Land-use change alters the mechanisms assembling rainforest mammal communities in Borneo

1. The assembly of species communities at local scales is thought to be driven by environmental filtering, species interactions and spatial processes such as dispersal limitation. Little is known about how the relative balance of these drivers of community assembly changes along environmental gradients, especially manmade environmental gradients associated with land-use change. 2. Using concurrent camera- and live-trapping, we investigated the local-scale assembly of mammal communities along a gradient of land-use intensity (old-growth forest, logged forest and oil palm plantations) in Borneo. We hypothesised that increasing land-use intensity would lead to an increasing dominance of environmental control over spatial processes in community assembly. Additionally, we hypothesised that competitive interactions among species might reduce in concert with declines in α-diversity (previously documented) along the land-use gradient. 3. To test our first hypothesis, we partitioned community variance into the fractions explained by environmental and spatial variables. To test our second hypothesis, we used probabilistic models of expected species co-occurrence patterns, in particular focussing on the prevalence of spatial avoidance between species. Spatial avoidance might indicate competition, but might also be due to divergent habitat preferences. 4. We found patterns that are consistent with a shift in the fundamental mechanics governing local community assembly. In support of our first hypothesis, the importance of spatial processes (dispersal limitation and fine-scale patterns of home-ranging) appeared to decrease from low to high intensity land-uses, whilst environmental control increased in importance (in particular due to fine-scale habitat structure). Support for our second hypothesis was weak: whilst we found that the prevalence of spatial avoidance decreased along the land-use gradient, in particular between congeneric species pairs most likely to be in competition, few instances of spatial avoidance were detected in any land-use, and most were likely due to divergent habitat preferences. 5. The widespread changes in land-use occurring in the tropics might be altering not just the biodiversity found in landscapes, but also the fundamental mechanics governing the local assembly of communities. A better understanding of these mechanics, for a range of taxa, could underpin more effective conservation and management of threatened tropical landscapes

Species richness and distribution of primates in disturbed and converted forest landscapes in northern Borneo

Knowledge of fundamental aspects of ecology such as species richness and distribution, and the factors affecting them, is increasingly used to identify priority areas for conservation and to effectively manage threatened species. We investigated the species richness and distribution pattern of non-human primate communities inhabiting 10 sampling sites in four different habitat classes corresponding to increasing habitat disturbance level, i.e. old growth forest, twice logged forest, repeatedly logged forest and oil palm plantation, in and around Kalabakan Forest Reserve, in central Sabah, Malaysian Borneo. By using direct and indirect survey methods, we confirmed the existence of nine, out of the total 10 primate species, found in Sabah, within the surveyed areas. Based on the monthly number of primate species detected, our results indicated a general trend of decreasing primate species richness with increasing habitat disturbance level. However, the response within the disturbed forest sites showed some variations with some sites in repeatedly logged forest displaying comparable primate species number to that of the undisturbed forest sites. We also found that within the forest habitats, tree density is a good predictor of the richness of the primate community with a positive effect. Hence, tree density may be a key indicator for evaluating primate communities in forest habitats. Overall, the results of our study suggest that although not equivalent to areas of undisturbed forest, degraded forests – including those that have been repeatedly logged – are still valuable for primate conservation. In contrast, oil palm plantations have mainly negative effects on the primate community

The distribution and persistence of primate species in disturbed and converted forest landscapes in Sabah, Malaysia: preliminary results

As disturbance and conversion of tropical rainforests due to man-made activities in many parts of the world continue at alarming rates, the future of many tropical rainforest species will depend more than ever on the effective management of a mixture of human-modified landscape. We studied the non-human primate community by direct and indirect sightings across a gradient of habitat disturbance - from old growth forest to heavily logged forest to oil palm plantation- in and around the Stability of Altered Forest Ecosystems (SAFE) Project experimental area in Kalabakan Forest Reserve, south central part of Sabah, Malaysian Borneo. Here we provide the preliminary analysis of our data. We confirmed the existence of nine, of the total of 10 species of non-human primates found in Sabah, within the surveyed areas. By using occupancy analysis we found no evidence of differential habitat disturbance effects on the primate community. We also found no evidence supporting differential habitat disturbance effects on the primate community based on animal body size or feeding habit. The lack in such evidences is surprising and it is likely due to the artifact of the small data set of this study. Interestingly, however, the presence of eight species of primates within the heavily logged forest sampling sites, which included Bornean endemic species and species of high conservation concern, e.g. orangutan, proboscis monkey and Bornean gibbon, shows that even highly disturbed forests in Sabah are still valuable for primate conservation

