Biodiversity decline and climate change are among the most important environmental issues society faces. Information to address these issues has benefited from increasing big data, advances in cloud computing, and subsequent new tools for analytics. Accessing such tools is streamlined by virtual laboratories for ecological analysis, like the ‘Biodiversity and Climate Change Virtual Laboratory’ (BCCVL) and ‘ecocloud’. These platforms help reduce time and effort spent on developing programming skills, data acquisition and curation, plus model building. Recently this functionality was extended, producing EcoCommons Australia—a web-based ecological modeling platform for environmental problem-solving—with upgraded infrastructure and improved ensemble modeling, post-model analysis, workflow transparency and reproducibility. We outline our user-centered approach to systems design, from initial surveys of stakeholder needs to user involvement in testing, and collaboration with specialists. We illustrate EcoCommons and compare model evaluation statistics through four case studies, highlighting how the modular platform meets users' needs.

The tropics harbour the highest species number on Earth, making them critical hotspots of biodiversity. However, there is an increased extinction risk towards the tropics, aka the tropical biodiversity crisis. Today, biodiversity loss is considered the main threat humanity faces. Yet, key locations may act as refugia (areas that ensure the persistence of biodiversity under environmental changes). Here, we used a set of five environmental variables (elevation, maximum temperature of the warmest month, temperature annual range, annual precipitation, and the human footprint index) to quantify the main drivers of extinction risk inside and outside protected areas for 7609 species of terrestrial animals and vascular plants distributed across Mexico. We used ordinal logistic regressions to assess drivers of extinction risk, as defined by the IUCN Red List, and evaluate the impact of the existing network of protected areas across Mexico to lower this risk. Outside protected areas, extinction risk was the highest for mammals and the lowest for reptiles. Protected areas had a positive impact by lowering the extinction risk of birds compared to outside these areas, while the opposite was observed for mammals, reptiles, vascular plants, amphibians, and arthropods. Extinction risk was greater in regions with high annual precipitation, high maximum temperature of the warmest month, low temperature annual range, as well as in areas with high elevations and human pressures on the environement. The network of protected areas in Mexico is crucial for the conservation of biodiversity; however, this network requires revision that accounts for climate change scenarios to better protect regions facing the greatest risks.

Human domination of landscapes is a key driver of biodiversity loss, with the fingerprint of climate change becoming increasingly pronounced. Frameworks and tools for identifying threats to biodiversity are required to meet Post-2020 Global Biodiversity Framework targets for 2030 that call for, among other things, reducing or halting species extinction rates ( 1 ). Hence, we compiled a phylogenetic tree for terrestrial tetrapods, mapped hotspots of geographically restricted and evolutionarily distinct lineages, and identified which hotspots may simultaneously face the highest magnitudes of land use impacts and climate change. Across a quarter of Earth’s surface, hotspots contain the entire ranges of 45% of tetrapods, representing 39% of terrestrial tetrapod evolutionary heritage. By 2070, we estimate 8–13% of this heritage to occur entirely within hotspots highly exposed to climate change, with 13–29% of hotspots projected to experience high exposure to both stressors simultaneously. Most hotspots at highest risk occur in countries least able to take action. Our analysis highlights the need for global ambition and coordination to avoid catastrophic loss of tetrapod evolutionary heritage.

Protected areas are the primary strategy for maintaining natural landscapes and separating biodiversity features from preventable anthropogenic threats. The Convention on Biological Diversity calls for the coverage of at least 17% of land by protected areas, and the strategic prioritization of important biodiversity areas. Using the spatially explicit reserve design software, Marxan, this study combines climate refugia modelled under future climates in the year 2070 and bioregions to identify priority sites for protected area expansion under climate change in the state of New South Wales (NSW), Australia. Priority sites for new protected areas that meet bioregion and climate refugia targets were identified in central-western, northeast and patches of southeast NSW. Seven existing parks, including Kosciuszko National Park, overlapped with regions identified repeatedly as climate refugia under 12 future climate scenarios. The recommendations from this study support policy-makers in prioritizing the protection of biodiversity under a changing and uncertain climate.

