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

Gut microbial community in proboscis monkeys (Nasalis larvatus): implications for effects of geographical and social factors

Recent technological advances have enabled comprehensive analyses of the previously uncharacterized microbial community in the gastrointestinal tracts of numerous animal species; however, the gut microbiota of several species, such as the endangered proboscis monkey (Nasalis larvatus) examined in this study, remains poorly understood. Our study sought to establish the first comprehensive data on the gut microbiota of free-ranging foregut-fermenting proboscis monkeys and to determine how their microbiota are affected locally by environmental factors, i.e. geographical distance, and social factors, i.e. the number of adult females within harem groups and the number of adults and subadults within non-harem groups, in a riverine forest in Sabah, Malaysian Borneo. Using 16S rRNA gene sequencing of 264 faecal samples collected from free-ranging proboscis monkeys, we demonstrated the trend that their microbial community composition is not particularly distinctive compared with other foregut- and hindgut-fermenting primates. The microbial alpha diversity was higher in larger groups and individuals inhabiting diverse vegetation (i.e. presumed to have a diverse diet). For microbial beta diversity, some measures were significant, showing higher values with larger geographical distances between samples. These results suggest that social factors such as increased inter-individual interactions, which can occur with larger groups, as well as physical distances between individuals or differences in dietary patterns, may affect the gut microbial communities.

A model for the noninvasive, habitat-inclusive estimation of upper limit abundance for synanthropes, exemplified by M. fascicularis

Accurately estimating population sizes for free-ranging animals through noninvasive methods, such as camera trap images, remains particularly limited by small datasets. To overcome this, we developed a flexible model for estimating upper limit populations and exemplified it by studying a group-living synanthrope, the long-tailed macaque (Macaca fascicularis). Habitat preference maps, based on environmental and GPS data, were generated with a maximum entropy model and combined with data obtained from camera traps, line transect distance sampling, and direct sightings to produce an expected number of individuals. The mapping between habitat preference and number of individuals was optimized through a tunable parameter ρ (inquisitiveness) that accounts for repeated observations of individuals. Benchmarking against published data highlights the high accuracy of the model. Overall, this approach combines citizen science with scientific observations and reveals the long-tailed macaque populations to be (up to 80%) smaller than expected. The model's flexibility makes it suitable for many species, providing a scalable, noninvasive tool for wildlife conservation.

Balancing economic and ecological functions in smallholder and industrial oil palm plantations

The expansion of the oil palm industry in Indonesia has improved livelihoods in rural communities, but comes at the cost of biodiversity and ecosystem degradation. Here, we investigated ways to balance ecological and economic outcomes of oil palm cultivation. We compared a wide range of production systems, including smallholder plantations, industrialized company estates, estates with improved agronomic management, and estates with native tree enrichment. Across all management types, we assessed multiple indicators of biodiversity, ecosystem functions, management, and landscape structure to identify factors that facilitate economic-ecological win-wins, using palm yields as measure of economic performance. Although, we found that yields in industrialized estates were, on average, twice as high as those in smallholder plantations, ecological indicators displayed substantial variability across systems, regardless of yield variations, highlighting potential for economic-ecological win-wins. Reducing management intensity (e.g., mechanical weeding instead of herbicide application) did not lower yields but improved ecological outcomes at moderate costs, making it a potential measure for balancing economic and ecological demands. Additionally, maintaining forest cover in the landscape generally enhanced local biodiversity and ecosystem functioning within plantations. Enriching plantations with native trees is also a promising strategy to increase ecological value without reducing productivity. Overall, we recommend closing yield gaps in smallholder cultivation through careful intensification, whereas conventional plantations could reduce management intensity without sacrificing yield. Our study highlights various pathways to reconcile the economics and ecology of palm oil production and identifies management practices for a more sustainable future of oil palm cultivation.

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.

