Boom-bust population dynamics drive rapid genetic change.

Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse (Pseudomys hermannsburgensis) experiences marked boom-bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation (FST) increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy-footed dunnart (Sminthopsis youngsoni), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts.

slimr: An R package for tailor-made integrations of data in population genomic simulations over space and time.

Software for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between standalone simulation software and R is currently not well developed. Here, we present slimr, an R package designed to create a seamless link between standalone software SLiM >3.0, one of the most powerful population genomic simulation frameworks, and the R development environment, with its powerful data manipulation and analysis tools. We show how slimr facilitates smooth integration between genetic data, ecological data and simulation in a single environment. The package enables pipelines that begin with data reading, cleaning and manipulation, proceed to constructing empirically based parameters and initial conditions for simulations, then to running numerical simulations and finally to retrieving simulation results in a format suitable for comparisons with empirical data - aided by advanced analysis and visualization tools provided by R. We demonstrate the use of slimr with an example from our own work on the landscape population genomics of desert mammals, highlighting the advantage of having a single integrated tool for both data analysis and simulation. slimr makes the powerful simulation ability of SLiM directly accessible to R users, allowing integrated simulation projects that incorporate empirical data without the need to switch between software environments. This should provide more opportunities for evolutionary biologists and ecologists to use realistic simulations to better understand the interplay between ecological and evolutionary processes.

Grow up, be persistent, and stay focused: keys for solving foraging problems by free-ranging possums.

Individuals within a species often vary in both their problem-solving approach and ability, affecting their capacity to access novel food resources. Testing problem-solving in free-ranging individuals is crucial for understanding the fundamental ecological implications of problem-solving capacity. To examine the factors affecting problem-solving in free-ranging animals, we presented three food-extraction tasks of increasing difficulty to urban common brushtail possums (Trichosurus vulpecula). We quantified two measures of problem-solving performance: trial outcome (success/failure) and time to solve and tested the influence of a range of potential drivers, including individual traits (personality, body weight, sex, and age), mechanistic behaviors that quantify problem-solving approach (work time, functional behavior time, behavioral diversity, and flexibility), and prior experience with the puzzles. We found that mechanistic behaviors were key drivers of performance. Individuals displaying greater persistence (higher work and functional behavior time) were more likely to solve a food-extraction task on their first attempt. Individuals also solved problems faster if they were more persistent and had lower behavioral flexibility. Personality indirectly affected time to solve one of the three problems by influencing time allocated to functional behaviors. Finally, adults solved the most difficult problem faster than juveniles. Overall, our study provides rare insight into the drivers underlying the problem-solving performance of wild animals. Such insight could be used to improve management strategies and conservation efforts, such as food or bait deployment, tailored to suit the innovative foraging abilities of target individuals in new and changing environments.

Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness.

In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks resulting from fragmentation should lower genetic diversity over time, yet species undergoing these fluctuations appear to maintain high levels of genetic diversity. To resolve this apparent paradox, we simulated a metapopulation of constant size undergoing repeat episodes of fragmentation and change in gene flow to mimic outcomes experienced by mammals in an Australian desert. We show that episodic fragmentation and gene flow have contrasting effects on two measures of genetic diversity: heterozygosity and allelic richness. Specifically, fragmentation into many, small subpopulations, coupled with periods of infrequent gene flow, preserves allelic richness at the expense of heterozygosity. In contrast, fragmentation into a few, large subpopulations maintains heterozygosity at the expense of allelic richness. The strength of the trade-off between heterozygosity and allelic richness depends on the amount of gene flow and the frequency of gene flow events. Our results imply that the type of genetic diversity maintained among species living in strongly fluctuating environments will depend on the way populations fragment, with our results highlighting different mechanisms for maintaining allelic richness and heterozygosity in small, fragmented populations.

Long-term livestock exclusion increases plant richness and reproductive capacity in arid woodlands.

