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Sympatric species are known to host the same parasites species. Nevertheless, surveys examining parasite assemblages in sympatric species are rare. To understand how parasite assemblages in sympatric host species differ in a given locality, we used a noninvasive identification method based on high-throughput sequencing. We collected fecal samples from sympatric species in Ranomafana National Park, Madagascar, from September to December in 2010, 2011, and 2012 and identified their parasites by metabarcoding, sequencing a region of the small ribosomal subunit (18S) gene. Our survey included 11 host species, including endemic primates, rodents, frogs, gastropods, and nonendemic rats and dogs. We collected 872 samples, of which 571 contained nematodes and 249 were successfully sequenced. We identified nine putative species of parasites, although their correspondence to actual parasite species is not clear as the resolution of the marker gene differs between nematode clades. For the host species that we successfully sampled with 10 or more positive occurrences of nematodes, i.e., mouse lemurs (Microcebus rufus), black rats (Rattus rattus), and frogs (Anura), the parasite assemblage compositions differed significantly among host species, sampling sites, and sampling years. Our metabarcoding method shows promise in interrogating parasite assemblages in sympatric host species and our results emphasize the importance of choosing marker regions for parasite identification accuracy.

The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit‐feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions). Abundance data were obtained by sampling butterflies using banana baited traps set at the forest canopy and understorey strata. Our results indicate a clear consistency in the kind of species or species groups observed at either the canopy or understorey in the three studied communities. Furthermore, we found significant correlation between some flight‐related morphological traits and species abundance at the forest canopy, but not at the understorey. Neutral theory's contribution to explaining our data lies largely in identifying dispersal limitation as a key process regulating fruit‐feeding butterfly community structure. Our study illustrates that using species abundance data alone in evaluating neutral theory can be informative, but is insufficient. Species‐level information such as habitat preference, host plants, geographical distribution, and phylogeny is essential in elucidating the processes that regulate biodiversity community structures and patterns.

Summary Understanding the responses of individual plant species along different edaphic gradients is a key question in ecology, with implications to community assembly, functioning of forest ecosystems, niche theory, and conservation planning. In tropical rain forests, responses to soil nutrients have been described only for a handful of species. Even abundant and conspicuous components of the forest, such as the palms (Arecaceae), are largely unknown in this respect. We inventoried all palm species and analysed soil chemistry in 96 sites across western Amazonia to (i) assess the relative importance of some micronutrients vs. macronutrients as drivers of patterns in palm species composition, (ii) model the response shapes of 61 palm taxa and of canopy vs. understory palms along gradients of selected soil nutrients, (iii) determine if the response shapes of conspecific palm varieties differ in relation to the most important observed soil nutrient, and (iv) assess if the rank-order of the most abundant canopy species changes along edaphic gradients. Patterns in palm species composition were best explained by Mehlich-III extractable exchangeable bases (Ca, K, Mg) and phosphorus (P), with the different palm species clearly separating along the soil cation concentration gradient. All 61 palm taxa exhibited statistical responses along soil nutrient gradients. Response shapes in relation to exchangeable bases varied among bimodal skewed (51% of species), unimodal skewed (47%), and monotonic (2%). There were no significant differences between canopy vs. understory species in their mean response shapes to the exchangeable bases, but canopy species had significantly higher mean optimum value for soil P and greater mean niche width along the Ca, K, Mg, P, and boron (B) gradients. Varieties of the same species of Bactris, Desmoncus and Geonoma generally had different response shapes and different optima for the exchangeable bases. Synthesis: Among the soil variables we studied, macronutrients (especially exchangeable bases and P) emerged as more important than micronutrients in predicting species abundances in palm communities of western Amazonian non-inundated forests. Non-gaussian responses were predominant, conspecific palm varieties exhibited different response types, and the rank-order of dominance of canopy palms varied along the gradients of exchangeable bases and P. Together, these findings advance niche theory about palms and may be used for generating better predictive models of palm species distributions and for experimental studies that search for the physiological mechanisms underlying inter- and infra-specific trade-offs along edaphic gradients. This article is protected by copyright. All rights reserved.

Half of Borneo's forest has been logged and oil palm plantations have replaced millions of hectares of forest since the 1970's. While this extensive land-use change has been shown to reduce species richness across landscapes, there is limited current knowledge on how deforestation affects the spatial arrangement of ecological communities. Identifying responses of beta-diversity to land-use change may reveal processes which could mitigate total biodiversity loss. We sampled weevils (superfamily: Curculionoidea) at multiple spatial scales across a land-use gradient at the Stability of Altered Forest Ecosystems (SAFE) Project in Sabah, Malaysia, in 2011–2012. We caught 160 taxa of weevil and calculated the response of alpha-diversity (1-ha scale) and beta-diversity (10-, 100-, and 1000-ha scales) to disturbance. Alpha-diversity of weevils was greatest in unlogged forest but landscape-level beta-diversity (100- and 1000-ha scale) was maintained across logged and unlogged due to high rates of spatial turnover. Turnover at smallest spatial scales (10-ha) in unlogged forest was highest in rough, flat terrain but smooth, sloping terrain had highest turnover in logged forest. Logging of flat terrain at small spatial scales has potential to decrease beta-diversity at greater scales. Beta-diversity at landscape-level in oil palm plantation remained high but was propagated by abundance shifts of few species instead of spatial turnover of many species. High temporal beta-diversity in unlogged forest was evident through periodic fluxes in abundance of many weevil species. We conclude that unlogged forest is irreplaceable for high beetle biodiversity but increased spatial turnover in some terrains may help conserve beetle communities in heavily-degraded landscapes.