Assessing the impact of forest structure disturbances on the arboreal movement and energetics of orangutans—An agent-based modeling approach

Agent-based models have been developed and widely employed to assess the impact of disturbances or conservation management on animal habitat use, population development, and viability. However, the direct impacts of canopy disturbance on the arboreal movement of individual primates have been less studied. Such impacts could shed light on the cascading effects of disturbances on animal health and fitness. Orangutans are an arboreal primate that commonly encounters habitat quality deterioration due to land-use changes and related disturbances such as forest fires. Forest disturbance may, therefore, create a complex stress scenario threatening orangutan populations. Due to forest disturbances, orangutans may adapt to employ more terrestrial, as opposed to arboreal, movements potentially prolonging the search for fruiting and nesting trees. In turn, this may lead to changes in daily activity patterns (i.e., time spent traveling, feeding, and resting) and available energy budget, potentially decreasing the orangutan's fitness. We developed the agent-based simulation model BORNEO (arBOReal aNimal movEment mOdel), which explicitly describes both orangutans' arboreal and terrestrial movement in a forest habitat, depending on distances between trees and canopy structures. Orangutans in the model perform activities with a motivation to balance energy intake and expenditure through locomotion. We tested the model using forest inventory data obtained in Sebangau National Park, Central Kalimantan, Indonesia. This allowed us to construct virtual forests with real characteristics including tree connectivity, thus creating the potential to expand the environmental settings for simulation experiments. In order to parameterize the energy related processes of the orangutans described in the model, we applied a computationally intensive evolutionary algorithm and evaluated the simulation results against observed behavioral patterns of orangutans. Both the simulated variability and proportion of activity budgets including feeding, resting, and traveling time for female and male orangutans confirmed the suitability of the model for its purpose. We used the calibrated model to compare the activity patterns and energy budgets of orangutans in both natural and disturbed forests . The results confirm field observations that orangutans in the disturbed forest are more likely to experience deficit energy balance due to traveling to the detriment of feeding time. Such imbalance is more pronounced in males than in females. The finding of a threshold of forest disturbances that affects a significant change in activity and energy budgets suggests potential threats to the orangutan population. Our study introduces the first agent-based model describing the arboreal movement of primates that can serve as a tool to investigate the direct impact of forest changes and disturbances on the behavior of species such as orangutans. Moreover, it demonstrates the suitability of high-performance computing to optimize the calibration of complex agent-based models describing animal behavior at a fine spatio-temporal scale (1-m and 1-s granularity).

Evidence for the latest fossil Pongo in southern China

Pongo fossils with precise absolute age brackets are rare, limiting our understanding of their taxonomy and spatiotemporal distribution in southern China during the Late Pleistocene. Twenty-four isolated teeth of fossil orangutans were recently discovered during excavations at Yicun Cave in Guangxi Zhuang Autonomous Region, southern China. Here, we dated the fossil-bearing layer using Uranium-series dating of the associated flowstone and soda straw stalactites. Our results date the Yicun orangutan fossils to between 66 ± 0.32 ka and 57 ± 0.26 ka; thus, these fossils currently represent the last appearance datum of Pongo in southern China. We further conducted a detailed morphological comparison of the Yicun fossil teeth with large samples of fossil (n = 2454) and extant (n = 441) orangutans from mainland and island Southeast Asia to determine their taxonomic position. Compared to other fossil and extant orangutan samples, the Yicun Pongo assemblage has larger teeth and displays greater variation in occlusal structure. Based on the high frequency of cingular remnants and light to moderate enamel wrinkling of the molars, we assigned the Yicun fossils to Pongo weidenreichi, a species that was widespread in southern China throughout the Pleistocene. Lastly, we used published stable carbon isotope data of Early to Late Pleistocene mammalian fossil teeth from mainland Southeast Asia to reconstruct changes in the paleoenvironment and to interpret dental size variation of Pongo assemblages in a broader temporal and environmental context. The carbon isotope data show that dental size reduction in Pongo is associated with environmental changes. These morphological changes in Pongo appear to coincide with the expansion of savannah biomes and the contraction of forest habitats from the Middle Pleistocene onward. The variation in dental size of forest-dwelling Pongo in mainland Southeast Asia may have resulted from habitat differentiation during the Pleistocene.

