Reid Tingley

Predicting species distributions for conservation decisions.

Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on-ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision-making contexts when used within a structured and transparent decision-making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of ‘translators’ between modellers and decision makers. We encourage species distribution modellers to get involved in real decision-making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.

Understanding co‐occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

Summary A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species’ and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co-occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co-occurrence data into a SDM. JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co-occurrence patterns into components describing shared environmental responses and residual patterns of co-occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia. Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co-occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities. Environmental and residual correlations estimated from JSDMs can help indicate whether co-occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.

Realized niche shift during a global biological invasion.

Significance Species’ distributions result from dispersal and physiological constraints, interactions with other species, and ultimately, evolution. Biological invasions result from the deliberate or accidental movement of species between regions they would not reach through natural dispersal and can cause major conservation, economic, and human health issues. However, invasions also provide fascinating insights into species’ distribution limits. We investigate the invasion of the cane toad from South America to Australia by comparing the results of two modeling approaches: one considering physiological constraints and the other considering the joint influences of physiology, dispersal, and biotic interactions. Our findings demonstrate that the cane toad is limited in its native distribution by biotic interactions but, in Australia, is free to fill its climatic potential. Accurate forecasts of biological invasions are crucial for managing invasion risk but are hampered by niche shifts resulting from evolved environmental tolerances (fundamental niche shifts) or the presence of novel biotic and abiotic conditions in the invaded range (realized niche shifts). Distinguishing between these kinds of niche shifts is impossible with traditional, correlative approaches to invasion forecasts, which exclusively consider the realized niche. Here we overcome this challenge by combining a physiologically mechanistic model of the fundamental niche with correlative models based on the realized niche to study the global invasion of the cane toad Rhinella marina. We find strong evidence that the success of R. marina in Australia reflects a shift in the species’ realized niche, as opposed to evolutionary shifts in range-limiting traits. Our results demonstrate that R. marina does not fill its fundamental niche in its native South American range and that areas of niche unfilling coincide with the presence of a closely related species with which R. marina hybridizes. Conversely, in Australia, where coevolved taxa are absent, R. marina largely fills its fundamental niche in areas behind the invasion front. The general approach taken here of contrasting fundamental and realized niche models provides key insights into the role of biotic interactions in shaping range limits and can inform effective management strategies not only for invasive species but also for assisted colonization under climate change.

Smart Moves: Effects of Relative Brain Size on Establishment Success of Invasive Amphibians and Reptiles

Brain size relative to body size varies considerably among animals, but the ecological consequences of that variation remain poorly understood. Plausibly, larger brains confer increased behavioural flexibility, and an ability to respond to novel challenges. In keeping with that hypothesis, successful invasive species of birds and mammals that flourish after translocation to a new area tend to have larger brains than do unsuccessful invaders. We found the same pattern in ectothermic terrestrial vertebrates. Brain size relative to body size was larger in species of amphibians and reptiles reported to be successful invaders, compared to species that failed to thrive after translocation to new sites. This pattern was found in six of seven global biogeographic realms; the exception (where relatively larger brains did not facilitate invasion success) was Australasia. Establishment success was also higher in amphibian and reptile families with larger relative brain sizes. Future work could usefully explore whether invasion success is differentially associated with enlargement of specific parts of the brain (as predicted by the functional role of the forebrain in promoting behavioural flexibility), or with a general size increase (suggesting that invasion success is facilitated by enhanced perceptual and motor skills, as well as cognitive ability).

Statistical approaches to account for false-positive errors in environmental DNA samples.

Environmental DNA (eDNA) sampling is prone to both false‐positive and false‐negative errors. We review statistical methods to account for such errors in the analysis of eDNA data and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false‐positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability and false‐positive rates. We advocate alternative approaches to account for false‐positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false‐positive errors. We illustrate the advantages of these approaches over ad hoc classifications of detections and provide practical advice and code for fitting these models in maximum likelihood and Bayesian frameworks. Given the severe bias induced by false‐negative and false‐positive errors, the methods presented here should be more routinely adopted in eDNA studies.

When trends intersect: The challenge of protecting freshwater ecosystems under multiple land use and hydrological intensification scenarios

Intensification of the use of natural resources is a world-wide trend driven by the increasing demand for water, food, fibre, minerals and energy. These demands are the result of a rising world population, increasing wealth and greater global focus on economic growth. Land use intensification, together with climate change, is also driving intensification of the global hydrological cycle. Both processes will have major socio-economic and ecological implications for global water availability. In this paper we focus on the implications of land use intensification for the conservation and management of freshwater ecosystems using Australia as an example. We consider this in the light of intensification of the hydrologic cycle due to climate change, and associated hydrological scenarios that include the occurrence of more intense hydrological events (extreme storms, larger floods and longer droughts). We highlight the importance of managing water quality, the value of providing environmental flows within a watershed framework and the critical role that innovative science and adaptive management must play in developing proactive and robust responses to intensification. We also suggest research priorities to support improved systemic governance, including adaptation planning and management to maximise freshwater biodiversity outcomes while supporting the socio-economic objectives driving land use intensification. Further research priorities include: i) determining the relative contributions of surface water and groundwater in supporting freshwater ecosystems; ii) identifying and protecting freshwater biodiversity hotspots and refugia; iii) improving our capacity to model hydro-ecological relationships and predict ecological outcomes from land use intensification and climate change; iv) developing an understanding of long term ecosystem behaviour; and v) exploring systemic approaches to enhancing governance systems, including planning and management systems affecting freshwater outcomes. A major policy challenge will be the integration of land and water management, which increasingly are being considered within different policy frameworks.

