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Summary: Stem respiration constitutes a substantial proportion of autotrophic respiration in forested ecosystems, but its drivers across different spatial scales and land‐use gradients remain poorly understood. This study quantifies and examines the impact of logging disturbance on stem CO2 efflux (EA) in Malaysian Borneo.EA was quantified at tree‐ and stand‐level in nine 1‐ha plots over a logging gradient from heavily logged to old‐growth using the static chamber method.Tree‐level results showed higher EA per unit stem area in logged vs old‐growth plots (37.0 ± 1.1 vs 26.92 ± 1.14 g C m−2 month−1). However, at stand‐level, there was no difference in EA between logged and old‐growth plots (6.7 ± 1.1 vs 6.0 ± 0.7 Mg C ha−1 yr−1) due to greater stem surface area in old‐growth plots. Allocation to growth respiration and carbon use efficiency was significantly higher in logged plots. Variation in EA at both tree‐ and stand‐level was driven by tree size, growth and differences in investment strategies between the forest types.These results reflect different resource allocation strategies and priorities, with a priority for growth in response to increased light availability in logged plots, while old‐growth plots prioritise maintenance and cell structure. [ABSTRACT FROM AUTHOR]

Urban environments provide opportunities for some species but are inhospitable for others. However, those which thrive can be found at higher densities in human‐dominated landscapes than in more rural habitats. This highlights the importance of understanding species responses to human environments. It is not only important for the conservation of urban wildlife but also may provide fundamental insights into human‐wildlife coexistence globally.Here, we use citizen science data to predict the habitat suitability of Greater London for the West European hedgehog (Erinaceus europaeus), the red fox (Vulpes vulpes), the European badger (Meles meles) and the Eastern grey squirrel (Sciurus carolinensis).Results indicate that the four target species prefer different urban habitats, indicating different levels of urbanisation potential. Foxes and grey squirrels are able to thrive in inner urban areas, with the highest values of habitat suitability for these species found in central London, whereas for hedgehogs and badgers, the highest habitat suitability occurs in suburban and more rural habitats in outer London, respectively.These results highlight a gradient in urban tolerance, from squirrels and foxes to hedgehogs and badgers. This work also shows the importance of urban green spaces as habitats for wildlife. [ABSTRACT FROM AUTHOR]

Understanding how community assembly processes drive biodiversity patterns is a central goal of community ecology. While it is generally accepted that ecological communities are assembled by both stochastic and deterministic processes, quantifying their relative importance remains challenging. Few studies have investigated how the relative importance of stochastic and deterministic community assembly processes vary among taxa and along gradients of habitat degradation. Using data on 1645 arthropod species across seven taxonomic groups in Malaysian Borneo, we quantified the importance of ecological stochasticity and of a suite of community assembly processes across a gradient of logging intensity. The relationship between logging and community assembly varied depending on the specific combination of taxa and stochasticity metric used, but, in general, the processes that govern invertebrate community assembly were remarkably robust to changes in land use intensity. [ABSTRACT FROM AUTHOR]

Addressing tropical deforestation in the palm oil sector involves a diverse range of stakeholders who engage or disengage with each other. Palm oil global value chain (GVC) firms (plantation companies, traders and processors, and consumer goods manufacturers and retailers), as well as nongovernmental organisations, financial institutions, consultancies and certification bodies, pursue their respective organisations' agendas through engagement practices, including through coalitions, in a palm oil sustainability network (POSN). Building on interviews with different stakeholder groups, this qualitative study characterises and critically analyses 'stakeholder engagement' by examining (1) the priority targets for engagement among different POSN stakeholders, (2) how mechanisms and tools are used in POSN stakeholder engagement or disengagement for addressing deforestation, and (3) the implications of stakeholder engagement or disengagement for addressing deforestation. Engagement and disengagement practices are shaped by and reshape GVC governance, with powerful stakeholders emerging as knowledge brokers and norm setters, raising important challenges for how deforestation is addressed. [ABSTRACT FROM AUTHOR]

Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual‐based demographic rates requires long‐term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, noninvasive method for individual‐based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogs is prohibitively time‐consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages. In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S‐Pattern, and WildID. As a case study, we consider the African wild dog, Lycaon pictus, a species whose conservation is limited by a lack of cost‐effective large‐scale monitoring. To evaluate intraspecific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat coloration patterns. The process of selecting suitable images was automated using convolutional neural networks that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image‐matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%). Our automated image preprocessing has immediate application for expanding monitoring based on image matching. However, the difference in accuracy between populations highlights that population‐specific detection rates are likely and may influence certainty in derived statistics. For species such as the African wild dog, where monitoring is both challenging and expensive, automated individual recognition could greatly expand and expedite conservation efforts. [ABSTRACT FROM AUTHOR]

Camera trap surveys are a popular ecological monitoring tool that produce vast numbers of images making their annotation extremely time‐consuming. Advances in machine learning, in the form of convolutional neural networks, have demonstrated potential for automated image classification, reducing processing time. These networks often have a poor ability to generalise, however, which could impact assessments of species in habitats undergoing change.Here, we (i) compare the performance of three network architectures in identifying species in camera trap images taken from tropical forest of varying disturbance intensities; (ii) explore the impacts of training dataset configuration; (iii) use habitat disturbance categories to investigate network generalisability and (iv) test whether classification performance and generalisability improve when using images cropped to bounding boxes.Overall accuracy (72.8%) was improved by excluding the rarest species and by adding extra training images (76.3% and 82.8%, respectively). Generalisability to new camera locations within a disturbance level was poor (mean F1‐score: 0.32). Performance across unseen habitat disturbance levels was worse (mean F1‐score: 0.27). Training the network on multiple disturbance levels improved generalisability (mean F1‐score on unseen disturbance levels: 0.41). Cropping images to bounding boxes improved overall performance (F1‐score: 0.77 vs. 0.47) and generalisability (mean F1‐score on unseen disturbance levels: 0.73), but at a cost of losing images that contained animals which the detector failed to detect.These results suggest researchers should consider using an object detector before passing images to a classifier, and an improvement in classification might be seen if labelled images from other studies are added to their training data. Composition of training data was shown to be influential, but including rarer classes did not compromise performance on common classes, providing support for the inclusion of rare species to inform conservation efforts. These findings have important implications for use of these methods for long‐term monitoring of habitats undergoing change, as they highlight the potential for misclassifications due to poor generalisability to impact subsequent ecological analyses. These methods therefore need to be considered as dynamic, in that changes to the study site would need to be reflected in the updated training of the network. [ABSTRACT FROM AUTHOR]

Agricultural expansion is a primary driver of biodiversity decline in forested regions of the tropics. Consequently, it is important to understand the conservation value of remnant forests in production landscapes. In a tropical landscape dominated by oil palm (Elaeis guineensis), we characterized faunal communities across eight taxa occurring within riparian forest buffers, which are legally protected alongside rivers, and compared them to nearby recovering logged forest. Buffer width was the main predictor of species richness and abundance, with widths of 40–100 m on each side of the river supporting broadly equivalent levels of biodiversity as compared to logged forest. However, width responses varied markedly among taxa, and buffers often lacked forest‐dependent species. Much wider buffers than are currently mandated are needed to safeguard most species. The largest biodiversity gains are achieved by increasing relatively narrow buffers. To provide optimal conservation outcomes in tropical production landscapes, we encourage policy makers to prescribe width requirements for key taxa and different landscape contexts. [ABSTRACT FROM AUTHOR]

