Author Correction: Environment and host as large-scale controls of ectomycorrhizal fungi.

Change history: In the HTML version of this Article, author 'Filipa Cox' had no affiliation in the author list, although she was correctly associated with affiliation 3 in the PDF. In addition, the blue circles for 'oak' were missing from Extended Data Fig. 1. These errors have been corrected online.

Environment and host as large-scale controls of ectomycorrhizal fungi.

Explaining the large-scale diversity of soil organisms that drive biogeochemical processes-and their responses to environmental change-is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is-to our knowledge-unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds for change across complex environmental gradients. We show the effect of 38 host, environment, climate and geographical variables on ectomycorrhizal diversity, and define thresholds of community change for key variables. We quantify host specificity and reveal plasticity in functional traits involved in soil foraging across gradients. We conclude that environmental and host factors explain most of the variation in ectomycorrhizal diversity, that the environmental thresholds used as major ecosystem assessment tools need adjustment and that the importance of belowground specificity and plasticity has previously been underappreciated.

Characterizing soundscapes across diverse ecosystems using a universal acoustic feature set.

Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labor-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we have developed a generalizable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolutional neural network to embed soundscapes from a variety of ecosystems into a common acoustic space. In both supervised and unsupervised modes, this allowed us to accurately quantify variation in habitat quality across space and in biodiversity through time. On the scale of seconds, we learned a typical soundscape model that allowed automatic identification of anomalous sounds in playback experiments, providing a potential route for real-time automated detection of irregular environmental behavior including illegal logging and hunting. Our highly generalizable approach, and the common set of features, will enable scientists to unlock previously hidden insights from acoustic data and offers promise as a backbone technology for global collaborative autonomous ecosystem monitoring efforts.

The Global Distribution and Drivers of Alien Bird Species Richness.

Alien species are a major component of human-induced environmental change. Variation in the numbers of alien species found in different areas is likely to depend on a combination of anthropogenic and environmental factors, with anthropogenic factors affecting the number of species introduced to new locations, and when, and environmental factors influencing how many species are able to persist there. However, global spatial and temporal variation in the drivers of alien introduction and species richness remain poorly understood. Here, we analyse an extensive new database of alien birds to explore what determines the global distribution of alien species richness for an entire taxonomic class. We demonstrate that the locations of origin and introduction of alien birds, and their identities, were initially driven largely by European (mainly British) colonialism. However, recent introductions are a wider phenomenon, involving more species and countries, and driven in part by increasing economic activity. We find that, globally, alien bird species richness is currently highest at midlatitudes and is strongly determined by anthropogenic effects, most notably the number of species introduced (i.e., "colonisation pressure"). Nevertheless, environmental drivers are also important, with native and alien species richness being strongly and consistently positively associated. Our results demonstrate that colonisation pressure is key to understanding alien species richness, show that areas of high native species richness are not resistant to colonisation by alien species at the global scale, and emphasise the likely ongoing threats to global environments from introductions of species.

Mediation of area and edge effects in forest fragments by adjacent land use.

Habitat loss, fragmentation, and degradation have pervasive detrimental effects on tropical forest biodiversity, but the role of the surrounding land use (i.e., matrix) in determining the severity of these impacts remains poorly understood. We surveyed bird species across an interior-edge-matrix gradient to assess the effects of matrix type on biodiversity at 49 different sites with varying levels of landscape fragmentation in the Brazilian Atlantic Forest-a highly threatened biodiversity hotspot. Both area and edge effects were more pronounced in forest patches bordering pasture matrix, whereas patches bordering Eucalyptus plantation maintained compositionally similar bird communities between the edge and the interior and exhibited reduced effects of patch size. These results suggest the type of matrix in which forest fragments are situated can explain a substantial amount of the widely reported variability in biodiversity responses to forest loss and fragmentation.

Mediación de los Efectos de Área y de Borde sobre los Fragmentos de Bosque Causados por el Uso de Suelo Adyacente Resumen La pérdida del hábitat, la fragmentación y la degradación tienen efectos nocivos generalizados sobre la biodiversidad de los bosques tropicales. A pesar de esto, el papel del uso de suelo de los terrenos adyacentes (es decir, la matriz) en la determinación de la gravedad de estos impactos todavía está poco entendido. Censamos las especies de aves a lo largo de un gradiente de borde interno de matriz para evaluar los efectos del tipo de matriz sobre la biodiversidad en al menos 49 sitios con diferentes niveles de fragmentación del paisaje en el Bosque Atlántico Brasileño - un punto caliente de biodiversidad que se encuentra severamente amenazado. Tanto los efectos de área como los de borde estuvieron más pronunciados en los fragmentos de bosque que limitan con la matriz de pasturas, mientras que los fragmentos que limitan con plantaciones de Eucalyptus mantuvieron comunidades de aves similares en composición con aquellas entre el borde y el interior y mostraron efectos reducidos del tamaño de fragmento. Estos resultados sugieren que el tipo de matriz en el cual están situados los fragmentos de bosque puede explicar una cantidad sustancial de la ampliamente reportada variabilidad de respuestas a la pérdida del bosque y a la fragmentación.

