CamTrapAsia: A dataset of tropical forest vertebrate communities from 239 camera trapping studies

Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land-use change and hunting, the latter frequently referred as "defaunation." This is especially true in tropical Asia where there is extensive land-use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non-invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera-derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large-scale pressence-only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10-, 20-, and 30-km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single-species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data.

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.

Selective Logging Shows No Impact on the Dietary Breadth of a Generalist Bat Species: The Fawn Leaf-Nosed Bat (Hipposideros cervinus)

Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Diptera, Blattodea, and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed per-bat in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites. Multiple bioinformatic parameters were used, to assess how they altered our perception of sampling completeness. While parameter choice altered estimates of completeness, a very high sampling effort was always required to detect the entire prey community.

Fungal communities in bat guano, speleothem surfaces, and cavern water in Madai cave, Northern Borneo (Malaysia)

The island of Borneo is a global biodiversity hotspot. However, its limestone caves are one of its least-studied ecosystems. We report for the first time the fungal species richness, diversity and abundance from Madai cave, situated in north-eastern Borneo. Environmental samples from inside the cave environment were collected (guano, speleothem, and cavern water) via opportunistic sampling. The dilution method was performed for isolation of fungi. Morphological characterisation and molecular analysis of the ITS region were utilised for the identification of isolates. Fifty-five pure cultures of fungi were attained, comprising 32 species from 15 genera, eight orders, and two divisions, Ascomycota and Basidiomycota. Ascomycetes dominated the fungal composition, accounting for 53 (96%) out of 55 total isolates. Penicillium spp. accounted for more than 47.1% of fungal abundance in all sample types. However, Aspergillus spp. had the highest occurrence rate, being isolated from all environmental samples except one. Purpureocillium lilacinum was isolated most frequently, appearing in five separate samples across all three substrates. Annulohypoxylon nitens, Ganoderma australe, Pyrrhoderma noxium, and Xylaria feejeensis were discovered and reported for the first time from the cave environment. This study provides additional data for further research on the mycoflora of Sabah’s various ecosystems, especially limestone caves.

Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats

The application of metabarcoding to environmental and invertebrate‐derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land‐use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood‐feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human‐modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.

Factors influencing riverine utilization patterns in two sympatric macaques

Many species of terrestrial animals, including primates, live in varied association with the aquatic (e.g., riverine or coastal) environment. However, the benefits that each species receive from the aquatic environment are thought to vary depending on their social and ecological characteristics, and thus, elucidating those benefits to each species is important for understanding the principles of wild animal behaviour. In the present study, to gain a more complete picture of aquatic environment use, including social and ecological factors in primates, factors affecting riverine habitat utilization of two macaque species (Macaca nemestrina and M. fascicularis) were identified and qualitative comparisons were made with sympatric proboscis monkeys (Nasalis larvatus), which have different social and ecological characteristics. Temporal variation in sighting frequency of macaques at the riverbanks was positively related to the fruit availability of a dominant riparian plant species and negatively related to the river water level which affects the extent of predation pressure. Riverine utilization of macaques was greatly influenced by distribution and abundance of food (especially fruit) resources, possibly in association with predation pressure. Additionally, qualitative ecological comparisons with sympatric proboscis monkeys suggest that the drivers of riverine utilization depend on the feeding niches of the species, and different anti-predator strategies resulting from their differing social structures.

Habitat use by a primate community in a lowland dipterocarp forest in Danum Valley, Borneo

