Limits to the accurate and generalizable use of soundscapes to monitor biodiversity

Although eco-acoustic monitoring has the potential to deliver biodiversity insight on vast scales, existing analytical approaches behave unpredictably across studies. We collated 8,023 audio recordings with paired manual avifaunal point counts to investigate whether soundscapes could be used to monitor biodiversity across diverse ecosystems. We found that neither univariate indices nor machine learning models were predictive of species richness across datasets but soundscape change was consistently indicative of community change. Our findings indicate that there are no common features of biodiverse soundscapes and that soundscape monitoring should be used cautiously and in conjunction with more reliable in-person ecological surveys.

Optimizing the automated recognition of individual animals to support population monitoring

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.

Logged tropical forests have amplified and diverse ecosystem energetics

Old-growth tropical forests are widely recognized as being immensely important for their biodiversity and high biomass1. Conversely, logged tropical forests are usually characterized as degraded ecosystems2. However, whether logging results in a degradation in ecosystem functions is less clear: shifts in the strength and resilience of key ecosystem processes in large suites of species have rarely been assessed in an ecologically integrated and quantitative framework. Here we adopt an ecosystem energetics lens to gain new insight into the impacts of tropical forest disturbance on a key integrative aspect of ecological function: food pathways and community structure of birds and mammals. We focus on a gradient spanning old-growth and logged forests and oil palm plantations in Borneo. In logged forest there is a 2.5-fold increase in total resource consumption by both birds and mammals compared to that in old-growth forests, probably driven by greater resource accessibility and vegetation palatability. Most principal energetic pathways maintain high species diversity and redundancy, implying maintained resilience. Conversion of logged forest into oil palm plantation results in the collapse of most energetic pathways. Far from being degraded ecosystems, even heavily logged forests can be vibrant and diverse ecosystems with enhanced levels of ecological function.

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.

Oil palm expansion increases the vectorial capacity of dengue vectors in Malaysian Borneo

Changes in land-use and the associated shifts in environmental conditions can have large effects on the transmission and emergence of mosquito-borne disease. Mosquito-borne disease are particularly sensitive to these changes because mosquito growth, reproduction, survival and susceptibility to infection are all thermally sensitive traits, and land use change dramatically alters local microclimate. Predicting disease transmission under environmental change is increasingly critical for targeting mosquito-borne disease control and for identifying hotspots of disease emergence. Mechanistic models offer a powerful tool for improving these predictions. However, these approaches are limited by the quality and scale of temperature data and the thermal response curves that underlie predictions. Here, we used fine-scale temperature monitoring and a combination of empirical, laboratory and temperature-dependent estimates to estimate the vectorial capacity of Aedes albopictus mosquitoes across a tropical forest–oil palm plantation conversion gradient in Malaysian Borneo. We found that fine-scale differences in temperature between logged forest and oil palm plantation sites were not sufficient to produce differences in temperature-dependent demographic trait estimates using published thermal performance curves. However, when measured under field conditions a key parameter, adult abundance, differed significantly between land-use types, resulting in estimates of vectorial capacity that were 1.5 times higher in plantations than in forests. The prediction that oil palm plantations would support mosquito populations with higher vectorial capacity was robust to uncertainties in our adult survival estimates. These results provide a mechanistic basis for understanding the effects of forest conversion to agriculture on mosquito-borne disease risk, and a framework for interpreting emergent relationships between land-use and disease transmission. As the burden of Ae. albopictus-vectored diseases, such as dengue virus, increases globally and rising demand for palm oil products drives continued expansion of plantations, these findings have important implications for conservation, land management and public health policy at the global scale.

A protocol for a longitudinal, observational cohort study of infection and exposure to zoonotic and vector-borne diseases across a land-use gradient in Sabah, Malaysian Borneo: a socio-ecological systems approach