Trait-based indicators of bird species sensitivity to habitat loss are effective within but not across data sets.

Species' traits have been widely championed as the key to predicting which species are most threatened by habitat loss, yet previous work has failed to detect trends that are consistent enough to guide large-scale conservation and management. Here we explore whether traits and environmental variables predict species sensitivity to habitat loss across two data sets generated by independent avifaunal studies in the Atlantic Forest of Brazil, both of which detected a similar assemblage of species, and similar species-specific responses to habitat change, across an overlapping sample of sites. Specifically, we tested whether 25 distributional, climatic, ecological, behavioral, and morphological variables predict sensitivity to habitat loss among 196 bird species, both within and across studies, and when data were analysed as occurrence or abundance. We found that four to nine variables showed high explanatory power within a single study or data set, but none performed as strong predictors across all data sets. Our results demonstrate that the use of species traits to predict sensitivity to anthropogenic habitat loss can produce predictions that are species- and site-specific and not scalable to whole regions or biomes, and thus should be used with caution.

Toward reassessing data-deficient species.

One in 6 species (13,465 species) on the International Union for Conservation of Nature (IUCN) Red List is classified as data deficient due to lack of information on their taxonomy, population status, or impact of threats. Despite the chance that many are at high risk of extinction, data-deficient species are typically excluded from global and local conservation priorities, as well as funding schemes. The number of data-deficient species will greatly increase as the IUCN Red List becomes more inclusive of poorly known and speciose groups. A strategic approach is urgently needed to enhance the conservation value of data-deficient assessments. To develop this, we reviewed 2879 data-deficient assessments in 6 animal groups and identified 8 main justifications for assigning data-deficient status (type series, few records, old records, uncertain provenance, uncertain population status or distribution, uncertain threats, taxonomic uncertainty, and new species). Assigning a consistent set of justification tags (i.e., consistent assignment to assessment justifications) to species classified as data deficient is a simple way to achieve more strategic assessments. Such tags would clarify the causes of data deficiency; facilitate the prediction of extinction risk; facilitate comparisons of data deficiency among taxonomic groups; and help prioritize species for reassessment. With renewed efforts, it could be straightforward to prevent thousands of data-deficient species slipping unnoticed toward extinction.

Speciation and extinction drive the appearance of directional range size evolution in phylogenies and the fossil record.

While the geographic range of a species is a fundamental unit of macroecology and a leading predictor of extinction risk, the evolutionary dynamics of species' ranges remain poorly understood. Based on statistical associations between range size and species age, many studies have claimed support for general models of range evolution in which the area occupied by a species varies predictably over the course of its life. Such claims have been made using both paleontological data and molecular estimates of the age of extant species. However, using a stochastic model, we show that the appearance of trends in range size with species' age can arise even when range sizes have evolved at random through time. This occurs because the samples of species used in existing studies are likely to be biased with respect to range size: for example, only those species that happened to have large or expanding ranges are likely to survive to the present, while extinct species will tend to be those whose ranges, by chance, declined through time. We compared the relationship between the age and range size of species arising under our stochastic model to those observed across 1,269 species of extant birds and mammals and 140 species of extinct Cenozoic marine mollusks. We find that the stochastic model is able to generate the full spectrum of empirical age-area relationships, implying that such trends cannot be simply interpreted as evidence for models of directional range size evolution. Our results therefore challenge the theory that species undergo predictable phases of geographic expansion and contraction through time.

Predicting the conservation status of data-deficient species.

There is little appreciation of the level of extinction risk faced by one-sixth of the over 65,000 species assessed by the International Union for Conservation of Nature. Determining the status of these data-deficient (DD) species is essential to developing an accurate picture of global biodiversity and identifying potentially threatened DD species. To address this knowledge gap, we used predictive models incorporating species' life history, geography, and threat information to predict the conservation status of DD terrestrial mammals. We constructed the models with 7 machine learning (ML) tools trained on species of known status. The resultant models showed very high species classification accuracy (up to 92%) and ability to correctly identify centers of threatened species richness. Applying the best model to DD species, we predicted 313 of 493 DD species (64%) to be at risk of extinction, which increases the estimated proportion of threatened terrestrial mammals from 22% to 27%. Regions predicted to contain large numbers of threatened DD species are already conservation priorities, but species in these areas show considerably higher levels of risk than previously recognized. We conclude that unless directly targeted for monitoring, species classified as DD are likely to go extinct without notice. Taking into account information on DD species may therefore help alleviate data gaps in biodiversity indicators and conserve poorly known biodiversity.