Knowledge of niche partitioning with respect to habitat is indispensable to understand the mechanism of coexistence of multiple species. Among primates, however, data are still deficient because repeated survey for a sufficiently long time, covering seasonal changes over a large area, is the only way to clarify habitat segregation within a seasonally fluctuating environment. Southeast Asia is particularly interesting because of the supra-annual, highly unpredictable seasonality in fruiting known as mast fruiting. We conducted repeated route census, habitat monitoring, and group tracking for 25 months in two study sites (ca. 10 km apart) in the largely primary lowland dipterocarp forest of the Danum Valley Conservation Area, eastern Sabah, northern Borneo, Malaysia. The five species of diurnal primates (Bornean orangutan Pongo pygmaeus, Müeller's gibbon Hylobates muelleri, red leaf monkey Presbytis rubicunda, long-tailed macaque Macaca fascicularis, and southern pig-tailed macaque M. nemestrina) did not show horizontal spatial segregation. Red leaf monkeys showed preferences for places with short tree height, but their distribution was not confined to such places. In response to the fruiting peak observed once during the study period, orangutans increased their numbers simultaneously in the two study sites. The average tree height used by the five species was different, but their range overlapped substantially. Compared with other primate communities, the lack of horizontal spatial segregation and the suggested long-distance movement of orangutans seem to be unique characteristics in Borneo, although the use of different forest strata is a widespread phenomenon among primate communities throughout the world.

Densities of Bornean orang-utans (Pongo pygmaeus morio) in heavily degraded forest and oil palm plantations in Sabah, Borneo

The conversion of forest to agriculture continues to contribute to the loss and fragmentation of remaining orang-utan habitat. There are still few published estimates of orang-utan densities in these heavily modified agricultural areas to inform range-wide population assessments and conservation strategies. In addition, little is known about what landscape features promote orang-utan habitat use. Using indirect nest count methods, we implemented surveys and estimated population densities of the Northeast Bornean orang-utan (Pongo pygmaeus morio) across the continuous logged forest and forest remnants in a recently salvage-logged area and oil palm plantations in Sabah, Malaysian Borneo. We then assessed the influence of landscape features and forest structural metrics obtained from LiDAR data on estimates of orang-utan density. Recent salvage logging appeared to have a little short-term effect on orang-utan density (2.35 ind/km ² ), which remained similar to recovering logged forest nearby (2.32 ind/km ² ). Orang-utans were also present in remnant forest patches in oil palm plantations, but at significantly lower numbers (0.82 ind/km ² ) than nearby logged forest and salvage-logged areas. Densities were strongly influenced by variation in canopy height but were not associated with other potential covariates. Our findings suggest that orang-utans currently exist, at least in the short-term, within human-modified landscapes, providing that remnant forest patches remain. We urge greater recognition of the role that these degraded habitats can have in supporting orang-utan populations, and that future range-wide analyses and conservation strategies better incorporate data from human-modified landscapes.

Improvement in body composition following a supervised exercise-training program of adult patients with cystic fibrosis

OBJECTIVES

Maintenance of optimal nutritional status is a crucial issue for cystic fibrosis (CF) patients. Here, we evaluate the effects of an 8-week exercise training (ET) program on body composition in CF patients.

METHODS

This prospective pilot observational study was conducted in adult CF subjects in stable condition following their annual check-up. The ET program consisted of three sessions per week and included aerobic training (≥30min), muscle strengthening, circuit training, and relaxation. Exercise tolerance (6-minute walk test, 6MWT), pulmonary function, quadriceps isometric strength, and body composition (bioelectrical impedance analysis of fat-free mass [FFM], fat mass, and body cell mass) were analyzed before and immediately after the ET program. A control group of CF patients who preferred not to participate in the ET program received the same evaluations.

RESULTS

A total of 43 CF patients were enrolled and offered the ET program; 28 accepted (aged 28±5 years, forced expiratory volume in 1s [FEV₁] 48.8±19% predicted) and 15 declined the ET program but agreed to be part of the control group (matched for age and CF severity: 30.8±9 years, FEV₁ 51.8±16.5%). Pulmonary function was unchanged at the end of the ET program, but significant improvements were observed in 6MWT distance (from 520±96m to 562±105m, P<0.001) and muscle strength (331±141N to 379±168N, P<0.001). Although mean body mass index did not change, the ET group showed significantly increased FFM (43.85±8kg to 44.5±9.2kg, P=0.03) and a trend towards increased body cell mass (21.4±6 to 22.1±6.6kg, P=0.06). All other parameters were unchanged by ET. There were no significant correlations between the increase in FFM and the improvements in either 6MWT distance or muscle strength. The CF control group exhibited no significant changes in any parameters between evaluations.