Accurate occurrence data is necessary for the conservation of keystone or endangered species, but acquiring it is usually slow, laborious and costly. Automated acoustic monitoring offers a scalable alternative to manual surveys but identifying species vocalisations requires large manually annotated training datasets, and is not always possible (e.g. for lesser studied or silent species). A new approach is needed that rapidly predicts species occurrence using smaller and more coarsely labelled audio datasets. We investigated whether local soundscapes could be used to infer the presence of 32 avifaunal and seven herpetofaunal species in 20 min recordings across a tropical forest degradation gradient in Sabah, Malaysia. Using acoustic features derived from a convolutional neural network (CNN), we characterised species indicative soundscapes by training our models on a temporally coarse labelled point‐count dataset. Soundscapes successfully predicted the occurrence of 34 out of the 39 species across the two taxonomic groups, with area under the curve (AUC) metrics from 0.53 up to 0.87. The highest accuracies were achieved for species with strong temporal occurrence patterns. Soundscapes were a better predictor of species occurrence than above‐ground carbon density – a metric often used to quantify habitat quality across forest degradation gradients. Our results demonstrate that soundscapes can be used to efficiently predict the occurrence of a wide variety of species and provide a new direction for data driven large‐scale assessments of habitat suitability. [ABSTRACT FROM AUTHOR]

Habitat fragmentation has become one of the largest areas of research in conservation biology. Empirical studies into habitat fragmentation impacts typically measure ecological responses to metrics describing fragmentation processes, for example 'distance to the nearest forest edge', 'forest fragment area' and 'landscape habitat amount'. However, these studies often fail to sample across representative ranges of fragmentation metrics characterising the study region. They therefore lack the data to account for correlation among multiple fragmentation metrics and for spatial autocorrelation among sample sites, which reduces the strength of derived predictive models.Here, we draw on approaches used in the mining and soil science industry to develop standardised and repeatable protocols for designing optimised sampling schemes of biodiversity in fragmented landscapes that meet three criteria: the distance between sample sites is maximised to reduce spatial autocorrelation, the full range of values of the metrics of interest are sampled and the confounding effects of correlated metrics are minimised.We show that our computational methods can optimise the placement of sample sites in fragmented landscapes to minimise, and in some cases to entirely avoid, over‐ or under‐sampling of fragmentation metrics. Our method is flexible enough to cater for any continuous (e.g. maps of percentage tree cover) or categorical (e.g. habitat and land use types) fragmentation metric, and to simultaneously handle combinations of multiple fragmentation metrics and habitat types. We implement our methods as open‐source code which includes options to mask invalid or inaccessible regions, update designs to adapt to unforeseen constraints in the field and suggest optimal numbers of sample sites for given design criteria.Using a case study landscape, we demonstrate how the approach improves on manually generated sampling designs. We also show that the methods are flexible enough to be applied to landscape studies beyond the field of habitat fragmentation. We introduce our package as a novel research tool that is able to streamline the experimental design process for biodiversity sampling and monitoring at landscape scales, leading to improved data quality and representativeness. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Forest degradation through logging is pervasive throughout the world's tropical forests, leading to changes in the three‐dimensional canopy structure that have profound consequences for wildlife, microclimate and ecosystem functioning. Quantifying these structural changes is fundamental to understanding the impact of degradation, but is challenging in dense, structurally complex forest canopies.We exploited discrete‐return airborne LiDAR surveys across a gradient of logging intensity in Sabah, Malaysian Borneo, and assessed how selective logging had affected canopy structure (Plant Area Index, PAI, and its vertical distribution within the canopy).LiDAR products compared well to independent, analogue models of canopy structure produced from detailed ground‐based inventories undertaken in forest plots, demonstrating the potential for airborne LiDAR to quantify the structural impacts of forest degradation at landscape scale, even in some of the world's tallest and most structurally complex tropical forests.Plant Area Index estimates across the plot network exhibited a strong linear relationship with stem basal area (R2 = 0.95). After at least 11–14 years of recovery, PAI was ~28% lower in moderately logged plots and ~52% lower in heavily logged plots than that in old‐growth forest plots. These reductions in PAI were associated with near‐complete lack of trees >30‐m tall, which had not been fully compensated for by increasing plant area lower in the canopy. This structural change drives a marked reduction in the diversity of canopy environments, with the deep, dark understorey conditions characteristic of old‐growth forests far less prevalent in logged sites. Full canopy recovery is likely to take decades.Synthesis and applications. Effective management and restoration of tropical forests requires detailed monitoring of the forest and its environment. We demonstrate that airborne LiDAR can effectively map the canopy architecture of the complex tropical forests of Borneo, capturing the three‐dimensional impact of degradation on canopy structure at landscape scales, therefore facilitating efforts to restore and conserve these ecosystems. [ABSTRACT FROM AUTHOR]

Logging and habitat conversion create hotter microclimates in tropical forest landscapes, representing a powerful form of localised anthropogenic climate change. It is widely believed that these emergent conditions are responsible for driving changes in communities of organisms found in modified tropical forests, although the empirical evidence base for this is lacking.Here we investigated how interactions between the physiological traits of genera and the environmental temperatures they experience lead to functional and compositional changes in communities of ants, a key organism in tropical forest ecosystems.We found that the abundance and activity of ant genera along a gradient of forest disturbance in Sabah, Malaysian Borneo, was defined by an interaction between their thermal tolerance (CTmax) and environmental temperature. In more disturbed, warmer habitats, genera with high CTmax had increased relative abundance and functional activity, and those with low CTmax had decreased relative abundance and functional activity.This interaction determined abundance changes between primary and logged forest that differed in daily maximum temperature by a modest 1.1°C, and strengthened as the change in microclimate increased with disturbance. Between habitats that differed by 5.6°C (primary forest to oil palm) and 4.5°C (logged forest to oil palm), a 1°C difference in CTmax among genera led to a 23% and 16% change in relative abundance, and a 22% and 17% difference in functional activity. CTmax was negatively correlated with body size and trophic position, with ants becoming significantly smaller and less predatory as microclimate temperatures increased.Our results provide evidence to support the widely held, but never directly tested, assumption that physiological tolerances underpin the influence of disturbance‐induced microclimate change on the abundance and function of invertebrates in tropical landscapes. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

GLO:69VH/01apr21:bes21826-fig-0002.jpg PHOTO (COLOR): . gl Photo 2: Freshwater fieldwork at the SAFE project in Sabah, Malaysia - A logged forest stream to sample. GLO:69VH/01apr21:bes21826-fig-0003.jpg PHOTO (COLOR): . gl Photo 3: Freshwater fieldwork at the SAFE project in Sabah, Malaysia. [Extracted from the 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 implementation of an autonomous acoustic monitoring network deployed in the tropical rainforests of Borneo. Real‐time audio is uploaded remotely from the field, indexed by a central database, and delivered via an API to a public‐facing website.We provide the open‐source code and design of our monitoring devices, the central web2py database, and the ReactJS website. Furthermore, we demonstrate an extension of this infrastructure to deliver real‐time analyses of the eco‐acoustic data.By detailing a fully functional, open source, and extensively tested design, our work will accelerate the rate at which fully autonomous monitoring networks mature from technological curiosities, and towards genuinely impactful tools in ecology. [ABSTRACT FROM AUTHOR]