Climatic changes have profound effects on the distribution of biodiversity, but untangling the links between climatic change and ecosystem functioning is challenging, particularly in high diversity systems such as tropical forests. Tropical forests may also show different responses to a changing climate, with baseline climatic conditions potentially inducing differences in the strength and timing of responses to droughts. Trait-based approaches provide an opportunity to link functional composition, ecosystem function and environmental changes. We demonstrate the power of such approaches by presenting a novel analysis of long-term responses of different tropical forest to climatic changes along a rainfall gradient. We explore how key ecosystem's biogeochemical properties have shifted over time as a consequence of multi-decadal drying. Notably, we find that drier tropical forests have increased their deciduous species abundance and generally changed more functionally than forests growing in wetter conditions, suggesting an enhanced ability to adapt ecologically to a drying environment.

Logged tropical forests represent a major opportunity for preserving biodiversity and sequestering carbon, playing a large role in meeting global forest restoration targets. Left alone, these ecosystems have been expected to undergo natural regeneration and succession towards old growth forests, but extreme drought events may challenge this process. While old growth forests possess a certain level of resilience, we lack understanding as to how logging may affect forest responses to drought. This study examines the drought–logging interaction in seedling dynamics within a landscape of logged and unlogged forests in Sabah Malaysia, based on 73 plots monitored before and after the 2015-16 El Niño drought. Drought increased seedling mortality in all forests, but the magnitude of this impact was modulated by logging intensity, with forests with lower canopy leaf area index (LAI) and above ground biomass (AGB) experiencing greater drought induced mortality. Moreover, community traits in more heavily logged forests shifted towards being more ruderal after drought, suggesting that the trajectory of forest succession had been reversed. These results indicate that with reoccurring strong droughts under a changing climate, logged forests that have had over half of their biomass removed may suffer permanently arrested succession. Targeted management interventions may therefore be necessary to lift the vulnerable forests above the biomass threshold.

Vast areas of degraded tropical forest, combined with increasing interest in mitigating climate change and conserving biodiversity, demonstrate the potential value of restoring tropical forest. However, there is a lack of long-term studies assessing active management for restoration. Here we investigate Above Ground Biomass (AGB), forest structure, and biodiversity, before degradation (in old-growth forest), after degradation (in abandoned agricultural savanna grassland), and within a forest that is actively being restored in Kibale National Park, Uganda. In 1995 degraded land in Kibale was protected from fire and replanted with native seedlings (39 species) at a density of 400 seedlings ha(-1). Sixty-five plots (50 m x 10 m) were established in restoration areas in 2005 and 50 of these were re-measured in 2013, allowing changes to be assessed over 18 years. Degraded plots have an Above Ground Biomass (AGB) of 5.1 Mg dry mass ha(-1), of which 80% is grass. By 2005 AGB of trees >= 10 cm DBH was 9.5 Mg ha(-1), increasing to 40.6 Mg ha(-1) by 2013, accumulating at a rate of 3.9 Mg ha(-1) year(-1). A total of 153 planted individuals ha(-1) (38%) remained by 2013, contributing 28.9 Mg ha(-1) (70%) of total AGB. Eighteen years after restoration, AGB in the plots was 12% of old-growth (419 Mg ha(-1)). If current accumulation rates continue restoration forest would reach old-growth AGB in a further 96 years. Biodiversity of degraded plots prior to restoration was low with no tree species and 2 seedling species per sample plot (0.05 ha). By 2005 restoration areas had an average of 3 tree and 3 seedling species per sample plot, increasing to 5 tree and 9 seedling species per plot in 2013. However, biodiversity was still significantly lower than old-growth forest, at 8 tree and 16 seedling species in an equivalent area. The results suggest that forest restoration is beneficial for AGB accumulation with planted stems storing the majority of AGB. Changes in biodiversity appear slower; possibly due to low stem turnover. Overall this restoration treatment is an effective means of restoring degraded land in the area, as can be seen from the lack of regeneration in degraded plots, which remain low-AGB and diversity, largely due to the impacts of fire and competition with grasses. (C) 2016 The Authors. Published by Elsevier B.V.

Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle(1). However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use(2-4). Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major environmental gradients in the Neotropics. The studied secondary forests are highly productive and resilient. Aboveground biomass recovery after 20 years was on average 122 megagrams per hectare (Mg ha(-1)), corresponding to a net carbon uptake of 3.05 Mg C ha(-1) yr(-1), 11 times the uptake rate of old-growth forests. Aboveground biomass stocks took a median time of 66 years to recover to 90% of old-growth values. Aboveground biomass recovery after 20 years varied 11.3-fold ( from 20 to 225 Mg ha(-1)) across sites, and this recovery increased with water availability (higher local rainfall and lower climatic water deficit). We present a biomass recovery map of Latin America, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth. The map will support policies to minimize forest loss in areas where biomass resilience is naturally low (such as seasonally dry forest regions) and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.

