Impacts of fire and prospects for recovery in a tropical peat forest ecosystem.

Uncontrolled fires place considerable burdens on forest ecosystems, compromising our ability to meet conservation and restoration goals. A poor understanding of the impacts of fire on ecosystems and their biodiversity exacerbates this challenge, particularly in tropical regions where few studies have applied consistent analytical techniques to examine a broad range of ecological impacts over multiyear time frames. We compiled 16 y of data on ecosystem properties (17 variables) and biodiversity (21 variables) from a tropical peatland in Indonesia to assess fire impacts and infer the potential for recovery. Burned forest experienced altered structural and microclimatic conditions, resulting in a proliferation of nonforest vegetation and erosion of forest ecosystem properties and biodiversity. Compared to unburned forest, habitat structure, tree density, and canopy cover deteriorated by 58 to 98%, while declines in species diversity and abundance were most pronounced for trees, damselflies, and butterflies, particularly for forest specialist species. Tracking ecosystem property and biodiversity datasets over time revealed most to be sensitive to recurrent high-intensity fires within the wider landscape. These megafires immediately compromised water quality and tree reproductive phenology, crashing commercially valuable fish populations within 3 mo and driving a gradual decline in threatened vertebrates over 9 mo. Burned forest remained structurally compromised long after a burn event, but vegetation showed some signs of recovery over a 12-y period. Our findings demonstrate that, if left uncontrolled, fire may be a pervasive threat to the ecological functioning of tropical forests, underscoring the importance of fire prevention and long-term restoration efforts, as exemplified in Indonesia.

Implications of large-scale infrastructure development for biodiversity in Indonesian Borneo.

Indonesia is embarking on an ambitious relocation of its capital city to Kalimantan, Borneo, bringing with it major urban and road infrastructure. Yet, despite being one of the world's most biologically diverse regions, the potential implications of this development for wildlife have yet to be fully assessed. We explored the potential impacts of the capital relocation, and road expansion and upgrades to critical habitat for medium-large mammals (>1 kg) using camera trap data from 11 forested landscapes. We applied Bayesian multi-species occupancy models to predict community and species-level responses to anthropogenic and environmental factors. We extrapolated spatial patterns of occupancy and species diversity across the forests of Kalimantan and identified "critical habitats" as the top 20th percentile of occupancy and species richness values. We subsequently overlapped these critical habitat layers with infrastructure impact zones to estimate the area that could potentially be affected by direct or secondary impacts. At both the community and species-level, distance to primary roads had the strongest negative influence on habitat-use. Occupancy was also influenced by forest quality and multidimensional poverty conditions in adjacent villages, demonstrating the sensitivity of biodiversity to socio-ecological pressures. Less than 1 % of the critical habitat for the threatened mammal community lay within the direct impact zone (30 km radius) of the capital relocation. However, approximately 16 % was located within 200 km and could potentially be affected by uncontrolled secondary impacts such as urban sprawl and associated regional development. The often-overlooked secondary implications of upgrading existing roads could also intersect a large amount of critical habitat for lowland species. Mitigating far-reaching secondary impacts of infrastructure development should be fully incorporated into environmental impact assessments. This will provide Indonesia with an opportunity to set an example of sustainable infrastructure development in the tropics.

Prevalence of bat viruses associated with land-use change in the Atlantic Forest, Brazil.