Introduction. Landscape changes disrupt environmental, social and biological systems, altering pathogen spillover and transmission risks. This study aims to quantify the impact of specific land management practices on spillover and transmission rates of zoonotic and vector-borne diseases within Malaysian Borneo. This protocol describes a cohort study with integrated ecological sampling to assess how deforestation and agricultural practices impact pathogen flow from wildlife and vector populations to human infection and detection by health facilities. This will focus on malaria, dengue and emerging arboviruses (Chikungunya and Zika), vector-borne diseases with varying contributions of simian reservoirs within this setting. Methods. A prospective longitudinal observational cohort study will be established in communities residing or working within the vicinity of the Stability of Altered Forest Ecosystems (SAFE) Project, a landscape gradient within Malaysian Borneo encompassing different plantation and forest types. The primary outcome of this study will be transmission intensity of selected zoonotic and vector-borne diseases, as quantified by changes in pathogen-specific antibody levels. Exposure will be measured using paired population-based serological surveys conducted at the beginning and end of the two-year cohort study. Secondary outcomes will include the distribution and infection rates of Aedes and Anopheles mosquito vectors, human risk behaviours and clinical cases reported to health facilities. Longitudinal data on human behaviour, contact with wildlife and GPS tracking of mobility patterns will be collected throughout the study period. This will be integrated with entomological surveillance to monitor densities and pathogen infection rates of Aedes and Anopheles mosquitoes relative to land cover. Within surrounding health clinics, continuous health facility surveillance will be used to monitor reported infections and febrile illnesses. Models will be developed to assess spillover and transmission rates relative to specific land management practices and evaluate abilities of surveillance systems to capture these risks.

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

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

Fine root dynamics across pantropical rainforest ecosystems

Fine roots constitute a significant component of the net primary productivity (NPP) of forest ecosystems but are much less studied than aboveground NPP. Comparisons across sites and regions are also hampered by inconsistent methodologies, especially in tropical areas. Here, we present a novel dataset of fine root biomass, productivity, residence time, and allocation in tropical old-growth rainforest sites worldwide, measured using consistent methods, and examine how these variables are related to consistently determined soil and climatic characteristics. Our pantropical dataset spans intensive monitoring plots in lowland (wet, semi-deciduous, and deciduous) and montane tropical forests in South America, Africa, and Southeast Asia (n = 47). Large spatial variation in fine root dynamics was observed across montane and lowland forest types. In lowland forests, we found a strong positive linear relationship between fine root productivity and sand content, this relationship was even stronger when we considered the fractional allocation of total NPP to fine roots, demonstrating that understanding allocation adds explanatory power to understanding fine root productivity and total NPP. Fine root residence time was a function of multiple factors: soil sand content, soil pH, and maximum water deficit, with longest residence times in acidic, sandy, and water-stressed soils. In tropical montane forests, on the other hand, a different set of relationships prevailed, highlighting the very different nature of montane and lowland forest biomes. Root productivity was a strong positive linear function of mean annual temperature, root residence time was a strong positive function of soil nitrogen content in montane forests, and lastly decreasing soil P content increased allocation of productivity to fine roots. In contrast to the lowlands, environmental conditions were a better predictor for fine root productivity than for fractional allocation of total NPP to fine roots, suggesting that root productivity is a particularly strong driver of NPP allocation in tropical mountain regions.

Recovery of logged forest fragments in a human-modified tropical landscape during the 2015-16 El Niño

The past 40 years in Southeast Asia have seen about 50% of lowland rainforests converted to oil palm and other plantations, and much of the remaining forest heavily logged. Little is known about how fragmentation influences recovery and whether climate change will hamper restoration. Here, we use repeat airborne LiDAR surveys spanning the hot and dry 2015-16 El Niño Southern Oscillation event to measure canopy height growth across 3,300 ha of regenerating tropical forests spanning a logging intensity gradient in Malaysian Borneo. We show that the drought led to increased leaf shedding and branch fall. Short forest, regenerating after heavy logging, continued to grow despite higher evaporative demand, except when it was located close to oil palm plantations. Edge effects from the plantations extended over 300 metres into the forests. Forest growth on hilltops and slopes was particularly impacted by the combination of fragmentation and drought, but even riparian forests located within 40 m of oil palm plantations lost canopy height during the drought. Our results suggest that small patches of logged forest within plantation landscapes will be slow to recover, particularly as ENSO events are becoming more frequent.

It is unclear whether tropical forest fragments within plantation landscapes are resilient to drought. Here the authors analyse LiDAR and ground-based data from the 2015-16 El Niño event across a logging intensity gradient in Borneo. Although regenerating forests continued to grow, canopy height near oil palm plantations decreased, and a strong edge effect extended up to at least 300 m away.