Climate change threatens the health and survival of urban trees and the various benefits they deliver to urban inhabitants. Here, we show that 56% and 65% of species in 164 cities across 78 countries are currently exceeding temperature and precipitation conditions experienced in their geographic range, respectively. We assessed 3,129 tree and shrub species, using three metrics related to climate vulnerability: exposure, safety margin and risk. By 2050 under Representative Concentration Pathway 6.0, 2,387 (76%) and 2,220 (70%) species will be at risk from projected changes in mean annual temperature and annual precipitation, respectively. Risk is predicted to be greatest in cities at low latitudes—such as New Delhi and Singapore—where all urban tree species are vulnerable to climate change. These findings aid the evaluation of the impacts of climate change to secure long-term benefits provided by urban forests. Assessing 3,129 species of trees and shrubs found in 164 global urban areas shows that over half of the species currently experience non-ideal climates. They project increases in risk due to climate change by 2050 and highlight cities where all species are at risk.

Trait-based invasiveness studies typically categorize exotic species as invasive or noninvasive, implicitly assuming species form two homogenous groups. However, species can become invasive in different ways (e.g., high abundance, fast spread), likely relying on different functional traits to do so. As such, binary classification may obscure traits associated with invasiveness. We tested whether (1) the way in which invasiveness is quantified influences its correlation with functional traits and (2) different demography-based metrics are related to different sets of traits. Using a case study of 251 herbs exotic to Victoria, Australia, we quantified species' invasiveness using 10 metrics: four continuous, demography-based dimensions of invasiveness (spread rate, local abundance, geographic and environmental range sizes) and six binary classifications of invasiveness (based on alternative sources and invasion criteria). We examined the correlation between species' invasiveness and a set of four traits known to relate to plant demography and invasion. Then, we examined whether different demographic dimensions of invasiveness were better explained by different sets of traits. We found that the way invasiveness was quantified was important: different traits were linked with different invasiveness metrics, and some traits showed opposite effects across metrics. Species with fast spread were either tall with small seeds (i.e., good colonizers), or had heavy, animal-dispersed seeds. Plants with a large environmental range had greater plasticity for some traits. Locally abundant plants had low SLA and heavy seeds (i.e., strong competitors). Animal dispersal was also key to reach a large geographic range. No traits were consistently related to the six binary classifications. Our results indicate that exotic plants are invasive in different ways and rely on different combinations of traits to be so. Some traits (e.g., seed mass) had complex relationships with invasion: they apparently promote, hampered, or had no influence on different dimensions of invasiveness. Our findings are consistent with the notion that plant species use strategies that may be near optimal under some, but not all, ecological conditions. Compared to binary classifications of invasiveness, the use of invasiveness dimensions advances clearer hypothesis testing in invasion science.

The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionality was later added for model selection and simulation from ENMs, and the software package has been quite widely used. ENMTools was initially implemented as a Perl script, which was also compiled into an executable file for various platforms. However, the package had a number of significant limitations; it was only designed to fit models using Maxent, it relied on a specific Perl distribution to function, and its internal structure made it difficult to maintain and expand. Subsequently, the R programming language became the platform of choice for most ENM studies, making ENMTools less usable for many practitioners. Here we introduce a new R version of ENMTools that implements much of the functionality of its predecessor as well as numerous additions that simplify the construction, comparison and evaluation of niche models. These additions include new metrics for model fit, methods of measuring ENM overlap, and methods for testing evolutionary hypotheses. The new version of ENMTools is also designed to work within the expanding universe of R tools for ecological biogeography, and as such includes greatly simplified interfaces for analyses from several other R packages.