CONCLUSIONS

ET significantly improved FFM, but not body mass index, in CF patients. The results illustrate the superiority of bioimpedancemetry for assessing changes in body composition and reveal the importance of ET for improving not only exercise tolerance but also nutritional status in these patients.

The influence of logging on vertebrate responses to mast fruiting

Periods of extreme food abundance, such as irregular masting events, can dramatically affect animal populations and communities, but the extent to which anthropogenic disturbances alter animal responses to mast events is not clear. In South-East Asia, dipterocarp trees reproduce in mast fruiting events every 2-10 years in some of the largest masting events on the planet. These trees, however, are targeted for selective logging, reducing the intensity of fruit production and potentially affecting multiple trophic levels. Moreover, animal responses to resource pulse events have largely been studied in systems where the major mast consumers have been extirpated. We sought to evaluate the influence of human-induced habitat disturbance on animal responses to masting in a system where key mast consumers remain extant. We used motion-triggered camera traps to quantify terrestrial mammal and bird occurrences in Sabah, Malaysian Borneo, relative to variation in fruit biomass from 69 plant families during a major (2014) and minor (2015) masting event and a non-mast year (2013), in both logged and unlogged forests. Bearded pigs (Sus barbatus) showed the clearest responses to masting and occurrence rates were highest in unlogged forest in the year following the major mast, suggesting that the pulse in fruit availability increased immigration or reproduction. We also detected local-scale spatial tracking of dipterocarp fruits in bearded pigs in unlogged forest, while this was equivocal in other species. In contrast, pigs and other vertebrate taxa in our study showed limited response to spatial or temporal variation in fruit availability in logged forest. Our findings suggest that vertebrates, namely bearded pigs, may respond to masting via movement and increased reproduction, but that these responses may be attenuated by habitat disturbance.

Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo

The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.

Multiple stages of tree seedling recruitment are altered in tropical forests degraded by selective logging

Tropical forest degradation is a global environmental issue. In degraded forests, seedling recruitment of canopy trees is vital for forest regeneration and recovery. We investigated how selective logging, a pervasive driver of tropical forest degradation, impacts canopy tree seedling recruitment, focusing on an endemic dipterocarp Dryobalanops lanceolata in Sabah, Borneo. During a mast-fruiting event in intensively logged and nearby unlogged forest, we examined four stages of the seedling recruitment process: seed production, seed predation, and negative density-dependent germination and seedling survival. Our results suggest that each stage of the seedling recruitment process is altered in logged forest. The seed crop of D. lanceolata trees in logged forest was one-third smaller than that produced by trees in unlogged forest. The functional role of vertebrates in seed predation increased in logged forest while that of non-vertebrates declined. Seeds in logged forest were less likely to germinate than those in unlogged forest. Germination increased with local-scale conspecific seed density in unlogged forest, but seedling survival tended to decline. However, both germination and seedling survival increased with local-scale conspecific seed density in logged forest. Notably, seed crop size, germination, and seedling survival tended to increase for larger trees in both unlogged and logged forests, suggesting that sustainable timber extraction and silvicultural practices designed to minimize damage to the residual stand are important to prevent seedling recruitment failure. Overall, these impacts sustained by several aspects of seedling recruitment in a mast-fruiting year suggest that intensive selective logging may affect long-term population dynamics of D. lanceolata. It is necessary to establish if other dipterocarp species, many of which are threatened by the timber trade, are similarly affected in tropical forests degraded by intensive selective logging.

The combined impacts of experimental defaunation and logging on seedling traits and diversity

