Dr Chad Beranek

Drones are an effective tool for animal surveys, capable of generating an abundance of high-quality ecological data. However, the large volume of ecological data generated introduces an additional problem of the requisite human resources to process and analyse such data. Deep learning models offer a solution to this challenge, capable of autonomously processing drone footage to detect animals with higher fidelity and lower latency when compared with humans. This work aimed to develop an animal detection architecture that classifies animals in accordance to their location (terrestrial vs. arboreal). The model incorporates human pilot inspired techniques for greater performance and consistency across time. Thermal drone footage across the state of New South Wales, Australia from surveys over a 2+ year period was used to construct a diverse training and validation dataset. A high-resolution 3D simulation was developed to workload by autonomously generating labelled data to supplement manually labelled field data. The model was evaluated on 130 hours of thermal imagery (14 million images) containing 57 unique animal species where 1637 out of 1719 (95.23%) of human pilot recorded animals were detected. The model achieved an F1 score of 0.9410, a 4.36 percentage point increase in performance over a benchmark YOLOv8 model. Simulated data improved model performance by 1.7x for low data scenarios, lowering data labelling costs due to higher quality image pre-labels. The proposed animal detection model demonstrates strong reporting accuracy in the detection and tracking of animals. The approach enables widespread adoption of drone-capturing technology by providing in-field real-time assistance, allowing novice pilots to detect animals at the level of experienced pilots, whilst also reducing the burden of report generation and data labelling costs.

Habitat fragmentation poses challenges to arboreal mammals relying on tree hollows for denning. Knowledge of species-specific den preferences is needed to realise the full potential of restoration actions. Current advice regarding artificial den design is often highly rigid and specific, where there may be intra- and interspecific variation in den use that is not considered. We investigated denning preferences of the Sugar Glider (Petaurus breviceps) and Squirrel Glider (Petaurus norfolcensis) in remnant forest reserves, exploring the use of natural hollows and nest boxes, and which attributes of the dens were predictive of use. We radio-tracked 15 Squirrel Gliders and seven Sugar Gliders to denning locations where den characteristics were assessed and compared to randomly selected hollows not known to be used within the home range of the radio-tracked gliders. The hollow entrance size was the only variable that predicted den use in both species. Contrary to expectations, nest boxes were used proportionally more than natural hollows. This highlights that nest boxes can be an effective temporary solution to provide interim den sites for gliders in degraded forest remnants. Also contrary to expectations, hollow height showed only a weak correlation with den use. Seasonal variation and individual behaviours may influence glider preferences, emphasizing the need for nuanced management strategies. Based on these findings, we recommend against a one-size-fits-all approach in the application of artificial hollows for the restoration of glider denning habitat, especially in terms of the aspect and entry height, so that intra- and interspecific variation in den use can be accommodated.

Temporary exclusion fencing is used around development and remediation sites to protect amphibians. However, by focusing so closely on mitigating potential for harm to individuals, managers may not see the "forest for the trees" and inadvertently cause more harm than good for the populations they are trying to protect. Land developments are necessary, and managers need to be capable of selecting the most appropriate solution that does not impede work activities or animal welfare. Yet, we suggest that adapted fencing solutions or non-fencing alternatives are not being explored that may reduce impacts on amphibians. Our focus is on project managers so that an open discussion can be had on the extent of fencing that is selected for each project.

With large wildfires becoming more frequent1,2, 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 unprecedented3,4 2019¿2020 Australian megafires burnt more than 10 million hectares5, 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.

Many animals create their own microhabitats that are not naturally present in the environment, such as nests and burrows, which are extended phenotypes that perform tasks related to survival and reproduction. Animals may be able to avoid the costs of implementing their own extended phenotypes by exploiting those already created by other species, including structures that are not actively in use or abandoned. Herein, we report on the striped marsh frog, Limnodynastes peronii, from Australia utilizing crayfish burrows for depositing their egg clutches. Field observations revealed large numbers of recently hatched L. peronii tadpoles in two flooded burrows likely created by the hunter hairy crayfish, Cherax setosus, near an ephemeral wetland pond on Kooragang Island, Australia that had partially dried. Our observations indicate that L. peronii may opportunistically exploit crayfish burrows which, when flooded, become suitable aquatic sites for breeding. These small waterbodies may provide fitness benefits to offspring, reducing exposure to aquatic predators found in naturally occurring aquatic systems but at the expense of increasing competition and cannibalism among confined siblings. These burrows may provide suitable microhabitat refuge during droughts, and breeding habitat for amphibians when other typical breeding habitats may not exist due to wetland drying. This is an example of an amphibian using an extended phenotype of a crustacean for the purposes of reproduction, revealing a unique interaction between these species that has not been reported.

