It can be challenging to reliably detect rare or cryptic species. Environmental DNA (eDNA) is an emerging tool for detecting species and is increasingly being used to detect reptiles in terrestrial environments that are costly or difficult to survey or monitor using traditional methods. Here, we trialled eDNA metabarcoding to detect one of Australia’s most threatened and least known reptile species, the Arnhem rock skink (Bellatorias obiri). At the only site where they were known to persist, we sampled soil from 12 rock crevices, including four with high levels of activity of the target species, as well as water from three adjacent pools. We were unable to identify DNA of B. obiri in any of the soil or water samples, suggesting multiple false-negative errors, despite our successful amplification of B. obiri DNA from an incidental scat sample. We were able to identify 15 non-target vertebrate taxa from our samples. Given that samples were taken from a site where B. obiri was known to be present, the eDNA metabarcoding technique trialled here does not appear to be an effective method for detecting this species. Whilst eDNA metabarcoding is an emerging and powerful tool in ecology and conservation, our pilot study highlights that challenges remain in its application for detecting rare or cryptic terrestrial reptiles.

Biodiversity loss is often attributable to multiple interacting pressures that are moderated across environmental gradients. These processes contribute to complex responses that are challenging to interpret and understand. Well-designed and well-implemented monitoring can play a vital role in this but is rarely undertaken.Mounting evidence suggests that current fire regimes across Savanna ecosystems have contributed to the decline of a range of biota. Hence, contemporary fire regimes are at odds with conservation goals.Using an extensive spatiotemporal monitoring dataset from three large National Parks in northern Australia, we applied generalised linear mixed models to examine: (1) trends in mammal richness and abundance through time and variation across environmental gradients such as productivity or landscape position (e.g. terrain ruggedness); and (2) how fire, a potential driver, is moderated by environmental gradients.Across 24 years, major declines in mammal richness and abundance were observed with greater reductions in less rugged and less mesic habitats. Patterns of decline were related to multiple aspects of fire regimes, but not changes in vegetation structure and composition, or cane toads, Rhinella marina, arrival and concomitant poisoning of predatory animals during consumption. More pronounced declines occurred in sites that were exposed to larger fires, had less long unburnt (>5 years without fire) vegetation and were more distant from large, long unburnt patches.Relationships between mammal persistence and fire varied among vegetation communities, with the strongest fire effects observed in lowland woodland-drier with few barriers to fire spread-where the availability of long unburnt areas moderated declines more than in other vegetation communities.Synthesis and applications. Current fire regimes are contributing to mammal declines in northern Australian Savanna. Collectively, our results highlight: (1) the value of long term monitoring, and importance of considering landscape position when assessing faunal responses to landscape-level perturbations like fire; (2) that significant improvements in fire regimes are required to ameliorate mammal declines; and (3) the need to shift management focus from retaining small, short-lived unburnt patches toward preserving relatively large contiguous areas of long unburnt habitat, particularly in less rugged lowland and sandstone woodlands.

Assessments of ecosystem restoration have traditionally focused on soil and vegetation, often with little consideration of fauna. It is critical to include fauna in such assessments, not just because of their intrinsic biodiversity value but also because of the many ecological roles that animals play in restoration processes. However, a widely accepted framework for specifying faunal standards for restoration is lacking. Here we present such a framework, incorporating: (1) the identification of appropriate reference conditions; (2) the taxa to be targeted for assessment; (3) the attributes of these taxa to be measured; (4) acceptable similarity with reference conditions; and (5) robust sampling methodologies for reliable assessment. We illustrate this framework using the restoration program at Ranger Uranium Mine in the Australian seasonal tropics, which aims to establish an environment similar to the surrounding World Heritage‐listed Kakadu National Park, corresponding to “full recovery” according to Society for Ecosystem Restoration's standards. Our case study has especially high restoration standards, but our framework has wide applicability to the specification of faunal standards for ecosystem restoration.

