Broad-scale acoustic monitoring of koala populations suggests metapopulation stability, but varying bellow rate, in the face of major disturbances and climate extremes.

Population trends are lacking for most threatened species, especially those that are cryptic and difficult to survey. Recent developments in passive acoustics and semi-automated call recognition provide a cost-effective option to systematically monitor populations of vocal species. We assessed recent trends for the koala Phascolarctos cinereus, an iconic marsupial, based on 7 years of acoustic monitoring across 224 forested sites. The study period overlapped with a severe drought and extensive megafires in 2019 followed by 2 years of extremely high rainfall. Dynamic occupancy modelling with a range of covariates at multiple landscape scales found that initial occupancy was related to elevation (-ve), NDVI (+ve) and previous selective harvesting (16-30-year age class; weakly +ve). Extinction probability increased with the extent of high-severity fire. Colonisation probability was related to a range of factors, with the top model showing a decrease with increasing lagged annual rainfall. However, the null model was also supported, suggesting weak associations for colonisation. Using these relationships, koala occupancy was found to be high and stable over the study period. Fire did not influence regional trends because koalas often persisted with low- to moderate-severity fire and because high-severity fire was limited to 11% of their habitat. In contrast, bellow rate varied across years, being initially low and declining immediately after the 2019 fires, with the driver of these changes unclear. Neither timber harvesting nor low-severity fire influenced koala occupancy or bellow rate. Given the extensive area of koala habitat in the region, our results point to the presence of a large population in these public forests, and in recent years, stable occupancy (albeit with site-scale reductions in density with high-severity fire). Ongoing monitoring is crucial for tracking future changes, especially with predictions of more frequent, severe forest fires due to climate change.

Estimating density of forest bats and their long-term trends in a climate refuge.

For many species, estimating density is challenging, but it is important for conservation planning and understanding the functional role of species. Bats play key ecological roles, yet little is known about their free-ranging density. We used a long-term banding study of four species caught in an extensively forested climate refuge and spatial capture-recapture models (SCR) to estimate density and its change over time. Between 1999 and 2020, there were 3671 captures of four bat species, which were all edge-space foragers. Recaptures represented 16% (n = 587) of all captures, of which 89 were between-trap-cluster movements. Closed spatial mark-recapture models estimated plausible densities that varied with elevation. Preferred elevations differed between species, with density averaging 0.63 ha-1 for Vespadelus darlingtoni (high elevation), 0.43 ha-1 for V. pumilus (low elevation), 0.19 ha-1 for Chalinolobus morio (high elevation), and 0.08 ha-1 for V. regulus (high elevation). Overall, densities were higher than most previous published estimates for bats. Forest disturbance history (past timber harvesting) had no detectable effect on density. Density also varied substantially across years, and although annual maximum temperature and rainfall were not supported in models, some time periods showed an apparent relationship between density and annual rainfall (+ve) and/or annual maximum temperature (-ve). The most notable change was an increase in the density of V. pumilus after 2013, which tracked an increase in annual temperature at the site, reflecting a warming climate. Bat densities in forests outside of climate refugia are likely to be more sensitive to climate change, but more studies are needed in different habitats and continents and outside climate refugia to place the densities we estimated into a broader context.

Passive acoustics and sound recognition provide new insights on status and resilience of an iconic endangered marsupial (koala Phascolarctos cinereus) to timber harvesting.

Retention forestry aims to mitigate impacts of native forestry on biodiversity, but data are limited on its effectiveness for threatened species. We used acoustics to investigate the resilience of a folivorous marsupial, the koala Phascolarctos cinereus, to timber harvesting where a key mitigation practice is landscape exclusion of harvesting. We deployed acoustic recorders at 171 sites to record male bellows (~14,640 hours) for use in occupancy modelling and for comparisons of bellow rate (bellows night-1). Surveys targeted modelled medium-high quality habitat, with sites stratified by time since logging and logging intensity, including old growth as a reference. After scanning recordings with software to identify koala bellows, we found a high probability of detection (~0.45 per night), but this varied with minimum temperature and recorder type. Naïve occupancy was ~ 64% across a broad range of forests, which was at least five times more than expected based on previous surveys using alternative methods. After accounting for imperfect detection, probability of occupancy was influenced by elevation (-ve), cover of important browse trees (+ve), landscape NDVI (+ve) and extent of recent wildfire (-ve, but minor effect). Elevation was the most influential variable, though the relationship was non-linear and low occupancy was most common at tableland elevations (> 1000 m). Neither occupancy nor bellow rate were influenced by timber harvesting intensity, time since harvesting or local landscape extent of harvesting or old growth. Extrapolation of occupancy across modelled habitat indicates that the hinterland forests of north-east NSW support a widespread, though likely low density koala population that is considerably larger than previously estimated. Retention forestry has a significant role to play in mitigating harvesting impacts on biodiversity, including for forest specialists, but localised studies are needed to optimise prescriptions for koalas.

Forest bat population dynamics over 14 years at a climate refuge: Effects of timber harvesting and weather extremes.

