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There is a weak evidence base supporting the effective management of riparian ecosystems within tropical agriculture. Policies to protect riparian buffers—strips of non‐cultivated land alongside waterways—are vague and vary greatly between countries. From a rapid evidence appraisal, we find that riparian buffers are beneficial to hydrology, water quality, biodiversity and some ecosystem functions in tropical landscapes. However, effects on connectivity, carbon storage and emissions reduction remain understudied. Riparian functions are mediated by buffer width and habitat quality, but explicit threshold recommendations are rare. Policy implications. A one‐size fits all width criterion, commonly applied, will be insufficient to provide all riparian functions in all circumstances. Context‐specific guidelines for allocating, restoring and managing riparian buffers are necessary to minimise continued degradation of biodiversity and ecosystem functioning in tropical agriculture. A one‐size fits all width criterion, commonly applied, will be insufficient to provide all riparian functions in all circumstances. Context‐specific guidelines for allocating, restoring and managing riparian buffers are necessary to minimise continued degradation of biodiversity and ecosystem functioning in tropical agriculture.

1. Conversion of forest to oil palm agriculture is a significant and ongoing threat to tropical biodiversity. Despite this, little is known about the value of riparian reserves in oil palm and how these conservation set-asides might best be managed to maintain biodiversity. 2. We characterized bird communities of 28 sites in an oil palm-forest mosaic in Sabah, Malaysia using 6,104 encounters from 840 point counts. Sites included oil palm riparian reserves of various vegetation quality and reserve widths, which were compared to oil palm streams without a riparian reserve as well as riparian and nonriparian control areas in continuous logged forest. 3. Riparian reserves, oil palm waterways, and control sites in riparian and nonriparian forest supported distinct avifaunal communities. Riparian reserve width, forest quality, and amount of forest cover were the strongest predictors of bird species richness. For forest-dependent species, each of these predictors had a stronger effect size when compared with all species. On average, reserves held 31% of all species and 30% of forest specialists, whereas riparian forest controls averaged 32% of all species, but 38% of forest species. 4. Riparian reserves with >40 m of natural vegetation on each bank supported similar bird diversity to riparian forest control habitats found in continuous forest. However, to support equivalent numbers of forest-dependent species and species of conservation concern, reserves would need to be at least 100-m wide on each bank. The largest numbers of species were found in riparian reserves with aboveground carbon densities exceeding 75 tC/ha, highlighting the importance of forest quality, as well as width, in supporting riparian bird communities. 5. Synthesis and applications. If designed and protected appropriately, riparian reserves in oil palm estates support diverse bird communities, including many species of conservation concern. This can be achieved by designating large reserves (80-200 m total width). But, to maximize species numbers, forest disturbance should also be minimized prior to conversion as well as during plantation operations.

The Wallacea biogeographic region of Sulawesi, the Moluccas and Lesser Sunda is globally renowned for exceptional endemism, but is currently emerging as a development frontier in Indonesia. We assessed patterns and drivers of forest loss and fragmentation across the region, and used dynamic deforestation models to project future deforestation to 2053. Up to 10 231 km 2 was deforested between 2000 and 2018, and a further 49 570 km 2 is expected to be lost by 2053, with annual deforestation rates ranging between 0.09% and 2.17% in different sub-regions (average: 1.23%). Key biodiversity areas (priority sites for endemic and threatened biodiversity) are particularly vulnerable to deforestation if they are small, coastal and unprotected. Sub-regional variation in deforestation patterns and drivers must be acknowledged if conservation interventions are to be targeted and effective. We provide a valuable baseline from which to monitor Wallacea’s new development course, as Indonesia undergoes profound policy changes that will provide both challenges and opportunities for environmental governance and conservation.