Between forest and croplands: Nocturnal behavior in wild chimpanzees of Sebitoli, Kibale National Park, Uganda

Some animal species have been presumed to be purely diurnal. Yet, they show flexibility in their activity rhythm, and can occasionally be active at night. Recently, it has been suggested that chimpanzees may rarely engage in nocturnal activities in savannah forests, in contrast to the frequent nocturnal feeding of crops observed at Sebitoli, Kibale National Park, Uganda. Here we thus aimed to explore the factors that might trigger such intense nocturnal activity (e.g. harsher weather conditions during daytime, low wild food availability or higher diurnal foraging risk) in this area. We used camera-traps set over 18 km2 operating for 15 months. We report activities and group composition from records obtained either within the forest or at the forest interface with maize fields, the unique crop consumed. Maize is an attractive and accessible food source, although actively guarded by farmers, particularly during daytime. Out of the 19 156 clips collected, 1808 recorded chimpanzees. Of these, night recordings accounted for 3.3% of forest location clips, compared to 41.8% in the maize fields. Most nocturnal clips were obtained after hot days, and most often during maize season for field clips. At night within the forest, chimpanzees were travelling around twilight hours, while when at the border of the fields they were foraging on crops mostly after twilight and in smaller parties. These results suggest that chimpanzees change their activity rhythm to access cultivated resources when human presence and surveillance is lower. This survey provides evidence of behavioral plasticity in chimpanzees in response to neighboring human farming activities, and emphasizes the urgent need to work with local communities to mitigate human-wildlife conflict related to crop-feeding.

Disentangling LiDAR Contribution in Modelling Species–Habitat Structure Relationships in Terrestrial Ecosystems Worldwide. A Systematic Review and Future Directions

Global biodiversity is threatened by unprecedented and increasing anthropogenic pressures, including habitat loss and fragmentation. LiDAR can become a decisive technology by providing accurate information about the linkages between biodiversity and ecosystem structure. Here, we review the current use of LiDAR metrics in ecological studies regarding birds, mammals, reptiles, amphibians, invertebrates, bryophytes, lichens, and fungi (BLF). We quantify the types of research (ecosystem and LiDAR sources) and describe the LiDAR platforms and data that are currently available. We also categorize and harmonize LiDAR metrics into five LiDAR morphological traits (canopy cover, height and vertical distribution, understory and shrubland, and topographic traits) and quantify their current use and effectiveness across taxonomic groups and ecosystems. The literature review returned 173 papers that met our criteria. Europe and North America held most of the studies, and birds were the most studied group, whereas temperate forest was by far the most represented ecosystem. Globally, canopy height was the most used LiDAR trait, especially in forest ecosystems, whereas canopy cover and terrain topography traits performed better in those ecosystems where they were mapped. Understory structure and shrubland traits together with terrain topography showed high effectiveness for less studied groups such as BLF and invertebrates and in open landscapes. Our results show how LiDAR technology has greatly contributed to habitat mapping, including organisms poorly studied until recently, such as BLF. Finally, we discuss the forthcoming opportunities for biodiversity mapping with different LiDAR platforms in combination with spectral information. We advocate (i) for the integration of spaceborne LiDAR data with the already available airborne (airplane, drones) and terrestrial technology, and (ii) the coupling of it with multispectral/hyperspectral information, which will allow for the exploration and analyses of new species and ecosystems.