Forest conversion to oil palm compresses food chain length in tropical streams

In Southeast Asia, biodiversity-rich forests are being extensively logged and converted to oil palm monocultures. Although the impacts of these changes on biodiversity are largely well documented, we know addition to samples we collected in 201 little about how these large-scale impacts affect freshwater trophic ecology. We used stable isotope analyses (SIA) to determine the impacts of land-use changes on the relative contribution of allochthonous and autochthonous basal resources in 19 stream food webs. We also applied compound-specific SIA and bulk-SIA to determine the trophic position of fish apex predators and meso-predators (invertivores and omnivores). There was no difference in the contribution of autochthonous resources in either consumer group (70-82%) among streams with different land-use type. There was no change in trophic position for meso-predators, but trophic position decreased significantly for apex predators in oil palm plantation streams compared to forest streams. This change in maximum food chain length was due to turnover in identity of the apex predator among land-use types. Disruption of aquatic trophic ecology, through reduction in food chain length and shift in basal resources, may cause significant changes in biodiversity as well as ecosystem functions and services. Understanding this change can help develop more focused priorities for mediating the negative impacts of human activities on freshwater ecosystems.

Imaging spectroscopy reveals the effects of topography and logging on the leaf chemistry of tropical forest canopy trees

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.

Extinction filters mediate the global effects of habitat fragmentation on animals

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 responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world’s tropical forests.

Canopy structure and topography jointly constrain the microclimate of human-modified tropical landscapes

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.

Logging disturbance shifts net primary productivity and its allocation in Bornean tropical forests

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.

Effect of tropical forest disturbance on the competitive interactions within a diverse ant community

Understanding how anthropogenic disturbance influences patterns of community composition and the reinforcing interactive processes that structure communities is important to mitigate threats to biodiversity. Competition is considered a primary reinforcing process, yet little is known concerning disturbance effects on competitive interaction networks. We examined how differences in ant community composition between undisturbed and disturbed Bornean rainforest, is potentially reflected by changes in competitive interactions over a food resource. Comparing 10 primary forest sites to 10 in selectively-logged forest, we found higher genus richness and diversity in the primary forest, with 18.5% and 13.0% of genera endemic to primary and logged respectively. From 180 hours of filming bait cards, we assessed ant-ant interactions, finding that despite considered aggression over food sources, the majority of ant interactions were neutral. Proportion of competitive interactions at bait cards did not differ between forest type, however, the rate and per capita number of competitive interactions was significantly lower in logged forest. Furthermore, the majority of genera showed large changes in aggression-score with often inverse relationships to their occupancy rank. This provides evidence of a shuffled competitive network, and these unexpected changes in aggressive relationships could be considered a type of competitive network re-wiring after disturbance.

The effects of catchment and riparian forest quality on stream environmental conditions across a tropical rainforest and oil palm landscape in Malaysian Borneo

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.

Increasing land-use intensity reverses the relative occupancy of two quadrupedal scavengers

Human land use is continuously altering the natural environment, yet the greater ecological implications of this change for many groups that are key to healthy ecosystem functioning remains uncharacterised in the tropics. Terrestrial scavenging vertebrates are one such group, providing integral ecosystem services through the removal of carrion which is a crucial component of both nutrient cycling and disease dynamics. To explore how anthropogenic processes may affect forest scavengers, we investigated the changes in the relative occupancy of two important terrestrial scavengers along a gradient of land use intensity, ranging from protected forest to oil palm plantation in Borneo. We found the Malay civet (Viverra tangalunga) had highest, albeit variable, occupancy in areas of low land use intensity and the Southeast Asian water monitor (Varanus salvator macromaculatus) had highest occupancy in areas of high land use intensity. Land use had no effect on the combined occupancy of the two species. In high land use intensity sites, individual water monitors were larger and had better body condition, but at population level had a highly biased sex ratio with more males than females and increased signs of intraspecific conflict. We did not assess scavenging rate or efficiency as a process, but the high occupancy rates and apparent health of the scavengers in high land use intensity landscapes suggests this ecological process is robust to land use change.

