Environmental DNA (eDNA) surveys have become a popular tool for assessing the distribution of species. However, it is known that false positive and false negative observation error can occur at both stages of eDNA surveys, namely the field sampling stage and laboratory analysis stage. We present an RShiny app that implements the Griffin et al. (2020) statistical method, which accounts for false positive

Remnant trees and forest fragments in agricultural landscapes can be important sources of propagules to facilitate forest recovery. However, many studies simply quantify forest cover in the surrounding landscape as a percentage, with little attention given to species composition, and subsequently fail to detect an effect on recruitment patterns. We assessed the relative importance of the spatial distribution

Understanding how species ranges shift as climates rapidly change informs us how to effectively conserve vulnerable species. Species distribution models (SDMs) are an important method for examining these range shifts. The tools for performing SDMs are ever improving. Here, we present the megaSDM R package. This package facilitates realistic spatiotemporal SDM analyses by incorporating dispersal probabilities

The large-scale conversion of natural mangroves to aquaculture reduces species richness and diversity. Large areas of abandoned aquaculture ponds in areas where mangroves formerly predominated in China and southeast Asia represent important potential effective targets for mangrove restoration. Here, we empirically assessed the α-diversity (species richness) and β-diversity (variation in community composition)

Although contemporary climate has been identified as one of the major determinants of large-scale species diversity patterns, its effect on species diversity greatly varies among clades. Understanding the drivers of the variation in species diversity–climate relationships (DCRs) across clades, which is critical for developing general mechanisms underlying the effects of climate on species diversity

Introduction of species by humans breaks down biogeographic boundaries and results in the homogenization of species composition, yet empirical tests of this impact in marine forest ecosystems are still scarce. Large-scale planting aimed at reversing losses of mangroves has been the dominant strategy for mangrove restoration adopted by many organizations in the past decades, but there is a lack of quantitative

Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSFs) or spatially extensive locational data without individual

Species are not uniformly distributed across the landscape. For every species, there should be few favoured sites where abundance is high and many other sites of lower suitability where abundance is low. Consequently, local abundance could be thought of as a natural expression of species response to local conditions. The correlation between abundance and environmental suitability has been well documented

Dispersal is one of the most important drivers of community assembly. Understanding how dispersal impacts spatial variations in community composition (beta diversity) is crucial for predicting biodiversity change during the Anthropocene. Classic theories and a large amount of empirical evidence have led to a common belief that increasing dispersal rate should lead to regional community homogenization

Biological invasions are one of the most defining features of the Anthropocene. Most studies on biological invasions focus on the later stages of the invasion process, that is after species have already become naturalized. It is frequently overlooked, however, that patterns in origin, phylogeny and traits of naturalized alien species might largely reflect which species have been introduced in the first

The aim of the GARPTools package is to provide tools to prepare data for input into the desktop version of the genetic algorithm for rule-set prediction (GARP), for the evaluation of the accuracy of output models, and for summary/examination of environmental coverages used in GARP rule sets for best models in an experiment. GARP is a software package for biodiversity and ecological research that allows

Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling

Cities are considered hotspots of biological invasions, yet it remains unclear why non-indigenous species are so successful in environments that most local native species do not tolerate. Here, we explore the intriguing possibility that humans may be unintentionally introducing species preadapted to persist in such environments. Combining data on historical introductions with information of avian assemblages

Understanding the key mechanisms that control northern treelines is important to accurately predict biome shifts and terrestrial feedbacks to climate. At a global scale, it has long been observed that elevational and latitudinal treelines occur at similar mean growing season air temperature (GSAT) isotherms, inspiring the growth limitation hypothesis (GLH) that cold GSAT limits aboveground growth of

Farmers' use of fungicides and insecticides constitutes a major threat to biodiversity that is also endangering agriculture itself. Landscapes could be designed to take advantage of the dependencies of pests, pathogens and their natural enemies on elements of the landscape. Yet the complexity of the interactions makes it difficult to establish general rules. In our study, we sought to characterize

Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and

Process-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability

Determining population growth across large scales is difficult because it is often impractical to collect data at large scales and over long timespans. Instead, the growth of a population is often only measured at a small, plot-level scale and then extrapolated to derive a mean field estimate. However, this approach is prone to error since it simplifies spatial processes such as the neighbourhood effects