Logging, pervasive across the lowland tropics, affects millions of hectares of forest, yet its influence on nutrient cycling remains poorly understood. One hypothesis is that logging influences phosphorus (P) cycling, because this scarce nutrient is removed in extracted timber and eroded soil, leading to shifts in ecosystem functioning and community composition. However, testing this is challenging because P varies within landscapes as a function of geology, topography and climate. Superimposed upon these trends are compositional changes in logged forests, with species with more acquisitive traits, characterized by higher foliar P concentrations, more dominant. It is difficult to resolve these patterns using traditional field approaches alone. Here, we use airborne light detection and ranging‐guided hyperspectral imagery to map foliar nutrient (i.e. P, nitrogen [N]) concentrations, calibrated using field measured traits, over 400 km2 of northeastern Borneo, including a landscape‐level disturbance gradient spanning old‐growth to repeatedly logged forests. The maps reveal that canopy foliar P and N concentrations decrease with elevation. These relationships were not identified using traditional field measurements of leaf and soil nutrients. After controlling for topography, canopy foliar nutrient concentrations were lower in logged forest than in old‐growth areas, reflecting decreased nutrient availability. However, foliar nutrient concentrations and specific leaf area were greatest in relatively short patches in logged areas, reflecting a shift in composition to pioneer species with acquisitive traits. N:P ratio increased in logged forest, suggesting reduced soil P availability through disturbance. Through the first landscape scale assessment of how functional leaf traits change in response to logging, we find that differences from old‐growth forest become more pronounced as logged forests increase in stature over time, suggesting exacerbated phosphorus limitation as forests recover. [ABSTRACT FROM AUTHOR]

Beyond broad‐scale investigations of species diversity and abundance, there is little information on how land conversion in the tropics is affecting the behavior and demographics of surviving species. To fill these knowledge gaps, we explored the effects of land‐use change on the ecologically important and threatened bearded pig (Sus barbatus) over seven years in Borneo. Random placement of camera traps across a land‐use gradient of primary forest, logged forest, and oil palm plantations (32,542 trap nights) resulted in 2,303 independent capture events. Land‐use was associated with changes in the age structure and activity patterns of photographed individuals, alongside large changes in abundance shown previously. The proportion of adults recorded declined from 92% in primary forests to 76% in logged forests, and 67% in plantations, likely indicating increased fecundity in secondary forests. Activity level (capture rate) did not vary, but activity patterns changed markedly, from diurnal in primary forests, crepuscular in logged forests, to nocturnal in plantations. These changes corresponded with avoidance of diurnal human activity and may also protect bearded pigs from increased thermal stress in warmer degraded forests. The percentage of adult captures that were groups rather than individuals increased five‐fold from primary forests (4%) to logged forests (20%), possibly due to increased mating or in response to perceived threats from indirect human disturbance. We recommend further investigation of the demographic and behavioral effects of land‐use change on keystone species as altered population structure, activity patterns, and social behavior may have knock‐on effects for entire ecosystems. [ABSTRACT FROM AUTHOR]

Selective logging is driving the proliferation of roads throughout tropical rain forests, particularly narrow, unpaved logging roads. However, little is known about the extent of road edge effects or their influence on the movements of tropical understory animal species. Here, we used forest rats to address the following questions: (a) Does the occupancy of rats differ from road edges to forest interior within logged forests? (b) Do roads inhibit the movements of rats within these forests? We established trapping grids along a road edge‐to‐forest interior gradient at four roads and in three control sites within a logged forest in Sabah, Malaysia. To quantify the probability of road crossing, rats were captured, translocated across a road, and then recaptured on subsequent nights. We caught 216 individuals of eight species on 3,024 trap nights. Rat occupancy did not differ across the gradient from road edge to interior, and 48 percent of the 105 translocated individuals crossed the roads and were recaptured. This proportion was not significantly different from that of rats returning in control sites (38% of 60 individuals), suggesting that small roads were not barriers to rat movements within logged forests. Subadults were significantly more likely to return from translocation than adults in both road and control sites. Our results are encouraging for the ecology of small mammal communities in heavily logged forests, because small logging roads do not restrict the movements of rats and therefore are unlikely to create an edge effect or influence habitat selection. [ABSTRACT FROM AUTHOR]

The assembly of species communities at local scales is thought to be driven by environmental filtering, species interactions and spatial processes such as dispersal limitation. Little is known about how the relative balance of these drivers of community assembly changes along environmental gradients, especially man‐made environmental gradients associated with land‐use change.Using concurrent camera‐ and live‐trapping, we investigated the local‐scale assembly of mammal communities along a gradient of land‐use intensity (old‐growth forest, logged forest and oil palm plantations) in Borneo. We hypothesised that increasing land‐use intensity would lead to an increasing dominance of environmental control over spatial processes in community assembly. Additionally, we hypothesised that competitive interactions among species might reduce in concert with declines in α‐diversity (previously documented) along the land‐use gradient.To test our first hypothesis, we partitioned community variance into the fractions explained by environmental and spatial variables. To test our second hypothesis, we used probabilistic models of expected species co‐occurrence patterns, in particular focussing on the prevalence of spatial avoidance between species. Spatial avoidance might indicate competition, but might also be due to divergent habitat preferences.We found patterns that are consistent with a shift in the fundamental mechanics governing local community assembly. In support of our first hypothesis, the importance of spatial processes (dispersal limitation and fine‐scale patterns of home‐ranging) appeared to decrease from low to high intensity land‐uses, whilst environmental control increased in importance (in particular due to fine‐scale habitat structure). Support for our second hypothesis was weak: whilst we found that the prevalence of spatial avoidance decreased along the land‐use gradient, in particular between congeneric species pairs most likely to be in competition, few instances of spatial avoidance were detected in any land‐use, and most were likely due to divergent habitat preferences.The widespread changes in land‐use occurring in the tropics might be altering not just the biodiversity found in landscapes, but also the fundamental mechanics governing the local assembly of communities. A better understanding of these mechanics, for a range of taxa, could underpin more effective conservation and management of threatened tropical landscapes. Mammal community variation explained by environmental and spatial variables across a tropical land‐use gradient. [ABSTRACT FROM AUTHOR]

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 unit for capturing and remotely transmitting continuous data streams from field sites over long time‐periods. We provide a modular software framework for deploying various sensors, together with implementations to demonstrate proof of concept for continuous audio monitoring and time‐lapse photography.We show how our system can outperform comparable technologies for fractions of the cost, provided a local mobile network link is available. The system is robust to unreliable network signals and has been shown to function in extreme environmental conditions, such as in the tropical rainforests of Sabah, Borneo.We provide full details on how to assemble the hardware, and the open‐source software. Paired with appropriate automated analysis techniques, this system could provide spatially dense, near real‐time, continuous insights into ecosystem and biodiversity dynamics at a low cost. [ABSTRACT FROM AUTHOR]