Background The coastal floodplains of northern Australia are fire-prone, but the impact of fire on floodplain biota is not well understood. Aims In this study, we sought to characterise the fire history of six adjacent floodplains in coastal Northern Territory, Australia. Methods We built a fine-scale 31-year fire history (1988–2018) to compare fire regimes on floodplains across land tenures and floodplain fire regimes with the surrounding savanna fire regime, determine the extent to which current fire regimes are meeting existing ecological fire thresholds, and investigate the relationship between rainfall totals and the extent of burning. Key results Floodplains in conservation reserves burnt more frequently than those on pastoral lands, and savannas burnt more often than floodplains. Current floodplain fire regimes comfortably meet existing ecological fire thresholds. The proportion of floodplain burning is inversely proportional to the amount of rain in the previous wet season. Conclusions Floodplain fire regimes vary markedly between land-use types, and floodplain fire regimes differ to those of savannas. The current management thresholds for floodplain fire regimes would benefit from further evidence of conservation outcomes. Implications For more effective floodplain fire management, research is needed to generate floodplain-specific thresholds that best conserve their considerable conservation value.

Summary Knowledge of where a threatened species occurs in a landscape is crucial for determining its habitat requirements and informing its conservation planning and management. We conducted the first broad-scale survey of the Endangered Alligator Rivers Yellow Chat Epthianura crocea tunneyi across much of its known range on drying coastal floodplains in northern Australia. Presence-absence records from 257 sites surveyed in the late dry season (August–December) of 2018 and 2019 were modelled using occupancy/detectability models. Occupancy was estimated to be 0.10 ± 0.04 with a high detection probability (0.89 ± 0.07). Modelling of 13 site-level environmental covariates found that chats were more likely to be detected at sites where the native shrub Sesbania sesban was present, were close to hydrogeological features such as depressions or channels, were long unburnt (5+ years) and/or with topsoil damage caused by feral pigs. Our estimates of chat occupancy, detectability, and the covariates that influence their occupancy, have improved our understanding of the role that fire and feral animals have on chat distribution and habitat selection, and can be used as a baseline for future monitoring. We also provide recommendations on how to design and implement future monitoring of this subspecies.

Aim An interaction between reduced habitat structural complexity and predation by feral cats (Felis catus) has been hypothesized as the primary driver of mammal decline in northern Australia. However, we have a limited understanding of the drivers of the distribution and abundance of feral cats at a landscape scale, including whether the occurrence of a top predator, the dingo (Canis familiaris [dingo]), limits feral cat populations. We modelled feral cat and dingo site occurrence, to provide the first broad-scale assessment of their distributional patterns and co-occurrence within monsoonal Australia. Location About 370,000 km(2) of monsoonal area in the Northern Territory. Methods We surveyed 376 sites using camera traps. We used single- and two-species occupancy models to investigate feral cat and dingo site occurrence and the influence of dingoes on feral cat occupancy. We included predictor variables that relate to hypotheses of predator occurrence, including both environmental and disturbance-related variables. Results Feral cat occurrence and dingo occurrence were best predicted by indices of habitat structural complexity; feral cat occurrence declined with increasing productivity, except in areas of relatively high fire activity (fire frequency and extent), and dingo occurrence declined with terrain ruggedness. We found no evidence that dingoes are spatially limiting feral cat occurrence. Main conclusions Our findings suggest the protection and enhancement of habitat structural complexity at both the local and landscape scale could enable conservation managers to reduce the exposure of small- and medium-sized mammals to feral cats and dingoes. This can most likely be achieved through improved fire and feral herbivore management, which is a more feasible management option than lethal predator control.