Animals can have both positive (e.g. via seed dispersal) and negative (e.g. via herbivory) impacts on plants. The net effects of these interactions remain difficult to predict and may be affected by overhunting and habitat disturbance, two widespread threats to tropical forests. Recent studies have documented their separate effects on plant recruitment but our understanding of how defaunation and logging interact to influence tropical tree communities is limited. From 2013 to 2016, we followed the fate of marked tree seedlings (n = 1489) from 81 genera in and outside experimental plots. Our plots differentially excluded small, medium and large-bodied mammal herbivores in logged and unlogged forest in Malaysian Borneo. We assessed the effects of experimental defaunation and logging on taxonomic diversity and plant trait (wood density, specific leaf area, fruit size) composition of seedling communities. Although seedling mortality was highest in the presence of all mammal herbivores (44%), defaunation alone did not alter taxonomic diversity nor plant trait composition. However, herbivores (across all body sizes) significantly reduced mean fruit size across the seedling community over time (95% confidence interval (CI): -0.09 to -0.01), particularly in logged forest (95% CI: -0.12 to -0.003). Our findings suggest that impacts of mammal herbivores on plant communities may be greater in forests with a history of disturbance and could subsequently affect plant functional traits and ecological processes associated with forest regeneration.

Lowland biotic attrition revisited: body size and variation among climate change 'winners' and 'losers'

The responses of lowland tropical communities to climate change will critically influence global biodiversity but remain poorly understood. If species in these systems are unable to tolerate warming, the communities-currently the most diverse on Earth-may become depauperate ('biotic attrition'). In response to temperature changes, animals can adjust their distribution in space or their activity in time, but these two components of the niche are seldom considered together. We assessed the spatio-temporal niches of rainforest mammal species in Borneo across gradients in elevation and temperature. Most species are not predicted to experience changes in spatio-temporal niche availability, even under pessimistic warming scenarios. Responses to temperature are not predictable by phylogeny but do appear to be trait-based, being much more variable in smaller-bodied taxa. General circulation models and weather station data suggest unprecedentedly high midday temperatures later in the century; predicted responses to this warming among small-bodied species range from 9% losses to 6% gains in spatio-temporal niche availability, while larger species have close to 0% predicted change. Body mass may therefore be a key ecological trait influencing the identity of climate change winners and losers. Mammal species composition will probably change in some areas as temperatures rise, but full-scale biotic attrition this century appears unlikely.

Fecal Nutrients Suggest Diets of Higher Fiber Levels in Free-Ranging than in Captive Proboscis Monkeys (Nasalis larvatus)

Understanding the natural diet of species may provide useful information that can contribute to successful captive maintenance. A common problem experienced with captive foregut-fermenting primate (colobine) diets is that they are deficient in fiber and therefore highly digestible. This may contribute to gastrointestinal disorders often observed in zoos. An approach to obtain information relevant for the improvement of diets is to compare the nutrient composition of feces from free-ranging and captive individuals. In theory, fecal material can be considered a proxy for diet intake integrated over a certain period of time. We collected fecal samples from eight free-ranging proboscis monkey (Nasalis larvatus, a highly endangered colobine species) groups from a secondary forest along the Kinabatangan River and four from a mixed mangrove-riverine forest along the Garama River, Sabah, Borneo, Malaysia. We also collected fecal samples from 12 individual captive adult/sub-adult proboscis monkeys from three different zoos. We confirmed that feces from free-ranging monkeys contained more fiber and less metabolic fecal nitrogen than those from captive specimens, indicating a less digestible diet in the wild. Modifying the diets of captive colobines to include more fiber, comparable to those of free-ranging ones, may contribute to their health and survival.

Defaunation and habitat disturbance interact synergistically to alter seedling recruitment

Vertebrate granivores destroy plant seeds, but whether animal-induced seed mortality alters plant recruitment varies with habitat context, seed traits, and among granivore species. An incomplete understanding of seed predation makes it difficult to predict how widespread extirpations of vertebrate granivores in tropical forests might affect tree communities, especially in the face of habitat disturbance. Many tropical forests are simultaneously affected by animal loss as well as habitat disturbance, but the consequences of each for forest regeneration are often studied separately or additively, and usually on a single plant demographic stage. The combined impacts of these threats could affect plant recruitment in ways that are not apparent when studied in isolation. We used wire cages to exclude large (elephants), medium, (sambar deer, bearded pigs, muntjac deer), and small (porcupines, chevrotains) ground-dwelling mammalian granivores and herbivores in logged and unlogged forests in Malaysian Borneo. We assessed the interaction between habitat disturbance (selective logging) and experimental defaunation on seed survival, germination, and seedling establishment in five dominant dipterocarp tree species spanning a 21-fold gradient in seed size. Granivore-induced seed mortality was consistently higher in logged forest. Germination of unpredated seeds was reduced in logged forest and in the absence of small to large-bodied mammals. Experimental defaunation increased germination and reduced seed removal but had little effect on seed survival. Seedling recruitment however, was more likely where logging and animal loss occurred together. The interacting effects of logging and hunting could therefore, actually increase seedling establishment, suggesting that the loss of mammals in disturbed forest could have important consequences for forest regeneration and composition.

