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Biomes are large‐scale ecosystems occupying large spaces. The biome concept should theoretically facilitate scientific synthesis of global‐scale studies of the past, present, and future biosphere. However, there is neither a consensus biome map nor universally accepted definition of terrestrial biomes, making joint interpretation and comparison of biome‐related studies difficult. "Desert," "rainforest," "tundra," "grassland," or "savanna," while widely used terms in common language, have multiple definitions and no universally accepted spatial distribution. Fit‐for‐purpose classification schemes are necessary, so multiple biome‐mapping methods should for now co‐exist. In this review, we compare biome‐mapping methods, first conceptually, then quantitatively. To facilitate the description of the diversity of approaches, we group the extant diversity of past, present, and future global‐scale biome‐mapping methods into three main families that differ by the feature captured, the mapping technique, and the nature of observation used: (1) compilation biome maps from expert elicitation, (2) functional biome maps from vegetation physiognomy, and (3) simulated biome maps from vegetation modeling. We design a protocol to measure and quantify spatially the pairwise agreement between biome maps. We then illustrate the use of such a protocol with a real‐world application by investigating the potential ecological drivers of disagreement between four broadly used, modern global biome maps. In this example, we quantify that the strongest disagreement among biome maps generally occurs in landscapes altered by human activities and moderately covered by vegetation. Such disagreements are sources of bias when combining several biome classifications. When aiming to produce realistic biome maps, biases could be minimized by promoting schemes using observations rather than predictions, while simultaneously considering the effect of humans and other ecosystem engineers in the definition. Throughout this review, we provide comparison and decision tools to navigate the diversity of approaches to encourage a more effective use of the biome concept. [ABSTRACT FROM AUTHOR]

Water extraction and climate change are altering the availability of surface water globally, thereby contributing to amphibian population declines. The managed delivery of water to benefit environmental values (environmental watering) is a promising conservation technique that can support amphibian recruitment and maintain viable populations. Environmental water can be delivered in various spatial patterns and with different frequencies, but comparing the effectiveness of competing strategies is complicated by variable and interactive environmental processes. We built a spatially explicit, stochastic, hydroecological metapopulation model to compare the effects of five environmental‐watering scenarios on the probability of persistence of threatened southern bell frogs (Litoria raniformis) in a major river reach in southern Australia. We compared a no‐intervention control to two managed watering frequencies (moderate and frequent) delivered in two spatial designs (managed wetlands grouped or spread across the reach). More frequent water provision to intervention sites improved the reach‐wide (metapopulation) probability of persistence, and spreading intervention sites across the reach improved persistence more than grouping intervention sites together. When re‐examined under severe drought conditions, L. raniformis had a 0.04 probability of persistence without intervention, which improved to 0.56 with high watering frequency. Model‐guided environmental water provision can improve reach‐wide persistence of amphibian metapopulations by guiding spatial and temporal delivery patterns to reduce the risk of extinction. [ABSTRACT FROM AUTHOR]

The biosphere is changing rapidly due to human endeavour. Because ecological communities underlie networks of interacting species, changes that directly affect some species can have indirect effects on others. Accurate tools to predict these direct and indirect effects are therefore required to guide conservation strategies. However, most extinction‐risk studies only consider the direct effects of global change—such as predicting which species will breach their thermal limits under different warming scenarios—with predictions of trophic cascades and co‐extinction risks remaining mostly speculative. To predict the potential indirect effects of primary extinctions, data describing community interactions and network modelling can estimate how extinctions cascade through communities. While theoretical studies have demonstrated the usefulness of models in predicting how communities react to threats like climate change, few have applied such methods to real‐world communities. This gap partly reflects challenges in constructing trophic network models of real‐world food webs, highlighting the need to develop approaches for quantifying co‐extinction risk more accurately. We propose a framework for constructing ecological network models representing real‐world food webs in terrestrial ecosystems and subjecting these models to co‐extinction scenarios triggered by probable future environmental perturbations. Adopting our framework will improve estimates of how environmental perturbations affect whole ecological communities. Identifying species at risk of co‐extinction (or those that might trigger co‐extinctions) will also guide conservation interventions aiming to reduce the probability of co‐extinction cascades and additional species losses. [ABSTRACT FROM AUTHOR]