Coconut farming contributes to the livelihoods of millions of people in tropical countries but is less frequently considered as a threat to biodiversity compared to other palm commodities such as oil palm. The expansion of coconut farming alongside other smallholder agriculture in Sulawesi, Indonesia, is of potential concern as the region is a centre of species endemism. We studied bird diversity and community structure in forests, coconut palm plantations and mixed farmland in Gorontalo Province, northern Sulawesi. Forest and non-forest sites supported similar numbers of species overall, but compared to agricultural areas, forest sites had communities that were more diverse and more even (i.e. different species were present at similar abundances). We found far fewer endemic species in agricultural areas compared to forests, and the communities in palm plantations and mixed farmland sites were dominated by generalist birds, with few indicator taxa. Nevertheless, there was a higher number of endemic species in coconut palm plantations than in mixed farmland sites. These findings mirror patterns of biotic homogenization documented elsewhere in the Wallacea centre of endemism, and imply that coconut palm plantations have comparable biodiversity value to other farmland systems. Increased protection of lowland forests and improved management of coconut farms could be important for supporting the conservation of the endemic birds of Sulawesi in the long term, but this warrants further study.

Zero‐deforestation commitments seek to decouple agricultural production and forest loss to improve prospects for biodiversity. However, the effectiveness of methods designed to meet these commitments is poorly understood. In a highly fragmented tropical landscape dominated by oil palm, we tested the capacity for the High Carbon Stock (HCS) Approach to prioritize forest remnants that sustain mammal diversity. Patches afforded high priority by HCS protocols (100 ha core area) provided important refuges for IUCN‐threatened species and megafauna. However, patch‐scale HCS area recommendations conserved only 35% of the mammal community. At least 3,000 ha would be required to retain intact mammal assemblages, with nearly 10 times this area needed if hunting pressure was high. While current HCS protocols will safeguard patches capable of sustaining biodiversity, highly fragmented tropical landscapes typical of zero‐deforestation pledges will require thinking beyond the patch toward strategically configured forest remnants at the landscape level and enforcing strict controls on hunting.

Effects of logging on species composition in tropical rainforests are well known but may fail to reveal key changes in species interactions. We used nitrogen stable-isotope analysis of 73 species of understory birds to quantify trophic responses to repeated intensive logging of rainforest in northern Borneo and to test 4 hypotheses: logging has significant effects on trophic positions and trophic-niche widths of species, and the persistence of species in degraded forest is related to their trophic positions and trophic-niche widths in primary forest. Species fed from higher up the food chain and had narrower trophic-niche widths in degraded forest. Species with narrow trophic-niche widths in primary forest were less likely to persist after logging, a result that indicates a higher vulnerability of dietary specialists to local extinction following habitat disturbance. Persistence of species in degraded forest was not related to a species' trophic position. These results indicate changes in trophic organization that were not apparent from changes in species composition and highlight the importance of focusing on trophic flexibility over the prevailing emphasis on membership of static feeding guilds. Our results thus support the notion that alterations to trophic organization and interactions within tropical forests may be a pervasive and functionally important hidden effect of forest degradation. Los efectos de la tala sobre la composición de especies en bosques lluviosos tropicales son bien conocidos pero pueden fallar en la revelación de cambios clave en las interacciones de especies. Utilizamos análisis de isotopos estables de nitrógeno de 73 especies de aves de sotobosque para cuantificar las respuestas tróficas a la tala intensiva del bosque lluvioso en el norte de Borneo y para probar 4 hipótesis: la tala tiene efectos significativos sobre posiciones tróficas y la amplitud de nicho de las especies, y la persistencia de especies en el bosque degradado está relacionado con sus posiciones tróficas y amplitud de nicho trófico en el bosque primario. Las especies se alimentaron más arriba en la cadena trófica y tuvieron nichos más angostos en el bosque degradado. Las especies con nichos angostos en bosques primarios tuvieron menor probabilidad de persistir después de la tala, resultado que indica que especies con dietas especializadas tienen mayor vulnerabilidad a la extinción local después de una perturbación de hábitat. La persistencia de especies en bosque degradado no se relacionó con la posición trófica. Este resultado indica cambios en la organización trófica que no fueron aparentes con los cambios en la composición de especies y resaltan la importancia de concentrase en la flexibilidad trófica en vez del énfasis prevaleciente en la membresía de gremios alimenticios estáticos. Por lo tanto, nuestros resultados soportan la noción de que las alteraciones de la organización trófica y las interacciones en los bosques tropicales pueden ser un efecto oculto, dominante e importante funcionalmente, de la degradación de bosques.