1. Public aquaria globally display numerous threatened fish species captured from wild populations. Potential impacts of harvests are rarely evaluated despite the need for improved management and conservation practices. 2. Sawfishes (Family Pristiidae) are one of the world's most at-risk fish families. Most commonly displayed (30+ wild caught individuals) is the Critically Endangered largetooth sawfish,Pristis pristis. 3. Two Australian aquaria release captiveP. prististo the wild as they outgrow displays, intending to offset impacts of the original harvests. The fate of released sawfish is unknown. 4. Using acoustic telemetry, the behaviour (rates of movement, patterns of habitat use) and survival of aquarium released sawfish (n= 5) were compared to a control group of wild sawfish (n= 5). 5. Aquarium sawfish had reduced rates of movement, were more sedentary, and occupied smaller activity spaces than wild sawfish; but diel activity and habitat use patterns were similar. 6. Collectively, mortality was high. Two aquarium sawfish survived to the end of the monitoring period (391 days and 117 days, respectively), and no wild sawfish survived. The mean duration of survival for aquarium and wild sawfish was 157 and 58 days, respectively. 7. Whilst captivity affected behaviours, the lower mortality rates of aquarium sawfish indicates that releases may partially offset the impact of the original harvest. Further data are required to investigate potential long-term ecological impacts. 8. If P. pristis are to be used for aquarium displays, the best conservation outcomes could be achieved by harvesting in the first year of life when natural mortality is highest, followed by release into the freshwater reaches of the natal river where predation risk may be minimized. Size on release should be less than similar to 2,800 mm total length to allow for migration from the river system as part of their natural life cycle.

Abstract Invertebrates are commonly ignored in conservation planning due to their vast diversity, difficulties with species identification, a poor understanding of their spatial patterns, and the impracticability of carrying out comprehensive sampling. Conservation planning for fauna is therefore often based on patterns of diversity and distribution of vertebrates, under the assumption that these are representative of animal diversity more generally. Here, we evaluate how well vertebrates act as umbrellas for invertebrate diversity and distribution in a highly diverse tropical savanna landscape, and we investigate the effect of vertebrate sampling intensity (i.e., number of surveys) on congruence results. We assessed congruence between each of the four classes of terrestrial vertebrates (amphibians, reptiles, birds, and mammals) and twelve invertebrate families (representing four dominant invertebrate taxa: ants, beetles, flies, and spiders) by applying a range of modeling approaches to analyze patterns of cross‐taxon congruence in species richness and composition across sampling sites. To investigate drivers of congruence, we applied generalized and distance‐based linear models to identify environmental associations of richness and composition for each taxon, then examined variation in environmental associations across taxa. Vertebrate and invertebrate richness was weakly (<30%) associated, and ~60% of the significant associations were negative. Correlations in species composition between vertebrate and invertebrate taxa were also weak, with a maximum of 13% congruence. In most cases, pairwise correlation scores using data from single surveys of vertebrates were only marginally lower than those from multiple surveys. Poor among‐site congruence between vertebrates and invertebrates was reflected by marked variation among taxa in their environmental associations. Our findings show that vertebrates are poor umbrellas for invertebrates in the tropical savannas of northern Australia in terms of geographic patterns of diversity and distribution and that this is not just an artifact of low vertebrate sampling intensity. Our study is one of the most comprehensive regional analyses of the congruence of vertebrate and invertebrate diversity, and it significantly adds to the growing evidence that empirical data on invertebrate diversity and distribution are required for conservation planning that effectively protects all faunal diversity.

Assessing the statistical power to detect changes in wildlife populations is a crucial yet often overlooked step when designing and evaluating monitoring programs. Here, we developed a simulation framework to perform spatially explicit statistical power analysis of biological monitoring programs for detecting temporal trends in occupancy for multiple species. Using raster layers representing the spatial variation in current occupancy and species-level detectability for one or multiple observation methods, our framework simulates changes in occupancy over space and time, with the capacity to explicitly model stochastic disturbances at monitoring sites (i.e., dynamic landscapes). Once users specify the number and location of sites, the frequency and duration of surveys, and the type of detection method(s) for each species, our framework estimates power to detect occupancy trends, both across the landscape and/or within nested management units. As a case study, we evaluated the power of a long-term monitoring program to detect trends in occupancy for 136 species (83 birds, 33 reptiles, and 20 mammals) across and within Kakadu, Litchfield, and Nitmiluk National Parks in northern Australia. We assumed continuation of an original monitoring design implemented since 1996, with the addition of camera trapping. As expected, power to detect trends was sensitive to the direction and magnitude of the change in occupancy, detectability, initial occupancy levels, and the rarity of species. Our simulations suggest that monitoring has at least an 80% chance at detecting a 50% decline in occupancy for 22% of the modeled species across the three parks over the next 15 yr. Monitoring is more likely to detect increasing occupancy trends, with at least an 80% chance at detecting a 50% increase in 87% of species. The addition of camera-trapping increased average power to detect a 50% decline in mammals compared with using only live trapping by 63%. We provide a flexible tool that can help decision-makers design and evaluate monitoring programs for hundreds of species at a time in a range of ecological settings, while explicitly considering the distribution of species and alternative sampling methods.