Species interactions play a fundamental role in ecosystems. However, few ecological communities have complete data describing such interactions, which is an obstacle to understanding how ecosystems function and respond to perturbations. Because it is often impractical to collect empirical data for all interactions in a community, various methods have been developed to infer interactions. Machine learning is increasingly being used for making interaction predictions, with random forest being one of the most frequently used of these methods. However, performance of random forest in inferring predator‐prey interactions in terrestrial vertebrates and its sensitivity to training data quality remain untested. We examined predator–prey interactions in two diverse, primarily terrestrial vertebrate classes: birds and mammals. Combining data from a global interaction dataset and a specific community (Simpson Desert, Australia), we tested how well random forest predicted predator–prey interactions for mammals and birds using species' ecomorphological and phylogenetic traits. We also tested how variation in training data quality – manipulated by removing records and switching interaction records to non‐interactions – affected model performance. We found that random forest could predict predator–prey interactions for birds and mammals using ecomorphological or phylogenetic traits, correctly predicting up to 88 and 67% of interactions and non‐interactions in the global and community‐specific datasets, respectively. These predictions were accurate even when there were no records in the training data for focal species. In contrast, false non‐interactions for focal predators in training data strongly degraded model performance. Our results demonstrate that random forest can identify predator–prey interactions for birds and mammals that have few or no interaction records. Furthermore, our study provides guidance on how to prepare training data to optimise machine learning classifiers for predicting species interactions, which could help ecologists 1) address knowledge gaps and explore network‐related questions in data‐poor situations, and 2) predict interactions for range‐expanding species. [ABSTRACT FROM AUTHOR]

The regulation of river systems alters hydrodynamics and often reduces lateral connectivity between river channels and floodplains. For taxa such as frogs that rely on floodplain wetlands to complete their life cycle, decreasing inundation frequency can reduce recruitment and increase the probability of local extinction. We virtually reconstructed the inundation patterns of wetlands under natural and regulated flow conditions and built stochastic population models to quantify the probability of local extinction under different inundation scenarios. Specifically, we explored the interplay of habitat size, inundation frequency, and successive dry years on the local extinction probability of the threatened southern bell frog Litoria raniformis in the Murray River floodplains of South Australia. We hypothesized that the changes to wetland inundation resulting from river regulation are driving L. raniformis declines in this semiarid system. Regulation has reduced the inundation frequency of essential habitats below critical thresholds for the persistence of many fresh water‐dependent species. Successive dry years raise the probability of local extinction, and these effects are strongest in smaller wetlands. Larger wetlands and those with more frequent average inundation are less susceptible to these effects. Elucidating these trends informs the prioritization of intervention sites and the frequency of conservation interventions. Environmental water provision (through pumping or the operation of flow‐regulating structures) is a promising tool to reduce the probability of breeding failure and local extinction. Our modeling approach can be used to prioritize the delivery of environmental water to L. raniformis and potentially many other frog species. [ABSTRACT FROM AUTHOR]

Extinctions stemming from environmental change often trigger trophic cascades and coextinctions. Bottom–up cascades occur when changes in the primary producers in a network elicit flow‐on effects to higher trophic levels. However, it remains unclear what determines a species' vulnerability to bottom–up cascades and whether such cascades were a large contributor to the megafauna extinctions that swept across several continents in the Late Pleistocene. The pathways to megafauna extinctions are particularly unclear for Sahul (landmass comprising Australia and New Guinea), where extinctions happened earlier than on other continents. We investigated the potential role of bottom–up trophic cascades in the megafauna extinctions in Late Pleistocene Sahul by first developing synthetic networks that varied in topology to identify how network position (trophic level, diet breadth, basal connections) influences vulnerability to bottom–up cascades. We then constructed pre‐extinction (~80 ka) network models of the ecological community of Naracoorte, south‐eastern Sahul, to assess whether the observed megafauna extinctions could be explained by bottom–up cascades. Synthetic networks showed that node vulnerability to bottom–up cascades decreased with increasing trophic level, diet breadth and basal connections. Extinct species in the Naracoorte community were more vulnerable overall to these cascades than were species that survived. The position of extinct species in the network – tending to be of low trophic level and therefore having relatively narrow diet breadths and fewer connections to plants – made them vulnerable. However, these species also tended to have few or no predators, a network‐position attribute that suggests they might have been particularly vulnerable to new predators. Together, these results suggest that trophic cascades and naivety to predators could have contributed to the megafauna extinction event in Sahul. [ABSTRACT FROM AUTHOR]