Introduction: Bats are critical to maintaining healthy ecosystems and many species are threatened primarily due to global habitat loss. Bats are also important hosts of a range of viruses, several of which have had significant impacts on global public health. The emergence of these viruses has been associated with land-use change and decreased host species richness. Yet, few studies have assessed how bat communities and the viruses they host alter with land-use change, particularly in highly biodiverse sites. Methods: In this study, we investigate the effects of deforestation on bat host species richness and diversity, and viral prevalence and richness across five forested sites and three nearby deforested sites in the interior Atlantic Forest of southern Brazil. Nested-PCR and qPCR were used to amplify and detect viral genetic sequence from six viral families (corona-, adeno-, herpes-, hanta-, paramyxo-, and astro-viridae) in 944 blood, saliva and rectal samples collected from 335 bats. Results: We found that deforested sites had a less diverse bat community than forested sites, but higher viral prevalence and richness after controlling for confounding factors. Viral detection was more likely in juvenile males located in deforested sites. Interestingly, we also found a significant effect of host bat species on viral prevalence indicating that viral taxa were detected more frequently in some species than others. In particular, viruses from the Coronaviridae family were detected more frequently in generalist species compared to specialist species. Discussion: Our findings suggest that deforestation may drive changes in the ecosystem which reduce bat host diversity while increasing the abundance of generalist species which host a wider range of viruses.

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.

Safeguarding Imperiled Biodiversity and Evolutionary Processes in the Wallacea Center of Endemism.

Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently.

Effectiveness of 20 years of conservation investments in protecting orangutans.

Conservation strategies are rarely systematically evaluated, which reduces transparency, hinders the cost-effective deployment of resources, and hides what works best in different contexts. Using data on the iconic and critically endangered orangutan (Pongo spp.), we developed a novel spatiotemporal framework for evaluating conservation investments. We show that around USD 1 billion was invested between 2000 and 2019 into orangutan conservation by governments, nongovernmental organizations, companies, and communities. Broken down by allocation to different conservation strategies, we find that habitat protection, patrolling, and public outreach had the greatest return on investment for maintaining orangutan populations. Given the variability in threats, land-use opportunity costs, and baseline remunerations in different regions, there were differential benefits per dollar invested across conservation activities and regions. We show that although challenging from a data and analysis perspective, it is possible to fully understand the relationships between conservation investments and outcomes and the external factors that influence these outcomes. Such analyses can provide improved guidance toward a more effective biodiversity conservation. Insights into the spatiotemporal interplays between the costs and benefits driving effectiveness can inform decisions about the most suitable orangutan conservation strategies for halting population declines. Although our study focuses on the three extant orangutan species of Sumatra and Borneo, our findings have broad application for evidence-based conservation science and practice worldwide.

Altered structure of bat-prey interaction networks in logged tropical forests revealed by metabarcoding.

Habitat degradation is pervasive across the tropics and is particularly acute in Southeast Asia, with major implications for biodiversity. Much research has addressed the impact of degradation on species diversity; however, little is known about how ecological interactions are altered, including those that constitute important ecosystem functions such as consumption of herbivores. To examine how rainforest degradation alters trophic interaction networks, we applied DNA metabarcoding to construct interaction networks linking forest-dwelling insectivorous bat species and their prey, comparing old-growth forest and forest degraded by logging in Sabah, Borneo. Individual bats in logged rainforest consumed a lower richness of prey than those in old-growth forest. As a result, interaction networks in logged forests had a less nested structure. These network structures were associated with reduced network redundancy and thus increased vulnerability to perturbations in logged forests. Our results show how ecological interactions change between old-growth and logged forests, with potentially negative implications for ecosystem function and network stability.

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.

The environmental impacts of palm oil in context.

Delivering the Sustainable Development Goals (SDGs) requires balancing demands on land between agriculture (SDG 2) and biodiversity (SDG 15). The production of vegetable oils and, in particular, palm oil, illustrates these competing demands and trade-offs. Palm oil accounts for ~40% of the current global annual demand for vegetable oil as food, animal feed and fuel (210 Mt), but planted oil palm covers less than 5-5.5% of the total global oil crop area (approximately 425 Mha) due to oil palm's relatively high yields. Recent oil palm expansion in forested regions of Borneo, Sumatra and the Malay Peninsula, where >90% of global palm oil is produced, has led to substantial concern around oil palm's role in deforestation. Oil palm expansion's direct contribution to regional tropical deforestation varies widely, ranging from an estimated 3% in West Africa to 50% in Malaysian Borneo. Oil palm is also implicated in peatland draining and burning in Southeast Asia. Documented negative environmental impacts from such expansion include biodiversity declines, greenhouse gas emissions and air pollution. However, oil palm generally produces more oil per area than other oil crops, is often economically viable in sites unsuitable for most other crops and generates considerable wealth for at least some actors. Global demand for vegetable oils is projected to increase by 46% by 2050. Meeting this demand through additional expansion of oil palm versus other vegetable oil crops will lead to substantial differential effects on biodiversity, food security, climate change, land degradation and livelihoods. Our Review highlights that although substantial gaps remain in our understanding of the relationship between the environmental, socio-cultural and economic impacts of oil palm, and the scope, stringency and effectiveness of initiatives to address these, there has been little research into the impacts and trade-offs of other vegetable oil crops. Greater research attention needs to be given to investigating the impacts of palm oil production compared to alternatives for the trade-offs to be assessed at a global scale.

