David Orme

Imperial College London | Imperial · Department of Life Sciences

The myriad interactions among individual plants, animals, microbes and their abiotic environment generate emergent phenomena that will determine the future of life on Earth. Here, we argue that holistic ecosystem models – incorporating key biological domains and feedbacks between biotic and abiotic processes and capable of predicting emergent pheno...

Multi‐microphone recording adds spatial information to recorded audio with emerging applications in ecosystem monitoring. Specifically placing sounds in space can improve animal count accuracy, locate illegal activity like logging and poaching, track animals to monitor behaviour and habitat use and allow for ‘beamforming’ to amplify sounds from tar...

Aim: We used two fungal data sources for occurrence records (fruitbodies and roots) to (1) test the influence of data source on estimating the environmental niche of ecto- mycorrhizal (ECM) fungi and (2) compare the differences in estimated niche area and density for ECM fungal species with conspicuous (easily observed, i.e. mushrooms) versus incon...

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems¹ that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value⁴. Here we present empirically defined thresholds for categorizing the cons...

The myriad interactions among individual plants, animals, microbes and their abiotic environment generate emergent phenomena that will determine the future of life on Earth. Here, we argue that holistic ecosystem models – incorporating key biological domains and feedbacks between biotic and abiotic processes – capable of predicting emergent phenome...

African Swine Fever (ASF) reached the island of Borneo at the end of 2020. The first mortalities occurred in wild bearded pigs ( Sus barbatus ) in Sabah, north-east Borneo. The virus then began to spread across the island but, confounded by COVID 19 lockdowns the spread was difficult to monitor on the ground. The Babi Hutan Project was launched in...

Aim Ecoregions and the distance decay in community similarity are fundamental concepts in biogeography and conservation biology that are well supported across plants and animals, but not fungi. Here we test the relevance of these concepts for ectomycorrhizal (ECM) fungi in temperate and boreal regions. Location Europe. Time Period 2008–2015. Maj...

Aim Ecoregions and the distance decay in community similarity are fundamental concepts in biogeography and conservation biology that are well supported across plants and animals, but not fungi. Here we test the relevance of these concepts for ectomycorrhizal (ECM) fungi in temperate and boreal regions. Location Europe. Time period 2008 – 2015. M...

The functional stability of ecosystems depends greatly on interspecific differences in responses to environmental perturbation. However, responses to perturbation are not necessarily invariant among populations of the same species, so intraspecific variation in responses might also contribute. Such inter-population response diversity has recently b...

1 – Acoustic localisation, which relies on simultaneous multi-microphone recording, adds spatial information to recorded audio and has been used in ecosystem monitoring to count individuals to improve abundance estimates, locate illegal activities such as logging/poaching, and monitor behaviour such as habitat use or species interactions. Studies h...

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 speci...

The relative effects of habitat loss and fragmentation on biodiversity have been a topic of discussion for decades. While it is acknowledged that habitat amount can mediate the effects of habitat fragmentation, it is unclear what other factors may drive inter- and intraspecific variation in fragmentation effects and their implications for conservat...

As vital ecosystems across the globe enter unchartered pressure from climate change and industrial land use, understanding the processes driving ecosystem viability has never been more critical. Nuanced ecosystem understanding comes from well-collected field data and a wealth of associated interpretations. In recent years the most popular methods o...

While the COVID-19 pandemic, caused by SARS-CoV-2, has renewed genomic surveillance efforts in wildlife, there has been limited characterisation of bat-borne coronaviruses in Europe. We collected 48 faecal samples from all but one of the 17 bat species breeding in the UK, through an extensive network of bat rehabilitators and conservationists, and...

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...

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 va...

1. Environmental soundscapes are increasingly being used as descriptors of 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...

The question of whether migratory birds track a specific climatic niche by seasonal movements has important implications for understanding the evolution of migration, the factors affecting species' distributions, and the responses of migrants to climate change. Despite much research, previous studies of bird migration have produced mixed results. H...

Significance Human pressures are causing natural ecosystems to change at an unprecedented rate. Understanding these changes is important (e.g., to inform policy decisions), but we are hampered by the slow, labor-intensive nature of traditional ecological surveys. In this study, we show that automated analysis of the sounds of an ecosystem—its sound...

Automated monitoring approaches offer an avenue to unlocking large‐scale insight into how ecosystems respond to human pressures. However, since data collection and data analyses are often treated independently, there are currently no open‐source examples of end‐to‐end, real‐time ecological monitoring networks. Here, we present the complete implemen...

Automated monitoring approaches offer an avenue to deep, large-scale insight into how ecosystems respond to human pressures. Since sensor technology and data analyses are often treated independantly, there are no open-source examples of end-to-end, real-time ecological monitoring networks. Here, we present the complete implementation of an autonomo...

Vulnerability to habitat fragmentation Habitat fragmentation caused by human activities has consequences for the distribution and movement of organisms. Betts et al. present a global analysis of how exposure to habitat fragmentation affects the composition of ecological communities (see the Perspective by Hargreaves). In a dataset consisting of 448...

Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labour-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we developed a generalisable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolu...

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 biod...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

It is generally assumed that deforestation affects a species consistently across space, however populations near their geographic range edge may exist at their niche limits and therefore be more sensitive to disturbance. We found that both within and across Atlantic Forest bird species, populations are more sensitive to deforestation when near thei...

Habitat loss and fragmentation reduce population sizes and increase isolation between populations. To better understand how functional connectivity is affected by habitat modification over large scales, we here applied a meta-population framework to the Brazilian Atlantic Forest, a highly degraded and fragmented biodiversity hotspot. Other studies...

Automated methods of monitoring ecosystems provide a cost-effective way to track changes in natural system’s dynamics across temporal and spatial scales. However, methods of recording and storing data captured from the field still require significant manual effort. Here we introduce an open source, inexpensive, fully autonomous ecosystem monitoring...

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 (Earth & Environmental Sciences, University of Manchester, Manchester, UK) in the PDF. In addition, the blue circles for 'oak' were missing from Extended Data Fig. 1. These errors have been correct...

Automated methods of monitoring ecosystems provide a cost‐effective way to track changes in natural system's dynamics across temporal and spatial scales. However, methods of recording and storing data captured from the field still require significant manual effort. Here, we introduce an open source, inexpensive, fully autonomous ecosystem monitorin...

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...

p>In the version of this Article originally published, grant no. 2015/20215-7 for C.N. was omitted from the Acknowledgements section. This has now been corrected in all versions of the Article.</p

The distributions of amphibians, birds and mammals have underpinned global and local conservation priorities, and have been fundamental to our understanding of the determinants of global biodiversity. In contrast, the global distributions of reptiles, representing a third of terrestrial vertebrate diversity, have been unavailable. This prevented th...

In this Article originally published, owing to a technical error, the author ‘Laurent Chirio’ was mistakenly designated as a corresponding author in the HTML version, the PDF was correct. This error has now been corrected in the HTML version. Further, in Supplementary Table 3, the authors misspelt the surname of ‘Danny Meirte’; this file has now be...

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 acro...

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 inf...

The number of species from different biogeographic regions that have been introduced outside of their native range in the historic and modern eras. Prop. historic = the proportion of species introduced in the first quartile of bird introductions (historical era) from each biogeographic region; Prop. modern = the proportion of species introduced in...

Global maps showing the richness of the native ranges of the alien bird species. Global maps showing the richness of the native ranges of the alien bird species introduced during (a) the second quartile (1904–1956AD) and (b) the third quartile (1957–1982AD) of the data (the first and fourth quartiles are shown in Fig 2A and 2C). Cold colours repres...

Diagnostic plots for INLA regression. (a) Histogram of the posterior means of the predictive distribution, with low number of low and high probabilities, (b) regression of observed on fitted values, showing the strong fit between the two. (TIF)

Spatial patterns of residuals from an INLA regression. (a) Residuals with full covariates but without a spatial term; (b) Residuals with a spatially structured random effect. Redder colours indicate more positive residuals and bluer more negative, with yellow closer to zero. (TIF)

The numbers of introductions by country for the first and fourth quartiles of introductions, as ranked by date, and lists of the introduced bird species for these quartiles. (XLSX)

Data on GDP and number introductions by country for the first and fourth quartiles of introductions, as ranked by date. (XLSX)

Hexagonal grid cell data used to plot Fig 2 and S1 Fig. (XLSX)

Univariate relationships to log (1 + Alien Species Richness). (a) log (1 + Colonisation Pressure), (b) log time since first introduction, (c) sqrt distance to historic port, and (d) sqrt native species richness. The coefficients for the relationships are given in S5 Table, and further details of the variables in the Methods. (TIF)

Correlograms to examine the patterns of spatial autocorrelation. Correlograms concern (a) alien bird richness; (b) the residuals of the most likely SARerr model. (DOCX)

The distribution of introduced birds by family. The number of species introduced from a family in the first quartile (historical) and fourth quartile (modern), the total number of species in the family (Total) [46], and the probability (Psim calculated using simulations; see Methods) of observing as many or more introductions (or fewer introduction...

Outputs from single predictor INLA models where log+1 alien species richness is the response variable. S.E. = standard error for the variable. ∑CPO = the sum of the probabilities of each data point given the model. For comparison, fitting an intercept only model gives wAIC = –11,610.6 and CPO = 4,457.5. (DOCX)

Impact of predictor variables included in each of the holdout cross validation INLA models measured in AIC units. The shaded column indicates the selected predictors and values for the minimum adequate model using all of the data. Goodness-of-fit was calculated with Pearson’s correlation coefficients between the response variables and the fitted va...

Spatial correlates of alien bird richness for the minimum adequate model excluding colonisation pressure. Parameter estimates are given fitting a Gaussian random field to the data to approximate the patterns of spatial autocorrelation in a Bayesian additive regression model inferred using INLA. wAIC = –12,449, conditional predictive ordinate (CPO)...