Long-term data are needed to explore the interaction of weather extremes with habitat alteration; in particular, can 'refugia' buffer population dynamics against climate change and are they robust to disturbances such as timber harvesting. Because forest bats are good indicators of ecosystem health, we used 14 years (1999-2012) of mark-recapture data from a suite of small tree-hollow roosting bats to estimate survival, abundance and body condition in harvested and unharvested forest and over extreme El Niño and La Niña weather events in southeastern Australia. Trapping was replicated within an experimental forest, located in a climate refuge, with different timber harvesting treatments. We trapped foraging bats and banded 3043 with a 32% retrap rate. Mark-recapture analyses allowed for dependence of survival on time, species, sex, logging treatment and for transients. A large portion of the population remained resident, with a maximum time to recapture of nine years. The effect of logging history (unlogged vs 16-30 years post-logging regrowth) on apparent survival was minor and species specific, with no detectable effect for two species, a positive effect for one and negative for the other. There was no effect of logging history on abundance or body condition for any of these species. Apparent survival of residents was not strongly influenced by weather variation (except for the smallest species), unlike previous studies outside of refugia. Despite annual variation in abundance and body condition across the 14 years of the study, no relationship with extreme weather was evident. The location of our study area in a climate refuge potentially buffered bat population dynamics from extreme weather. These results support the value of climate refugia in mitigating climate change impacts, though the lack of an external control highlights the need for further studies on the functioning of climate refugia. Relatively stable population dynamics were not compromised by timber harvesting, suggesting ecologically sustainable harvesting may be compatible with climate refugia.

Development and field validation of a regional, management-scale habitat model: A koala Phascolarctos cinereus case study.

Species distribution models have great potential to efficiently guide management for threatened species, especially for those that are rare or cryptic. We used MaxEnt to develop a regional-scale model for the koala Phascolarctos cinereus at a resolution (250 m) that could be used to guide management. To ensure the model was fit for purpose, we placed emphasis on validating the model using independently-collected field data. We reduced substantial spatial clustering of records in coastal urban areas using a 2-km spatial filter and by modeling separately two subregions separated by the 500-m elevational contour. A bias file was prepared that accounted for variable survey effort. Frequency of wildfire, soil type, floristics and elevation had the highest relative contribution to the model, while a number of other variables made minor contributions. The model was effective in discriminating different habitat suitability classes when compared with koala records not used in modeling. We validated the MaxEnt model at 65 ground-truth sites using independent data on koala occupancy (acoustic sampling) and habitat quality (browse tree availability). Koala bellows (n = 276) were analyzed in an occupancy modeling framework, while site habitat quality was indexed based on browse trees. Field validation demonstrated a linear increase in koala occupancy with higher modeled habitat suitability at ground-truth sites. Similarly, a site habitat quality index at ground-truth sites was correlated positively with modeled habitat suitability. The MaxEnt model provided a better fit to estimated koala occupancy than the site-based habitat quality index, probably because many variables were considered simultaneously by the model rather than just browse species. The positive relationship of the model with both site occupancy and habitat quality indicates that the model is fit for application at relevant management scales. Field-validated models of similar resolution would assist in guiding management of conservation-dependent species.

Cascading effects of climate extremes on vertebrate fauna through changes to low-latitude tree flowering and fruiting phenology.

Forest vertebrate fauna provide critical services, such as pollination and seed dispersal, which underpin functional and resilient ecosystems. In turn, many of these fauna are dependent on the flowering phenology of the plant species of such ecosystems. The impact of changes in climate, including climate extremes, on the interaction between these fauna and flora has not been identified or elucidated, yet influences on flowering phenology are already evident. These changes are well documented in the mid to high latitudes. However, there is emerging evidence that the flowering phenology, nectar/pollen production, and fruit production of long-lived trees in tropical and subtropical forests are also being impacted by changes in the frequency and severity of climate extremes. Here, we examine the implications of these changes for vertebrate fauna dependent on these resources. We review the literature to establish evidence for links between climate extremes and flowering phenology, elucidating the nature of relationships between different vertebrate taxa and flowering regimes. We combine this information with climate change projections to postulate about the likely impacts on nectar, pollen and fruit resource availability and the consequences for dependent vertebrate fauna. The most recent climate projections show that the frequency and intensity of climate extremes will increase during the 21st century. These changes are likely to significantly alter mass flowering and fruiting events in the tropics and subtropics, which are frequently cued by climate extremes, such as intensive rainfall events or rapid temperature shifts. We find that in these systems the abundance and duration of resource availability for vertebrate fauna is likely to fluctuate, and the time intervals between episodes of high resource availability to increase. The combined impact of these changes has the potential to result in cascading effects on ecosystems through changes in pollinator and seed dispersal ecology, and demands a focused research effort.

Are regional habitat models useful at a local-scale? A case study of threatened and common insectivorous bats in South-Eastern Australia.