Rare and cryptic species require effective monitoring methods in order to track populations over time. Monitoring surveys utilizing artificial refugia are an increasingly applied tool for detecting herpetofauna; yet for many species, limited information is available on the factors that influence optimal detectability. Most monitoring programs utilize only one type of artificial refuge. This approach has limitations as it may overlook the dynamic habitat needs of some species, with different refugia required under different conditions. Here we investigate whether using two different types of artificial refugia could maximize overall detection of the endangered Monaro grassland earless dragon Tympanocryptis osbornei by providing refugia that match habitat use. Tympanocryptis osbornei is a grassland specialist endemic to the Monaro Plains of southern NSW which occurs within a fragmented and altered agricultural landscape. Artificial refuge habitat in the form of customized replica 'spider' tubes and concrete roof tiles were utilized to infer the highest detection probability when compared to traditional rock rolling techniques. We found tubes to be more successful than tiles (mean: 0.021, 0.010¿0.037 95% Bayesian credible interval (BCI) vs mean: 0.0096, 0.0045¿0.018 95% BCI). However, this was dependent on air temperature, as tiles became more effective between 25 and 30 °C when dragons were more likely to be using surface shelters. Artificial refugia on a transect level (12 tubes and 12 tiles) had the greatest detection probability (mean: 0.11, 0.04¿0.23 95% BCI) compared to individually checked objects. Our results identify the best current methods and conditions to detect T. osbornei and provide insights into additional considerations for optimizing survey efforts, timing, and detectability for other small reptiles in temperate climates. We recommend a combination of artificial refugia be considered in future surveys for cryptic reptiles.

Aim: Changes to the extent and severity of wildfires driven by anthropogenic climate change are predicted to have compounding negative consequences for ecological communities. While there is evidence that severe weather events like drought impact amphibian communities, the effects of wildfire on such communities are not well understood. The impact of wildfire on amphibian communities and species is likely to vary, owing to the diversity of their life-history traits. However, no previous research has identified commonalities among the amphibians at most risk from wildfire, limiting conservation initiatives in the aftermath of severe wildfire. We aimed to investigate the impacts of the unprecedented 2019¿2020 black summer bushfires on Australian forest amphibian communities. Location: Eastern coast of New South Wales, Australia. Methods: We conducted visual encounter surveys and passive acoustic monitoring across 411 sites within two regions, one in northeast and one in southeast New South Wales. We used fire severity and extent mapping in two multispecies occupancy models to assess the impacts of fire on 35 forest amphibian species. Results: We demonstrate a negative influence of severe fire extent on metacommunity occupancy and species richness in the south with weaker effects in the north¿reflective of the less severe fires that occurred in this region. Both threatened and common species were impacted by severe wildfire extent. Occupancy of burrowing species and rain forest specialists had mostly negative relationships with severe wildfire extent, while arboreal amphibians had neutral relationships. Main Conclusion: Metacommunity monitoring and adaptive conservation strategies are needed to account for common species after severe climatic events. Ecological, morphological and life-history variation drives the susceptibility of amphibians to wildfires. We document the first evidence of climate change-driven wildfires impacting temperate forest amphibian communities across a broad geographic area, which raises serious concern for the persistence of amphibians under an increasingly fire-prone climate.

Traditional methods for identifying individual amphibians in capture¿mark¿recapture (CMR) studies have been primarily confined to post-metamorphic stages, using artificial markers that come with a variety of limitations. An alternative that may open CMR studies to earlier life stages involves the use of a species' natural external markers in photo-based identification. In this study, we investigated whether it was possible to distinguish tadpoles of the threatened green and golden bell frog (Litoria aurea) at the individual level based on tail venation patterns. We collected photographs of the tails of captive-raised tadpoles using a smartphone over a 4-week period. This photo-library was used to create an electronic survey where participants were asked to detect matches for query tadpoles from small image pools. We found that most participants agreed on a match for each query, with perfect consensus achieved for most queries (83%). We detected a 14% decline in perfect consensus when participants were asked to match images of tadpoles separated by longer time intervals, suggesting that it is more difficult to visually identify recapture events of L.¿aurea tadpoles over extended periods due to changes to tail appearance. However, consensus was obtained by participants for all queries, with all matches verified as being correct by the primary researcher. The strength of agreement among participants with no prior experience in matching tadpole tails suggests that there is sufficient inter-individual variation in this feature for individuals to be manually identified. We thus propose that photo-identification is likely to be a valid, non-invasive technique that can be used for short-term studies on tadpole populations that display tail venation. This offers an alternative to artificial markers that may not allow for individual identification, while also opening up tadpole monitoring programmes to citizen scientists who can be recruited online to process image data from home.