Understanding where species occur and how difficult they are to detect during surveys is crucial for designing and evaluating monitoring programs, and has broader applications for conservation planning and management. In this study, we modelled occupancy and the effectiveness of six sampling methods at detecting vertebrates across the Top End of northern Australia. We fitted occupancy-detection models to 136 species (83 birds, 33 reptiles, 20 mammals) of 242 recorded during surveys of 333 sites in eight conservation reserves between 2011 and 2016. For modelled species, mean occupancy was highly variable: birds and reptiles ranged from 0.01-0.81 and 0.01-0.49, respectively, whereas mammal occupancy was lower, ranging from 0.02-0.30. Of the 11 environmental covariates considered as potential predictors of occupancy, topographic ruggedness, elevation, maximum temperature, and fire frequency were retained more readily in the top models. Using these models, we predicted species occupancy across the Top End of northern Australia (293,017 km2) and generated species richness maps for each species group. For mammals and reptiles, high richness was associated with rugged terrain, while bird richness was highest in coastal lowland woodlands. On average, detectability of diurnal birds was higher per day of surveys (0.33 ± 0.09) compared with nocturnal birds per night of spotlighting (0.13 ± 0.06). Detectability of reptiles was similar per day/night of pit trapping (0.30 ± 0.09) as per night of spotlighting (0.29 ± 0.11). On average, mammals were highly detectable using motion-sensor cameras for a week (0.36 ± 0.06), with exception of smaller-bodied species. One night of Elliott trapping (0.20 ± 0.06) and spotlighting (0.19 ± 0.06) was more effective at detecting mammals than cage (0.08 ± 0.03) and pit trapping (0.05 ± 0.04). Our estimates of species occupancy and detectability will help inform decisions about how best to redesign a long-running vertebrate monitoring program in the Top End of northern Australia.

An unprecedented rate of global environmental change is predicted for the next century. The response to this change by ecosystems around the world is highly uncertain. To address this uncertainty, it is critical to understand the potential drivers and mechanisms of change in order to develop more reliable predictions. Australia's Long Term Ecological Research Network (LTERN) has brought together some of the longest running (10-60years) continuous environmental monitoring programs in the southern hemisphere. Here, we compare climatic variables recorded at five LTERN plot network sites during their period of operation and place them into the context of long-term climatic trends. Then, using our unique Australian long-term datasets (total 117 survey years across four biomes), we synthesize results from a series of case studies to test two hypotheses: 1) extreme weather events for each plot network have increased over the last decade, and; 2) trends in biodiversity will be associated with recent climate change, either directly or indirectly through climate-mediated disturbance (wildfire) responses. We examined the biodiversity responses to environmental change for evidence of non-linear behavior. In line with hypothesis 1), an increase in extreme climate events occurred within the last decade for each plot network. For hypothesis 2), climate, wildfire, or both were correlated with biodiversity responses at each plot network, but there was no evidence of non-linear change. However, the influence of climate or fire was context-specific. Biodiversity responded to recent climate change either directly or indirectly as a consequence of changes in fire regimes or climate-mediated fire responses. A national long-term monitoring framework allowed us to find contrasting species abundance or community responses to climate and disturbance across four of the major biomes of Australia, highlighting the need to establish and resource long-term monitoring programs across representative ecosystem types, which are likely to show context-specific responses.