Herbivore exclusion is implemented globally to recover ecosystems from grazing by introduced and native herbivores, but evidence for large-scale biodiversity benefits is inconsistent in arid ecosystems. We examined the effects of livestock exclusion on dryland plant richness and reproductive capacity. We collected data on plant species richness and seeding (reproductive capacity), rainfall, vegetation productivity and cover, soil strength and herbivore grazing intensity from 68 sites across 6500 km2 of arid Georgina gidgee (Acacia georginae) woodlands in central Australia between 2018 and 2020. Sites were on an actively grazed cattle station and two destocked conservation reserves. We used structural equation modeling to examine indirect (via soil or vegetation modification) versus direct (herbivory) effects of grazing intensity by two introduced herbivores (cattle, camels) and a native herbivore (red kangaroo), on seasonal plant species richness and seeding of all plants, and the richness and seeding of four plant groups (native grasses, forbs, annual chenopod shrubs, and palatable perennial shrubs). Non-native herbivores had a strong indirect effect on plant richness and seeding by reducing vegetative ground cover, resulting in decreased richness and seeding of native grasses and forbs. Herbivores also had small but negative direct impacts on plant richness and seeding. This direct effect was explained by reductions in annual chenopod and palatable perennial shrub richness under grazing activity. Responses to grazing were herbivore-dependent; introduced herbivore grazing reduced native plant richness and seeding, while native herbivore grazing had no significant effect on richness or seeding of different plant functional groups. Soil strength decreased under grazing by cattle but not camels or kangaroos. Cattle had direct effects on palatable perennial shrub richness and seeding, whereas camels had indirect effects, reducing richness and seeding by reducing the abundance of shrubs. We show that considering indirect pathways improves evaluations of the effects of disturbances on biodiversity, as focusing only on direct effects can mask critical mechanisms of change. Our results indicate substantial biodiversity benefits from excluding livestock and controlling camels in drylands. Reducing introduced herbivore impacts will improve soil and vegetation condition, ensure reproduction and seasonal persistence of species, and protect native plant diversity.

Top-down response to spatial variation in productivity and bottom-up response to temporal variation in productivity in a long-term study of desert ants.

Under the Ecosystem Exploitation Hypothesis ecosystem productivity predicts trophic complexity, but it is unclear if spatial and temporal drivers of productivity have similar impacts. Long-term studies are necessary to capture temporal impacts on trophic structure in variable ecosystems such as deserts. We sampled ants and measured plant resources in the Simpson Desert, central Australia over a 22-year period, during which rainfall varied 10-fold. We sampled dune swales (higher nutrient) and crests (lower nutrient) to account for spatial variation in productivity. We asked how temporal and spatial variation in productivity affects the abundance of ant trophic guilds. Precipitation increased vegetation cover, with the difference more pronounced on dune crests; seeding and flowering also increased with precipitation. Generalist activity increased over time, irrespective of productivity. Predators were more active in more productive (swale) habitat, i.e. spatial impacts of productivity were greatest at the highest trophic level. By contrast, herbivores (seed harvesters and sugar feeders) increased with long-term rainfall; seed harvesters also increased as seeding increased. Temporal impacts of productivity were therefore greatest for low trophic levels. Whether productivity variation leads to top-down or bottom-up structured ecosystems thus depends on the scale and dimension (spatial or temporal) of productivity.

Characterising the spatiotemporal dynamics of drought and wet events in Australia.

Global climate change has altered precipitation patterns and disrupted the characteristics of drought and rainfall events. Climate projections confirm that more frequent, intense, and extreme droughts and rainfall events will continue. However, knowledge around how drought and wet events move dynamically through space and time is limited, especially in the southern hemisphere. Australia is the driest inhabited continent, renowned as the land of droughts and flooding rains, but recent climate-driven changes to the severity of wildfires and floods have garnered global attention. Here we used S-TRACK, a novel method for spatial drought tracking, to build pathways for past drought and wet events in Australia to examine their spatiotemporal dynamics. Characteristics such as duration, severity, and intensity were obtained from these pathways, and modified Mann-Kendall tests and Sen's slope were used to detect significant trends in characteristics over time. Drought conditions in southern Australia have intensified, particularly in the southwest of Australia and Tasmania, while the north of the country is experiencing longer, more severe, and more intense wet conditions. We also found that the location of drought and wet hotspots has clearly shifted in response to precipitation changes since the 1970's. Finally, pathways for the most extreme events show peak severity is reached in the middle to late stages of pathways, and that the largest drought and wet areas of a pathway have moved further west in recent times. The findings in this study provide the necessary knowledge to improve preparedness for extreme precipitation events as they become more common and to inform predictions for agricultural output or the extent of other climate events such as wildfires and flooding.