Urban forests (i.e. all vegetation present in urban areas), provide environmental and socioeconomic benefits[1][1] to more than half of the global population[2][2]. Projected climate change threatens these benefits to society[3][3]–[5][4]. Here, we assess vulnerability to climate change of 16,006 plant species present in the urban forests of 1,010 cities within 93 countries, using three vulnerability metrics: exposure, safety margin and risk. Exposure expresses the magnitude of projected changes in climate in a given area, safety margin measures species’ sensitivity to climate change, and risk is the difference between exposure and safety margin[6][5]. We identified 9,676 (60.5%) and 8,344 (52.1%) species exceeding their current climatic tolerance (i.e. safety margin) for mean annual temperature (MAT) and annual precipitation (AP), respectively. By 2050, 13,479 (84.2%) and 9,960 (62.2%) species are predicted to be at risk from projected changes in MAT and AP, respectively, with risk increasing in cities at lower latitudes. Our results can aid evaluation of the impacts of climate change on urban forests and identify the species most at risk. Considering future climates when selecting species for urban plantings will enhance the long-term societal benefits provided by urban forests, including their contribution to mitigating the magnitude and impacts of climate change.### Competing Interest StatementThe authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-5 [5]: #ref-6

Conservation strategies based on charismatic flagship species, such as tigers, lions, and elephants, successfully attract funding from individuals and corporate donors. However, critics of this species-focused approach argue it wastes resources and often does not benefit broader biodiversity. If true, then the best way of raising conservation funds excludes the best way of spending it. Here we show that this conundrum can be resolved, and that the flagship species approach does not impede cost-effective conservation. Through a tailored prioritization approach, we identify places containing flagship species while also maximizing global biodiversity representation (based on 19,616 terrestrial and freshwater species). We then compare these results to scenarios that only maximized biodiversity representation, and demonstrate that our flagship-based approach achieves 79−89% of our objective. This provides strong evidence that prudently selected flagships can both raise funds for conservation and help target where these resources are best spent to conserve biodiversity.

Knowledge of threatened species' distributions is essential for effective conservation decision-making. Species distribution models (SDMs) are widely used to map species' geographic ranges, identify new areas of suitable habitat and guide field surveys. In New South Wales (NSW), Australia, there are grave doubts about whether populations of the critically endangered long-footed potoroo (Potorous longipes) remain extant, and identification of occupied sites is a high priority for its conservation. We used an SDM (Maxent) to identify regions in NSW that may have suitable habitat for the potoroo. The SDM was built with seven climate layers and had strong predictive performance (cross-validated AUC = 0.94). We then combined this information on habitat suitability with vegetation and topography, to identify 58 survey sites across NSW. From April 2016 to May 2017, we undertook six field trips deploying six to eight cameras at each site for 52-63 days, resulting in 25 120 camera trap nights. A total of 215 759 images captured 43 native and feral animal species, but no long-footed potoroos. Following the survey, newly available, independent presence and absence data were used to validate our model. A Kruskal-Wallis H test indicated that habitat suitability values were significantly higher at presence locations than absence locations (H = 58.66, d.f. = 1, P < 0.001). Finally, we refitted the Maxent model with the new data and identified additional regions that future surveys could explore. We conclude, however, that if the long-footed potoroo remains extant in NSW, it is extremely rare.

Tephritid fruit flies are among the most destructive horticultural pests posing risks to Australia's multi-billion-dollar horticulture industry. Currently, there are 11 pest fruit fly species of economic concern in Australia. Of these, nine are native to this continent (Bactrocera aquilonis, B. bryoniae, B. halfordiae, B. jarvisi, B. kraussi, B. musae, B. neohumeralis, B. tryoni and Zeugodacus cucumis), while B. frauenfeldi and Ceratitis capitata are introduced. To varying degrees these species are costly to Australia's horticulture through in-farm management, monitoring to demonstrate pest freedom, quarantine and trade restrictions, and crop losses. Here, we used a common species distribution model, Maxent, to assess climate suitability for these 11 species under baseline (1960-1990) and future climate scenarios for Australia. Projections indicate that the Wet Tropics is likely to be vulnerable to all 11 species until at least 2070, with the east coast of Australia also likely to remain vulnerable to multiple species. While the Cape York Peninsula and Northern Territory are projected to have suitable climate for numerous species, extrapolation to novel climates in these areas decreases confidence in model projections. The climate suitability of major horticulture areas currently in eastern Queensland, southern-central New South Wales and southern Victoria to these pests may increase as climate changes. By highlighting areas at risk of pest range expansion in the future our study may guide Australia's horticulture industry in developing effective monitoring and management strategies.