Seasonal Fluctuations of Astrovirus, But Not Coronavirus Shedding in Bats Inhabiting Human-Modified Tropical Forests

Emerging infectious diseases (EIDs) are considered a major threat to global health. Most EIDs appear to result from increased contact between wildlife and humans, especially when humans encroach into formerly pristine habitats. Habitat deterioration may also negatively affect the physiology and health of wildlife species, which may eventually lead to a higher susceptibility to infectious agents and/or increased shedding of the pathogens causing EIDs. Bats are known to host viruses closely related to important EIDs. Here, we tested in a paleotropical forest with ongoing logging and fragmentation, whether habitat disturbance influences the occurrence of astro- and coronaviruses in eight bat species. In contrast to our hypothesis, anthropogenic habitat disturbance was not associated with corona- and astrovirus detection rates in fecal samples. However, we found that bats infected with either astro- or coronaviruses were likely to be coinfected with the respective other virus. Additionally, we identified two more risk factors influencing astrovirus shedding. First, the detection rate of astroviruses was higher at the beginning of the rainy compared to the dry season. Second, there was a trend that individuals with a poor body condition had a higher probability of shedding astroviruses in their feces. The identification of risk factors for increased viral shedding that may potentially result in increased interspecies transmission is important to prevent viral spillovers from bats to other animals, including humans.

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.

Factors Affecting Leaf Selection by Foregut-fermenting Proboscis Monkeys: New Insight from in vitro Digestibility and Toughness of Leaves

Free-living animals must make dietary choices in terms of chemical and physical properties, depending on their digestive physiology and availability of food resources. Here we comprehensively evaluated the dietary choices of proboscis monkeys (Nasalis larvatus) consuming young leaves. We analysed the data for leaf toughness and digestibility measured by an in vitro gas production method, in addition to previously reported data on nutrient composition. Leaf toughness, in general, negatively correlated with the crude protein content, one of the most important nutritional factors affecting food selection by leaf-eating primates. This result suggests that leaf toughness assessed by oral sensation might be a proximate cue for its protein content. We confirmed the importance of the leaf chemical properties in terms of preference shown by N. larvatus; leaves with high protein content and low neutral detergent fibre levels were preferred to those of the common plant species. We also found that these preferred leaves were less tough and more digestible than the alternatives. Our in vitro results also suggested that N. larvatus were little affected by secondary plant compounds. However, the spatial distribution pattern of plant species was the strongest factor explaining the selection of the preferred leaf species.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Habitat disturbance results in chronic stress and impaired health status in forest-dwelling paleotropical bats

Anthropogenic habitat disturbance is a major threat to biodiversity worldwide. Yet, before population declines are detectable, individuals may suffer from chronic stress and impaired immunity in disturbed habitats, making them more susceptible to pathogens and adverse weather conditions. Here, we tested in a paleotropical forest with ongoing logging and fragmentation, whether habitat disturbance influences the body mass and immunity of bats. We measured and compared body mass, chronic stress (indicated by neutrophil to lymphocyte ratios) and the number of circulating immune cells between several bat species with different roost types living in recovering areas, actively logged forests, and fragmented forests in Sabah, Malaysia. In a cave-roosting species, chronic stress levels were higher in individuals from fragmented habitats compared with conspecifics from actively logged areas. Foliage-roosting species showed a reduced body mass and decrease in total white blood cell counts in actively logged areas and fragmented forests compared with conspecifics living in recovering habitats. Our study highlights that habitat disturbance may have species-specific effects on chronic stress and immunity in bats that are potentially related to the roost type. We identified foliage-roosting species as particularly sensitive to forest habitat deterioration. These species may face a heightened extinction risk in the near future if anthropogenic habitat alterations continue.