Night of the hunter: using cameras to quantify nocturnal activity in desert spiders.

Invertebrates dominate the animal world in terms of abundance, diversity and biomass, and play critical roles in maintaining ecosystem function. Despite their obvious importance, disproportionate research attention remains focused on vertebrates, with knowledge and understanding of invertebrate ecology still lacking. Due to their inherent advantages, usage of camera traps in ecology has risen dramatically over the last three decades, especially for research on mammals. However, few studies have used cameras to reliably detect fauna such as invertebrates or used cameras to examine specific aspects of invertebrate ecology. Previous research investigating the interaction between wolf spiders (Lycosidae: Lycosa spp.) and the lesser hairy-footed dunnart (Sminthopsis youngsoni) found that camera traps provide a viable method for examining temporal activity patterns and interactions between these species. Here, we re-examine lycosid activity to determine whether these patterns vary with different environmental conditions, specifically between burned and unburned habitats and the crests and bases of sand dunes, and whether cameras are able to detect other invertebrate fauna. Twenty-four cameras were deployed over a 3-month period in an arid region in central Australia, capturing 2,356 confirmed images of seven invertebrate taxa, including 155 time-lapse images of lycosids. Overall, there was no clear difference in temporal activity with respect to dune position or fire history, but twice as many lycosids were detected in unburned compared to burned areas. Despite some limitations, camera traps appear to have considerable utility as a tool for determining the diel activity patterns and habitat use of larger arthropods such as wolf spiders, and we recommend greater uptake in their usage in future.

Impact of 2019-2020 mega-fires on Australian fauna habitat.

Australia's 2019-2020 mega-fires were exacerbated by drought, anthropogenic climate change and existing land-use management. Here, using a combination of remotely sensed data and species distribution models, we found these fires burnt ~97,000 km2 of vegetation across southern and eastern Australia, which is considered habitat for 832 species of native vertebrate fauna. Seventy taxa had a substantial proportion (>30%) of habitat impacted; 21 of these were already listed as threatened with extinction. To avoid further species declines, Australia must urgently reassess the extinction vulnerability of fire-impacted species and assist the recovery of populations in both burnt and unburnt areas. Population recovery requires multipronged strategies aimed at ameliorating current and fire-induced threats, including proactively protecting unburnt habitats.

Ecological forecasts to inform near-term management of threats to biodiversity.

Ecosystems are being altered by rapid and interacting changes in natural processes and anthropogenic threats to biodiversity. Uncertainty in historical, current and future effectiveness of actions hampers decisions about how to mitigate changes to prevent biodiversity loss and species extinctions. Research in resource management, agriculture and health indicates that forecasts predicting the effects of near-term or seasonal environmental conditions on management greatly improve outcomes. Such forecasts help resolve uncertainties about when and how to operationalize management. We reviewed the scientific literature on environmental management to investigate whether near-term forecasts are developed to inform biodiversity decisions in Australia, a nation with one of the highest recent extinction rates across the globe. We found that forecasts focused on economic objectives (e.g. fisheries management) predict on significantly shorter timelines and answer a broader range of management questions than forecasts focused on biodiversity conservation. We then evaluated scientific literature on the effectiveness of 484 actions to manage seven major terrestrial threats in Australia, to identify opportunities for near-term forecasts to inform operational conservation decisions. Depending on the action, between 30% and 80% threat management operations experienced near-term weather impacts on outcomes before, during or after management. Disease control, species translocation/reintroduction and habitat restoration actions were most frequently impacted, and negative impacts such as increased species mortality and reduced recruitment were more likely than positive impacts. Drought or dry conditions, and rainfall, were the most frequently reported weather impacts, indicating that near-term forecasts predicting the effects of low or excessive rainfall on management outcomes are likely to have the greatest benefits. Across the world, many regions are, like Australia, becoming warmer and drier, or experiencing more extreme rainfall events. Informing conservation decisions with near-term and seasonal ecological forecasting will be critical to harness uncertainties and lower the risk of threat management failure under global change.

Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793.