Maximizing the value of forest restoration for tropical mammals by detecting three-dimensional habitat associations.

Tropical forest ecosystems are facing unprecedented levels of degradation, severely compromising habitat suitability for wildlife. Despite the fundamental role biodiversity plays in forest regeneration, identifying and prioritizing degraded forests for restoration or conservation, based on their wildlife value, remains a significant challenge. Efforts to characterize habitat selection are also weakened by simple classifications of human-modified tropical forests as intact vs. degraded, which ignore the influence that three-dimensional (3D) forest structure may have on species distributions. Here, we develop a framework to identify conservation and restoration opportunities across logged forests in Borneo. We couple high-resolution airborne light detection and ranging (LiDAR) and camera trap data to characterize the response of a tropical mammal community to changes in 3D forest structure across a degradation gradient. Mammals were most responsive to covariates that accounted explicitly for the vertical and horizontal characteristics of the forest and actively selected structurally complex environments comprising tall canopies, increased plant area index throughout the vertical column, and the availability of a greater diversity of niches. We show that mammals are sensitive to structural simplification through disturbance, emphasizing the importance of maintaining and enhancing structurally intact forests. By calculating occurrence thresholds of species in response to forest structural change, we identify areas of degraded forest that would provide maximum benefit for multiple high-conservation value species if restored. The study demonstrates the advantages of using LiDAR to map forest structure, rather than relying on overly simplistic classifications of human-modified tropical forests, for prioritizing regions for restoration.

Quantifying the impacts of defaunation on natural forest regeneration in a global meta-analysis.

Intact forests provide diverse and irreplaceable ecosystem services that are critical to human well-being, such as carbon storage to mitigate climate change. However, the ecosystem functions that underpin these services are highly dependent on the woody vegetation-animal interactions occurring within forests. While vertebrate defaunation is of growing policy concern, the effects of vertebrate loss on natural forest regeneration have yet to be quantified globally. Here we conduct a meta-analysis to assess the direction and magnitude of defaunation impacts on forests. We demonstrate that real-world defaunation caused by hunting and habitat fragmentation leads to reduced forest regeneration, although manipulation experiments provide contrasting findings. The extirpation of primates and birds cause the greatest declines in forest regeneration, emphasising their key role in maintaining carbon stores, and the need for national and international climate change and conservation strategies to protect forests from defaunation fronts as well as deforestation fronts.

FragSAD: A database of diversity and species abundance distributions from habitat fragments.

Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species' assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

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.

Tolerating tigers: Gaining local and spiritual perspectives on human-tiger interactions in Sumatra through rural community interviews.