Biodiversity is in global decline during the Anthropocene. Declines have been caused by multiple factors, such as habitat removal, invasive species, and disease, which are often targets for conservation management. However, conservation interventions are under threat from climate change induced weather extremes. Weather extremes are becoming more frequent and devastating and an example of this was the 2019/2020 Australian drought and mega-fires. We provide a case study the impacts of these extreme weather events had on a population of the threatened frog Litoria aurea that occurs in a constructed habitat which was designed to reduce the impact of introduced fish and chytrid-induced disease. We aimed to determine what factors influenced persistence so that the design of wetlands can be further optimised to future-proof threatened amphibians. We achieved this with 4 years (2016¿2020) of intensive capture¿recapture surveys during austral spring and summer across nine wetlands (n = 94 repeat surveys). As hypothesized, drought caused a sharp reduction in population size, but persistence was achieved. The most parsimonious predictor of survival was an interaction between maximum air temperature and rainfall, indicating that weather extremes likely caused the decline. Survival was positively correlated with wetland vegetation coverage, positing this is an important feature to target to enhance resilience in wetland restoration programs. Additionally, the benefits obtained from measures to reduce chytrid prevalence were not compromised during drought, as there was a positive correlation between salinity and survival. We emphasize that many species may not be able to persist under worse extreme weather scenarios. Despite the potential for habitat augmentation to buffer effects of extreme weather, global action on climate change is needed to reduce extinction risk.

Introduced rodents, particularly the black rat (Rattus rattus), have caused serious ecological impacts due to their ability to interact with native species as both predators, and by eliciting competitive pressure. However, impacts of black rats upon many Australian mammals have yet to be determined, particularly when those mammals are arboreal. Here, we present novel observations in the form of camera trap footage and photographs of interspecific competition between the introduced black rat and two species of arboreal gliding marsupial (sugar gliders (Petaurus breviceps) and squirrel gliders (Petaurus norfolcensis)) in urban bushland reserves in New South Wales, Australia. Gliders were found to flee or were prevented from exploiting food resources due to antagonistic posturing and physical attacks by black rats. While interspecific aggression and interference competition between black rats and native mammal species has been demonstrated previously, this appears to be the first observation of such interactions for Australian gliders. Our findings may have implications for the future management of glider populations in urban bushland where they co-occur with rats; however, further research needs to be undertaken to determine the extent of this potential threat.

Understanding biodiversity patterns as well as drivers of population declines, and range losses provides crucial baselines for monitoring and conservation. However, the information needed to evaluate such trends remains unstandardised and sparsely available for many taxonomic groups and habitats, including the cave-dwelling bats and cave ecosystems. We developed the DarkCideS 1.0 (https://darkcides.org/), a global database of bat caves and species synthesised from publicly available information and datasets. The DarkCideS 1.0 is by far the largest database for cave-dwelling bats, which contains information for geographical location, ecological status, species traits, and parasites and hyperparasites for 679 bat species are known to occur in caves or use caves in part of their life histories. The database currently contains 6746 georeferenced occurrences for 402 cave-dwelling bat species from 2002 cave sites in 46 countries and 12 terrestrial biomes. The database has been developed to be collaborative and open-access, allowing continuous data-sharing among the community of bat researchers and conservation biologists to advance bat research and comparative monitoring and prioritisation for conservation.

Amphibians are under threat from many drivers resulting in declining populations. Restoration and creation of habitat is a method used to reverse amphibian declines. The green and golden bell frog (Litoria aurea) is distributed in southeastern Australia, and is threatened by the fungal pathogen Batrachochytrium dendobatidis (chytrid), an introduced fish (the plague minnow, Gambusia holbrooki), and habitat loss. There have been numerous wetland restoration attempts to combat population declines in this species, which have been largely unsuccessful in producing persisting populations. Here we present a robust model for the creation of breeding habitat for the L. aurea population on Kooragang Island, New South Wales, which is based off thorough review of the literature and past pilot studies and experiments. We describe in detail the habitat, land use history, and wetland habitat design formulation and construction so that the context of the habitat creation is understood and so construction can be repeatable and the design can be further refined. The habitat features passive controls for chytrid and G. holbrooki, and contains the most optimum breeding habitat for L. aurea based upon current knowledge. This is the first attempt in our knowledge to create wetlands in an open system that have the potential to passively manage chytrid.

