadly distributed before aridification began. In Australia, this process started around 20 million years ago (Ma), leading to gradual speciation as the climate became increasingly arid. Here, we use genomic data to investigate the biogeography and timing of divergence of native allotetraploid tobaccos, Nicotiana section Suaveolentes (Solanaceae). The original allotetraploid migrants from South America were adapted to mesic areas of Australia and recently radiated in the EZ, including in sandy dune fields (only 1.2 Ma old), after developing drought adaptations. Coalescent and maximum likelihood analyses suggest that Nicotiana section Suaveolentes arrived on the continent around 6 Ma, with the ancestors of the Pilbara (Western Australian) lineages radiating there at the onset of extreme aridity 5 Ma by locally adapting to these various ancient, highly stable habitats. The Pilbara thus served as both a mesic refugium and cradle for adaptations to harsher conditions, due to its high topographical diversity, providing microhabitats with varying moisture levels and its proximity to the ocean, which buffers against extreme aridity. This enabled species like Nicotiana to survive in mesic refugia and subsequently adapt to more arid conditions. These results demonstrate that initially poorly adapted plant groups can develop novel adaptations in situ, permitting extensive and rapid dispersal despite the highly variable and unpredictable extreme conditions of the EZ., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Waterways that drain the Great Barrier Reef catchment area (GBRCA) transport pollutants to marine habitats, provide a critical corridor between freshwater and marine habitats for migratory fish species, and are of high socioecological value. Some of these waterways contain concentrations of pesticide active ingredients (PAIs) that exceed Australian ecotoxicity threshold values (ETVs) for ecosystem protection. In this article, we use a "pathway to harm" model with five key criteria to assess whether the available information supports the hypothesis that PAIs are or could have harmful effects on fish and arthropod populations. Strong evidence of the first three criteria and circumstantial weaker evidence of the fourth and fifth criteria are presented. Specifically, we demonstrate that exceedances of Australian and New Zealand ETVs for ecosystem protection are widespread in the GBRCA, that the PAI contaminated water occurs (spatially and temporally) in important habitats for fisheries, and that there are clear direct and indirect mechanisms by which PAIs could cause harmful effects. The evidence of individuals and populations of fish and arthropods being adversely affected species is more circumstantial but consistent with PAIs causing harmful effects in the freshwater ecosystems of Great Barrier Reef waterways. We advocate strengthening the links between PAI concentrations and fish health because of the cultural values placed on the freshwater ecosystems by relevant stakeholders and Traditional Owners, with the aim that stronger links between elevated PAI concentrations and changes in recreationally and culturally important fish species will inspire improvements in water quality. Integr Environ Assess Manag 2024;20:1256-1279. © 2023 Commonwealth of Australia and The Commonwealth Scientific and Industrial Research Organisation. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC)., (© 2023 Commonwealth of Australia and The Commonwealth Scientific and Industrial Research Organisation. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).)

At a time when ambitious environmental management initiatives are required to protect and restore aquatic ecosystems, public trust in the science that underpins environmental policy and decision-making is waning. This decline in public trust coincides with a rise in misinformation, and threatens to undermine public support for, and participation in, environmental protection. Our study investigates the prevalence and predictors of mistrust in science associated with the protection and management of the Great Barrier Reef (GBR) and its catchments. Using survey data from 1,877 residents of the GBR region, we identify environmental values, perceptions, and attitudes that are associated with science mistrust. Our results include a typology of GBR science trust and scepticism. Science-sceptical respondents, representing 31% of our sample, were likely to perceive waterway management decisions as being unfair, felt less responsible, and were less motivated to contribute to improving waterway health than those with greater trust in science. Science-sceptical respondents also had differing perceptions of some threats to waterways, in particular climate change. However, similarities and 'common ground' between respondents with varying levels of trust in science included a shared recognition of the importance of waterways' ecosystem services, and a shared perception of the relative health and problems within their regions' waterways. Our findings can help to break down assumptions about science-sceptical groups in the GBR region and elsewhere. We offer recommendations to guide more constructive engagement that seeks to restore trust and build consensus on mutual goals and pathways to protect vital ecosystem functions and services., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Curnock et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Manipulation of host plant physiology by leaf-galling insects is a multifaceted process. Among fundamental knowledge gaps surrounding this scientifically intriguing phenomenon is the appropriation of plant mineral nutrients and moisture for galling advantage. Small, soluble mineral ions and watery cell contents in dense gall tissues risk disruption during routine sample preparations. In this study, an X-ray microanalysis was applied to investigate gall mineral nutrition. Morphologically diverse leaf galls were sampled from three Australian rainforest tree species. Using cryo-analytical scanning electron microscopy, real-time X-ray analytical maps of cellular mineral nutrients and water were integrated with anatomical images of gall and leaf cross-sectional surfaces. A comparison of host-leaf and gall anatomies bore direct evidence of drastic changes to leaf cells through the galling process. Distinct "wet" and "dry" regions within galls were anatomically and/or chemically differentiated, suggesting specific functionality. "Wet" regions comprising hydrated cells including soft gall-cavity linings where larvae are known to feed contained soluble plant mineral nutrients, while C-rich "dry" tissues largely devoid of mineral nutrients likely contribute structural support. Mapping immobile nutrients such as Mn may provide a means of "matching" specific gall cell types to those in ungalled host-leaf tissues. The findings here provided otherwise inaccessible insights into leaf-gall mineral nutrition., Competing Interests: Conflict of Interest The authors declare that they have no competing interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Microscopy Society of America.)