Vertical transmission of fungal endophytes is widespread in forbs

To date, it has been thought that endophytic fungi in forbs infect the leaves of their hosts most commonly by air-borne spores (termed “horizontal transmission”). Here, we show that vertical transmission from mother plant to offspring, via seeds, occurs in six forb species (Centaurea cyanus, C. nigra,Papaver rhoeas,Plantago lanceolata,Rumex acetosa, and Senecio vulgaris), suggesting that this may be a widespread phenomenon. Mature seeds were collected from field-grown plants and endophytes isolated from these, and from subsequent cotyledons and true leaves of seedlings, grown in sterile conditions. Most seeds contain one species of fungus, although the identity of the endophyte differs between plant species. Strong evidence for vertical transmission was found for two endophyte species, Alternaria alternata and Cladosporium sphaerospermum. These fungi were recovered from within seeds, cotyledons, and true leaves, although the plant species they were associated with differed. Vertical transmission appears to be an imperfect process, and germination seems to present a bottleneck for fungal growth. We also found that A. alternata and C. sphaerospermum occur on, and within pollen grains, showing that endophyte transmission can be both within and between plant generations. Fungal growth with the pollen tube is likely to be the way in which endophytes enter the developing seed. The fact that true vertical transmission seems common suggests a more mutualistic association between these fungi and their hosts than has previously been thought, and possession of endophytes by seedling plants could have far-reaching ecological consequences. Seedlings may have different growth rates and be better protected against herbivores and pathogens, dependent on the fungi that were present in the mother plant. This would represent a novel case of trans-generational resistance in plants

Terrestrial mammal species richness and composition in three small forest patches within an oil palm landcape in Sabah, Malaysian Borneo

Small and highly degraded forest patches are usually scattered across oil palm plantation landscapes and often exist as permanent features. By using a combination of camera-trapping and line-transect methods, we evaluated the usefulness of three such forest patches (< 30 ha) for terrestrial mammal species conservation in a mature oil palm plantation located near (< 1.7 km) a large continuous tract of logged forest in eastern Sabah, Malaysian Borneo. Of the 29 terrestrial mammal species recorded in this study, 28 were found in the continuous logged forest habitat including six species that are either large-bodied, wide ranging, locally rare or are of high conservation concern. In comparison, 18 species were recorded across the three forest patches collectively; consisting mostly of species that are widespread, well-adapted to living in highly modified habitats and of low conservation concern. The presence of small forest patches within the oil palm habitat matrix seemed to be useful to some extent for some mammal species. However, many of the species were likely only transient in this habitat. The maintenance of large continuous tracts of natural forest is critical to the continued survival of many terrestrial mammal species on Borneo, particularly for species that are of high conservation value

Life in the Canopy: Using Camera-Traps to Inventory Arboreal Rainforest Mammals in Borneo

Arboreal mammals form a diverse group providing ecologically important functions such as predation, pollination and seed dispersal. However, their cryptic and elusive nature, and the heights at which they live, makes studying these species challenging. Consequently, our knowledge of rainforest mammals is heavily biased towards terrestrial species, limiting our understanding of overall community structure and the possible impacts of human-induced disturbance. We undertook the first in-depth appraisal of an arboreal mammal community in Southeast Asia, using camera-traps set in unlogged and logged tropical rainforest in Sabah, Borneo. Using paired canopy and terrestrial camera-traps at 50 locations (25 in unlogged forest, 25 in logged), we assessed the effectiveness of camera-trapping at characterising the arboreal versus terrestrial community, and tested the influence of strata and forest type on community structure and composition. The paired design detected 55 mammal species across 15,817 camera-trap nights, and additional canopy sampling in a subset of trees added a further two arboreal species to the inventory. In total, thirty species were detected exclusively by terrestrial camera-traps, eighteen exclusively by canopy camera-traps, and nine by units set at both heights, demonstrating significant differences between arboreal and terrestrial communities. This pattern was strongest in unlogged forest, reflecting greater structural diversity of this habitat, but held in logged forest as well. Species accumulation curves revealed that canopy camera-trapping significantly boosted species inventories compared to terrestrial-only sampling, and was particularly effective at detecting gliding mammals, rodents and primates. Canopy inventories took longer to reach an asymptote, suggesting that a greater sampling effort is required when deploying canopy camera-traps compared to those set on the ground. We demonstrate that arboreal mammals in Borneo’s rainforest form a diverse and distinct community, and can be sampled effectively using canopy camera-traps. However, the additional costs incurred by sampling in the canopy can be substantial. We provide recommendations to maximise sampling effectiveness, while bringing down costs, to help encourage further study into one of the last frontiers of tropical forest research