The taxonomic status and systematic nomenclature of the Australian dingo remain contentious, resulting in decades of inconsistent applications in the scientific literature and in policy. Prompted by a recent publication calling for dingoes to be considered taxonomically as domestic dogs (Jackson et al. 2017, Zootaxa 4317, 201-224), we review the issues of the taxonomy applied to canids, and summarise the main differences between dingoes and other canids. We conclude that (1) the Australian dingo is a geographically isolated (allopatric) species from all other Canis, and is genetically, phenotypically, ecologically, and behaviourally distinct; and (2) the dingo appears largely devoid of many of the signs of domestication, including surviving largely as a wild animal in Australia for millennia. The case of defining dingo taxonomy provides a quintessential example of the disagreements between species concepts (e.g., biological, phylogenetic, ecological, morphological). Applying the biological species concept sensu stricto to the dingo as suggested by Jackson et al. (2017) and consistently across the Canidae would lead to an aggregation of all Canis populations, implying for example that dogs and wolves are the same species. Such an aggregation would have substantial implications for taxonomic clarity, biological research, and wildlife conservation. Any changes to the current nomen of the dingo (currently Canis dingo Meyer, 1793), must therefore offer a strong, evidence-based argument in favour of it being recognised as a subspecies of Canis lupus Linnaeus, 1758, or as Canis familiaris Linnaeus, 1758, and a successful application to the International Commission for Zoological Nomenclature - neither of which can be adequately supported. Although there are many species concepts, the sum of the evidence presented in this paper affirms the classification of the dingo as a distinct taxon, namely Canis dingo.

Animal movements in fire-prone landscapes.

Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire-prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer-term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire-prone ecosystems.

Understanding selective predation: Are energy and nutrients important?

For generalist predators, a mixed diet can be advantageous as it allows individuals to exploit a potentially broad range of profitable food types. Despite this, some generalist predators show preferences for certain types of food and may forage selectively in places or at times when these foods are available. One such species is the lesser hairy-footed dunnart (Sminthopsis youngsoni). Usually considered to be a generalist insectivore, in the Simpson Desert, Australia, this small marsupial predator has been found to selectively consume wolf spiders (Family Lycosidae), for reasons yet unknown. Here, we tested whether lycosids have relatively high energy or nutrient contents compared to other invertebrates, and hence whether these aspects of food quality can explain selective predation of lycosids by S. youngsoni. Energy, lipid and protein composition of representatives of 9 arthropod families that are eaten by S. youngsoni in the Simpson Desert were ascertained using microbomb calorimetry, chloroform-methanol extraction and Dumas combustion, respectively. Although lycosids contained a high proportion of energy and nutrients, they were not found to yield statistically greater amounts of these food components than many other available arthropod prey that are not selected by S. youngsoni. Our results therefore suggest that alternative factors may be more influential in shaping dietary selection in this marsupial predator, such as high rates of encounter between lycosids and S. youngsoni.

Assessing the potential for intraguild predation among taxonomically disparate micro-carnivores: marsupials and arthropods.

Interspecific competition may occur when resources are limited, and is often most intense between animals in the same ecological guild. Intraguild predation (IGP) is a distinctive form of interference competition, where a dominant predator selectively kills subordinate rivals to gain increased access to resources. However, before IGP can be identified, organisms must be confirmed as members of the same guild and occur together in space and time. The lesser hairy-footed dunnart (Sminthopsis youngsoni, Dasyuridae) is a generalist marsupial insectivore in arid Australia, but consumes wolf spiders (Lycosa spp., Lycosidae) disproportionately often relative to their availability. Here, we test the hypothesis that this disproportionate predation is a product of frequent encounter rates between the interactants due to high overlap in their diets and use of space and time. Diet and prey availability were determined using direct observations and invertebrate pitfall trapping, microhabitat use by tracking individuals of both species-groups, and temporal activity using spotlighting and camera traps. Major overlap (greater than 75% similarity) was found in diet and temporal activity, and weaker overlap in microhabitat use. Taken together, these findings suggest reasonable potential, for the first time, for competition and intraguild predation to occur between taxa as disparate as marsupials and spiders.

Biodiversity responds to increasing climatic extremes in a biome-specific manner.

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.

Top predators constrain mesopredator distributions.