Phylogenetic turnover has emerged as a powerful tool to identify the mechanisms by which biological communities assemble. When significantly structured along environmental gradients, phylogenetic turnover evidences phylogenetic niche conservatism, a critical principle explaining patterns of species distributions at different spatio–temporal scales. Here, we quantify the contribution of geographic and

Metacommunity ecology currently lacks a consistent functional trait perspective across trophic levels. To foster new cross-taxa experiments and field studies, we present hypotheses on how three trait dimensions change along gradients of density of individuals, resource supply and habitat isolation. The movement dimension refers to the ability to move and navigate in space, the tolerance dimension addresses

Accurately predicting the distribution of emerging invasive species is crucial for early detection and eradication. While ecological niche models are often used to forecast invasions, such models are limited when invasive populations of a species have realized niches that differ from native populations, or when invasive populations are not at equilibrium. One technique to potentially overcome these

The current erosion of biodiversity is a major concern that threatens the ecological integrity of ecosystems and the ecosystem services they provide. Due to global change, an increasing proportion of river networks are drying and changes from perennial to non-perennial flow regimes represent dramatic ecological shifts with potentially irreversible alterations of community and ecosystem dynamics. However

The time that animals spend travelling at various speeds and the tortuosity of their movement paths are two of the many things that affect space-use by animals. In this, high turn rates are predicted to be energetically costly, especially at high travel speeds, which implies that animals should modulate their speed according to path characteristics. When animals move so as to maximize distance and

Presence-only data are typical occurrence information used in species distribution modelling. Data may be originated from different sources, and their integration is a challenging exercise in spatial ecology as detection biases are rarely fully considered. We propose a new protocol for presence-only data fusion, where information sources include social media platforms, to investigate several possible

Animals follow specific movement patterns and search strategies to maximize encounters with essential resources (e.g. prey, favourable habitat) while minimizing exposures to suboptimal conditions (e.g. competitors, predators). While describing spatiotemporal patterns in animal movement from tracking data is common, understanding the associated search strategies employed continues to be a key challenge

A fundamental goal of scientific research is to identify the underlying variables that govern crucial processes of a system. This is especially difficult in ecology, which is intrinsically rich in candidate predictors. An efficient statistical procedure to evaluate the relative importance of predictors in regression models is highly desirable. However, previous studies criticised the most universally

Habitat loss and fragmentation reduce biodiversity and alter species composition in local communities. β diversity describes the variation in species composition between or among communities in fragmented landscapes and has two components: species turnover and nestedness. In this study, we assessed β diversity of ant assemblages on 24 island fragments in the Thousand Island Lake, China. We constructed

The potential for megafauna restoration is unevenly distributed across the world, along with the socio-political capacity of countries to support these restoration initiatives. We show that choosing a recent baseline to identify species' indigenous range puts a higher burden for megafauna restoration on countries in the Global South, which also have less capacity to support these restoration initiatives

The midpoint attractor (MPA) models of species richness integrate a unimodal environmental favourability gradient and neutral effects forced by geometric constraints and thus extend the ecologically neutral mid-domain model. However, both alternative MPA algorithms assume that underlying environmental favourability peaks within the modelling domain. Here, we used elevational distribution data for 1054

Conservation planning involves identifying and selecting actions to best achieve objectives for managing natural, social and cultural resources. Conservation problems are often high dimensional when specified as combinatorial or portfolio problems and when multiple competing objectives are considered at varying spatial and temporal scales. Although analytical techniques such as modern portfolio theory

Niche conservatism is the hypothesis that a species' niche remains stable in space and time. This concept is central to understanding phenomena ranging from the role of climate change impacts on species biogeography to community dynamics. Marine zooplankton have been used as indicators of global change in the ocean, and niche conservatism is usually assumed for these organisms due to their high dispersal

Megaherbivores (adult body mass > 1000 kg) are suggested to disproportionately shape ecosystem and Earth system functioning. We systematically reviewed the empirical basis for this general thesis and for the more specific hypotheses that 1) megaherbivores have disproportionately larger effects on Earth system functioning than their smaller counterparts, 2) this is true for all extant megaherbivore