Religious beliefs and spiritual connections to biodiversity have the potential to reduce animosity towards wildlife that might otherwise present a real or perceived threat to local people. Understanding this social dynamic can therefore be important for formulating locally-appropriate species-specific conservation strategies. Using semi-structured interviews which incorporated human-tiger conflict scenarios, we investigated how beliefs towards tigers varied between ethnic groups living around a large protected area that is home to the largest tiger population in Sumatra. We gathered this information to determine the degree to which cultural tolerance may contribute to the survival of the tiger in the Kerinci Seblat landscape, Indonesia. From 154 interviewees, 133 respondents came from three main ethnic groups, Minangkabau, Kerincinese and Melayu. The majority (73.5%) of Minangkabau interviewees cited that their ethnic group had customary laws regarding tigers, as did 52% of Melayu and 44% of Kerincinese. Irrespective of ethnicity, most participants did not perceive there to be a connection between Islam and tigers. All participants acknowledged the existence of zoological tigers and two groups (Minangkabau and Kerincinese) held a strong common belief that different types of spirit tigers also existed. From presenting different human-tiger conflict scenarios, with varying levels of severity towards livestock or human life, an unprovoked tiger attack in the village elicited the most calls for the tiger to be killed. Yet, if a village or family member was killed by a tiger whilst hunting in the forest then most respondents across all ethnic groups said to do nothing. The frequency of this response increased if a tiger killed someone in the village who had committed adultery, reflecting beliefs associated with the role of the tiger as an enforcer of moral rule. Our study highlights the importance of consulting with local communities who live in close proximity to large and potentially dangerous carnivores when developing conflict mitigation strategies, which hitherto has not been the case in Sumatra.

Addressing human-tiger conflict using socio-ecological information on tolerance and risk.

Tigers are critically endangered due to deforestation and persecution. Yet in places, Sumatran tigers (Panthera tigris sumatrae) continue to coexist with people, offering insights for managing wildlife elsewhere. Here, we couple spatial models of encounter risk with information on tolerance from 2386 Sumatrans to reveal drivers of human-tiger conflict. Risk of encountering tigers was greater around populated villages that neighboured forest or rivers connecting tiger habitat; geographic profiles refined these predictions to three core areas. People's tolerance for tigers was related to underlying attitudes, emotions, norms and spiritual beliefs. Combining this information into socio-ecological models yielded predictions of tolerance that were 32 times better than models based on social predictors alone. Pre-emptive intervention based on these socio-ecological predictions could have averted up to 51% of attacks on livestock and people, saving 15 tigers. Our work provides further evidence of the benefits of interdisciplinary research on conservation conflicts.

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.

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.

Reconciling timber extraction with biodiversity conservation in tropical forests using reduced-impact logging.

Over 20% of the world's tropical forests have been selectively logged, and large expanses are allocated for future timber extraction. Reduced-impact logging (RIL) is being promoted as best practice forestry that increases sustainability and lowers CO2 emissions from logging, by reducing collateral damage associated with timber extraction. RIL is also expected to minimize the impacts of selective logging on biodiversity, although this is yet to be thoroughly tested.We undertake the most comprehensive study to date to investigate the biodiversity impacts of RIL across multiple taxonomic groups. We quantified birds, bats and large mammal assemblage structures, using a before-after control-impact (BACI) design across 20 sample sites over a 5-year period. Faunal surveys utilized point counts, mist nets and line transects and yielded >250 species. We examined assemblage responses to logging, as well as partitions of feeding guild and strata (understorey vs. canopy), and then tested for relationships with logging intensity to assess the primary determinants of community composition.Community analysis revealed little effect of RIL on overall assemblages, as structure and composition were similar before and after logging, and between logging and control sites. Variation in bird assemblages was explained by natural rates of change over time, and not logging intensity. However, when partitioned by feeding guild and strata, the frugivorous and canopy bird ensembles changed as a result of RIL, although the latter was also associated with change over time. Bats exhibited variable changes post-logging that were not related to logging, whereas large mammals showed no change at all.Indicator species analysis and correlations with logging intensities revealed that some species exhibited idiosyncratic responses to RIL, whilst abundance change of most others was associated with time.Synthesis and applications. Our study demonstrates the relatively benign effect of reduced-impact logging (RIL) on birds, bats and large mammals in a neotropical forest context, and therefore, we propose that forest managers should improve timber extraction techniques more widely. If RIL is extensively adopted, forestry concessions could represent sizeable and important additions to the global conservation estate - over 4 million km2.

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.