The Environmental Legacy of Modern Tropical Deforestation

Tropical deforestation has caused a significant share of carbon emissions and species losses, but historical patterns have rarely been explicitly considered when estimating these impacts [1]. A deforestation event today leads to a time-delayed future release of carbon, from the eventual decay either of forest products or of slash left at the site [2]. Similarly, deforestation often does not result in the immediate loss of species, and communities may exhibit a process of “relaxation” to their new equilibrium over time [3]. We used a spatially explicit land cover change model [4] to reconstruct the annual rates and spatial patterns of tropical deforestation that occurred between 1950 and 2009 in the Amazon, in the Congo Basin, and across Southeast Asia. Using these patterns, we estimated the resulting gross vegetation carbon emissions [2, 5] and species losses over time [6]. Importantly, we accounted for the time lags inherent in both the release of carbon and the extinction of species. We show that even if deforestation had completely halted in 2010, time lags ensured there would still be a carbon emissions debt of at least 8.6 petagrams, equivalent to 5–10 years of global deforestation, and an extinction debt of more than 140 bird, mammal, and amphibian forest-specific species, which if paid, would increase the number of 20^th-century extinctions in these groups by 120%. Given the magnitude of these debts, commitments to reduce emissions and biodiversity loss are unlikely to be realized without specific actions that directly address this damaging environmental legacy.

•

Time lags in historical tropical deforestation ensure an emission debt of 8.6 PgC

•

Tropical deforestation resulted in a debt of more than 140 forest-specific vertebrates

•

The carbon emissions debt is equivalent to 5–10 years of global deforestation

•

The extinction debt would increase 20^th-century extinctions in vertebrates by 120%

Vertical stratification of adult mosquitoes (Diptera: Culicidae) within a tropical rainforest in Sabah, Malaysia

Background

Malaria cases caused by Plasmodium knowlesi, a simian parasite naturally found in long-tailed and pig-tailed macaques, are increasing rapidly in Sabah, Malaysia. One hypothesis is that this increase is associated with changes in land use. A study was carried out to identify the anopheline vectors present in different forest types and to observe the human landing behaviour of mosquitoes.

Methods

Mosquito collections were carried out using human landing catches at ground and canopy levels in the Tawau Division of Sabah. Collections were conducted along an anthropogenic disturbance gradient (primary forest, lightly logged virgin jungle reserve and salvage logged forest) between 18:00 and 22:00 h.

Results

Anopheles balabacensis, a vector of P. knowlesi, was the predominant species in all collection areas, accounting for 70 % of the total catch, with a peak landing time of 18:30–20:00 h. Anopheles balabacensis had a preference for landing on humans at ground level compared to the canopy (p < 0.0001). A greater abundance of mosquitoes were landing in the logged forest compared to the primary forest (p < 0.0001). There was no difference between mosquito abundance in the logged forest and lightly logged forest (p = 0.554). A higher evening temperature (p < 0.0001) and rainfall (p < 0.0001) significantly decreased mosquito abundance during collection nights.

Conclusions

This study demonstrates the potential ability of An. balabacensis to transmit P. knowlesi between canopy-dwelling simian hosts and ground-dwelling humans, and that forest disturbance increases the abundance of this disease vector. These results, in combination with regional patterns of land use change, may partly explain the rapid rise in P. knowlesi cases in Sabah. This study provides essential data on anthropophily for the principal vector of P. knowlesi which is important for the planning of vector control strategies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1416-1) contains supplementary material, which is available to authorized users.

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside

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.

Road networks predict human influence on Amazonian bird communities

Road building can lead to significant deleterious impacts on biodiversity, varying from direct road-kill mortality and direct habitat loss associated with road construction, to more subtle indirect impacts from edge effects and fragmentation. However, little work has been done to evaluate the specific effects of road networks and biodiversity loss beyond the more generalized effects of habitat loss. Here, we compared forest bird species richness and composition in the municipalities of Santarém and Belterra in Pará state, eastern Brazilian Amazon, with a road network metric called 'roadless volume (RV)' at the scale of small hydrological catchments (averaging 3721 ha). We found a significant positive relationship between RV and both forest bird richness and the average number of unique species (species represented by a single record) recorded at each site. Forest bird community composition was also significantly affected by RV. Moreover, there was no significant correlation between RV and forest cover, suggesting that road networks may impact biodiversity independently of changes in forest cover. However, variance partitioning analysis indicated that RV has partially independent and therefore additive effects, suggesting that RV and forest cover are best used in a complementary manner to investigate changes in biodiversity. Road impacts on avian species richness and composition independent of habitat loss may result from road-dependent habitat disturbance and fragmentation effects that are not captured by total percentage habitat cover, such as selective logging, fire, hunting, traffic disturbance, edge effects and road-induced fragmentation.