Natural perturbations, including hurricanes and severe droughts, are becoming more frequent and intense in the tropics, yet our understanding of forest responses to these events is still limited. While the relationships between extreme climatic events and tree mortality are frequently studied, responses of trees that survived such perturbations have been rarely reported. Perturbations and their effects

Identifying physical and ecological boundaries that limit where species can occur is important for predicting how those species will respond to global change. The island of Borneo encompasses a wide range of habitats that support some of the highest richness on Earth, making it an ideal location for investigating ecological mechanisms underlying broad patterns of species distribution. We tested variation

Willows (Salix) are some of the most abundant shrubs in cold alpine and tundra biomes. In alpine regions, seed dispersal is not limiting upwards willow expansion, so the upslope shift of willow shrublines is assumed to be a response to climatic warming. Very little, however, is known about the recent spatiotemporal dynamics of alpine willow shrublines. The world's highest willow shrublines (ca 4900

The paleotropics harbor many biodiversity hotspots and show many different species richness patterns. However, it remains unclear which factors are the most important in directly shaping richness patterns among regions in the paleotropics (i.e. diversification rates, colonization times, and dispersal frequency). Here we used Cycadaceae as a model system to test the causes of regional richness patterns

The idea that several small, rather than a single large, habitat areas should hold the highest total species richness (the so-called SLOSS debate) brings into question the importance of habitat fragmentation to extinction risk. SLOSS studies are generally addressed over a short time scale, potentially ignoring the long-term dimension of extinction risk. Here, we provide the first long-term evaluation

Rewilding is gaining importance across Europe, as agricultural abandonment trajectories provide opportunities for large-scale ecosystem restoration. However, its effective implementation is hitherto limited, in part due to a lack of monitoring of rewilding interventions and their interactions. Here, we provide a first assessment of rewilding progress across seven European sites. Using an iterative

Kelp forests are highly productive coastal habitats that serve as biodiversity hotspots and provide valuable ecosystem services. Despite being one the largest marine biomes, kelp forests have been drastically understudied relative to other marine systems. Notably, while the role of kelp as habitat-forming, or ‘foundation species', is well-documented, a comprehensive understanding of kelp forest food

Endothermic organisms typically maintain high and relatively constant body temperatures in the face of environmental variation by regulating their metabolic and water loss rates in conjunction with behavioural and postural adjustments. A mechanistic understanding of these processes provides a perspective of the fundamental niches of endotherms by quantifying their energy and water requirements, restrictions

Coastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi-enclosed system that experiences hypoxia in deeper waters which occasionally shoals onto shallow coral reefs, suffocating most aerobic benthic life. To explore the long-term history of reefs in

Macroecological relationships provide insights into rules that govern ecological systems. Bergmann's rule posits that members of the same clade are larger at colder temperatures. Whether temperature drives this relationship is debated because several other potential drivers covary with temperature. We conducted a near-global comparative analysis on marine copepods (97 830 samples, 388 taxa) to test

The digitization of museum collections as well as an explosion in citizen science initiatives has resulted in a wealth of data that can be useful for understanding the global distribution of biodiversity, provided that the well-documented biases inherent in unstructured opportunistic data are accounted for. While traditionally used to model imperfect detection using structured data from systematic

Maintaining the diversity of wild bees is a priority for preserving ecosystem function and promoting stability and productivity of agroecosystems. However, wild bee communities face many threats and beekeeping could be one of them, because honey bees may have a strong potential to outcompete wild pollinators when placed at high densities. Yet, we still know little about how beekeeping intensity affects

Temperature and productivity appear as universal positive large-scale correlates of species richness. However, the strength and the shape of species–temperature (STR) and species–productivity (SPR) relationships vary widely, and the causes of this variation are poorly known. We analysed 1) published species richness data for multiple taxa sampled in various regions and 2) different clades within vertebrate

Climate-driven changes in phenology have widespread effects on ecological interactions and species' abundances. Most predictions of changes in phenology and the consequences for ecology and conservation are based on research in temperate systems. Climate-driven changes in phenology are largely undocumented in subtropical regions, which host much of the world's biodiversity. Factors important to regulating