Knowledge on how life history traits affect distribution in range-restricted and endemic plants is paramount for conservation and management, particularly for threatened species. Traits relating to dispersal ability are important in the ongoing persistence of range restricted species and may present a pathway to extinction or invasion. This is evident in the highly diverse and cosmopolitan genus Senecio (Asteraceae), where both threatened and invasive species occur within Australia. In this study, propagule geometry, settling velocity and dispersal potential for two range-restricted and threatened native taxa (S. linearifolious var. dangarensis Belcher ex I.Thomps., S. spathulatus var. attenuatus I.Thomps.) are contrasted with four native taxa that occupy wider ranges (S. amygdalifolius F.Muell., S. l. var. arachnoideus I.Thomps., S. l. var. macrodontus (DC.) I.Thomps., S. pinnatifolius A.Rich. var. pinnatifolius) and one introduced, wide-ranging species (S. madagascariensis Poir.). Differences were found in settling velocity and propagule morphology across all taxa. Based on propagule morphology, S. amygdalifolius has the greatest dispersal potential, S. spathulatus var. attenuatus the smallest, whereas all other taxa were similar. Although useful, dispersal potential alone does not fully explain distributional differences between all range-restricted and widespread taxa, and close assessment of habitat attributes may be required to further elucidate dispersal limitations in some taxa.

The 'Compassionate Conservation' movement is gaining momentum through its promotion of 'ethical' conservation practices based on self-proclaimed principles of 'first-do-no-harm' and 'individuals matter'. We argue that the tenets of 'Compassionate Conservation' are ideological - that is, they are not scientifically proven to improve conservation outcomes, yet are critical of the current methods that do. In this paper we envision a future with 'Compassionate Conservation' and predict how this might affect global biodiversity conservation. Taken literally, 'Compassionate Conservation' will deny current conservation practices such as captive breeding, introduced species control, biocontrol, conservation fencing, translocation, contraception, disease control and genetic introgression. Five mainstream conservation practices are used to illustrate the far-reaching and dire consequences for global biodiversity if governed by 'Compassionate Conservation'. We acknowledge the important role of animal welfare science in conservation practices but argue that 'Compassionate Conservation' aligns more closely with animal liberation principles protecting individuals over populations. Ultimately we fear that a world of 'Compassionate Conservation' could stymie the global conservation efforts required to meet international biodiversity targets derived from evidenced based practice, such as the Aichi targets developed by the Convention on Biological Diversity and adopted by the International Union for the Conservation of Nature and the United Nations.

The Brown Goshawk Accipiter fasciatus has a variable diet comprising mainly avian prey and mammals, and most observations suggest that it employs a range of ambush tactics but rarely uses long-distance aerial pursuits. Here I document a rare instance of a successful long-distance aerial pursuit of an Australian Raven Corvus coronoides by a Brown Goshawk, on 29 March 2015, on Broughton Island, New South Wales. After multiple unsuccessful aerial attacks, the Goshawk eventually succeeded. Although corvids are abundant and widespread throughout Australia and are within the preferred avian prey size range, they are rarely observed in the Goshawk's diet. Two ecological factors probably contributed to this observation: (1) there is little woodland here and thus little concealment for ambush tactics and (2) prey availability on Broughton Island and the surrounding islands has been altered by programs to eradicate pest mammals, thereby limiting the prey available to this species in this area.

Although the Little Eagle Hieraaetus morphnoides is broadly distributed across much of Australia, it appears to be declining in New South Wales. The key threatening process is the removal of habitat, leading to loss of suitable nesting and foraging sites and changes in prey abundance. Here we present the frst report of successful nesting of the Little Eagle in greater Sydney (i.e. in the County of Cumberland), and recommend guidelines for management. The nest, discovered in a Smooth-barked Apple Angophora costata in the suburb of Ingleside on 15 October 2016, was visited one to three times per week, and observations on behaviour, diet and habitat of the Eagles were noted. The most common prey species taken was the European Rabbit Oryctolagus cuniculus. The chick fledged at c. 9 weeks old. The nest-site is at risk from a proposed development in the area and needs to be adaptively managed to ensure the continued presence and nesting of this species at this site.