Predicted relationships between alien bird species richness and anthropogenic and environmental variables. The predicted relationship and studies that provide support for each prediction are given. (DOCX)

Details of the anthropogenic and environmental predictor variables selected for use in model building. (DOCX)

Data on number of introductions in different time periods used in Fig 1. (XLSX)

Correlation matrix of all transformed predictor variables. r is above the diagonal and P is below it. (DOCX)

The data frame for the analysis of alien species richness. (XLSX)

Monocots account for a quarter of angiosperm species richness and are among the most economically and culturally important plants, including cereals (grasses), palms, orchids and lilies. Previous investigations of correlates of monocot species diversity have varied in scale and usually concentrated on a few drivers of diversification. Here, to dise...

A recent paper by Mori [1] states the need for a unification of studies of ‘engineering’ and ‘ecological’ frameworks of resilience. Engineering resilience focuses on the capacity of a system to recover to equilibrium following some kind of perturbation, while ecological resilience (ER) explicitly recognizes multiple stable states and the capacity f...

Accelerating rates of environmental change and the continued loss of global biodiversity threaten functions and services delivered by ecosystems. Much ecosystem monitoring and management is focused on the provision of ecosystem functions and services under current environmental conditions, yet this could lead to inappropriate management guidance an...

Cost‐effective reduction of uncertainty in global biodiversity indicators is a central goal of conservation. Comprising a sixth of the 74 000+ species currently on the IUCN Red List, Data Deficient species contribute to considerable uncertainty in estimates of extinction risk. Estimating levels of risk in Data Deficient species will require large r...

The ICP Forests network can be a platform for large-scale mycorrhizal studies. Mapping and monitoring of mycorrhizas have untapped potential to inform science, management, conservation and policy regarding distributions, diversity hotspots, dominance and rarity, and indicators of forest changes. A dearth of information about fungi at large scales...

Predictive frameworks of climate change extinction risk generally focus on the magnitude of climate change a species is expected to experience and the potential for that species to track suitable climate. A species' risk of extinction from climate change will depend, in part, on the magnitude of climate change the species experiences, its exposure....

At present, few studies exist that consider the relationship between species interactions and key environmental variables, with the added influence of offshore marine renewable energy technologies. Video footage and ADCP survey techniques were used, to examine the presence of fish and velocity flow rates within the vicinity of a deployed tidal ener...

The addition of man-made structures to the marine environment is known to increase the physical complexity of the seafloor, which can influence benthic species community patterns and habitat structure. However, knowledge of how deployed tidal energy device structures influence benthic communities is currently lacking. Here we examined species biodi...

Few studies of global diversity gradients in plants exist, largely because the data are not available for all species involved. Instead, most global studies have focussed on vertebrates, as these taxa have historically been associated with the most complete data. Here, we address this shortfall by first investigating global diversity gradients in m...

Cross-taxon congruence of monocots and vertebrates using the conservative method (see Methods) of assigning species to L3B units. All Spearman's rank correlations, apart from those marked with ?, were significant at the 0.05/30 = 0.00167 level according to Dutilleul's test accounting for spatial autocorrelation of neighbouring units and incorporati...

Patterns of monocot diversity using a ‘conservative’ method of assigning species to units. For those genera that occur in more than one biome within a single L3 unit, we assigned each genus' species into the set of L3B units in proportion to the size of each unit (see Methods for more details). White units are unoccupied. Results using the conserva...

Estimated parameters for multiple regression models summarised in Table 3. Units <10,000 km2 were not included, leaving 601 units in each model. The continent effect is relative to Africa. Precipitation variables were square-root transformed, and all other variables, except mean annual temperature, were log10 transformed. Estimated parameters for m...

Given the heavy reliance placed on and investment in protected areas for biological conservation, there has been much debate as to how effective these are in representing biodiversity features within their boundaries. The majority of studies addressing this issue have been conducted on a regional or national basis, precluding a broad picture of pat...

R package: betapart allows computing pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity. Available at: https://cran.r-project.org/web/packages/betapart/index.html

This vignette documents the use of the caper package for R (R Development Core Team, 2011) in carrying out a range of comparative analysis methods for phylogenetic data. The caper package, and the code in this vignette, requires the ape package (Paradis et˜al., 2004) along with the packages mvtnorm and MASS.

Aim To investigate the impact of different treatments of the IUCN D ata D eficient ( DD ) category on taxonomic and geographical patterns of extinction risk in crayfish, freshwater crabs and dragonflies. Location Global. Methods We used contingency tables to evaluate taxonomic and geographical selectivity of data deficiency and extinction risk fo...

Predation is a complex behavioural process and it is only through identifying the different factors influencing each stage that is it possible to understand the evolutionary processes driving the arms race between predators and prey. Using a long-term data set from Serengeti National Park in Tanzania, we investigated the importance of demographic,...

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 c...