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs., Competing Interests: Conflict of Interest K.M.C. is a scientific advisor to the Australian Dingo Foundation, the New Guinea Singing Dog Conservation Society, and the New Guinea Highland Wild Dog Foundation. K.M.C. and L.B. are members of the IUCN Canid Specialist Group Dingo Working Group., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY 1 Y 2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations., (© 2024. The Author(s).)

The gold rush at the end of the nineteenth century in south-eastern Australia resulted in the mobilization and re-deposition of vast quantities of tailings that modified the geomorphology of the associated river valleys. Previous studies of contamination risk in these systems have either been performed directly on mine wastes (e.g., battery sand) or at locations close to historical mine sites but have largely ignored the extensive area of riverine alluvial deposits extending downstream from gold mining locations. Here we studied the distribution of contaminant metal(loids) in the Loddon River catchment, one of the most intensively mined areas of the historical gold-rush period in Australia (1851-1914). Floodplain alluvium along the Loddon River was sampled to capture differences in metal and metalloid concentrations between the anthropogenic floodplain deposits and the underlying original floodplain. Elevated levels of arsenic up to 300 mg-As/kg were identified within the anthropogenic alluvial sediment, well above sediment guidelines (ISQG-high trigger value of 70 ppm) and substantially higher than in the pre-mining alluvium. Maximum arsenic concentrations were found at depth within the anthropogenic alluvium (plume-like), close to the contact with the original floodplain. The results obtained here indicate that arsenic may pose a significantly higher risk within this river catchment than previously assessed through analysis of surface floodplain soils. The risks of this submerged arsenic plume will require further investigation of its chemical form (speciation) to determine its mobility and potential bioavailability. Our work shows the long-lasting impact of historical gold mining on riverine landscapes., (© 2024. The Author(s).)

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N 2 ) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii)., (© 2024. The Author(s).)

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier Ltd. All rights reserved.)

Turtles are a potential sentinel species of aquatic ecosystem health as they inhabit aquatic ecosystems, are long lived, and potentially have high exposure to anthropogenic chemicals via food and water. This study investigated per- and polyfluoroalkyl substances (PFAS) tissue partitioning in female Emydura macquarii macquarii turtle, and the maternal offloading of (PFAS) into eggs and then hatchlings as well as the accumulation of PFAS in male and female Emydura macquarii macquarii serum. Significantly higher levels of perfluorosulfonic acids (PFSAs) and perfluorocarboxylic acids (PFCAs) were measured in the male serum compared to the female turtle serum, whereas perfluoroalkane sulfonamides (FASAs) were significantly higher in the female turtle serum. Perfluorooctane sulfonate (PFOS) was the predominant PFAS in the turtles whereas PFHxA was the predominant PFAS found in the surrounding water. PFHxA was not reported in any turtle tissue or the serum. The short-chain PFSAs and FASAs appeared to be highly associated with blood; long-chain PFSAs and PFCAs were more likely to be associated with tissue. Half of the PFHxS and all the long-chain PFSAs and PFCAs reported in the yolks were transferred into the hatchlings (by mass), suggesting a potential intergenerational effect., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier B.V. All rights reserved.)