Habitat modelling and predictive mapping are important tools for conservation planning, particularly for lesser known species such as many insectivorous bats. However, the scale at which modelling is undertaken can affect the predictive accuracy and restrict the use of the model at different scales. We assessed the validity of existing regional-scale habitat models at a local-scale and contrasted the habitat use of two morphologically similar species with differing conservation status (Mormopterus norfolkensis and Mormopterus species 2). We used negative binomial generalised linear models created from indices of activity and environmental variables collected from systematic acoustic surveys. We found that habitat type (based on vegetation community) best explained activity of both species, which were more active in floodplain areas, with most foraging activity recorded in the freshwater wetland habitat type. The threatened M. norfolkensis avoided urban areas, which contrasts with M. species 2 which occurred frequently in urban bushland. We found that the broad habitat types predicted from local-scale models were generally consistent with those from regional-scale models. However, threshold-dependent accuracy measures indicated a poor fit and we advise caution be applied when using the regional models at a fine scale, particularly when the consequences of false negatives or positives are severe. Additionally, our study illustrates that habitat type classifications can be important predictors and we suggest they are more practical for conservation than complex combinations of raw variables, as they are easily communicated to land managers.

Odour cues influence predation risk at artificial bat roosts in urban bushland.

Odours that accumulate from roosting can attract predators and increase predation risk. Consequently, selection should favour strategies that allow prey to evade detection by predators, including changing roosts. Insectivorous bats that roost in tree hollows regularly switch roosts and roost in different sized groups, strategies that would alter the accumulation of roost odours and are hypothesized to reduce predation risk. We experimentally manipulated the amount and refresh rate of roosting odour cues at 90 artificial bat roosts in Sydney, Australia, to test the hypothesis that odours increase predator visitation. Predators visited roosts with bat faeces significantly more often than untreated control roosts. Roosts with small amounts of faeces mimicking sites used by solitary bats had the greatest rate of visitation. This suggests that bats roosting alone, rather than in groups, have a greater likelihood of disturbance or predation. Roost switching probably decreases the predictability of finding occupied roosts; however, we show that all roosts (those currently or recently occupied) were visited by predators, suggesting generalist urban predators readily investigate potential roosts. This is the first demonstration that bat odours are attractive to predators that use olfactory cues, showing that bats are at risk of predation in visually cryptic roosts.

Influence of landscape structure and human modifications on insect biomass and bat foraging activity in an urban landscape.

Urban landscapes are often located in biologically diverse, productive regions. As such, urbanization may have dramatic consequences for this diversity, largely due to changes in the structure and function of urban communities. We examined the influence of landscape productivity (indexed by geology), housing density and vegetation clearing on the spatial distribution of nocturnal insect biomass and the foraging activity of insectivorous bats in the urban landscape of Sydney, Australia. Nocturnal insect biomass (g) and bat foraging activity were sampled from 113 sites representing backyard, open space, bushland and riparian landscape elements, across urban, suburban and vegetated landscapes within 60 km of Sydney's Central Business District. We found that insect biomass was at least an order of magnitude greater within suburban landscapes in bushland and backyard elements located on the most fertile shale influenced geologies (both p<0.001) compared to nutrient poor sandstone landscapes. Similarly, the feeding activity of bats was greatest in bushland, and riparian elements within suburbs on fertile geologies (p = 0.039). Regression tree analysis indicated that the same three variables explained the major proportion of the variation in insect biomass and bat foraging activity. These were ambient temperature (positive), housing density (negative) and the percent of fertile shale geologies (positive) in the landscape; however variation in insect biomass did not directly explain bat foraging activity. We suggest that prey may be unavailable to bats in highly urbanized areas if these areas are avoided by many species, suggesting that reduced feeding activity may reflect under-use of urban habitats by bats. Restoration activities to improve ecological function and maintain the activity of a diversity of bat species should focus on maintaining and restoring bushland and riparian habitat, particularly in areas with fertile geology as these were key bat foraging habitats.

Tree decline and the future of Australian farmland biodiversity.

Farmland biodiversity is greatly enhanced by the presence of trees. However, farmland trees are declining worldwide, including in North America, Central America, and parts of southern Europe. We show that tree decline and its likely consequences are particularly severe in Australia's temperate agricultural zone, which is a threatened ecoregion. Using field data on trees, remotely sensed imagery, and a demographic model for trees, we predict that by 2100, the number of trees on an average farm will contract to two-thirds of its present level. Statistical habitat models suggest that this tree decline will negatively affect many currently common animal species, with predicted declines in birds and bats of up to 50% by 2100. Declines were predicted for 24 of 32 bird species modeled and for all of six bat species modeled. Widespread declines in trees, birds, and bats may lead to a reduction in economically important ecosystem services such as shade provision for livestock and pest control. Moreover, many other species for which we have no empirical data also depend on trees, suggesting that fundamental changes in ecosystem functioning are likely. We conclude that Australia's temperate agricultural zone has crossed a threshold and no longer functions as a self-sustaining woodland ecosystem. A regime shift is occurring, with a woodland system deteriorating into a treeless pasture system. Management options exist to reverse tree decline, but new policy settings are required to encourage their widespread adoption.