Ecological communities are assembled in a spatial–temporal continuum. However, we still have a poor understanding of the relative importance of different mechanisms structuring community composition (i.e. beta-diversity) in space and time. In this study, we start by introducing a conceptual model that capitalizes upon the core-occasional species concept to predict that the assembly process in tropical

How communities assemble is a central and fundamental question in ecology. However, it has been mired by conflicting conclusions about whether community assembly is driven by environmental filtering, biotic interactions, and/or dispersal processes. Elevational gradients provide an ideal system for exploring the biotic and abiotic forces influencing the processes of community assembly, as these both

A distribution with high spatial variability may impair the bet-hedging capacity of a population, threatening population sustainability. Although the association between aggregation and life history traits of a species (e.g. body size) has been documented, the relationship between aggregation and size within a population has rarely been explored. As selective over-fishing may induce size truncation

We are living in a time of rapid environmental changes caused by anthropogenic pressures. Besides direct human exploitation of plant and animal populations and habitat transformation, biodiversity changes in the Anthropocene are affected by less trivial processes including rapid spreading of non-native species, emergence of novel communities and modifications of ecosystem functioning due to changing

Although many studies have focused on the effects of the environment and area on local patterns of species richness, few studies have demonstrated how to reconcile the availability of more niches with smaller habitat areas in heterogeneous localities. Here, the environmental range that a species prefers was defined as a niche; a space was defined as an available space if the environmental range of

The amount of observational and specimen-based biodiversity data available to researchers is increasing exponentially, yet the ability to manage and cite large, complex biodiversity datasets lags behind. This management and citation gap impedes reproducibility for data users and the ability for data publishers to track use and accumulate use citations, ultimately harming the longer-term sustainability

Indirect effects resulting from species sharing the same enemy can shape spatio-temporal variations in species occurrence. The strength of such effects remains poorly known in natural communities composed of species from different trophic levels interacting in heterogeneous landscapes. Benefiting from a well-known arctic vertebrate community and marked spatio-temporal variations in the density of key

The theory of island biogeography postulates that size and isolation are key drivers of biodiversity on islands. This theory has been applied not only to true (e.g. oceanic) islands but also to terrestrial island-like systems (e.g. edaphic islands). Recently, a debate has opened as to whether terrestrial island-like systems function like true islands. However, identifying the effect of insularity in

Maintaining functional connectivity is critical for the long-term conservation of wildlife populations. Landscape genomics provides an opportunity to assess long-term functional connectivity by relating environmental variables to spatial patterns of genomic variation resulting from generations of movement, dispersal and mating behaviors. Identifying landscape features associated with gene flow at large

Effective assessments of the current status of biodiversity conservation are needed to support planning, policy and action, from local to global levels. Of particular use would be well documented, reproducible methods based on openly accessible data and tools. Such methods should provide an accurate estimate of the state of conservation of diversity, identifying gaps in current conservation systems

Retreating glaciers, icons of climate change, release new potential habitats for both aquatic and terrestrial organisms. High-elevation species are threatened by temperature increases and the upward migration of lowlands species. Improving our understanding of successional processes after glacier retreat becomes urgent, especially in the tropics, where glacier shrinkage is particularly fast. We examined

Disturbances, such as wildfires, are one of the main drivers of biodiversity dynamics, and their frequency and intensity are expected to increase due to global change. Such disturbances generate a mosaic of affected and unaffected patches that change landscape structure and, consequently, metacommunity networks. Therefore, to fully understand the consequences of such disturbances, a landscape perspective

The context-depency of biological invasions makes it difficult to understand why some species become succesfull invaders and others not. Such understanding requires studying closely-related invasive and non-invasive alien taxa sharing the same introduction history in the same environment. We identified this unusual situation in Kenya where the individuals that founded invasive Prosopis juliflora and

The island species area relationship (ISAR) is an important tool for measuring variation in species diversity in variety of insular systems, from true-island archipelagoes to fragmented terrestrial landscapes. However, it suffers from several limitations. For example, due to the sample-area effect, positive relationships between species and area cannot be directly interpreted as evidence for deterministic