Resilience-based management is essential to protect ecosystems in the Anthropocene. Unlike large-scale climate threats to Great Barrier Reef (GBR) corals, outbreaks of coral-eating crown-of-thorns starfish (COTS; Acanthaster cf. solaris) can be directly managed through targeted culling. Here, we evaluate the outcomes of a decade of strategic COTS management in suppressing outbreaks and protecting corals during the 4th COTS outbreak wave at reef and regional scales (sectors). We compare COTS density and coral cover dynamics during the 3rd and 4th outbreak waves. During the 4th outbreak wave, sectors that received limited to no culling had sustained COTS outbreaks causing significant coral losses. In contrast, in sectors that received timely and sufficient cull effort, coral cover increased substantially, and outbreaks were suppressed with COTS densities up to six-fold lower than in the 3rd outbreak wave. In the Townsville sector for example, despite exposure to comparable disturbance regimes during the 4th outbreak wave, effective outbreak suppression coincided with relative increases in sector-wide coral cover (44%), versus significant coral cover declines (37%) during the 3rd outbreak wave. Importantly, these estimated increases span entire sectors, not just reefs with active COTS control. Outbreaking reefs with higher levels of culling had net increases in coral cover, while the rate of coral loss was more than halved on reefs with lower levels of cull effort. Our results also indicate that outbreak wave progression to adjoining sectors has been delayed, probably via suppression of COTS larval supply. Our findings provide compelling evidence that proactive, targeted, and sustained COTS management can effectively suppress COTS outbreaks and deliver coral growth and recovery benefits at reef and sector-wide scales. The clear coral protection outcomes demonstrate the value of targeted manual culling as both a scalable intervention to mitigate COTS outbreaks, and a potent resilience-based management tool to "buy time" for coral reefs, protecting reef ecosystem functions and biodiversity as the climate changes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Matthews et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Pesticide active ingredients (PAIs) are one of the main contributors affecting water quality in the Great Barrier Reef Catchment Area (GBRCA). While an extensive list of pesticides is monitored in the GBRCA, only a limited number have water quality guideline values (WQGs), meaning it is not possible to know whether these PAIs are present at concentrations that may pose a hazard to the aquatic environment. In the current study, we derived 66 ecotoxicity threshold values (ETVs) for PAIs, the equivalent of WQGs, with a focus on PAIs applied to sugar cane. The hazard posed by PAIs monitored as part of the Great Barrier Reef Catchment Loads Monitoring Program (GBRCLMP) was assessed by comparing the derived ETVs with monitoring data from 2016/2017 to 2021/2022. The derived ETVs included herbicides, insecticides and fungicides, with the values that should protect 99 or 95 % of aquatic species (PC99 or PC95) spanning nine orders of magnitude. The concentrations of 10 PAIs exceeded their respective ETVs, giving a hazard quotient (HQ) >1. Of particular concern were insecticides chlorpyrifos, diazinon and methomyl, which have maximum HQ values >10. However, joint probability plots indicated that the PAIs generally pose a low risk to the aquatic environment, with most samples below the limit of reporting. As PAIs are predominantly found in mixtures in the GBRCA, the hazard posed by PAI mixtures was assessed by summing all individual HQ values in a sample for all PAIs with an ETV or WQG. On average, the insecticide active ingredient imidacloprid and herbicide active ingredients metolachlor, metsulfuron methyl, diuron and imazepic were the drivers of combined mixture hazard. Methomyl was an important contributor at some sites, suggesting that this pesticide should be considered for inclusion in any future PAI mixture hazard and/or risk assessment of the GBRCA., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Catastrophic fish death events are increasing in frequency and severity globally. A series of major recent fish deaths in the semi-arid lower Darling-Baaka river system (LDBR) of Australia are emblematic of these issues with tens of millions of native fish perishing. In 2018-2019 there was a major death event for Australia's largest freshwater fish, Murray cod (Maccullochella peelii). To aid the recovery and guide restoration activities of local Murray cod populations, it is essential to gather information on the mating strategies and effective population size following the fish death event. After the fish deaths, we collected larvae during the 2020 and 2021 breeding seasons and used single nucleotide polymorphisms (SNPs) to provide insight mating strategies and to estimate effective population size. Larvae were detected in both years along the entire length of the LDBR. Sixteen percent of the inferred breeding individuals were found to contribute to multiple pairings, confirming a complex and polygamous mating system. A high frequency of polygamy was evident both within and between years with 100 % polygamy identified among parents that produced offspring in both 2020 and 2021 and 95 % polygamy identified among parents involved in multiple spawning events within years. Post-larval Murray cod samples collected between 2016 and 2021 were co-analysed to further inform kinship patterns. Again, monogamy was rare with no confirmed cases of the same male-female pair contributing to multiple breeding events within or between seasons. Effective population size based on Murray cod collected after the fish death event was estimated at 721.6 (CI 471-1486), though this has likely declined following a subsequent catastrophic fish death event in the LDBR in March 2023. Our data provide insight into the variability of Murray cod mating strategies, and we anticipate that this knowledge will assist in planning conservation actions to ultimately help recover a species in crisis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier B.V. All rights reserved.)

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation., (© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation.)

In Brief: Seahorses exhibit male pregnancy and are thus valuable comparative models for the study of the physiology and evolution of pregnancy. This study shows that protein is transported from fathers to developing embryos during gestation, and provides new knowledge about paternal contributions to embryonic development., Abstract: Syngnathid embryos (seahorses, pipefishes and seadragons) develop on or in the male in a specialised brooding structure (brood pouch). Seahorse brood pouches supply nutrients, including lipids, to developing embryos (patrotrophy). We tested the hypothesis that proteins, vital for gene regulation and tissue growth during embryogenesis, are also transported from father to embryos, using the Australian pot-bellied seahorse, Hippocampus abdominalis. We used dry masses and total nitrogen content to estimate the total protein content of newly fertilised egg and neonate H. abdominalis. Neonates contained significantly greater protein mass than newly fertilised eggs. This result indicates that paternal protein transport to developing embryos occurs during H. abdominalis pregnancy. This study is the first to show paternal protein transport during pregnancy in seahorses, and furthers our understanding of paternal influence on embryonic development in male pregnant vertebrates.

Ambient air samples were collected in Brisbane (Australia), Dalian (China), and Hanoi (Vietnam) during Mar 2013-Feb 2018 using polyurethane foam based passive air samplers. A sampling rate calibration experiment was conducted for chlorinated paraffins (CPs, i.e., short-chain, medium-chain, and long-chain CPs), where the sampling rates were 4.5 ± 0.7, 4.8 ± 0.3, and 4.8 ± 2.1 m 3 day -1 for SCCPs, MCCPs, and LCCPs, respectively. The atmospheric concentration of CPs was then calculated and the medians of ∑CPs were 0.079, 1.0, and 0.89 ng m -3 in Brisbane, Dalian, and Hanoi, respectively. The concentration of CPs in Brisbane's air remained at low levels, with no significant differences observed between the city background site and the city center site, indicating limited usage and production of CPs in this city. The highest concentration of MCCPs was detected in Dalian, while the highest concentration of SCCPs was detected in Hanoi. A decrease of SCCP concentration and an increase of MCCPs' were found in Brisbane's air from 2016 to 2018, while increasing trends for both SCCPs and MCCPs were observed in Dalian. These results indicated impacts from different sources of CPs in the investigated cities.