Development and behavior of wild infant-juvenile East Bornean orangutans (Pongo pygmaeus morio) in Danum Valley

Orangutans have a long period of immaturity and the longest inter-birth interval (IBI) of all mammals, which can be explained by their solitary life style, preventing the mother from rearing two offspring simultaneously (solitary life hypothesis) [corrected]. We collected data on mother-offspring dyads living in a primary lowland forest in Danum Valley, East Borneo in an effort to examine the developmental and behavioral patterns of the subspecies Pongo pygmaeus morio. We analyzed developmental changes in mother-offspring distance, contact, and activity budgets in orangutans ranging from 1 to 7 years of age. The results indicated decreased resting and playing with increasing age, whereas feeding, traveling and social play all increased significantly. Mothers' feeding and traveling time were good predictors of their offspring's feeding and traveling activities. Mother-offspring contact lasted longer in resting contexts; contact during traveling was almost non-existent after 4 years of age. Comparisons with previously published data on the Sumatran species Pongo abelli revealed no fundamental differences in these behavioral measures. However, a shorter association time with the mother after behavioral independence is documented for this East Bornean population in comparison to Sumatran populations. These results are best explained by the solitary life hypothesis, in agreement with previous studies. We suggest that environmental constraints in Bornean forests, as well as a lower population density, should be considered when interpreting the differences between Sumatran and Bornean orangutans in both the period of association with mother and the IBI.

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.

Euarchontan Opsin Variation Brings New Focus to Primate Origins

Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination.

The First Estimates of Marbled Cat Pardofelis marmorata Population Density from Bornean Primary and Selectively Logged Forest

The marbled cat Pardofelis marmorata is a poorly known wild cat that has a broad distribution across much of the Indomalayan ecorealm. This felid is thought to exist at low population densities throughout its range, yet no estimates of its abundance exist, hampering assessment of its conservation status. To investigate the distribution and abundance of marbled cats we conducted intensive, felid-focused camera trap surveys of eight forest areas and two oil palm plantations in Sabah, Malaysian Borneo. Study sites were broadly representative of the range of habitat types and the gradient of anthropogenic disturbance and fragmentation present in contemporary Sabah. We recorded marbled cats from all forest study areas apart from a small, relatively isolated forest patch, although photographic detection frequency varied greatly between areas. No marbled cats were recorded within the plantations, but a single individual was recorded walking along the forest/plantation boundary. We collected sufficient numbers of marbled cat photographic captures at three study areas to permit density estimation based on spatially explicit capture-recapture analyses. Estimates of population density from the primary, lowland Danum Valley Conservation Area and primary upland, Tawau Hills Park, were 19.57 (SD: 8.36) and 7.10 (SD: 1.90) individuals per 100 km², respectively, and the selectively logged, lowland Tabin Wildlife Reserve yielded an estimated density of 10.45 (SD: 3.38) individuals per 100 km². The low detection frequencies recorded in our other survey sites and from published studies elsewhere in its range, and the absence of previous density estimates for this felid suggest that our density estimates may be from the higher end of their abundance spectrum. We provide recommendations for future marbled cat survey approaches.

Oil palm plantations fail to support mammal diversity

Agricultural expansion is the largest threat to global biodiversity. In particular, the rapid spread of tree plantations is a primary driver of deforestation in hyperdiverse tropical regions. Plantations tend to support considerably lower biodiversity than native forest, but it remains unclear whether plantation traits affect their ability to sustain native wildlife populations, particularly for threatened taxa. If animal diversity varies across plantations with different characteristics, these traits could be manipulated to make plantations more "wildlife friendly." The degree to which plantations create edge effects that degrade habitat quality in adjacent forest also remains unclear, limiting our ability to predict wildlife persistence in mixed-use landscapes. We used systematic camera trapping to investigate mammal occurrence and diversity in oil palm plantations and adjacent forest in Sabah, Malaysian Borneo. Mammals within plantations were largely constrained to locations near native forest; the occurrence of most species and overall species richness declined abruptly with decreasing forest proximity from an estimated 14 species at the forest ecotone to -1 species 2 km into the plantation. Neither tree height nor canopy cover within plantations strongly affected mammal diversity or occurrence, suggesting that manipulating tree spacing or planting cycles might not make plantations more wildlife friendly. Plantations did not appear to generate strong edge effects; mammal richness within forest remained high and consistent up to the plantation ecotone. Our results suggest that land-sparing strategies, as opposed to efforts to make plantations more wildlife-friendly, are required for regional wildlife conservation in biodiverse tropical ecosystems.

