David Orme

David Orme
Imperial College London | Imperial

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122
Publications
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Publications

Publications (122)
Article
Full-text available
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...
Article
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Abstract 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 para...
Preprint
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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...
Article
Full-text available
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...
Article
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 con...
Article
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...
Preprint
Full-text available
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...
Article
Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity-affected by avoidance of habitat edges-should be driven by historical exposure to, and therefore species' evolutionary respo...
Preprint
Full-text available
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...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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...
Article
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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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
1.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. 2.Here we introduce an open source, inexpensive, fully autonomous ecosystem monito...
Article
Full-text available
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...
Article
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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
Article
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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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Data
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...
Data
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...
Data
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)
Data
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)
Data
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
Data on GDP and number introductions by country for the first and fourth quartiles of introductions, as ranked by date. (XLSX)
Data
Hexagonal grid cell data used to plot Fig 2 and S1 Fig. (XLSX)
Data
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)
Data
Correlograms to examine the patterns of spatial autocorrelation. Correlograms concern (a) alien bird richness; (b) the residuals of the most likely SARerr model. (DOCX)
Data
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...
Data
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)
Data
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...
Data
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)...
Data
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)
Data
Details of the anthropogenic and environmental predictor variables selected for use in model building. (DOCX)
Data
Data on number of introductions in different time periods used in Fig 1. (XLSX)
Data
Correlation matrix of all transformed predictor variables. r is above the diagonal and P is below it. (DOCX)
Data
The data frame for the analysis of alien species richness. (XLSX)
Article
Full-text available
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...
Article
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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...
Article
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...
Article
Full-text available
1.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...
Article
Full-text available
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...
Article
Full-text available
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....
Article
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...
Article
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...
Article
Full-text available
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...
Data
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...
Data
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...
Data
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...
Article
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...
Code
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
Article
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.
Article
Full-text available
Aim: To investigate the impact of different treatments of the IUCN Data Deficient (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 for t...
Article
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,...
Article
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...
Article
Aim Chorological relationships describe the patterns of distributional overlap among species. In addition to revealing biogeographical structure, the resulting clusters of species with similar geographical distributions can serve as natural units in conservation planning. Here, we assess the extent to which temporal, methodological and taxonomical...
Data
Bird and mammal phylogenetic trees. (ZIP)
Data
The relationship between the range size and the age of extant species expected under the stochastic model when rates of speciation (ν) are high. Variation in Spearman's correlation (ρ) between species' age and geographic range area under different combinations of asymmetry in range size inheritance and rate of change in range size where probability...
Data
Classification of curve shapes from the regression of log range size on log species age. Of the quadratic models, curve shapes are classified using the sign of the quadratic coefficient and the position of the curve vertex in relation to the observed species age values (grey panels). The corresponding models under the nine-category classification s...
Data
Age–area relationships for individual clades of birds and mammals. (DOC)
Data
The relationship between the range size and the age of extant species expected under the stochastic model when rates of speciation (ν) are low. Variation in Spearman's correlation (ρ) between species' age and geographic range area under different combinations of asymmetry in range size inheritance and rate of change in range size where probability...
Data
The relative proportions of observed and expected age–area trajectories across reconstructed phylogenies and extinct species using nine model types. The grey bars show the 95% confidence limits of the expected relative proportion of different age–area relationship classes under different combinations of asymmetry and range size inheritance for exta...
Data
Age–area relationships across clades of birds and mammals with relationships classified into nine types. (DOC)
Data
Range trajectories for fossil mollusks. (DOC)