Feral cats are some of the most destructive invasive predators worldwide, particularly in insular environments; hence, density‐reduction campaigns are often applied to alleviate the predation mortality they add to native fauna. Density‐reduction and eradication efforts are costly procedures with important outcomes for native fauna recovery, so they require adequate planning to be successful. These plans should include empirical density‐reduction models that can guide yearly culling quotas, and resource roll‐out for the duration of the culling period. This ensures densities are reduced over the long term and that resources are not wasted. We constructed a stochastic population model with cost estimates to test the relative effectiveness and cost‐efficiency of two main culling scenarios for a 10‐year eradication campaign of cats on Kangaroo Island, Australia: (a) constant proportional annual cull (one‐phase), and (b) high initial culling followed by a constant proportional maintenance cull (two‐phase). A one‐phase cull of at least 0.35 of the annual population size would reduce the final population to 0.1 of its original size, while a two‐phase cull with an initial cull of minimum 0.6 and minimum 0.5 maintenance cull would reduce the final population to 0.01 of its initial size within the 10‐year time frame. Cost estimates varied widely depending on the methods applied (shooting, trapping, aerial poison baits, Felixer™ poison‐delivery system), but using baiting, trapping and Felixers with additional shooting to meet culling quotas was the most cost‐effective combination (minimum cost: AU$19.56 million; range: AU$16.87 million–AU$20.69 million). Our model provides an adaptable and general assessment tool for cat reductions in Australia and potentially elsewhere, and provides relative culling costs for the Kangaroo Island campaign specifically. [ABSTRACT FROM AUTHOR]

Aim: Correlative species distribution models (SDMs) are typically trained using only the contemporary distribution of species; however, recent records might reflect an incomplete description of a species' niche, limiting the reliability of predictions. SDMs linking fossil records have the potential to improve conservation decisions under human‐induced climate change. Here, we built SDMs using presence records from contemporary and Holocene records to enable estimations of climatically suitable area under current and future climate scenarios. Location: Aotearoa New Zealand Taxon: Tuatara, Sphenodon punctatus Methods: For an evolutionary relict found in Aotearoa New Zealand, the tuatara (Sphenodon punctatus), we built SDMs using presence records from contemporary and Holocene records to estimate climatically suitable area under current and future climate scenarios. We also use our detailed knowledge of the Holocene distribution and remnant populations to examine niche shifts following the arrival of humans and associated introduction of mammalian predators. To build SDMs, we use presence records from four sources: (a) remnant populations, (b) radiocarbon‐dated fossil deposits from the Holocene, (c) other fossil deposits containing tuatara bones of Holocene age and iv) islands from which tuatara are known or highly likely to have become extinct. Results: We found shifts in the niche of tuatara due to niche unfilling. Incorporating locations of Holocene deposits and/or all past locations in SDMs led to larger areas of climatically suitable area being identified compared to SDMs derived from remnant populations only. Using all presence records, under climate change projections for 2090, climatically suitable area increased slightly. However, many areas retain potential as translocation sites (e.g. northern South Island), some areas become unsuitable (e.g. inland Canterbury) and/or involve extrapolation into novel climates (e.g. Northland). Main Conclusion: SDMs incorporating locations of Holocene deposits and/or all past locations identified areas of critical habitat for tuatara under current and future climate scenarios, that would not have been identified using contemporary occurrences only. Our results highlight the need to consider past locations when assessing habitat suitability for conservation translocations, both for tuatara and other relict species. [ABSTRACT FROM AUTHOR]

In its invasive range in Australia, the European rabbit threatens the persistence of native flora and fauna and damages agricultural production. Understanding its distribution and ecological niche is critical for developing management plans to reduce populations and avoid further biodiversity and economic losses.We developed an ensemble of species distribution models (SDMs) to determine the geographic range limits and habitat suitability of the rabbit in Australia. We examined the advantage of incorporating data collected by citizens (separately and jointly with expert data) and explored issues of spatial biases in occurrence data by implementing different approaches to generate pseudo‐absences. We evaluated the skill of our model using three approaches: cross‐validation, out‐of‐region validation, and evaluation of the covariate response curves according to expert knowledge of rabbit ecology.Combining citizen and expert occurrence data improved model skill based on cross‐validation, spatially reproduced important aspects of rabbit ecology, and reduced the need to extrapolate results beyond the studied areas.Our ensemble model projects that rabbits are distributed across approximately two thirds of Australia. Annual maximum temperatures >25°C and annual minimum temperatures >10°C define, respectively, the southern and northern most range limits of its distribution. In the arid and central regions, close access to permanent water (≤~ 0.4 km) and reduced clay soil composition (~20%–50%) were the major factors influencing the probability of occurrence of rabbits.Synthesis and applications. Our results show that citizen science data can play an important role in managing invasive species by providing missing information on occurrences in regions not surveyed by experts because of logistics or financial constraints. The additional sampling effort provided by citizens can improve the capacity of SDMs to capture important elements of a species ecological niche, improving the capacity of statistical models to accurately predict the geographic range of invasive species. [ABSTRACT FROM AUTHOR]