SUMMARY The choice of particular nesting sites can be important for seabirds breeding in colonies exposed to harsh environments. For polar seabirds of small to medium body size, cavity nesting provides shelter from predators as well as from harsh weather, but cavities may also accumulate snow, which is detrimental to breeding. We studied these relative influences on Snow Petrel Pagodroma nivea nest selection at a colony exposed to moderate snowfall and substantial windblown snow from regular katabatic winds. Nest selection was assessed using 13 habitat characteristics compared through three stages of breeding (initial occupancy, incubation and chick provisioning), during two consecutive years of varied weather. Snow Petrels occupied a wide range of cavities, but hatching success and chick survival were greater in more sheltered nests with a flat nest bowl. Ice accumulation was detrimental to laying and breeding success and was related to aspect: nesting cavities on the lee of the island provided some protection against prevailing winds yet were more prone to ice accumulation. The most successful nests had a degree of exposure to winds that allowed them to remain ice-free but enough shelter to retain loose substrate and presumably provide protection from predators.

To understand how animals cope with environmental variability it is necessary to identify the degree of flexibility in a species' diet and foraging mode and the consequences of this flexibility for reproduction. We examined rates of feeding and energy delivery to chicks by a long-lived pelagic seabird, the Short-tailed Shearwater (Puffinus tenuirostris). Individual adults alternated between foraging trips of short and long duration in a dual foraging strategy, but the allocation of time on those trips varied significantly from year to year. In two years when sea-surface temperatures of feeding grounds exploited during short trips were cooler (2005, 2006) adults initially fed their chick more often, then feeding decreased through the chick-rearing period. In the following year of warmer sea-surface temperature (2007), the number of feedings per day was initially low but increased through chick rearing. Despite varied feeding patterns, breeding success was consistently high, yet in 2006 the chicks' poor condition indicates the capacity for buffering chicks from these effects was lower than in other years. The relative contribution of short and long trips to the amount of energy delivered to chicks also varied by year. During local food shortages, shearwaters appeared to deliver more oil from long trips and increased the frequency of short trips. Yet in 2006, low-calorie prey from short trips coincided with low volume of stomach oil from long trips, resulting in chicks' poorer condition. Oil volume and increased short-trip foraging provide potential mechanisms of flexibility enabling adults to buffer prey delivery to chicks during food shortages.

The Spotted Handfish (Brachionichthys hirsutus) is a small, benthic fish whose current known distribution is limited to a number of discrete locations in the Derwent Estuary, south eastern Tasmania. It is listed as ‘critically endangered’ by the IUCN and is considered vulnerable to extinction due to habitat loss and modification and invasive species. This project was developed to generate momentum and community engagement for ongoing monitoring and recovery actions of key handfish populations in the Derwent Estuary, with the ultimate aim of establishing a mechanism for long-term sustainability of handfish recovery and monitoring efforts.

BACKGROUND:Sooty (Puffinus griseus) and short-tailed (P. tenuirostris) shearwaters are abundant seabirds that range widely across global oceans. Understanding the foraging ecology of these species in the Southern Ocean is important for monitoring and ecosystem conservation and management.METHODOLOGY/PRINCIPAL FINDINGS:Tracking data from sooty and short-tailed shearwaters from three regions of New Zealand and Australia were combined with at-sea observations of shearwaters in the Southern Ocean, physical oceanography, near-surface copepod distributions, pelagic trawl data, and synoptic near-surface winds. Shearwaters from all three regions foraged in the Polar Front zone, and showed particular overlap in the region around 140 degrees E. Short-tailed shearwaters from South Australia also foraged in Antarctic waters south of the Polar Front. The spatial distribution of shearwater foraging effort in the Polar Front zone was matched by patterns in large-scale upwelling, primary production, and abundances of copepods and myctophid fish. Oceanic winds were found to be broad determinants of foraging distribution, and of the flight paths taken by the birds on long foraging trips to Antarctic waters.CONCLUSIONS/SIGNIFICANCE:The shearwaters displayed foraging site fidelity and overlap of foraging habitat between species and populations that may enhance their utility as indicators of Southern Ocean ecosystems. The results highlight the importance of upwellings due to interactions of the Antarctic Circumpolar Current with large-scale bottom topography, and the corresponding localised increases in the productivity of the Polar Front ecosystem.