Global effects of land use on local terrestrial biodiversity

Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

Logging cuts the functional importance of invertebrates in tropical rainforest

Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests.

Habitat fragmentation and its lasting impact on Earth's ecosystems

We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest's edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.

The relationship between leaf area index and microclimate in tropical forest and oil palm plantation: Forest disturbance drives changes in microclimate

Land use change is a major threat to biodiversity. One mechanism by which land use change influences biodiversity and ecological processes is through changes in the local climate. Here, the relationships between leaf area index and five climate variables - air temperature, relative humidity, vapour pressure deficit, specific humidity and soil temperature - are investigated across a range of land use types in Borneo, including primary tropical forest, logged forest and oil palm plantation. Strong correlations with the leaf area index are found for the mean daily maximum air and soil temperatures, the mean daily maximum vapour pressure deficit and the mean daily minimum relative humidity. Air beneath canopies with high leaf area index is cooler and has higher relative humidity during the day. Forest microclimate is also found to be less variable for sites with higher leaf area indices. Primary forest is found to be up to 2.5 °C cooler than logged forest and up to 6.5 °C cooler than oil palm plantations. Our results indicate that leaf area index is a useful parameter for predicting the effects of vegetation upon microclimate, which could be used to make small scale climate predictions based on remotely sensed data.

Untangling interactions: do temperature and habitat fragmentation gradients simultaneously impact biotic relationships?

Gaining insight into the impact of anthropogenic change on ecosystems requires investigation into interdependencies between multiple drivers of ecological change and multiple biotic responses. Global environmental change drivers can act simultaneously to impact the abundance and diversity of biota, but few studies have also measured the impact across trophic levels. We firstly investigated whether climate (using temperature differences across a latitudinal gradient as a surrogate) interacts with habitat fragmentation (measured according to fragment area and distance to habitat edges) to impact a New Zealand tri-trophic food chain (plant, herbivore and natural enemy). Secondly, we examined how these interactions might differentially impact both the density and biotic processes of species at each of the three trophic levels. We found evidence to suggest that these drivers act non-additively across trophic levels. The nature of these interactions however varied: location synergistically interacted with fragmentation measures to exacerbate the detrimental effects on consumer density; and antagonistically interacted to ameliorate the impact on plant density and on the interactions between trophic levels (herbivory and parasitoid attack rate). Our findings indicate that the ecological consequences of multiple global change drivers are strongly interactive and vary according to the trophic level studied and whether density or ecological processes are investigated.

The transparency, reliability and utility of tropical rainforest land-use and land-cover change models

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.

Modelling land cover change in the Brazilian Amazon: temporal changes in drivers and calibration issues

Land cover change (LCC) models are used in many studies of human impacts on the environment, but knowing how well these models predict observed changes in the landscape is a challenge. We used nearly three decades of LCC maps to run several LCC simulations to: (1) determine which parameters associated with drivers of LCC (e.g. roads) get selected for which transition (forest to deforested, regeneration to deforested or deforested to regeneration); (2) investigate how the parameter values vary through time with respect to the different activities (e.g. farming); and (3) quantify the influence of choosing a particular time period for model calibration and validation on the performance of LCC models. We found that deforestation of primary forests tends to occur along roads (included in 95 % of models) and outside protected areas (included in all models), reflecting farming establishment. Regeneration tends to occur far from roads (included in 78 % of the models) and inside protected areas (included in 38 % of the models), reflecting the processes of land abandonment. Our temporal analysis of model parameters revealed a degree of variation through time (e.g. effectiveness of protected areas rose by 73 %, p < 0.001), but for the majority of parameters there was no significant trend. The degree to which model predictions agreed with observed change was heavily dependent on the year used for calibration (p < 0.001). The next generation of LCC models may need to embed trends in parameter values to allow the processes determining LCC to change through time and exert their influence on model predictions.