Multiple linear regression (MLR) models were developed for predicting chronic zinc toxicity to a freshwater microalga, Chlorella sp., using three toxicity-modifying factors (TMFs): pH, hardness, and dissolved organic carbon (DOC). The interactive effects between pH and hardness and between pH and DOC were also included. Models were developed at three different effect concentration (EC) levels: EC10, EC20, and EC50. Models were independently validated using six different zinc-spiked Australian natural waters with a range of water chemistries. Stepwise regression found hardness to be an influential TMF in model scenarios and was retained in all final models, while pH, DOC, and interactive terms had variable influence and were only retained in some models. Autovalidation and residual analysis of all models indicated that models generally predicted toxicity and that there was little bias based on individual TMFs. The MLR models, at all effect levels, performed poorly when predicting toxicity in the zinc-spiked natural waters during independent validation, with models consistently overpredicting toxicity. This overprediction may be from another unaccounted for TMF that may be present across all natural waters. Alternatively, this consistent overprediction questions the underlying assumption that models developed from synthetic laboratory test waters can be directly applied to natural water samples. Further research into the suitability of applying synthetic laboratory water-based models to a greater range of natural waters is needed. Environ Toxicol Chem 2023;42:2630-2641. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC., (© 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.)

Litoria rothii is a widespread pelodryadid frog with a charismatic laughing advertisement call, distributed across the Australian Monsoon Tropics and southern New Guinea. Given its large distribution spanning well-known biogeographic barriers, variation in male advertisement calls and the prevalence of unresolved species complexes in the Australian frog fauna, we examine the genetic, morphological and acoustic diversity in the species from across its range. Our analyses reveal the presence of a previously unrecognised species in western parts of the range of L. rothii sensu lato, which we describe herein as a new species. Litoria ridibunda sp. nov. is distinguished from L. rothii on the basis of paraphyly of nuclear gene trees with L. everetti from Indonesia, colour patterns on the posterior thigh and male advertisement calls. Compared to L. rothii, the new species has a less contrasting pattern on the posterior thigh and a male advertisement call with a greater number of notes per call and a greater call duration. In particular, the magnitude of call differences between the species is highest where the ranges of the two species are in proximity in north-western Queensland. Our study further emphasises the undiagnosed diversity that remains in Australian frogs, even in relatively large, charismatic, frequently encountered species that often share human dwellings.

Extreme fire events have increased across south-eastern Australia owing to warmer and drier conditions driven by anthropogenic climate change. Fuel reduction burning is widely applied to reduce the occurrence and severity of wildfires; however, targeted assessment of the effectiveness of this practice is limited, especially under extreme climatic conditions. Our study utilises fire severity atlases for fuel reduction burns and wildfires to examine: (i) patterns in the extent of fuel treatment within planned burns (i.e., burn coverage) across different fire management zones, and; (ii) the effect of fuel reduction burning on the severity of wildfires under extreme climatic conditions. We assessed the effect of fuel reduction burning on wildfire severity across temporal and spatial scales (i.e., point and local landscape), while accounting for burn coverage and fire weather. Fuel reduction burn coverage was substantially lower (∼20-30%) than desired targets in fuel management zones focused on asset protection, but within the desired range in zones that focus on ecological objectives. At the point scale, wildfire severity was moderated in treated areas for at least 2-3 years after fuel treatment in shrubland and 3-5 years in forests, relative to areas that did not receive fuel reduction treatments (i.e., unburnt patches). Fuel availability strongly limited fire occurrence and severity within the first 18 months of fuel reduction burning, irrespective of fire weather. Fire weather was the dominant driver of high severity canopy defoliating fire by ∼3-5 years after fuel treatment. At the local landscape scale (i.e., 250 ha), the extent of high canopy scorch decreased marginally as the extent of recently (<5 years) treated fuels increased, though there was a high level of uncertainty around the effect of recent fuel treatment. Our findings demonstrate that during extreme fire events, very recent (i.e., <3 years) fuel reduction burning can aid wildfire suppression locally (i.e., near assets) but will have a highly variable effect on the extent and severity of wildfires at larger scales. The patchy coverage of fuel reduction burns in the wildland-urban interface indicates that considerable residual fuel hazard will often be present within the bounds of fuel reduction burns., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2023. Published by Elsevier Ltd. All rights reserved.)