Old-growth tropical forests are widely recognized as being immensely important for their biodiversity and high biomass 1 . Conversely, logged tropical forests are usually characterized as degraded ecosystems 2 . 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. Logged forests in Borneo have higher energy flow from vegetation to and broad range of bird and mammal species relative to old-growth forests and oil palm plantations, showing that they can be diverse and ecologically vibrant ecosystems.

The expansion of oil palm agriculture has contributed to biodiversity loss in Southeast Asia and elsewhere in the tropics. Riparian reserves (areas of native forest along waterways) have the potential to maintain forest biodiversity and associated ecological processes within these agricultural landscapes. Using acoustic sampling, we investigated the value of riparian reserves for insectivorous bats in oil palm plantations in Sabah, Malaysian Borneo. We compared general bat activity, foraging activity, and species occupancy between riparian areas in forest and riparian reserves in oil palm plantations. Overall bat activity varied little between riparian reserves in oil palm and riparian forest. Rather, activity was greatest in areas with a high forest canopy, irrespective of how much forest was available within or outside the riparian reserve. Bat foraging activity, as well as the occupancy of two species, was greatest in the forest sites, and while bats were detected in the oil palm riparian reserves, both foraging and occupancy were more associated with topographic ruggedness than forest amount or height. Our results indicate that habitat structure within riparian reserves may be more important than reserve size for supporting insectivorous bat diversity within oil palm landscapes. These findings provide important insights into the extent of the ecological benefits provided by conservation set-asides in forest-agricultural landscapes in the tropics.

Measuring the multidimensional diversity properties of a community is of great importance for ecologists, conservationists and stakeholders. Diversity profiles, a plotted series of Hill numbers, simultaneously capture the common diversity indices. However, diversity metrics require information on species abundance, often relying on raw count data without accounting for imperfect and varying detection. Hierarchical occupancy models account for variation in detectability, and Hill numbers have been expanded to allow estimation based on occupancy probability. But the ability of occupancy‐based diversity profiles to reproduce patterns in abundance‐based diversity has not been investigated. Here, we fit community occupancy models to simulated animal communities to explore how well occupancy‐based diversity profiles reflect patterns in true abundance‐based diversity. Because we expect occupancy‐based diversity to be overestimated, we further tested a occupancy thresholding approach to reduce potential biases in the estimated diversity profiles. Finally, we use empirical bird community data to present how the framework can be extended to consider species similarity. The simulation study showed that occupancy‐based diversity profiles produced among‐community patterns in diversity similar to true abundance diversity profiles, although within‐community diversity was generally overestimated. Applying an occupancy threshold reduced positive bias, but resulted in negative bias in richness estimates and slightly reduced the ability to reproduce true differences among the simulated communities; thus, we do not recommend application of this threshold. Application of our approach to a large bird dataset indicated differential species diversity patterns in communities of different habitat types. Accounting for phylogenetic and ecological similarities between species reduced variability in diversity among habitats. Our framework allows investigating the complexity of diversity from species detection data, while accounting for imperfect and varying detection probabilities, as well as species similarities. Visualizing results in the form of diversity profiles facilitates comparison of diversity between sites or across time. The approach offers opportunities for further development, for example by using local abundances estimated using the Royle–Nichols or N‐mixture models and further exploration of thresholding methods. In spite of some challenges, occupancy‐based diversity profiles are useful for studying and monitoring patterns in biodiversity.

Agricultural expansion is a primary driver of biodiversity decline in forested regions of the tropics. Consequently, it is important to understand the conservation value of remnant forests in production landscapes. In a tropical landscape dominated by oil palm (Elaeis guineensis), we characterized faunal communities across eight taxa occurring within riparian forest buffers, which are legally protected alongside rivers, and compared them to nearby recovering logged forest. Buffer width was the main predictor of species richness and abundance, with widths of 40–100 m on each side of the river supporting broadly equivalent levels of biodiversity as compared to logged forest. However, width responses varied markedly among taxa, and buffers often lacked forest-dependent species. Much wider buffers than are currently mandated are needed to safeguard most species. The largest biodiversity gains are achieved by increasing relatively narrow buffers. To provide optimal conservation outcomes in tropical production landscapes, we encourage policy makers to prescribe width requirements for key taxa and different landscape contexts.