Local‐scale microclimatic conditions in forest understoreys play a key role in shaping the composition, diversity and function of these ecosystems. Consequently, understanding what drives variation in forest microclimate is critical to forecasting ecosystem responses to global change, particularly in the tropics where many species already operate close to their thermal limits and rapid land‐use transformation is profoundly altering local environments. Yet our ability to characterize forest microclimate at ecologically meaningful scales remains limited, as understorey conditions cannot be directly measured from outside the canopy. To address this challenge, we established a network of microclimate sensors across a land‐use intensity gradient spanning from old‐growth forests to oil‐palm plantations in Borneo. We then combined these observations with high‐resolution airborne laser scanning data to characterize how topography and canopy structure shape variation in microclimate both locally and across the landscape. In the processes, we generated high‐resolution microclimate surfaces spanning over 350 km2, which we used to explore the potential impacts of habitat degradation on forest regeneration under both current and future climate scenarios. We found that topography and vegetation structure were strong predictors of local microclimate, with elevation and terrain curvature primarily constraining daily mean temperatures and vapour pressure deficit (VPD), whereas canopy height had a clear dampening effect on microclimate extremes. This buffering effect was particularly pronounced on wind‐exposed slopes but tended to saturate once canopy height exceeded 20 m—suggesting that despite intensive logging, secondary forests remain largely thermally buffered. Nonetheless, at a landscape‐scale microclimate was highly heterogeneous, with maximum daily temperatures ranging between 24.2 and 37.2°C and VPD spanning two orders of magnitude. Based on this, we estimate that by the end of the century forest regeneration could be hampered in degraded secondary forests that characterize much of Borneo's lowlands if temperatures continue to rise following projected trends. Written Summary:Local‐scale microclimatic conditions in forest understoreys play a key role in shaping the composition, diversity and function of these ecosystems. Yet our ability to capture microclimate at scales relevant for management and conservation remains inherently limited. By combining a network of microclimate sensors with high‐resolution airborne laser scanning data acquired across a land‐use intensity gradient in Borneo, here we characterise how topography and canopy structure shape variation in microclimate in human‐modified tropical landscapes. We estimate that by 2080 forest regeneration could be hampered in large tracts of degraded secondary forest that make up much of Borneo's lowlands. [ABSTRACT FROM AUTHOR]

Freshwater fish are a vital resource for local communities across the rural tropics. In Southeast Asia, biodiversity‐rich forests are being logged and converted to extensive oil palm monocultures. This clearly has impacts on associated freshwater ecosystems, but the impact on their biodiversity remains largely understudied and poorly understood, despite the important provisioning service that freshwater fishes provide for human well‐being.This study quantifies the biomass stocks of freshwater fish across a land‐use gradient encompassing primary forest, twice‐logged forest, and oil palm plantations in Sabah, Malaysia, in an area where local communities are known to harvest freshwater fish. Stream fish were sampled using a cast net, the dominant technique used by local fishermen, in 200‐m‐long transects in 16 streams over three sampling years (2011, 2013, and 2015).Unexpectedly, no impact from land use on total fish availability was detected. There were no significant differences in fish species richness or, most importantly, biomass per unit fishing effort across the land‐use gradient. There was variation in the responses of five known food species (Tor tambra, Hampala sabana, Barbodes sealei, Barbonymus balleroides, and Gastromyzon lepidogaster), and these small differences are attributed to variation in species habitat selection that co‐vary with land‐use change.Despite evidence to suggest that freshwater fish communities are resilient to land‐use change, they still face risks associated with disturbance, such as invasion by alien species; furthermore, several of the more stenotopic species were only present in primary forest catchments. Nonetheless, freshwater fish in small headwater streams appear to represent a sustainable food resource for villages established in human‐modified forests or in developed oil palm plantations. [ABSTRACT FROM AUTHOR]

Abstract: Aim: Thousands of kilometres of rainforest edges are created every year through forest fragmentation, but we have little knowledge of the impacts of edges on spatial patterns of species turnover and nestedness components of β‐diversity. Location: A quasi‐experimental landscape in the north‐east Brazilian Amazon. Methods: We sampled dung beetles and ants using a sampling design based on a fractal series of equilateral triangles that naturally allows examination at multiple spatial scales. We sampled two edge types (primary‐secondary and primary‐Eucalyptus forest) and three control sites immersed in primary, secondary and Eucalyptus forest. We measured β‐diversity between communities across the primary forest‐matrix edge and within communities at up to 1 km from the forest edge. We examined β‐diversity at multiple scales by partitioning the dissimilarity matrix into fractal orders representing inter‐point distances of ~32, ~100, ~316 and ~1,000 m and into turnover and nestedness components. Results: Turnover but not nestedness was greater across the primary‐Eucalyptus forest than primary‐secondary forest edge. There was spillover of species across edges in both directions. Across edges and within controls, turnover was the main driver of β‐diversity. Within community, β‐diversity was increased for dung beetles at large scales (~300–1,000 m) at both edge types. This increase, however, was driven by elevated nestedness. Levels of β‐diversity were affected even ~300 m into habitat interiors, but appeared to be at control levels by 1 km. Main conclusions: The effects of edges on the spatial dynamics of community composition penetrated far beyond the typical distances at which forest structure and microclimate are altered. This indicates that for a significant proportion of Amazonian communities, the underlying processes determining diversity may be impacted by deforestation. [ABSTRACT FROM AUTHOR]

Abstract: Tropical forests play a major role in the carbon cycle of the terrestrial biosphere. Recent field studies have provided detailed descriptions of the carbon cycle of mature tropical forests, but logged or secondary forests have received much less attention. Here, we report the first measures of total net primary productivity (NPP) and its allocation along a disturbance gradient from old‐growth forests to moderately and heavily logged forests in Malaysian Borneo. We measured the main NPP components (woody, fine root and canopy NPP) in old‐growth (n = 6) and logged (n = 5) 1 ha forest plots. Overall, the total NPP did not differ between old‐growth and logged forest (13.5 ± 0.5 and 15.7 ± 1.5 Mg C ha−1 year−1 respectively). However, logged forests allocated significantly higher fraction into woody NPP at the expense of the canopy NPP (42% and 48% into woody and canopy NPP, respectively, in old‐growth forest vs 66% and 23% in logged forest). When controlling for local stand structure, NPP in logged forest stands was 41% higher, and woody NPP was 150% higher than in old‐growth stands with similar basal area, but this was offset by structure effects (higher gap frequency and absence of large trees in logged forest). This pattern was not driven by species turnover: the average woody NPP of all species groups within logged forest (pioneers, nonpioneers, species unique to logged plots and species shared with old‐growth plots) was similar. Hence, below a threshold of very heavy disturbance, logged forests can exhibit higher NPP and higher allocation to wood; such shifts in carbon cycling persist for decades after the logging event. Given that the majority of tropical forest biome has experienced some degree of logging, our results demonstrate that logging can cause substantial shifts in carbon production and allocation in tropical forests. [ABSTRACT FROM AUTHOR]

Freshwaters provide valuable habitat and important ecosystem services but are threatened worldwide by habitat loss and degradation. In Southeast Asia, rainforest streams are particularly threatened by logging and conversion to oil palm, but we lack information on the impacts of this on freshwater environmental conditions, and the relative importance of catchment versus riparian-scale disturbance. We studied 16 streams in Sabah, Borneo, including old-growth forest, logged forest, and oil palm sites. We assessed forest quality in riparian zones and across the whole catchment and compared it with stream environmental conditions including water quality, structural complexity, and organic inputs. We found that streams with the highest riparian forest quality were nearly 4 °C cooler, over 20 cm deeper, had over 40% less sand, greater canopy cover, more stored leaf litter, and wider channels than oil palm streams with the lowest riparian forest quality. Other variables were significantly related to catchment-scale forest quality, with streams in the highest quality forest catchments having 40% more bedrock and 20 times more dead wood, along with higher phosphorus, and lower nitrate-N levels compared to streams with the lowest catchment-scale forest quality. Although riparian buffer strips went some way to protecting waterways, they did not maintain fully forest-like stream conditions. In addition, logged forest streams still showed signs of disturbance 10-15 years after selective logging. Our results suggest that maintenance and restoration of buffer strips can help to protect healthy freshwater ecosystems but logging practices and catchment-scale forest management also need to be considered. [ABSTRACT FROM AUTHOR]