Infections with the coccidian parasite Neospora caninum affect domestic and wild animals worldwide. In Australia, N. caninum infections cause considerable losses to the cattle industry with seroprevalence of 8.7% in beef and 10.9% in dairy cattle. Conversely, the role of wild animals, in maintaining the parasite cycle is also unclear. It is possible that native or introduced herbivorous species could be reservoir hosts of N. caninum in Australia, but to date, this has not been investigated. We report here the first large-scale screening of N. caninum antibodies in Australian wild deer, spanning three species (fallow, red and sambar deer). Consequently, we also assessed two commercial cELISA tests validated for detecting N. caninum in cattle for their ability to detect N. caninum antibodies in serum samples of wild deer. N. caninum antibodies were detected in 3.7% (7/189, 95% CI 1.8 - 7.45) of the wild deer serum samples collected in south-eastern Australia (n = 189), including 97 fallow deer (Dama dama), 14 red deer (Cervus elaphus), and 78 sambar deer (Rusa unicolor). Overall, our study provides the first detection of N. caninum antibodies in wild deer and quantifies deer's potential role in the sylvatic cycle of N. caninum., (© 2023. BioMed Central Ltd., part of Springer Nature.)

When a plant is introduced to a new ecosystem it may escape from some of its coevolved herbivores. Reduced herbivore damage, and the ability of introduced plants to allocate resources from defence to growth and reproduction can increase the success of introduced species. This mechanism is known as enemy release and is known to occur in some species and situations, but not in others. Understanding the conditions under which enemy release is most likely to occur is important, as this will help us to identify which species and habitats may be most at risk of invasion. We compared in situ measurements of herbivory on 16 plant species at 12 locations within their native European and introduced Australian ranges to quantify their level of enemy release and understand the relationship between enemy release and time, space and climate. Overall, plants experienced approximately seven times more herbivore damage in their native range than in their introduced range. We found no evidence that enemy release was related to time since introduction, introduced range size, temperature, precipitation, humidity or elevation. From here, we can explore whether traits, such as leaf defences or phylogenetic relatedness to neighbouring plants, are stronger indicators of enemy release across species.

Many of Australias smaller marsupial species have been taxonomically described in just the past 50 years, and the Dasyuridae, a speciose family of carnivores, is known to harbour many cryptic taxa. Evidence from molecular studies is being increasingly utilised to help revise species boundaries and focus taxonomic efforts, and research over the past two decades has identified several undescribed genetic lineages within the dasyurid genus Planigale. Here, we describe two new species, Planigale kendricki sp. nov. (formerly known as Planigale 1) and P. tealei sp. nov. (formerly known as Planigale sp. Mt Tom Price). The two new species have broadly overlapping distributions in the Pilbara region of Western Australia. The new species are genetically distinct from each other and from all other members of the genus, at both mitochondrial and nuclear loci, and morphologically, in both external and craniodental characters. The new species are found in regional sympatry within the Pilbara but occupy different habitat types at local scales. This work makes a start at resolving the cryptic diversity within Planigale at a time when small mammals are continuing to decline throughout Australia.

Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species' distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries., (© 2023. Crown.)

Experts can provide valuable information to fill knowledge gaps in published research on management effectiveness, particularly for threatened ecosystems, for which there is often limited evidence and the need for prompt intervention to ensure their persistence. One such ecosystem, alpine peatland, is threatened by climate change and other pressures, provides vital ecosystem services, and supports unique biodiversity. In a workshop, we gathered and synthesized into an accessible format information from experts on interventions used, threat context, and intervention effectiveness for Australian alpine peatland and used this knowledge to evaluate local relevance of the global literature for this threatened ecosystem. Experts identified 15 interventions used to conserve Australian peatlands, most of which enhanced or restored peatland condition and effectively addressed diverse threats. Experts' perspectives and global studies were strongly aligned, suggesting that research on peatland management may be broadly relevant across contexts, despite the distinct characteristics of Australian systems. Our workshop-based expert elicitation approach provided insights into current management practices unavailable in the literature., (© 2023 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches., (© 2023. The Author(s).)

Widespread coral bleaching was observed over the Great Barrier Reef, Australia, the world's largest coral reef during the 2021-2022 La Niña. This raised concerns that background global warming may have crossed a critical threshold causing thermal stress to corals during a climate state historically associated with increased cloud cover, rainfall and cooler summer water temperatures. Here we present an analysis of recent summer La Niña events focused on their synoptic meteorology and corresponding water temperatures over the Great Barrier Reef. Results show that the 2021-2022 summer La Niña caused accumulated coral heat stress to exceed previous La Niña conditions by 2.5 times. We find that weather patterns that favoured the build-up of heat in water overlying the Great Barrier Reef during the 2021-2022 summer were likely the result of repositioning of planetary scale atmospheric longwaves. This insight provides an additional means to predict potential future atmospheric conditions that increase the risk of extremely high water temperatures and coral bleaching in the Great Barrier Reef., (© 2023. The Author(s).)

True branching is a facultative characteristic only known from two cyanobacteria in the Aphanizomenonaceae, Umezakia natans and Dolichospermum brachiatum. In both cases, its expression has been associated with environmental stress, and its practical use as a diacritical feature has been previously evaluated. In this study, we undertook further evaluation of the phylogeny of Umezakia natans and its relationship to Chrysosporum ovalisporum as a previous study suggested the two were potentially congeneric. We used combined morphological, phylogenetic, and phylogenomic approaches to determine their relatedness using new strains available from a broad geographic range. Phylogenetic analysis based on 16S rRNA gene sequences showed that Australian C. ovalisporum and Japanese U. natans strains clustered together with accessions of C. ovalisporum originating from Australia, Israel, and Spain, with high p-distance similarity values (99.5%-99.9%). Additionally, differences between the two species in the 16S-23S ITS region was low (0%-2.5%). The average nucleotide identity of the U. natans and C. ovalisporum strains was also high (ANI of > 99.5 and AF > 0.9) and supported a genus-level separation from Chrysosporum bergii (83 ANI between clusters). Furthermore, in culture, strains of both species grown in vitamin-free media showed facultative true branching, a feature not previously known in C. ovalisporum. Collectively, the results support unification of C. ovalisporum and U. natans according to the principle of priority as Umezakia ovalisporum., (© 2023 Phycological Society of America.)