The koala's Phascolarctos cinereus distribution is currently restricted to eastern and south‐eastern Australia. However, fossil records dating from 70 ± 4 ka (ka = 103 yr) from south‐western Australia and the Nullarbor Plain are evidence of subpopulation extinctions in the southwest at least after the Last Interglacial (~128–116 ka). We hypothesize that koala sub‐population extinctions resulted from the eastward retraction of the koala's main browse species in response to unsuitable climatic conditions. We further posit a general reduction in the distribution of main koala‐browse trees in the near future in response climate change. We modelled 60 koala‐browse species and constructed a set of correlative species distribution models for five time periods: Last Interglacial (~128–116 ka), Last Glacial Maximum (~23–19 ka), Mid‐Holocene (~7–5 ka), present (interpolations of observed data, representative of 1960–1990), and 2070. We based our projections on five hindcasts and one forecast of climatic variables extracted from WorldClim based on two general circulation models (considering the most pessimistic scenario of high greenhouse‐gas emissions) and topsoil clay fraction. We used 17 dates of koala fossil specimens identified as reliable from 70 (± 4) to 535 (± 49) ka, with the last appearance of koalas at 70 ka in the southwest. The main simulated koala‐browse species were at their greatest modelled extent of suitability during the Last Glacial Maximum, with the greatest loss of koala habitat occurring between the Mid‐Holocene and the present. We predict a similar habitat loss between the present and 2070. The spatial patterns of habitat change support our hypothesis that koala extinctions in the southwest, Nullarbor Plain and central South Australia resulted from the eastward retraction of the dominant koala‐browse species in response to long‐term climate changes. Future climate patterns will likely increase the extinction risk of koalas in their remaining eastern ranges. [ABSTRACT FROM AUTHOR]

Abstract: The current distribution of species, environmental conditions and their interactions represent only one snapshot of a planet that is continuously changing, in part due to human influences. To distinguish human impacts from natural factors, the magnitude and pace of climate shifts, since the Last Glacial Maximum, are often used to determine whether patterns of diversity today are artefacts of past climate change. In the absence of high‐temporal resolution palaeoclimate reconstructions, this is generally done by assuming that past climate change occurred at a linear pace between widely spaced (usually, ≥1,000 years) climate snapshots. We show here that this is a flawed assumption because regional climates have changed significantly across decades and centuries during glacial–interglacial cycles, likely causing rapid regional replacement of biota. We demonstrate how recent atmosphere‐ocean general circulation model (AOGCM) simulations of the climate of the past 21,000 years can provide credible estimates of the details of climate change on decadal to centennial timescales, showing that these details differ radically from what might be inferred from longer timescale information. High‐temporal resolution information can provide more meaningful estimates of the magnitude and pace of climate shifts, the location and timing of drivers of physiological stress, and the extent of novel climates. They also produce new opportunities to directly investigate whether short‐term climate variability is more important in shaping biodiversity patterns rather than gradual changes in long‐term climatic means. Together, these more accurate measures of past climate instability are likely to bring about a better understanding of the role of palaeoclimatic change and variability in shaping current macroecological patterns in many regions of the world. [ABSTRACT FROM AUTHOR]

It has been difficult to access projections of global-scale climate change with high temporal resolution spaning the late Pleistocene and Holocene. This has limited our ability to discern how climate fluctuations have affected species' range dynamics and extinction processes, turn-over in ecological communities and changes in genetic diversity. PaleoView is a new freeware tool, which provides a comprehensive but easy-to-use way to generate and view paleoclimate data at temporal and spatial resolutions suitable for detecting biotic responses to major climate shifts since the last glacial maximum. Regional to global scale simulations of temperature, precipitation, humidity and mean sea level pressure can be generated from PaleoView as gridded or time series data at time intervals as short as a decade for any period during the last 21 000 yr. They can be viewed using a built-in geographical user interface or saved as data files. Modelled climate reconstructions are based on daily simulation output from the Community Climate System Model ver. 3 (CCSM3). This global coupled atmosphere-ocean-sea ice-land general circulation model accurately reproduces major climatic features associated with the most recent deglaciation event, and predicts present-day patterns of climate conditions with verified hindcast skill. By providing a portal for readily accessing climate reconstructions at high temporal resolutions, PaleoView can help to better establish the consequences of past climate fluctuations on macro-ecological patterns of biological and genetic diversity. [ABSTRACT FROM AUTHOR]