Establishment Success of Introduced Amphibians Increases in the Presence of Congeneric Species

Darwin’s naturalization hypothesis predicts that the success of alien invaders will decrease with increasing taxonomic similarity to the native community. Alternatively, shared traits between aliens and the native assemblage may preadapt aliens to their novel surroundings, thereby facilitating establishment (the preadaptation hypothesis). Here we examine successful and failed introductions of amphibian species across the globe and find that the probability of successful establishment is higher when congeneric species are present at introduction locations and increases with increasing congener species richness. After accounting for positive effects of congeners, residence time, and propagule pressure, we also find that invader establishment success is higher on islands than on mainland areas and is higher in areas with abiotic conditions similar to the native range. These findings represent the first example in which the preadaptation hypothesis is supported in organisms other than plants and suggest that preadaptation has played a critical role in enabling introduced species to succeed in novel environments.

Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader

Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental variables (water depth, rainfall, ambient temperature) were not clearly correlated with detection probabilities estimated via trapping, whereas eDNA detection probabilities were negatively correlated with water depth, possibly reflecting higher eDNA concentrations at lower water levels. Our findings demonstrate that eDNA sampling can be an order of magnitude more sensitive than traditional methods, and illustrate that traditional- and eDNA-based surveys can provide independent information on species distributions when occupancy surveys are conducted over short timescales.

Detecting extinction risk from climate change by IUCN red list criteria

Anthropogenic climate change is a key threat to global biodiversity. To inform strategic actions aimed at conserving biodiversity as climate changes, conservation planners need early warning of the risks faced by different species. The IUCN Red List criteria for threatened species are widely acknowledged as useful risk assessment tools for informing conservation under constraints imposed by limited data. However, doubts have been expressed about the ability of the criteria to detect risks imposed by potentially slow-acting threats such as climate change, particularly because criteria addressing rates of population decline are assessed over time scales as short as 10 years. We used spatially explicit stochastic population models and dynamic species distribution models projected to future climates to determine how long before extinction a species would become eligible for listing as threatened based on the IUCN Red List criteria. We focused on a short-lived frog species (Assa darlingtoni) chosen specifically to represent potential weaknesses in the criteria to allow detailed consideration of the analytical issues and to develop an approach for wider application. The criteria were more sensitive to climate change than previously anticipated; lead times between initial listing in a threatened category and predicted extinction varied from 40 to 80 years, depending on data availability. We attributed this sensitivity primarily to the ensemble properties of the criteria that assess contrasting symptoms of extinction risk. Nevertheless, we recommend the robustness of the criteria warrants further investigation across species with contrasting life histories and patterns of decline. The adequacy of these lead times for early warning depends on practicalities of environmental policy and management, bureaucratic or political inertia, and the anticipated species response times to management actions.

Desiccation Risk Drives the Spatial Ecology of an Invasive Anuran (Rhinella marina) in the Australian Semi-Desert

Some invasive species flourish in places that impose challenges very different from those faced in their native geographic ranges. Cane toads (Rhinella marina) are native to tropical and subtropical habitats of South and Central America, but have colonised extremely arid regions over the course of their Australian invasion. We radio-tracked 44 adult cane toads at a semi-arid invasion front to investigate how this invasive anuran has managed to expand its geographic range into arid areas that lie outside of its native climatic niche. As predicted from their low physiological control over rates of evaporative water loss, toads selected diurnal shelter sites that were consistently cooler and damper (and thus, conferred lower water loss rates) than nearby random sites. Desiccation risk also had a profound influence on rates of daily movement. Under wet conditions, toads that were far from water moved further between shelter sites than did conspecifics that remained close to water, presumably in an attempt to reach permanent water sources. However, this relationship was reversed under dry conditions, such that only toads that were close to permanent water bodies made substantial daily movements. Toads that were far from water bodies also travelled along straighter paths than did conspecifics that generally remained close to water. Thus, behavioural flexibility—in particular, an ability to exploit spatial and temporal heterogeneity in the availability of moist conditions—has allowed this invasive anuran to successfully colonize arid habitats in Australia. This finding illustrates that risk assessment protocols need to recognise that under some circumstances an introduced species may be able to thrive in conditions far removed from any that it experiences in its native range.