Monitoring is critical to assess management effectiveness, but broadscale systematic assessments of monitoring to evaluate and improve recovery efforts are lacking. We compiled 1808 time series from 71 threatened and near-threatened terrestrial and volant mammal species and subspecies in Australia (48% of all threatened mammal taxa) to compare relative trends of populations subject to different management strategies. We adapted the Living Planet Index to develop the Threatened Species Index for Australian Mammals and track aggregate trends for all sampled threatened mammal populations and for small (<35 g), medium (35-5500 g), and large mammals (>5500 g) from 2000 to 2017. Unmanaged populations (42 taxa) declined by 63% on average; unmanaged small mammals exhibited the greatest declines (96%). Populations of 17 taxa in havens (islands and fenced areas that excluded or eliminated introduced red foxes [Vulpes vulpes] and domestic cats [Felis catus]) increased by 680%. Outside havens, populations undergoing sustained predator baiting initially declined by 75% but subsequently increased to 47% of their abundance in 2000. At sites where predators were not excluded or baited but other actions (e.g., fire management, introduced herbivore control) occurred, populations of small and medium mammals declined faster, but large mammals declined more slowly, than unmanaged populations. Only 13% of taxa had data for both unmanaged and managed populations; index comparisons for this subset showed that taxa with populations increasing inside havens declined outside havens but taxa with populations subject to predator baiting outside havens declined more slowly than populations with no management and then increased, whereas unmanaged populations continued to decline. More comprehensive and improved monitoring (particularly encompassing poorly represented management actions and taxonomic groups like bats and small mammals) is required to understand whether and where management has worked. Improved implementation of management for threats other than predation is critical to recover Australia's threatened mammals., (© 2022 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Cynanchum viminale subsp. australe , more commonly known as caustic vine, is a leafless succulent that grows in the northern arid zone of Australia. Toxicity toward livestock has been reported for this species, along with use in traditional medicine and its potential anticancer activity. Disclosed herein are novel seco -pregnane aglycones cynavimigenin A ( 5 ) and cynaviminoside A ( 6 ), together with new pregnane glycosides cynaviminoside B ( 7 ) and cynavimigenin B ( 8 ). Cynavimigenin B ( 8 ) contains an unprecedented 7-oxobicyclo[2.2.1]heptane moiety in the seco -pregnane series, likely arising from a pinacol-type rearrangement. Interestingly, these isolates displayed only limited cytotoxicity in cancer and normal human cell lines, in addition to low activity against acetylcholinesterase and Sarcoptes scabiei bioassays, suggesting that 5 - 8 are not associated with the reported toxicity of this plant species.

Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed., Findings: We generated a high-quality chromosome-level reference genome assembly (Canfam&#95;ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog., Conclusions: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)

Rangelands worldwide have been subject to broadscale modification, such as widespread predator control, introduction of permanent livestock water and altered vegetation to improve grazing. In Australia, these landscape changes have resulted in kangaroos (i.e. large macropods) populations increasing over the past 200 years. Kangaroos are a key contributor to total grazing pressure and in conjunction with livestock and feral herbivores have been linked to land degradation. We used 22 years of aerial survey data to investigate whether the density of 3 macropod species in the southern rangelands of Western Australia was associated with: (i) land use, including type of livestock, total livestock, density of feral goats, type of land tenure, and kangaroo commercial harvest effort; (ii) predator management, including permitted dingo control effort, estimated dingo abundance, and presence of the State Barrier Fence (a dingo exclusion fence); and (iii) environmental variables: ruggedness, rainfall, fractional cover, and total standing dry matter. Red kangaroos (Osphranter rufus) were most abundant in flat, open vegetation, on pastoral land, where area permitted for dingo control was high, and numbers were positively associated with antecedent rainfall with a 12-month delay. Western grey kangaroos (Macropus fuliginosus) were most abundant on flat, agricultural land, but less abundant in areas with high permitted dingo control. Euros (Osphranter robustus) were most abundant in rugged pastoral land with open vegetation, where permitted dingo control was high. While environmental variables are key drivers of landscape productivity and kangaroo populations, anthropogenic factors such as land use and permitted dingo control are strongly associated with kangaroo abundance., (© 2022 The Authors. Integrative Zoology published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.)