Climate change threatens Earth's biodiversity, although its impacts are variable and depend on the capacity of species and ecosystems to cope with the magnitude and speed of change. Natural protected areas (NPAs) constitute potential refugia for species' persistence and for sustaining the provisioning of ecosystem services. Biosphere reserves are NPAs that are less altered by human actions and provide habitat to endemic, threatened or endangered species. Here, we aim to evaluate the threat imposed by climate change on the network of biosphere reserves in Mexico. Focusing on five bioclimatic variables, we computed the climatic space - measured as an n-dimensional hypervolume - of 40 NPAs. Increases in temperature are predicted for all NPAs by 2050, whereas decreases in annual rainfall are predicted for 30 NPAs. By 2050, 31 NPAs that provide habitat to 22,866 recorded species are predicted to lose 100% of their baseline climatic space, shifting to completely novel climates. On average, the other nine NPAs are predicted to lose 55.7% (SD = 26.7%) of their baseline climatic space, while 54.5% (SD = 32.5%) of the future climatic space will be novel. Seventeen NPAs may lose climate variability (homogenization), decreasing species' niches. The extent to which non-analogue conditions will remain within the tolerance of species and ecosystems is currently unknown. Finally, we propose a vulnerability index to categorise NPAs based on their loss of existing climatic space, total geographic area, species richness, and uniqueness of species composition, finding los Tuxtlas and Tiburon Ballena as the most and least vulnerable NPAs, respectively.

Globally, local governments are increasing investment in urban greening projects. However, there is little consideration of whether the species being planted will be resilient to climate change. We assessed the distribution of climatically suitable habitat, now and in the future, for 176 tree species native to Australia, commonly planted across Australia's Significant Urban Areas (SUAs) and currently grown by commercial nurseries. Species' occurrence records were obtained from inventories and herbaria, globally and across Australia, and combined with baseline climate data (WorldClim, 1960-1990) and six climate scenarios for 2030 and 2070 using climatic suitability models (CSMs). CSMs for each species were calibrated and projected onto baseline and future scenarios. We calculated changes in the size of climatically suitable habitat for each species across each SUA, and identified urban areas that are likely to have suitable climate for either fewer or more of our study species under future climate. By 2070, climatically suitable habitat in SUAs is predicted to decline for 73% of species assessed. For 18% of these species, climatically suitable area is predicted to be more than halved, relative to their baseline extent. Generally, for urban areas in cooler regions, climatically suitable habitat is predicted to increase. By contrast, for urban areas in warmer regions, a greater proportion of tree species may lose climatically suitable habitat. Our results highlight changing patterns of urban climatic space for commonly planted species, suggesting that local governments and the horticultural industry should take a proactive approach to identify new climate-ready species for urban plantings.

Climate refugia—areas that remain suitable for species during periods of climate disruption—have played an important role in species persistence over time. Identifying and protecting these refugia is a key climate change adaptation approach for conservation planning. To identify climate refugia for Australian tropical/sub-tropical rainforest flora, from the Last Glacial Maximum to 2070. Habitat suitability models were calibrated for 30 species using Maxent, and projected onto climate data for: Last Glacial Maximum (LGM, ~ 22,000 ybp); mid-Holocene (MH, ~ 6000 ybp); current period; and 2070. The intersection of suitable habitat over consecutive periods was assessed, identifying: current refugia (LGM–MH–Current); future refugia (Current–Future); and High Value Refugia (HVR, suitable over all four periods). Refugial hotspots (regions suitable for at least 15 species) were also identified. Suitable habitat was generally projected to span the greatest area in the current period. Four current refugial hotspots were identified: Wet Tropics, Central Mackay Coast, South Eastern Queensland, and North Coast (New South Wales). While suitable habitat for most species may decline in the future, HVRs will likely be retained for all species to at least 2070, although restricted in size. Future refugia was also projected in areas beyond species’ dispersal ranges. HVRs are highly important for the conservation of these rainforest species, given their generation times, limited dispersal capabilities and additional anthropogenic barriers to movement. This study assists in understanding long-term spatial shifts in rainforest flora in response to climate change and in designing future conservation strategies.