A great challenge for ecologists is predicting how communities in fragmented tropical landscapes will change in the future. Available evidence suggests that fragmented tropical tree communities are progressing along a trajectory of 'retrogressive succession', in which the community shifts towards an early or mid-successional state that will persist indefinitely. Here, we investigate the potential endpoint of retrogressive succession, examining whether it will eventually lead to the highly depauperate communities that characterise recently abandoned agricultural lands. We tested this hypothesis by using neural networks to construct an empirical model of Amazonian rainforest-tree-community responses to experimental habitat fragmentation. The strongest predictor of tree-community composition in the future was its composition in the present, modified by variables like the composition of the surrounding habitat matrix and distance to forest edge. We extrapolated network predictions over a 100 yr period and quantified trajectories of forest communities in multidimensional ordination space. We found no evidence that forest communities, including those near forest edges, were converging strongly towards a composition dominated by just one or two early successional genera. Retrogressive succession may well be stronger in fragmented landscapes altered by chronic disturbances, such as edge-related fires, selective logging, or intense windstorms, but in this experimental landscape in which other human disturbances are very limited, it is unlikely that forest edge communities will fully revert to the species poor assemblages observed in very early successional landscapes. [ABSTRACT FROM AUTHOR]

A variety of landscape models are used to conceptualize and interpret human impacts on ecosystems and their biodiversity. The simplest, a 'patch-matrix' model, is rooted in island biogeography theory and assumes a dichotomy between generic, easily-defined habitat patches and a surrounding matrix that is completely inhospitable. This dichotomy between patch and matrix habitats has been recently relaxed, with the 'continuum' model taking this relaxation to its extreme and logical endpoint - a species-based model with no a priori definition of habitat or matrix, but rather focusing on ecological gradients. Yet, because few empirical comparisons of these bookending models exist, we lack understanding of their relative utility or the merits of hybrid approaches that combine attributes of patch-matrix and continuum models. To guide such considerations, we first develop a decision-making framework for the application of patch-matrix, continuum, and hybrid models. The framework takes into account study objectives, attributes of the landscape, and species traits. We then evaluate this framework by empirically comparing how continuum, patch-matrix, and hybrid models explain beetle distributions across two contrasting fragmented landscapes, for species differing in trophic level and habitat specificity. Within the Hope River Forest Fragmentation Project, a system with strong landscape contrast and distinct ('hard') structural edges between forest fragments and grassland, we find broad support for hybrid models, particularly those incorporating surrounding landscape structure. Conversely, within the Wog Wog Habitat Fragmentation Experiment, a system with weak landscape contrast and 'soft' structural edges between natural and plantation forest, we find co-support for continuum and hybrid models. We find no support in either system for patch-matrix, relative to continuum and hybrid models. We conclude by considering key questions and areas of research for advancing the application of models to understand species responses and biodiversity patterns associated with land-use change. [ABSTRACT FROM AUTHOR]

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that β-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected β-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and β-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as β-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); β-diversity was quantified by comparing observed β-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the β-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant β-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The β-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to β-diversity at a range of spatial grains. [ABSTRACT FROM AUTHOR]

Invasive species pose one of the greatest threats to biodiversity. This study investigates the extent to which human disturbance to natural ecosystems facilitates the spread of non-native species, focusing on a small mammal community in selectively logged rain forest, Sabah, Borneo. The microhabitat preferences of the invasive Rattus rattus and three native species of small mammal were examined in three-dimensional space by combining the spool-and-line technique with a novel method for quantifying fine-scale habitat selection. These methods allowed the detection of significant differences for each species between the microhabitats used compared with alternative, available microhabitats that were avoided. Rattus rattus showed the greatest preference for heavily disturbed habitats, and in contrast to two native small mammals of the genus Maxomys, R. rattus showed high levels of arboreal behavior, frequently leaving the forest floor and traveling through the understory and midstory forest strata. This behavior may enable R. rattus to effectively utilize the complex three-dimensional space of the lower strata in degraded forests, which is characterized by dense vegetation. The behavioral flexibility of R. rattus to operate in both terrestrial and arboreal space may facilitate its invasion into degraded forests. Human activities that generate heavily disturbed habitats preferred by R. rattus may promote the establishment of this invasive species in tropical forests in Borneo, and possibly elsewhere. We present this as an example of a synergistic effect, whereby forest disturbance directly threatens biodiversity and indirectly increases the threat posed by invasive species, creating habitat conditions that facilitate the establishment of non-native fauna. [ABSTRACT FROM AUTHOR]

Land-use and land-cover ( LULC) change is one of the largest drivers of biodiversity loss and carbon emissions globally. We use the tropical rainforests of the Amazon, the Congo basin and South-East Asia as a case study to investigate spatial predictive models of LULC change. Current predictions differ in their modelling approaches, are highly variable and often poorly validated. We carried out a quantitative review of 48 modelling methodologies, considering model spatio-temporal scales, inputs, calibration and validation methods. In addition, we requested model outputs from each of the models reviewed and carried out a quantitative assessment of model performance for tropical LULC predictions in the Brazilian Amazon. We highlight existing shortfalls in the discipline and uncover three key points that need addressing to improve the transparency, reliability and utility of tropical LULC change models: (1) a lack of openness with regard to describing and making available the model inputs and model code; (2) the difficulties of conducting appropriate model validations; and (3) the difficulty that users of tropical LULC models face in obtaining the model predictions to help inform their own analyses and policy decisions. We further draw comparisons between tropical LULC change models in the tropics and the modelling approaches and paradigms in other disciplines, and suggest that recent changes in the climate change and species distribution modelling communities may provide a pathway that tropical LULC change modellers may emulate to further improve the discipline. Climate change models have exerted considerable influence over public perceptions of climate change and now impact policy decisions at all political levels. We suggest that tropical LULC change models have an equally high potential to influence public opinion and impact the development of land-use policies based on plausible future scenarios, but, to do that reliably may require further improvements in the discipline. [ABSTRACT FROM AUTHOR]

Landscape ecology plays a vital role in understanding the impacts of land-use change on biodiversity, but it is not a predictive discipline, lacking theoretical models that quantitatively predict biodiversity patterns from first principles. Here, we draw heavily on ideas from phylogenetics to fill this gap, basing our approach on the insight that habitat fragments have a shared history. We develop a landscape 'terrageny', which represents the historical spatial separation of habitat fragments in the same way that a phylogeny represents evolutionary divergence among species. Combining a random sampling model with a terrageny generates numerical predictions about the expected proportion of species shared between any two fragments, the locations of locally endemic species, and the number of species that have been driven locally extinct. The model predicts that community similarity declines with terragenetic distance, and that local endemics are more likely to be found in terragenetically distinctive fragments than in large fragments. We derive equations to quantify the variance around predictions, and show that ignoring the spatial structure of fragmented landscapes leads to over-estimates of local extinction rates at the landscape scale. We argue that ignoring the shared history of habitat fragments limits our ability to understand biodiversity changes in human-modified landscapes. [ABSTRACT FROM AUTHOR]