BIOFRAG - a new database for analyzing BIOdiversity responses to forest FRAGmentation

Habitat fragmentation studies have produced complex results that are challenging to synthesize. Inconsistencies among studies may result from variation in the choice of landscape metrics and response variables, which is often compounded by a lack of key statistical or methodological information. Collating primary datasets on biodiversity responses to fragmentation in a consistent and flexible database permits simple data retrieval for subsequent analyses. We present a relational database that links such field data to taxonomic nomenclature, spatial and temporal plot attributes, and environmental characteristics. Field assessments include measurements of the response(s) (e.g., presence, abundance, ground cover) of one or more species linked to plots in fragments within a partially forested landscape. The database currently holds 9830 unique species recorded in plots of 58 unique landscapes in six of eight realms: mammals 315, birds 1286, herptiles 460, insects 4521, spiders 204, other arthropods 85, gastropods 70, annelids 8, platyhelminthes 4, Onychophora 2, vascular plants 2112, nonvascular plants and lichens 320, and fungi 449. Three landscapes were sampled as long-term time series (>10 years). Seven hundred and eleven species are found in two or more landscapes. Consolidating the substantial amount of primary data available on biodiversity responses to fragmentation in the context of land-use change and natural disturbances is an essential part of understanding the effects of increasing anthropogenic pressures on land. The consistent format of this database facilitates testing of generalizations concerning biologic responses to fragmentation across diverse systems and taxa. It also allows the re-examination of existing datasets with alternative landscape metrics and robust statistical methods, for example, helping to address pseudo-replication problems. The database can thus help researchers in producing broad syntheses of the effects of land use. The database is dynamic and inclusive, and contributions from individual and large-scale data-collection efforts are welcome.

Assessing the status of wild felids in a highly-disturbed commercial forest reserve in Borneo and the implications for camera trap survey design

The proliferation of camera-trapping studies has led to a spate of extensions in the known distributions of many wild cat species, not least in Borneo. However, we still do not have a clear picture of the spatial patterns of felid abundance in Southeast Asia, particularly with respect to the large areas of highly-disturbed habitat. An important obstacle to increasing the usefulness of camera trap data is the widespread practice of setting cameras at non-random locations. Non-random deployment interacts with non-random space-use by animals, causing biases in our inferences about relative abundance from detection frequencies alone. This may be a particular problem if surveys do not adequately sample the full range of habitat features present in a study region. Using camera-trapping records and incidental sightings from the Kalabakan Forest Reserve, Sabah, Malaysian Borneo, we aimed to assess the relative abundance of felid species in highly-disturbed forest, as well as investigate felid space-use and the potential for biases resulting from non-random sampling. Although the area has been intensively logged over three decades, it was found to still retain the full complement of Bornean felids, including the bay cat Pardofelis badia, a poorly known Bornean endemic. Camera-trapping using strictly random locations detected four of the five Bornean felid species and revealed inter- and intra-specific differences in space-use. We compare our results with an extensive dataset of >1,200 felid records from previous camera-trapping studies and show that the relative abundance of the bay cat, in particular, may have previously been underestimated due to the use of non-random survey locations. Further surveys for this species using random locations will be crucial in determining its conservation status. We advocate the more wide-spread use of random survey locations in future camera-trapping surveys in order to increase the robustness and generality of inferences that can be made.

Predictive modelling of contagious deforestation in the Brazilian Amazon

Tropical forests are diminishing in extent due primarily to the rapid expansion of agriculture, but the future magnitude and geographical distribution of future tropical deforestation is uncertain. Here, we introduce a dynamic and spatially-explicit model of deforestation that predicts the potential magnitude and spatial pattern of Amazon deforestation. Our model differs from previous models in three ways: (1) it is probabilistic and quantifies uncertainty around predictions and parameters; (2) the overall deforestation rate emerges “bottom up”, as the sum of local-scale deforestation driven by local processes; and (3) deforestation is contagious, such that local deforestation rate increases through time if adjacent locations are deforested. For the scenarios evaluated–pre- and post-PPCDAM (“Plano de Ação para Proteção e Controle do Desmatamento na Amazônia”)–the parameter estimates confirmed that forests near roads and already deforested areas are significantly more likely to be deforested in the near future and less likely in protected areas. Validation tests showed that our model correctly predicted the magnitude and spatial pattern of deforestation that accumulates over time, but that there is very high uncertainty surrounding the exact sequence in which pixels are deforested. The model predicts that under pre-PPCDAM (assuming no change in parameter values due to, for example, changes in government policy), annual deforestation rates would halve between 2050 compared to 2002, although this partly reflects reliance on a static map of the road network. Consistent with other models, under the pre-PPCDAM scenario, states in the south and east of the Brazilian Amazon have a high predicted probability of losing nearly all forest outside of protected areas by 2050. This pattern is less strong in the post-PPCDAM scenario. Contagious spread along roads and through areas lacking formal protection could allow deforestation to reach the core, which is currently experiencing low deforestation rates due to its isolation.