Environmental niche models (ENM) and species distribution models (SDM) are used to estimate species’ environmental niches and the distribution of suitable habitat. ENMs are used to aid conservation decisions and to study niche evolution. Investigators use metrics of niche breadth (Levins 1968, Mandle et al. 2010) to quantify the estimated geographic distribution of projected habitat suitability, or overlap to measure similarity between ENMs (Warren et al. 2008, 2010, Rödder and Engler 2011).

Climate change presents a substantial threat to species unable to keep pace via migration or adaptation. In-situ climate refugia, areas currently occupied by a species and that remain suitable in the future, will be vital for species with dispersal limitations. Ex-situ refugia, areas beyond species' current ranges that remain suitable, may facilitate range shifts or provide options for translocation. Assessing both refugia is a conservation priority. Here, we identify refugia for 319 species threatened in New South Wales, using four plausible scenarios describing futures that are Warmer/Wetter, Warmer/Drier, Hotter/Wetter and Hotter/Little Precipitation change, relative to the present. Using Maxent, we identify (a) in-situ refugia for each species under each scenario; (b) regions of consensus – areas projected as in-situ refugia across all scenarios; (c) hotspots of in-situ refugia (regions suitable for >1 species); and (d) regions of consensus for ex-situ refugia. Species were categorised based on the extent of in- and ex-situ refugia. By 2070, refugia will likely be broadest, and narrowest, under the Warmer/Wetter and Hotter/Wetter scenarios, respectively. East coast regions currently suitable for multiple species are unlikely to remain as hotspots. Most species (65%) are projected to have limited regions of consensus for either refugia. Translocation should be explored for species with little-to-no in-situ refugia, but for which ex-situ refugia exist. Management of existing populations will be critical for species with in-situ refugia but limited ex-situ. We highlight how management decisions based on agreement across climate scenarios can be made, irrespective of uncertainty about the magnitude of climate change.

Identification of refugia from climate change is increasingly considered important for biodiversity conservation, but the distribution of putative refugia may vary across alternative climate scenarios, impeding conservation decision‐making. Based on 117 plant species representative of ecoregions within south‐eastern Australia, we provide a case study identifying in situ refugia across a spectrum of plausible future climates. We define in situ refugia as areas that currently contain populations of the target species, and are projected to remain climatically suitable in the future. Refugia were identified across scenarios describing futures that are, relative to 1990–2009, warmer and wetter, warmer/drier, hotter/wetter, and hotter with little precipitation change. Despite substantial variation in the spatial extent and longevity of climate refugia across species, ecoregions and climate scenarios, clear patterns emerged. By 2070, refugia for species in 1) deserts and xeric shrublands; 2) mediterranean forests, woodlands and shrublands; and 3) temperate and tropical grasslands are likely to be least extensive under a hotter/wetter future. Conversely, wetter conditions may lead to broader refugia for species in temperate forests. We identified areas of congruence where high richness refugia (refugia for ≥ 50% of representative species) were projected to occur irrespective of the climate scenario. These regions therefore appear robust to uncertainty about climate change, presenting clear targets for conservation attention. Our approach provides valuable information for decision‐makers, enabling them to identify and visualise the spatial arrangement of refugia under contrasting scenarios of environmental change. This reveals management options in the context of climate uncertainty and facilitates informed prioritisation of conservation resources.