The way in which species interactions are altered at habitat edges is an emerging concern in conservation biology, with some theories predicting edge-affected habitats to be less stable and exhibit intensified species interactions relative to interior habitats. One little-studied interaction is phoresy, where an individual of one species attaches itself to an individual of another species for the purpose of dispersal. Bumble bees ( Bombus spp.) are important crop pollinators around the world and at least 10 species of phoretic mites have been associated with various bumble bee species., Here, we investigated changes in the abundance of the introduced European B. terrestris across forest-grassland edges in the Southern Alps of New Zealand, and concomitant changes in the phoretic mite loads on these mobile pollinators., Bumble bees penetrated up to 250 m inside forest fragments, with abundance declining with distance from the anthropogenic matrix habitat. By contrast, phoretic mite loads increased towards the forest interior. Overall, phoretic mite loads on B. terrestris were greatest in the forest canopy, suggesting that this species interaction is intensified in natural habitat compared to that in the anthropogenic land use surrounding forest fragments., Our data indicate that phoretic loads on bumble bees are elevated in forest canopies. The functional significance of altered bumble bee - mite interactions for pollination services at forest edges remains to be tested. [ABSTRACT FROM AUTHOR]

Species turnover, β-diversity, underpins a number of ecological processes that define patterns of diversity. Estimates of β-diversity are dependent upon the spatial scale investigated, and patterns may vary across spatial scales. This presents us with a logistical problem of how to sample sufficiently at fine, local scales through to broad, landscape scales to provide accurate estimates of β-diversity at all spatial scales., Here, we present a scalable sampling design based on fractal geometry that is designed to explicitly address questions about β-diversity. Using simulated communities, we assessed the efficacy of the fractal design, along with two further designs representing subsamples of the fractal design and several classical ecological sampling designs (grids and transects) to estimate β-diversity across multiple spatial scales using two measures of β-diversity: community dissimilarity modelled against geographic distance and additive partitioning., All designs successfully modelled dissimilarity against distance, with the exception of grid sets and transects that were found to be unsuitable. When diversity was partitioned into multiple spatial scales, all sampling designs overestimated large-scale β-diversity., The accuracy of distance-decay estimates were primarily determined by the spatial configuration of sampling points. By contrast, the accuracy of diversity partitioning estimates was also influenced by sampling effort, with insufficient sampling effort and unsuitable sampling point configuration causing overestimates of β-diversity at larger spatial scales. We recommend that studies investigating β-diversity use a cluster-based configuration of sampling points, such as the fractal-based design presented here, to ensure accurate and comparable estimates at multiple spatial scales. Furthermore, when comparing results between studies, care should be taken to account for differences in sampling grain, sampling effort and the configuration of sampling points. [ABSTRACT FROM AUTHOR]

Communities in fragmented landscapes are often assumed to be structured by species extinction due to habitat loss, which has led to extensive use of the species-area relationship (SAR) in fragmentation studies. However, the use of the SAR presupposes that habitat loss leads species to extinction but does not allow for extinction to be offset by colonization of disturbed-habitat specialists. Moreover, the use of SAR assumes that species richness is a good proxy of community changes in fragmented landscapes. Here, we assessed how communities dwelling in fragmented landscapes are influenced by habitat loss at multiple scales; then we estimated the ability of models ruled by SAR and by species turnover in successfully predicting changes in community composition, and asked whether species richness is indeed an informative community metric. To address these issues, we used a data set consisting of 140 bird species sampled in 65 patches, from six landscapes with different proportions of forest cover in the Atlantic Forest of Brazil. We compared empirical patterns against simulations of over 8 million communities structured by different magnitudes of the power-law SAR and with species-specific rules to assign species to sites. Empirical results showed that, while bird community composition was strongly influenced by habitat loss at the patch and landscape scale, species richness remained largely unaffected. Modeling results revealed that the compositional changes observed in the Atlantic Forest bird metacommunity were only matched by models with either unrealistic magnitudes of the SAR or by models ruled by species turnover, akin to what would be observed along natural gradients. We show that, in the presence of such compositional turnover, species richness is poorly correlated with species extinction, and z values of the SAR strongly underestimate the effects of habitat loss. We suggest that the observed compositional changes are driven by each species reaching its individual extinction threshold: either a threshold of forest cover for species that disappear with habitat loss, or of matrix cover for species that benefit from habitat loss. [ABSTRACT FROM AUTHOR]

There is now an extensive literature on extinction debt following deforestation. However, the potential for species credit in landscapes that have experienced a change from decreasing to expanding forest cover has received little attention. Both delayed responses should depend on current landscape forest cover and on species life-history traits, such as longevity, as short-lived species are likely to respond faster than long-lived species., We evaluated the effects of historical and present-day local forest cover on two vertebrate groups with different longevities - understorey birds and non-flying small mammals − in forest patches at three Atlantic Forest landscapes. Our work investigated how the probability of extinction debt and species credit varies (i) amongst landscapes with different proportions of forest cover and distinct trajectories of forest cover change, and (ii) between taxa with different life spans., Our results suggest that the existence of extinction debt and species credit, as well as the potential for their future payment and/or receipt, is not only related to forest cover trajectory but also to the amount of remaining forest cover at the landscape scale. Moreover, differences in bird and small mammal life spans seem to be insufficient to affect differently their probability of showing time-delayed responses to landscape change., Synthesis and applications. Our work highlights the need for considering not only the trajectory of deforestation/regeneration but also the amount of forest cover at landscape scale when investigating time-delayed responses to landscape change. As many landscapes are experiencing a change from decreasing to expanding forest cover, understanding the association of extinction and immigration processes, as well as their interactions with the landscape dynamic, is a key factor to plan conservation and restoration actions in human-altered landscapes. [ABSTRACT FROM AUTHOR]

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Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on conservation management' includes (7) the intermediate landscape-complexity hypothesis-landscape-moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape-moderated biodiversity versus ecosystem service management hypothesis-landscape-moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape-moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management. [ABSTRACT FROM AUTHOR]

ABSTRACT Within-site variability in species detectability is a problem common to many biodiversity assessments and can strongly bias the results. Such variability can be caused by many factors, including simple counting inaccuracies, which can be solved by increasing sample size, or by temporal changes in species behavior, meaning that the way the temporal sampling protocol is designed is also very important. Here we use the example of mist-netted tropical birds to determine how design decisions in the temporal sampling protocol can alter the data collected and how these changes might affect the detection of ecological patterns, such as the species-area relationship (SAR). Using data from almost 3400 birds captured from 21,000 net-hours at 31 sites in the Brazilian Atlantic Forest, we found that the magnitude of ecological trends remained fairly stable, but the probability of detecting statistically significant ecological patterns varied depending on sampling effort, time of day and season in which sampling was conducted. For example, more species were detected in the wet season, but the SAR was strongest in the dry season. We found that the temporal distribution of sampling effort was more important than its total amount, discovering that similar ecological results could have been obtained with one-third of the total effort, as long as each site had been equally sampled over 2 yr. We discuss that projects with the same sampling effort and spatial design, but with different temporal sampling protocol are likely to report different ecological patterns, which may ultimately lead to inappropriate conservation strategies. [ABSTRACT FROM AUTHOR]