Continuous monitoring of oil discharges in coastal and open ocean waters using Earth Observation (EO) has undeniably contributed to diminishing their occurrence wherever a detection system was in place, such as in Europe (EMSA's CleanSeaNet) or in the United States (NOAA's OR&R). This study describes the development and testing of a semi-automated oil slick detection system tailored to the Great Barrier Reef (GBR) marine park solely based on EO data as no such service was routinely available in Australia until recently. In this study, a large, curated, historical global dataset of SAR imagery acquired by Sentinel-1 SAR, now publicly available, is used to assess classification techniques, namely an empirical approach and a deep learning model, to discriminate between oil-like features and look-alikes in the scenes acquired over the marine park. An evaluation of this detection system on 10 Sentinel-1 SAR images of the GBR using two performance metrics - the detection accuracy and the false-positive rate (FPR) - shows that the classifiers perform best when combined (accuracy >98 %; FPR 0.01) rather than when used separately. This study demonstrates the benefit of sequentially combining classifiers to improve the detection and monitoring of unreported oil discharge events in SAR imagery. The workflow has also been tested outside the GBR, demonstrating its robustness when applied to other regions such as Australia's Northwest Shelf, Southeast Asia and the Pacific., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2023. Published by Elsevier Ltd. All rights reserved.)

Coxiella burnetii causes significant reproduction losses in livestock and the disease Q fever in humans. Transmission of C. burnetii is facilitated by the stability of the bacterium in the environment and the susceptibility of a variety of host species to infection. Consequently, inter-species transmission occurs frequently through either direct or indirect contact. Wildlife may represent reservoirs of C. burnetii and could therefore be a source of infection for domestic animals. Understanding the prevalence of C. burnetii infections at the wildlife-livestock interface is important for disease control. This study aimed to investigate the extent of C. burnetii exposure in wild deer in eastern Australia. Serum samples were obtained from 413 wild deer from seven regions in four eastern Australian states from 2017 to 2020. Antibodies were detected using a commercial Q fever antibody kit validated for ruminants. Seroprevalence of C. burnetii antibodies in deer was determined and true prevalence estimated, for each region. The overall seroprevalence of C. burnetii antibodies in wild deer was 3.4% (14 seropositive of 413 deer sampled) with true prevalence estimated to be 4.3% (95% credible interval: 0.6%, 10.9%). Seropositive deer were identified only in Queensland (7/108 seropositive) and northern New South Wales (7/120 seropositive). This geospatial distribution is consistent with seropositivity in other animal species and indicative of the level of C. burnetii in the environment. The low seroprevalence suggests that wild deer are unlikely to be a major reservoir species for C. burnetii in eastern Australia but may still be implicated in inter-species transmission cycles., (© 2022 The Authors. Australian Veterinary Journal published by John Wiley & Sons Australia, Ltd on behalf of Australian Veterinary Association.)

Background and Aims: The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia., Methods: We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework., Key Results: RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids., Conclusions: The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Annals of Botany Company.)

All seven species of sea turtle are facing increasing pressures from human activities that are impacting their health. Changes in circulating blood proteins of an individual, or all members of a population, can provide an early indicator of adverse health outcomes. Non-targeted measurement of all detectable proteins in a blood sample can indicate physiological changes. In the context of wildlife toxicology, this technique can provide a powerful tool for discovering biomarkers of chemical exposure and effect. This study presents a non-targeted examination of the protein abundance in sea turtle plasma obtained from three geographically distinct foraging populations of green turtles (Chelonia mydas) on the Queensland coast. Relative changes in protein expression between sites were compared, and potential markers of contaminant exposure were investigated. Blood plasma protein profiles were distinct between populations, with 85 out of the 116 identified proteins differentially expressed (p < 0.001). The most strongly dysregulated proteins were predominantly acute phase proteins, suggestive of differing immune status between the populations. The highest upregulation of known markers of immunotoxicity, such as pentraxin fusion and complement factor h, was observed in the Moreton Bay turtles. Forty-five different organohalogens were also measured in green turtle plasma samples as exposure to some organohalogens (e.g., polychlorinated biphenyls) has previously been identified as a cause for immune dysregulation in marine animals. The few detected organohalogens were at very low (pg/mL) concentrations in turtles from all sites, and are unlikely to be the cause of the proteome differences observed. However, the changes in protein expression may be indicative of exposure to other chemicals or environmental stressors. The results of this study provide important information about differences in protein expression between different populations of turtles, and guide future toxicological and health studies on east-Australian green sea turtles., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Since their introduction in 1859, European rabbits ( Oryctolagus cuniculus ) have had a devastating impact on agricultural production and biodiversity in Australia, with competition and land degradation by rabbits being one of the key threats to agricultural and biodiversity values in Australia. Biocontrol agents, with the most important being the rabbit haemorrhagic disease virus 1 (RHDV1), constitute the most important landscape-scale control strategies for rabbits in Australia. Monitoring field strain dynamics is complex and labour-intensive. Here, using phylodynamic models to analyse the available RHDV molecular data, we aimed to: investigate the epidemiology of various strains, use molecular data to date the emergence of new variants and evaluate whether different strains are outcompeting one another. We determined that the two main pathogenic lagoviruses variants in Australia (RHDV1 and RHDV2) have had similar dynamics since their release, although over different timeframes (substantially shorter for RHDV2). We also found a strong geographic difference in their activities and evidence of overall competition between the two viruses.