Functional traits, the phylogeny of function, and ecosystem service vulnerability

People depend on benefits provided by ecological systems. Understanding how these ecosystem services - and the ecosystem properties underpinning them - respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species' effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms - which both depend on combinations of functional traits - correlate across species and how they are arranged on the species' phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology.

Optimising bait for pitfall trapping of Amazonian dung beetles (Coleoptera: Scarabaeinae)

The accurate sampling of communities is vital to any investigation of ecological processes and biodiversity. Dung beetles have emerged as a widely used focal taxon in environmental studies and can be sampled quickly and inexpensively using baited pitfalls. Although there is now a wealth of available data on dung beetle communities from around the world, there is a lack of standardisation between sampling protocols for accurately sampling dung beetle communities. In particular, bait choice is often led by the idiosyncrasies of the researcher, logistic problems and the dung sources available, which leads to difficulties for inter-study comparisons. In general, human dung is the preferred choice, however, it is often in short supply, which can severely limit sampling effort. By contrast, pigs may produce up to 20 times the volume. We tested the ability of human and pig dung to attract a primary forest dung beetle assemblage, as well as three mixes of the two baits in different proportions. Analyses focussed on the comparability of sampling with pig or human-pig dung mixes with studies that have sampled using human dung. There were no significant differences between richness and abundance sampled by each bait. The assemblages sampled were remarkably consistent across baits, and ordination analyses showed that the assemblages sampled by mixed dung baits were not significantly different from that captured by pure human dung, with the assemblages sampled by 10% and 90% pig mixes structurally most similar to assemblages sampled by human dung. We suggest that a 10:90 human:pig ratio, or similar, is an ideal compromise between sampling efficiency, inter-study comparability and the availability of large quantities of bait for sampling Amazonian dung beetles. Assessing the comparability of assemblage samples collected using different baits represents an important step to facilitating large-scale meta-analyses of dung beetle assemblages collected using non-standard methodology.

Using landscape history to predict biodiversity patterns in fragmented landscapes

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.

Unraveling the drivers of community dissimilarity and species extinction in fragmented landscapes

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.

Fragmentation impairs the microclimate buffering effect of tropical forests

BACKGROUND

Tropical forest species are among the most sensitive to changing climatic conditions, and the forest they inhabit helps to buffer their microclimate from the variable climatic conditions outside the forest. However, habitat fragmentation and edge effects exposes vegetation to outside microclimatic conditions, thereby reducing the ability of the forest to buffer climatic variation. In this paper, we ask what proportion of forest in a fragmented ecosystem is impacted by altered microclimate conditions driven by edge effects, and extrapolate these results to the whole Atlantic Forest biome, one of the most disturbed biodiversity hotspots. To address these questions, we collected above and below ground temperature for a full year using temperature sensors placed in forest fragments of different sizes, and at different distances from the forest edge.

PRINCIPAL FINDINGS

In the Atlantic forests of Brazil, we found that the buffering effect of forests reduced maximum outside temperatures by one third or more at ground level within a forest, with the buffering effect being stronger below-ground than one metre above-ground. The temperature buffering effect of forests was, however, reduced near forest edges with the edge effect extending up to 20 m inside the forest. The heavily fragmented nature of the Brazilian Atlantic forest means that 12% of the remaining biome experiences altered microclimate conditions.

CONCLUSIONS

Our results add further information about the extent of edge effects in the Atlantic Forest, and we suggest that maintaining a low perimeter-to-area ratio may be a judicious method for minimizing the amount of forest area that experiences altered microclimatic conditions in this ecosystem.