The conceptual foundations of habitat fragmentation research have not kept pace with empirical advances in our understanding of species responses to landscape change, nor with theoretical advances in the wider disciplines of ecology. There is now real debate whether explicit recognition of 'habitat fragmentation' as an over-arching conceptual domain will stimulate or hinder further progress toward understanding and mitigating the effects of landscape change. In this paper, we critically challenge the conceptual foundations of the discipline, and attempt to derive an integrated perspective on the best way to advance mechanistic understanding of fragmentation processes. We depict the inherent assumptions underlying the discipline as a 'conceptual phase space' of contrasting false dichotomies in fragmentation 'problem space'. In our opinion, the key determinant of whether 'habitat fragmentation' can remain a cohesive framework lies in the concept of 'interdependence': 1) interdependence of landscape effects on species and 2) interdependence of species responses to landscape change. If there is non-trivial interdependence among the various sub-components of habitat fragmentation, or non-trivial interdependence among species responses to landscape change, then there will be real heuristic value in 'habitat fragmentation' as a single conceptual domain. At present, the current paradigms entrenched in the fragmentation literature are implicitly founded on strict independence of landscape effects (e.g. the debate about the independent effects of habitat loss versus fragmentation per se) and strict independence of species responses (e.g. the individualistic species response models underpinning landscape continuum models), despite compelling evidence for interdependence in both effects and responses to fragmentation. We discuss how strong 'interdependence' of effects and responses challenges us to rethink long-held views, and re-cast the conceptual foundations of habitat fragmentation in terms of spatial context-dependence in the effects of multiple interacting spatial components of fragmentation, and community context-dependence in the responses of multiple interacting species to landscape change. [ABSTRACT FROM AUTHOR]

The article presents the study which examines whether production land use alters edge response functions in invertebrate diversity and community composition across native forest boundaries in Banks Peninsula, New Zealand. The study selected paired native forest-vs.-pasture and native forest-vs.-plantation edge gradients within four catchments. It is noted that variation in adjacent production land use altered the edge response function for over 80% of all beetle samples.

The use of indicators to identify areas of conservation importance has been challenged on several grounds, but nonetheless retains appeal as no more parsimonious approach exists. Among the many variants, two indicator strategies stand out: the use of indicator species and the use of metrics of landscape structure. While the first has been thoroughly studied, the same cannot be said about the latter. We aimed to contrast the relative efficacy of species-based and landscape-based indicators by: (i) comparing their ability to reflect changes in community integrity at regional and landscape spatial scales, (ii) assessing their sensitivity to changes in data resolution, and (iii) quantifying the degree to which indicators that are generated in one landscape or at one spatial scale can be transferred to additional landscapes or scales. We used data from more than 7000 bird captures in 65 sites from six 10 000-ha landscapes with different proportions of forest cover in the Atlantic Forest of Brazil. Indicator species and landscape-based indicators were tested in terms of how effective they were in reflecting changes in community integrity, defined as deviations in bird community composition from control areas. At the regional scale, indicator species provided more robust depictions of community integrity than landscape-based indicators. At the landscape scale, however, landscape-based indicators performed more effectively, more consistently and were also more transferable among landscapes. The effectiveness of high resolution landscape-based indicators was reduced by just 12% when these were used to explain patterns of community integrity in independent data sets. By contrast, the effectiveness of species-based indicators was reduced by 33%. Synthesis and applications. The use of indicator species proved to be effective; however their results were variable and sensitive to changes in scale and resolution, and their application requires extensive and time-consuming field work. Landscape-based indicators were not only effective but were also much less context-dependent. The use of landscape-based indicators may allow the rapid identification of priority areas for conservation and restoration, and indicate which restoration strategies should be pursued, using remotely sensed imagery. We suggest that landscape-based indicators might often be a better, simpler, and cheaper strategy for informing decisions in conservation. [ABSTRACT FROM AUTHOR]

Developing high-quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini-reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth-atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub-disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large-scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions. [ABSTRACT FROM AUTHOR]

Aim Few studies have attempted to assess the overall impact of fragmentation at the landscape scale. We quantify the impacts of fragmentation on plant diversity by assessing patterns of community composition in relation to a range of fragmentation measures. Location The investigation was undertaken in two regions of New Zealand – a relatively unfragmented area of lowland rain forest in south Westland and a highly fragmented montane forest on the eastern slopes of the Southern Alps. Methods We calculated an index of community similarity (Bray–Curtis) between forest plots we regarded as potentially affected by fragmentation and control forest plots located deep inside continuous forest areas. Using a multiple nonlinear regression technique that incorporates spatial autocorrelation effects, we analysed plant community composition in relation to measures of fragmentation at the patch and landscape levels. From the resulting regression equation, we predicted community composition for every forest pixel on land-cover maps of the study areas and used these maps to calculate a landscape-level estimate of compositional change, which we term ‘BioFrag’. BioFrag has a value of one if fragmentation has no detectable effect on communities within a landscape, and tends towards zero if fragmentation has a strong effect. Results We detected a weak, but significant, impact of fragmentation metrics operating at both the patch and landscape levels. Observed values of BioFrag ranged from 0.68 to 0.90, suggesting that patterns of fragmentation have medium to weak impacts on forest plant communities in New Zealand. BioFrag values varied in meaningful ways among landscapes and between the ground-cover and tree and shrub communities. Main conclusions BioFrag advances methods that describe spatial patterns of forest cover by incorporating the exact spatial patterns of observed species responses to fragmentation operating at multiple spatial scales. BioFrag can be applied to any landscape and ecological community across the globe and represents a significant step towards developing a biologically relevant, landscape-scale index of habitat fragmentation. [ABSTRACT FROM AUTHOR]

Bird communities in tropical forests are strongly affected by both patch area and habitat edges. The fact that both effects are intrinsically confounded in space raises questions about how these two widely reported ecological patterns interact, and whether they are independent or simply different spatial manifestations of the same phenomenon. Moreover, do small patches of secondary forest, in landscapes where the most sensitive species have gone locally extinct, exhibit similar patterns to those previously observed in fragmented and continuous primary forests? We addressed these questions by testing edge-related differences in vegetation structure and bird community composition at 31 sites in fragmented and continuous landscapes in the imperilled Atlantic forest of Brazil. Over a two-year period, birds were captured with mist nets to a standardized effort of 680 net-hours at each site (∼22 000 net-hours resulting in 3381 captures from 114 species). We found that the bird community in patches of secondary forest was degraded in species composition compared to primary continuous forest, but still exhibited a strong response to edge effects. In fragmented secondary forests, edge and area effects also interacted, such that the magnitude of edge to interior differences on bird community composition declined markedly with patch size. The change in bird species composition between forest interiors and edges was similar to the change in community composition between large and small patches (because species had congruent responses to edge and area), but after controlling for edge effects community composition was no longer affected by patch area. Our results show that although secondary forests hold an impoverished bird community, ecological patterns such as area and edge effects are similar to those reported for primary forests. Our data provide further evidence that edge effects are the main drivers of area effects in fragmented landscapes. [ABSTRACT FROM AUTHOR]

1. Ecosystem services are the benefits humans obtain from ecosystems. The importance of research into ecosystem services has been widely recognized, and rapid progress is being made. However, the prevailing approach to quantifying ecosystem services is still based on static analyses and single services, ignoring system dynamics, uncertainty and feedbacks. This is not only partly due to a lack of mechanistic understanding of processes and a dearth of empirical data, but also due to a failure to engage fully with the interdisciplinarity of the problem. 2. We argue that there is a tendency to ignore the feedbacks between and within both social and ecological systems, and a lack of explicit consideration of uncertainty. Metrics need to be developed that can predict thresholds, which requires strong linkages to underlying processes, while the development of policy for management of ecosystem services needs to be based on a broader understanding of value and drivers of human well-being. 3. We highlight the complexities, gaps in current knowledge and research, and the potentially promising avenues for future investigation in four priority research areas: agendas, processes, metrics and uncertainty. 4. Synthesis and applications. The research interest in the field of ecosystem services is rapidly expanding, and can contribute significantly to the sustainable management of natural resources. However, a narrow disciplinary approach, or an approach which does not consider feedbacks within and between ecological and social systems, has the potential to produce dangerously misleading policy recommendations. In contrast, if we explicitly acknowledge and address uncertainties and complexities in the provision of ecosystem services, progress may appear slower but our models will be substantially more robust and informative about the effects of environmental change. [ABSTRACT FROM AUTHOR]