Predicting dispersal distance in mammals: a trait-based approach.

Dispersal is one of the principal mechanisms influencing ecological and evolutionary processes but quantitative empirical data are unfortunately scarce. As dispersal is likely to influence population responses to climate change, whether by adaptation or by migration, there is an urgent need to obtain estimates of dispersal distance. Cross-species correlative approaches identifying predictors of dispersal distance can provide much-needed insights into this data-scarce area. Here, we describe the compilation of a new data set of natal dispersal distances and use it to test life-history predictors of dispersal distance in mammals and examine the strength of the phylogenetic signal in dispersal distance. We find that both maximum and median dispersal distances have strong phylogenetic signals. No single model performs best in describing either maximum or median dispersal distances when phylogeny is taken into account but many models show high explanatory power, suggesting that dispersal distance per generation can be estimated for mammals with comparatively little data availability. Home range area, geographic range size and body mass are identified as the most important terms across models. Cross-validation of models supports the ability of these variables to predict dispersal distances, suggesting that models may be extended to species where dispersal distance is unknown.

Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential.

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine complete genomes, including two novel coronavirus species, across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk warrants closer surveillance.

Global distribution and conservation of rare and threatened vertebrates.

Global conservation strategies commonly assume that different taxonomic groups show congruent geographical patterns of diversity, and that the distribution of extinction-prone species in one group can therefore act as a surrogate for vulnerable species in other groups when conservation decisions are being made. The validity of these assumptions remains unclear, however, because previous tests have been limited in both geographical and taxonomic extent. Here we use a database on the global distribution of 19,349 living bird, mammal and amphibian species to show that, although the distribution of overall species richness is very similar among these groups, congruence in the distribution of rare and threatened species is markedly lower. Congruence is especially low among the very rarest species. Cross-taxon congruence is also highly scale dependent, being particularly low at the finer spatial resolutions relevant to real protected areas. 'Hotspots' of rarity and threat are therefore largely non-overlapping across groups, as are areas chosen to maximize species complementarity. Overall, our results indicate that 'silver-bullet' conservation strategies alone will not deliver efficient conservation solutions. Instead, priority areas for biodiversity conservation must be based on high-resolution data from multiple taxa.

The macroecology of landscape ecology.

One of landscape ecology's main goals is to unveil how biodiversity is impacted by habitat transformation. However, the discipline suffers from significant context dependency in observed spatial and temporal trends, hindering progress towards understanding the mechanisms driving species declines and preventing the development of accurate estimates of future biodiversity change. Here, we discuss recent evidence that populations' and species' responses to habitat change at the landscape scale are modulated by factors and processes occurring at macroecological scales, such as historical disturbance rates, distance to geographic range edges, and climatic suitability. We suggest that placing landscape ecology studies in a macroecological lens will help to explain seemingly inconsistent results and will ultimately create better predictive models to help mitigate the biodiversity crisis.

Determinants of northerly range limits along the Himalayan bird diversity gradient.

The primary explanation for the latitudinal gradient in species diversity must lie in why species fail to expand ranges across different climatic regimes. Theories of species gradients based in niche conservatism assume that whole clades are confined to particular climatic regimes because the traits they share limit adaptation to alternative regimes. We assess these theories in an analysis of the twofold decline in bird species richness along the Himalayas from the southeast to the northwest. The presence of fewer species in the northwest is entirely due to a steep decline in the number of forest species; species occupying more open habitats show a reversed gradient. Forest species numbers are exceptionally high at midelevations (1,000-2,000 m) in the southeast, which experience a warm, wet climate not present in the northwest, and a high proportion of these species fail to expand their range to the northwest. Despite this, many species do have populations or close relatives that straddle different climatic regimes along altitudinal gradients and/or the regional gradient, implying that climate-based niche conservatism per se does not strongly constrain range limits. We argue that climate- and competition-mediated resource distributions are important in setting northerly range limits and show that one measure of forest resources (foliage density) is lower in the northwest.

Detecting shifts in diversity limits from molecular phylogenies: what can we know?

Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a--probably untenable--model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification 'rules' and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.

Global hotspots of species richness are not congruent with endemism or threat.