Plastics pollution is a global issue impacting every part of our environment. Tyre road wear particle (TRWP) plastics pollution is thought to be one of the largest pollution sources in urban environments. These plastics are also of concern due to the presence of additive chemicals, incorporated during manufacture, that can be released into the surrounding environment. This study aimed to provide information on concentrations of a range of anthropogenic plastics related pollutants in the Australian environment through a scoping study of surface water in 5 key urban centres around Queensland, Australia. Samples were analysed for a suite of 15 common tyre additive chemicals, TRWPs and 6 common high production polymers, and included the new transformation product of concern 6PPD-quinone which has recent reports of causing mass mortality events in certain aquatic species. The additives were ubiquitously detected (2.9-1440 ng/L) with 6PPD-quinone concentrations lower than in previous studies (<0.05-24 ng/L) and TRWPs detected at 18 of the 21 sites (

Invasive plants are considered to be one of the biggest threats to environmental assets, and once established, they can be immensely difficult to control. Nassella trichotoma is an aggressive, perennial grass species, and is considered to be one of the most economically damaging weeds to grazing systems due to its unpalatability, as well as being one of the leading causes of biodiversity loss in grassland communities. This species produces high density seedbanks that rapidly respond to disturbance events. Despite control programs being developing in Australia since the 1930s, this species is still widespread throughout south-east Australia, indicating that a new management approach is critical to control this Weed of National Significance at the landscape scale. The present study explored the effect of 12 different combinations of herbicide, fire, a second application of herbicide, grazing exclusion, tillage and broadcasting seeds in order to reduce the above and below-ground density of N. trichotoma. A control treatment was also included. The results were assessed using a Hierarchy analysis, whereby treatments of increasing complexity were compared for their efficacy in reducing N. trichotoma cover and seedbank density, while simultaneously increasing the establishment of the broadcast species. Whilst all integrated treatments effectively reduced N. trichotoma's seedbank, the treatments that included fire performed significantly better at simultaneously reducing N. trichotoma and increasing the establishment of broadcasted seeds. Overall, the integration of herbicide, fire and broadcasting native seeds was observed to provide the most economically feasible management strategy for the landscape scale restoration of a degraded temperate grassland dominated by N. trichotoma., (© 2022. The Author(s).)

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes., Competing Interests: The authors have declared that no competing interests exist.

A semiquantitative high-resolution mass spectrometry method was developed and applied to assess the occurrence of bromo-/chloro paraffins (BCPs) and olefins (BCOs) in the environment. More than 400 possible BCPs and BCO congener groups were detected in dust, air, and sewage sludge samples collected from Australia. Median chain analytes with the number of halogen atoms <7 (C n H m Cl x Br y , 14 ≤ n ≤ 17, x + y < 7) prevailed in the dust and sludge samples, while short chain analytes (C n H m Cl x Br y , 10 ≤ n ≤ 13, x + y < 7) predominated the air samples. The estimated concentrations of ∑BCPs and ∑BCOs in dust and sludge were approximately 20% that of the chlorinated paraffins (CPs) present, with the median concentrations of 5.4 μg/g (dust) and 0.18 μg/g (sludge) for ∑BCPs and 22 μg/g (in dust) and 0.50 μg/g (sludge) for BCOs. In the air samples, the concentrations of BCPs (0.020 pg/m 3 ) and BCOs (0.032 pg/m 3 ) were 3-4 orders of magnitudes lower than the concentrations of CPs (790 pg/m 3 ). Significant correlations ( P < 0.001) were found between the concentration of CPs, BCPs, and BCOs in all the matrices.

Background: Aboriginal peoples have occupied the island continent of Australia for millennia. Over 500 different clan groups or nations with distinctive cultures, beliefs, and languages have learnt to live sustainably and harmoniously with nature. They have developed an intimate and profound relationship with the environment, and their use of native plants in food and medicine is largely determined by the environment they lived in. Over 1511 plant species have been recorded as having been used medicinally in Australia. Most of these medicinal plants were recorded from the Aboriginal communities in Northern Territory, New South Wales, South Australia, and Western Australia. Not much has yet been reported on Aboriginal medicinal plants of Queensland. Therefore, the main aim of this review is to collect the literature on the medicinal plants used by Aboriginal peoples of Queensland and critically assess their ethnopharmacological uses., Methods: The information used in this review was collected from archival material and uploaded into the Tropical Indigenous Ethnobotany Centre (TIEC) database. Archival material included botanist's journals/books and old hard copy books. Scientific names of the medicinal plant species were matched against the 'World Flora Online Plant List', and 'Australian Plant Census' for currently accepted species names to avoid repetition. An oral traditional medical knowledge obtained through interviewing traditional knowledge holders (entered in the TIEC database) has not been captured in this review to protect their knowledge., Results: This review identified 135 species of Queensland Aboriginal medicinal plants, which belong to 103 genera from 53 families, with Myrtaceae being the highest represented plant family. While trees represented the biggest habit, leaves were the most commonly used plant parts. Of 62 different diseases treated by the medicinal plants, highest number of plants are used for treating skin sores and infections. Few plants identified through this review can be found in other tropical countries but many of these medicinal plants are native to Australia. Many of these medicinal plants are also used as bush food by Aboriginal peoples., Conclusion: Through extensive literature review, we found that 135 medicinal plants native to Queensland are used for treating 62 different diseases, especially skin infections. Since these medicinal plants are also used as bush food and are rarely studied using the Western scientific protocols, there is a huge potential for bioprospecting and bush food industry., (© 2022. The Author(s).)