Prey availability and temporal partitioning modulate felid coexistence in Neotropical forests

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids

High carbon stock forests provide co-benefits for tropical biodiversity

1. Carbon-based policies provide powerful opportunities to unite tropical forest conservation with climate change mitigation. However, their effectiveness in delivering biodiversity co-benefits is dependent on high levels of biodiversity being found in high carbon areas. Previous studies have focussed solely on the co-benefits associated with Reducing Emissions from Deforestation and forest Degradation (REDD+) over large spatial scales, with few empirically testing carbon-biodiversity correlations at management unit scales appropriate to decision-makers. Yet, in development frontiers, where most biodiversity and carbon loss occurs, carbon-based policies are increasingly driven by commodity certification schemes, which are applied at the concession-level. 2. Working in a typical human-modified landscape in Southeast Asia, we examined the biodiversity value of land prioritised via application of REDD+ or the High Carbon Stock (HCS) Approach, the emerging land-use planning tool for oil palm certification. Carbon stocks were estimated via low- and high-resolution datasets derived from global or local level biomass. Mammalian species richness was predicted using hierarchical Bayesian multi-species occupancy models of camera-trap data from forest and oil palm habitats. 3. At the community level, HCS forest supported comparable mammal diversity to control sites in continuous forest, while lower carbon strata exhibited reduced species occupancy. 4. No association was found between species richness and carbon when the latter was estimated using coarse-resolution data. However, when using high-resolution, field validated biomass data, diversity demonstrated positive relationships with carbon for threatened and disturbance-sensitive species, suggesting sensitivity of co-benefits to carbon data sources and the species considered. 5. Policy implications. Our work confirms the potential for environmental certification and REDD+ to work in tandem with conservation to mitigate agricultural impacts on tropical forest carbon stocks and biodiversity, especially if this directs development to low carbon, low biodiversity areas

Best practices and software for themanagement and sharing of camera trap data for small and large scales studies

Camera traps typically generate large amounts of bycatch data of non-target species that are secondary to the study’s objectives. Bycatch data pooled from multiple studies can answer secondary research questions; however, variation in field and data management techniques creates problems when pooling data from multiple sources. Multi-collaborator projects that use standardized methods to answer broad-scale research questions are rare and limited in geographical scope. Many small, fixed-term independent camera trap studies operate in poorly represented regions, often using field and data management methods tailored to their own objectives. Inconsistent data management practices lead to loss of bycatch data, or an inability to share it easily. As a case study to illustrate common problems that limit use of bycatch data, we discuss our experiences processing bycatch data obtained by multiple research groups during a range-wide assessment of sun bears Helarctos malayanus in Southeast Asia. We found that the most significant barrier to using bycatch data for secondary research was the time required, by the owners of the data and by the secondary researchers (us), to retrieve, interpret and process data into a form suitable for secondary analyses. Furthermore, large quantities of data were lost due to incompleteness and ambiguities in data entry. From our experiences, and from a review of the published literature and online resources, we generated nine recommendations on data management best practices for field site metadata, camera trap deployment metadata, image classification data and derived data products. We cover simple techniques that can be employed without training, special software and Internet access, as well as options for more advanced users, including a review of data management software and platforms. From the range of solutions provided here, researchers can employ those that best suit their needs and capacity. Doing so will enhance the usefulness of their camera trap bycatch data by improving the ease of data sharing, enabling collaborations and expanding the scope of research

Logged tropical forests have amplified and diverse ecosystem energetics

Old growth tropical forests are widely recognised as immensely important for their biodiversity and high biomass1. Conversely, selectively logged tropical forests are usually characterised 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 old growth forests, likely driven by greater resource accessibility and vegetation palatability. Most major 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