Biodiversity hotspots have a prominent role in conservation biology, but it remains controversial to what extent different types of hotspot are congruent. Previous studies were unable to provide a general answer because they used a single biodiversity index, were geographically restricted, compared areas of unequal size or did not quantitatively compare hotspot types. Here we use a new global database on the breeding distribution of all known extant bird species to test for congruence across three types of hotspot. We demonstrate that hotspots of species richness, threat and endemism do not show the same geographical distribution. Only 2.5% of hotspot areas are common to all three aspects of diversity, with over 80% of hotspots being idiosyncratic. More generally, there is a surprisingly low overall congruence of biodiversity indices, with any one index explaining less than 24% of variation in the other indices. These results suggest that, even within a single taxonomic class, different mechanisms are responsible for the origin and maintenance of different aspects of diversity. Consequently, the different types of hotspots also vary greatly in their utility as conservation tools.

Colloquium paper: phylogenetic trees and the future of mammalian biodiversity.

Phylogenies describe the origins and history of species. However, they can also help to predict species' fates and so can be useful tools for managing the future of biodiversity. This article starts by sketching how phylogenetic, geographic, and trait information can be combined to elucidate present mammalian diversity patterns and how they arose. Recent diversification rates and standing diversity show different geographic patterns, indicating that cradles of diversity have moved over time. Patterns in extinction risk reflect both biological differences among mammalian lineages and differences in threat intensity among regions. Phylogenetic comparative analyses indicate that for small-bodied mammals, extinction risk is governed mostly by where the species live and the intensity of the threats, whereas for large-bodied mammals, ecological differences also play an important role. This modeling approach identifies species whose intrinsic biology renders them particularly vulnerable to increased human pressure. We outline how the approach might be extended to consider future trends in anthropogenic drivers, to identify likely future battlegrounds of mammalian conservation, and the likely casualties. This framework could help to highlight consequences of choosing among different future climatic and socioeconomic scenarios. We end by discussing priority-setting, showing how alternative currencies for diversity can suggest very different priorities. We argue that aiming to maximize long-term evolutionary responses is inappropriate, that conservation planning needs to consider costs as well as benefits, and that proactive conservation of largely intact systems should be part of a balanced strategy.

How index selection, compression, and recording schedule impact the description of ecological soundscapes.

Acoustic indices derived from environmental soundscape recordings are being used to monitor ecosystem health and vocal animal biodiversity. Soundscape data can quickly become very expensive and difficult to manage, so data compression or temporal down-sampling are sometimes employed to reduce data storage and transmission costs. These parameters vary widely between experiments, with the consequences of this variation remaining mostly unknown.We analyse field recordings from North-Eastern Borneo across a gradient of historical land use. We quantify the impact of experimental parameters (MP3 compression, recording length and temporal subsetting) on soundscape descriptors (Analytical Indices and a convolutional neural net derived AudioSet Fingerprint). Both descriptor types were tested for their robustness to parameter alteration and their usability in a soundscape classification task.We find that compression and recording length both drive considerable variation in calculated index values. However, we find that the effects of this variation and temporal subsetting on the performance of classification models is minor: performance is much more strongly determined by acoustic index choice, with Audioset fingerprinting offering substantially greater (12%-16%) levels of classifier accuracy, precision and recall.We advise using the AudioSet Fingerprint in soundscape analysis, finding superior and consistent performance even on small pools of data. If data storage is a bottleneck to a study, we recommend Variable Bit Rate encoded compression (quality = 0) to reduce file size to 23% file size without affecting most Analytical Index values. The AudioSet Fingerprint can be compressed further to a Constant Bit Rate encoding of 64 kb/s (8% file size) without any detectable effect. These recommendations allow the efficient use of restricted data storage whilst permitting comparability of results between different studies.

The environmental limits to geographic range expansion in birds.

The environmental factors limiting species' ranges across broad geographic and taxonomic scales are central to questions regarding the geographic variation in biodiversity and impacts of environmental change. However, our understanding remains relatively limited owing to the small-scale, correlative nature of most previous analyses. In this study, we provide a global test of the environmental determinants of range limits in birds, using both stochastic and environmentally deterministic models of range expansion to simulate spatial patterns in the shape of species' distributions. We show that spatial variation in range shape can be well explained by the action of a few key climatic variables in limiting range expansion. Furthermore, we demonstrate that these patterns cannot be explained by random processes alone. In addition, our study also identifies important differences in the factors constraining range expansion between biogeographic realms and between widespread and rare species. Although temperature was the principal climatic determinant of range shape at a global scale, its effects were driven primarily by widespread species, with the ranges of rare taxa better predicted by gradients in precipitation or topography. These key results were robust with respect to the index used to quantify range shape. Our analysis helps resolve long running debates regarding the role of environmentally deterministic and stochastic processes in structuring biodiversity and extends our understanding of the factors limiting species' ranges and the response of broad scale biodiversity patterns to environmental change.