To conserve future biodiversity, a better understanding of the likely effects of climate and land-use change on the geographical distributions of species and the persistence of ecological communities is needed. Recent advances have integrated population dynamic processes into species distribution models ( SDMs), to reduce potential biases in predictions and to better reflect the demographic nuances of incremental range shifts. However, there is no clear framework for selecting the most appropriate demographic-based model for a given data set or scientific question., We review the computer-based modelling platforms currently used for the development of either population- or individual-based species range dynamics models. We describe the features and requirements of 20 software platforms commonly used to generate simulations of species ranges and abundances. We classify the platforms according to particular capabilities or features that account for user requirements and constraints, such as (i) ability to simulate simple to complex population dynamics, (ii) organism specificity or (iii) their computational capacities., Using this classification, we develop a protocol for choosing the most appropriate framework for modelling species range dynamics based in data availability and research requirements. We find that the main differences between modelling platforms are related to the way in which they simulate population dynamics, the type of organisms they are able to model and the ecological processes they incorporate. We show that some platforms can be used as generic modelling software to investigate a broad range of ecological questions related to the range dynamics of most species, and how these are likely to change in the future in response to forecast climate and land-use change. We argue that model predictions will be improved by reducing usage to a smaller number of highly flexible freeware platforms., Our approach provides ecologists and conservation biologists with a clear method for selecting the most appropriate software platform that meets their needs when developing SDMs coupled with population-dynamic processes. We argue that informed tool choice will translate to better predictions of species responses to climate and land-use change and improved conservation management. [ABSTRACT FROM AUTHOR]

Recent efforts to incorporate migration processes into species distribution models ( SDMs) are allowing assessments of whether species are likely to be able to track their future climate optimum and the possible causes of failing to do so. Here, we projected the range shift of European beech over the 21st century using a process-based SDM coupled to a phenomenological migration model accounting for population dynamics, according to two climate change scenarios and one land use change scenario. Our model predicts that the climatically suitable habitat for European beech will shift north-eastward and upward mainly because (i) higher temperature and precipitation, at the northern range margins, will increase survival and fruit maturation success, while (ii) lower precipitations and higher winter temperature, at the southern range margins, will increase drought mortality and prevent bud dormancy breaking. Beech colonization rate of newly climatically suitable habitats in 2100 is projected to be very low (1-2% of the newly suitable habitats colonised). Unexpectedly, the projected realized contraction rate was higher than the projected potential contraction rate. As a result, the realized distribution of beech is projected to strongly contract by 2100 (by 36-61%) mainly due to a substantial increase in climate variability after 2050, which generates local extinctions, even at the core of the distribution, the frequency of which prevents beech recolonization during more favourable years. Although European beech will be able to persist in some parts of the trailing edge of its distribution, the combined effects of climate and land use changes, limited migration ability, and a slow life-history are likely to increase its threat status in the near future. [ABSTRACT FROM AUTHOR]

Aim Despite the recent improvements made in species distribution models ( SDMs), assessing species' ability to migrate fast enough to track their climate optimum remains a challenge. This study achieves this goal and demonstrates the reliability of a process-based SDM to provide accurate projections by simulating the post-glacial colonization of European beech. Location Europe. Methods We simulated the post-glacial colonization of European beech over the last 12,000 years by coupling a process-based SDM ( PHENOFIT) and a new migration model based on Gibbs point processes, both parameterized with modern ecological data. Simulations were compared with palaeoarchives and phylogeographic data on European beech. Results Model predictions are consistent with palaeoarchives and phylogeographic data over the Holocene. The results suggest that post-glacial expansion of European beech was limited by climate on its north-eastern leading edge, while limited by its migration abilities on its north-western leading edge. The results show a mean migration rate of beech varying from 270 m yr −1 to 280 m yr−1 and a maximum migration rate varying from 560 m yr−1 to 630 m yr−1, when limited and not limited by climate, respectively. They also highlight the relative contribution of known and suspected glacial refugia in present beech distribution and confirm the results of phylogeographic studies. Main conclusions For the first time, we were able to reproduce accurately the colonization dynamics of European beech during the last 12 kyr using a process-based SDM and a migration model, both parameterized with modern ecological data. Our methodology has allowed us to identify the different factors that affected European beech migration during its post-glaciation expansion in different parts of its range. This method shows great potential to help palaeobotanists and phylogeographers locate putative glacial refugia, and to provide accurate projections of beech distribution change in the future. [ABSTRACT FROM AUTHOR]