Shifts in mosquito diversity and abundance along a gradient from oil palm plantations to conterminous forests in Borneo

Deforestation precipitates spillover of enzootic, vector-borne viruses into humans, but specific mechanisms for this effect have rarely been investigated. Expansion of oil palm cultivation is a major driver of deforestation. Here, we demonstrate that mosquito abundance decreased over ten stepwise distances from interior forest into conterminous palm plantations in Borneo. Diversity in interior plantation narrowed to one species, Aedes albopictus, a potential bridge vector for spillover of multiple viruses. A. albopictus was equally abundant across all distances in forests, forest-plantation edge, and plantations, while A. niveus, a known vector of sylvatic dengue virus, was found only in forests. A. albopictus collections were significantly female-biased in plantation but not in edge or forest. Our data reveal that the likelihood of encountering any mosquito is greater in interior forest and edge than plantation, while the likelihood of encountering A. albopictus is equivalent across the gradient sampled from interior plantation to interior forest.

Drivers of Bornean Orangutan Distribution across a Multiple-Use Tropical Landscape

Logging and conversion of tropical forests in Southeast Asia have resulted in the expansion of landscapes containing a mosaic of habitats that may vary in their ability to sustain local biodiversity. However, the complexity of these landscapes makes it difficult to assess abundance and distribution of some species using ground-based surveys alone. Here, we deployed a combination of ground-transects and aerial surveys to determine drivers of the critically endangered Bornean Orangutan (Pongo pygmaeus morio) distribution across a large multiple-use landscape in Sabah, Malaysian Borneo. Ground-transects and aerial surveys using drones were conducted for orangutan nests and hemi-epiphytic strangler fig trees (Ficus spp.) (an important food resource) in 48 survey areas across 76 km2, within a study landscape of 261 km2. Orangutan nest count data were fitted to models accounting for variation in land use, above-ground carbon density (ACD, a surrogate for forest quality), strangler fig density, and elevation (between 117 and 675 m). Orangutan nest counts were significantly higher in all land uses possessing natural forest cover, regardless of degradation status, than in monoculture plantations. Within these natural forests, nest counts increased with higher ACD and strangler fig density, but not with elevation. In logged forest (ACD 14–150 Mg ha−1), strangler fig density had a significant, positive relationship with orangutan nest counts, but this relationship disappeared in a forest with higher carbon content (ACD 150–209 Mg ha−1). Based on an area-to-area comparison, orangutan nest counts from ground transects were higher than from counts derived from aerial surveys, but this did not constitute a statistically significant difference. Although the difference in nest counts was not significantly different, this analysis indicates that both methods under-sample the total number of nests present within a given area. Aerial surveys are, therefore, a useful method for assessing the orangutan habitat use over large areas. However, the under-estimation of nest counts by both methods suggests that a small number of ground surveys should be retained in future surveys using this technique, particularly in areas with dense understory vegetation. This study shows that even highly degraded forests may be a suitable orangutan habitat as long as strangler fig trees remain intact after areas of forest are logged. Enrichment planting of strangler figs may, therefore, be a valuable tool for orangutan conservation in these landscapes.

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.

Grouping behavior of Sumatran orangutans (Pongo abelii) and Tapanuli orangutans (Pongo tapanuliensis) living in forest with low fruit abundance

In contrast to the African great apes, orangutans (Pongo spp.) are semisolitary: Individuals are often on their own, but form aggregations more often than expected by chance. These temporary aggregations provide social benefits such as mating opportunities. When fruit availability is high, costs of aggregating should be lower, because competition is less pronounced. Therefore, average party size is expected to be higher when fruit availability is high. This hypothesis would also explain why orangutans in highly fruit-productive habitats on Sumatra are more gregarious than in the usually less productive habitats of Borneo. Here, we describe the aggregation behavior of orangutans in less productive Sumatran habitats (Sikundur and Batang Toru), and compare results with those of previously surveyed field sites. Orangutans in Sikundur were more likely to form parties when fruit availability was higher, but the size of daily parties was not significantly affected by fruit availability. With regard to between-site comparisons, average party sizes of females and alone time of parous females in Sikundur and Batang Toru were substantially lower than those for two previously surveyed Sumatran sites, and both fall in the range of values for Bornean sites. Our results indicate that the assessment of orangutans on Sumatra as being more social than those on Borneo needs revision. Instead, between-site differences in sociality seem to reflect differences in average fruit availability.

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.