Pectin-Derived Acidic Oligosaccharides Improve the Outcome of Pseudomonas aeruginosa Lung Infection in C57BL/6 Mice

The administration of prebiotics as oligosaccharides (OS), by acting on intestinal microbiota, could modulate the immune and inflammatory response and represent a new strategy to improve the outcome of bacterial infection. The aim of this study was to determine whether pectin-derived acidic oligosaccharides (pAOS) could modulate the outcome of pulmonary P. aeruginosa (PA) infection in C57BL/6 mice, which develop a Th1 response to PA lung infection. Mice were randomized for 5 weeks to consume a control or a 5% pAOS diet and chronically infected by PA. Resistance to a second PA infection was also analyzed by reinfecting the surviving mice 2 weeks after the first infection. Compared with control mice, mice fed pAOS had reduced mortality (P<0.05). This improvement correlated with a better control of the inflammatory response with a lower neutrophil count on day 1 (P<0.05), a sustained neutrophil and macrophage recruitment on days 2 and 3 (P<0.01) a greater and sustained IL-10 release in lung (P<0.05) and a reduction of the Th1 response and M1 activation with a lower IFN-γ/IL-4 (P<0.01) and nos2/arg1 (P<0.05) ratios. These results coincided with a modulation of the intestinal microbiota as shown by an increased butyric acid concentration in feces (P<0.05). Moreover, pAOS decreased the bacterial load (P<0.01) in mice reinfected 2 weeks after the first infection, suggesting that pAOS could reduce pulmonary exacerbations. In conclusion, pAOS improved the outcome of PA infection in C57BL/6 mice by modulating the intestinal microbiota and the inflammatory and immune responses.

Further studies on the biological activity of hazelnut allergens

Background

Sensitization to hazelnut allergens vary depending on the geographic origin and age of the patients. The objective of this study was to further investigate the allergenic activity of hazelnut allergens using sera from patients recruited in various European regions and presenting different sensitization patterns to hazelnut proteins.

Methods

Natural Cor a 11 and Cor a 9 were purified from hazelnut whereas Cor a 1 and Cor a 8 were produced as recombinant proteins (rCor a 1.04 and rCor a 8). Sera from hazelnut allergic patients were collected in France (n = 5), Switzerland (n = 2), Greece (n = 11) and Spain (n = 3), within the Europrevall project. Total and allergen-specific IgE were quantified by enzyme allergosorbent test and IgE immunoblot were performed using pooled sera from birch-pollen endemic region or from Greece. Histamine Release (HR) assays were performed with stripped basophils passively sensitized with individual sera and challenged by a hazelnut extract or the different hazelnut allergens.

Results

As previously described, hazelnut allergic patients from Mediterranean countries are mainly sensitized to the nsLTP Cor a 8 whereas patients from France and Switzerland are sensitized to pollen-related allergens. Interestingly, an intermediate profile was evidenced in patients from Madrid. Hazelnut 7S globulin (Cor a 11) and 11S globulin (Cor a 9) were found to be minor allergens, recognized only by patients from Mediterranean countries. The biologic activity of the 4 tested allergens, analysed by HR assay, further confirmed the sensitization patterns, but also demonstrated the very high elicitation potency of Cor a 8.

Conclusions

This work, extending previously published researches, represents a step towards the better understanding of the complexity of hazelnut allergy and provides new data on the biological activity of hazelnut allergens and extracts.

Electronic supplementary material

The online version of this article (doi:10.1186/s13601-015-0066-7) contains supplementary material, which is available to authorized users.

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.