Top predators can suppress mesopredators by killing them, competing for resources and instilling fear, but it is unclear how suppression of mesopredators varies with the distribution and abundance of top predators at large spatial scales and among different ecological contexts. We suggest that suppression of mesopredators will be strongest where top predators occur at high densities over large areas. These conditions are more likely to occur in the core than on the margins of top predator ranges. We propose the Enemy Constraint Hypothesis, which predicts weakened top-down effects on mesopredators towards the edge of top predators' ranges. Using bounty data from North America, Europe and Australia we show that the effects of top predators on mesopredators increase from the margin towards the core of their ranges, as predicted. Continuing global contraction of top predator ranges could promote further release of mesopredator populations, altering ecosystem structure and contributing to biodiversity loss.

75 years of dryland science: Trends and gaps in arid ecology literature.

Growth in the publication of scientific articles is occurring at an exponential rate, prompting a growing need to synthesise information in a timely manner to combat urgent environmental problems and guide future research. Here, we undertake a topic analysis of dryland literature over the last 75 years (8218 articles) to identify areas in arid ecology that are well studied and topics that are emerging. Four topics-wetlands, mammal ecology, litter decomposition and spatial modelling, were identified as 'hot topics' that showed higher than average growth in publications from 1940 to 2015. Five topics-remote sensing, climate, habitat and spatial, agriculture and soils-microbes, were identified as 'cold topics', with lower than average growth over the survey period, but higher than average numbers of publications. Topics in arid ecology clustered into seven broad groups on word-based similarity. These groups ranged from mammal ecology and population genetics, broad-scale management and ecosystem modelling, plant ecology, agriculture and ecophysiology, to populations and paleoclimate. These patterns may reflect trends in the field of ecology more broadly. We also identified two broad research gaps in arid ecology: population genetics, and habitat and spatial research. Collaborations between population genetics and ecologists and investigations of ecological processes across spatial scales would contribute profitably to the advancement of arid ecology and to ecology more broadly.

Desert mammal populations are limited by introduced predators rather than future climate change.

Climate change is predicted to place up to one in six species at risk of extinction in coming decades, but extinction probability is likely to be influenced further by biotic interactions such as predation. We use structural equation modelling to integrate results from remote camera trapping and long-term (17-22 years) regional-scale (8000 km2) datasets on vegetation and small vertebrates (greater than 38 880 captures) to explore how biotic processes and two key abiotic drivers influence the structure of a diverse assemblage of desert biota in central Australia. We use our models to predict how changes in rainfall and wildfire are likely to influence the cover and productivity of the dominant vegetation and the impacts of predators on their primary rodent prey over a 100-year timeframe. Our results show that, while vegetation cover may decline due to climate change, the strongest negative effect on prey populations in this desert system is top-down suppression from introduced predators.

Spatial and temporal synchrony in reptile population dynamics in variable environments.

Resources are seldom distributed equally across space, but many species exhibit spatially synchronous population dynamics. Such synchrony suggests the operation of large-scale external drivers, such as rainfall or wildfire, or the influence of oasis sites that provide water, shelter, or other resources. However, testing the generality of these factors is not easy, especially in variable environments. Using a long-term dataset (13-22 years) from a large (8000 km(2)) study region in arid Central Australia, we tested firstly for regional synchrony in annual rainfall and the dynamics of six reptile species across nine widely separated sites. For species that showed synchronous spatial dynamics, we then used multivariate follow a multivariate auto-regressive state-space (MARSS) models to predict that regional rainfall would be positively associated with their populations. For asynchronous species, we used MARSS models to explore four other possible population structures: (1) populations were asynchronous, (2) differed between oasis and non-oasis sites, (3) differed between burnt and unburnt sites, or (4) differed between three sub-regions with different rainfall gradients. Only one species showed evidence of spatial population synchrony and our results provide little evidence that rainfall synchronizes reptile populations. The oasis or the wildfire hypotheses were the best-fitting models for the other five species. Thus, our six study species appear generally to be structured in space into one or two populations across the study region. Our findings suggest that for arid-dwelling reptile populations, spatial and temporal dynamics are structured by abiotic events, but individual responses to covariates at smaller spatial scales are complex and poorly understood.