Feeding a rapidly expanding human population will require a large increase in the supply of agricultural products during the coming decades. This may lead to the transformation of many landscapes from natural vegetation cover to agricultural land use, unless increases in crop yields reduce the need for new farmland. Here, we assess the evidence that past increases in agricultural yield have spared land for wild nature. We investigated the relationship between the change in the combined energy yield of the 23 most energetically important food crops over the period 1979–1999 and the change in per capita cropland area for 124 countries over the same period. Per capita area of the 23 staple crops tended to decrease in developing countries where large yield increases occurred. However, this was counteracted by a tendency for the area used to grow crops other than staples to increase in the countries where staple crop yields increased. There remained a weak tendency in developing countries for the per capita area of all cropland to decline as staple crop yield increased, a pattern that was most evident in developing countries with the highest per capita food supplies. In developed countries, there was no evidence that higher staple crop yields were associated with decreases in per capita cropland area. This may be because high agricultural subsidies in developed countries override any land-sparing pattern that might otherwise occur. Declines in the area of natural forest were smaller in countries where the yield of staple crops increased most, when the negative effects of human population increases on forest area were controlled for. Our results show that land-sparing is a weak process that occurs under a limited set of circumstances, but that it can have positive outcomes for the conservation of wild nature. [ABSTRACT FROM AUTHOR]

The future of tropical forest biodiversity depends more than ever on the effective management of human-modified landscapes, presenting a daunting challenge to conservation practitioners and land use managers. We provide a critical synthesis of the scientific insights that guide our understanding of patterns and processes underpinning forest biodiversity in the human-modified tropics, and present a conceptual framework that integrates a broad range of social and ecological factors that define and contextualize the possible future of tropical forest species. A growing body of research demonstrates that spatial and temporal patterns of biodiversity are the dynamic product of interacting historical and contemporary human and ecological processes. These processes vary radically in their relative importance within and among regions, and have effects that may take years to become fully manifest. Interpreting biodiversity research findings is frequently made difficult by constrained study designs, low congruence in species responses to disturbance, shifting baselines and an over-dependence on comparative inferences from a small number of well studied localities. Spatial and temporal heterogeneity in the potential prospects for biodiversity conservation can be explained by regional differences in biotic vulnerability and anthropogenic legacies, an ever-tighter coupling of human-ecological systems and the influence of global environmental change. These differences provide both challenges and opportunities for biodiversity conservation. Building upon our synthesis we outline a simple adaptive-landscape planning framework that can help guide a new research agenda to enhance biodiversity conservation prospects in the human-modified tropics. [ABSTRACT FROM AUTHOR]

Tree-holes provide an important microhabitat that is used for feeding, roosting and breeding by numerous species around the world. Yet despite their ecological importance for many of New Zealand's endangered species, few studies have investigated the abundance or distribution of tree-holes in native forests. We used complementary ground and climbed tree surveys to determine the abundance, distribution and characteristics of tree-holes in undisturbed Nothofagus forest in the Lewis Pass, New Zealand. We found that hole-bearing trees were surprisingly abundant compared with many other studies, including Australian Eucalyptus species and American beech. In fact, we estimated as many as 3906 tree-holes per hectare, of which 963 holes per hectare were potentially large enough to provide roost sites for hole-nesting bats in New Zealand, while only eight holes per hectare were potentially suitable for specialist hole-nesting birds. This was of great interest as primary cavity-excavating animals are absent from New Zealand forests, compared with North America and Australia. Moreover, tree-hole formation in New Zealand is likely to be dominated by abiotic processes, such as branch breakage from windstorms and snow damage. As has been found in many other studies, tree-holes were not uniformly distributed throughout the forest. Tree-holes were significantly more abundant on the least abundant tree species, Nothofagus fusca, than on either N. menziesii or N. solandri. In addition to tree species, tree size was also an important factor influencing the structural characteristics of tree-holes and their abundance in this forest. Moreover, these trends were not fully evident without climbed tree surveys. Our results revealed that ground-based surveys consistently underestimated the number of tree-holes present on Nothofagus trees, and illustrate the importance of using climbed inspections where possible in tree-hole surveys. We compare our results with other studies overseas and discuss how these are linked to the biotic and abiotic processes involved in tree-hole formation. We consider the potential implications of our findings for New Zealand's hole-dwelling fauna and how stand dynamics and past and future forest management practices will influence the structural characteristics of tree-holes and their abundance in remnant forest throughout New Zealand. [ABSTRACT FROM AUTHOR]

1. Edge effects are a highly cited issue in conservation biology with a wealth of empirically described impacts on invertebrates, but the mechanisms underlying the responses of individual species to habitat edges have been seldom tested. One often-raised hypothesis is that individual species vary in their ability to survive along a gradient of changing microclimatic conditions across habitat edges. 2. I used a phylogenetically controlled, translocation experiment to investigate edge-driven variation in adult mortality rate for two closely related species that have contrasting abundance patterns with respect to forest-grassland edges; the habitat generalist Mecodema fulgidum Broun (Coleoptera: Carabidae) and the forest-dwelling Mecodema rugiceps Sharp. 3. Adult individuals of both species were live-caught and translocated into containers at varying distances along an edge gradient extending from 1024 m inside a large forest fragment and 64 m into the surrounding grassland matrix. Experimental containers were connected to the above- and below-ground environments via mesh-covered panels, and beetle mortality over a 4-month period in the 2006/2007 austral summer was recorded. 4. Overall, mortality was higher for the habitat specialist M. rugiceps than for the generalist M. fulgidum. Neither species exhibited an edge-related trend in mortality, nor were mortality rates correlated with microclimatic gradients across the edge. 5. Weather records for the summer indicated that M. rugiceps was more sensitive than M. fulgidum to a soil moisture deficit that became more pronounced as summer progressed. Analysis of a 10-year climate record shows that soil moisture deficits occur annually, suggesting that seasonal variation in soil moisture may contribute to the variation in the distribution and abundance of the two species. [ABSTRACT FROM AUTHOR]

Habitat fragmentation causes extinction of local animal populations by decreasing the amount of viable “core” habitat area and increasing edge effects. It is widely accepted that larger fragments make better nature reserves because core-dwelling species have a larger amount of suitable habitat. Nevertheless, fragments in real landscapes have complex, irregular shapes. We modeled the population sizes of species that have a representative range of preferences for or aversions to habitat edges at five spatial scales (within 10, 32, 100, 320, and 1000 m of an edge) in a nation-wide analysis of forest remnants in New Zealand. We hypothesized that the irregular shapes of fragments in real landscapes should generate statistically significant correlations between population density and fragment area, purely as a “geometric” effect of varying species responses to the distribution of edge habitat. Irregularly shaped fragments consistently reduced the population size of core-dwelling species by 10–100%, depending on the scale over which species responded to habitat edges. Moreover, core populations within individual fragments were spatially discontinuous, containing multiple, disjunct populations that inhabited small spatial areas and had reduced population size. The geometric effect was highly nonlinear and depended on the range of fragment sizes sampled and the scale at which species responded to habitat edges. Fragment shape played a strong role in determining population size in fragmented landscapes; thus, habitat restoration efforts may be more effective if they focus on connecting disjunct cores rather than isolated fragments. [ABSTRACT FROM AUTHOR]