Photoassimilate distribution inside leaves is less studied than photosynthesis, and yet the topic is important as it gives insights into the vital roles played by leaves in plant survival. We combined greenhouse measurements of light response curves with 11C-labelling using leaves of 3-year-old potted Maesopsis eminii Engl. trees to improve our understanding of its leaf carbon physiology. This fast-growing pioneer tree species showed low photosynthetic rates for a common tropical pioneer during well-watered reference conditions (5.0 ± 0.7 µmol m−2 s−1), which further decreased in response to drought. 11C-autoradiography indicated active phloem loading and/or rapid phloem transport rates. Active loading is uncommon in tree species, but might be related to deciduousness traits and continuous investment in growth, like in herbaceous active loaders. Active loading involves higher carbon allocation to growth, which might explain why low photosynthetic rates were observed in this fast-growing species. These findings suggest that examining photoassimilate distribution and transport may be critical for understanding the role tree physiology plays in terrestrial carbon cycling.

Evapotranspiration (ET) of Amazon forests is a main driver of regional climate patterns and an important indicator of ecosystem functioning. Despite its importance, the seasonal variability of ET over Amazon forests, and its relationship with environmental drivers, is still poorly understood. In this study, we carry out a water balance approach to analyse seasonal patterns in ET and their relationships with water and energy drivers over five sub-basins across the Amazon basin. We used in-situ measurements of river discharge, and remotely sensed estimates of terrestrial water storage, rainfall, and solar radiation. We show that the characteristics of ET seasonality in all sub-basins differ in timing and magnitude. The highest mean annual ET was found in the northern Rio Negro basin (~ 1497 mm year−1) and the lowest values in the Solimões River basin (~ 986 mm year−1). For the first time in a basin-scale study, using observational data, we show that factors limiting ET vary across climatic gradients in the Amazon, confirming local-scale eddy covariance studies. Both annual mean and seasonality in ET are driven by a combination of energy and water availability, as neither rainfall nor radiation alone could explain patterns in ET. In southern basins, despite seasonal rainfall deficits, deep root water uptake allows increasing rates of ET during the dry season, when radiation is usually higher than in the wet season. We demonstrate contrasting ET seasonality with satellite greenness across Amazon forests, with strong asynchronous relationships in ever-wet watersheds, and positive correlations observed in seasonally dry watersheds. Finally, we compared our results with estimates obtained by two ET models, and we conclude that neither of the two tested models could provide a consistent representation of ET seasonal patterns across the Amazon.

Disturbances play an important role in forest dynamics across the globe. Researchers have mainly focused on the temporal context of disturbances, but have largely ignored the spatial patterns of tree recruitment they create. Geostatistical tools enable the analysis of spatial patterns and variability in tropical forest disturbance histories. Here, we examine the potential of combining dendroecological analysis and spatial statistics to reconstruct the disturbance history of a seasonal dry evergreen tropical forest plot at the Huai Kha Khaeng Wildlife Sanctuary (HKK), western Thailand. We used tree-ring-derived age estimates for 70 individuals of the shade-intolerant pioneer species Melia azederach (Meliaceae) and tree locations across a 316-ha study plot to identify the timing and spatial extent of past disturbances. Although the age distribution for Melia suggested that regeneration had been continuous over the past 60 yr, spatial analyses (mark correlation function and kriging) demonstrated the presence of three spatially discrete age cohorts. Two of these cohorts suggested a severe disturbance ~20 yr before present. A third cohort appears to have established ~50 years ago. Using historical records, we conclude that fire disturbance is the most likely disturbance factor affecting HKK. Nevertheless, we do not rule out other disturbance factors. The combined application of tree-ring analysis and spatial statistics as applied in this study could be readily applied to reconstruct disturbance histories in other tropical regions where tree species with annual growth rings are present.

South East Asia has the highest rate of lowland forest loss of any tropical region, with logging and deforestation for conversion to plantation agriculture being flagged as the most urgent threats. Detecting and mapping logging impacts on forest structure is a primary conservation concern, as these impacts feed through to changes in biodiversity and ecosystem functions. Here, we test whether high-spatial resolution satellite remote sensing can be used to map the responses of aboveground live tree biomass (AGB), canopy leaf area index (LAI) and fractional vegetation cover (FCover) to selective logging and deforestation in Malaysian Borneo. We measured these attributes in permanent vegetation plots in rainforest and oil palm plantations across the degradation landscape of the Stability of Altered Forest Ecosystems project. We found significant mathematical relationships between field-measured structure and satellite-derived spectral and texture information, explaining up to 62% of variation in biophysical structure across forest and oil palm plots. These relationships held at different aggregation levels from plots to forest disturbance types and oil palms allowing us to map aboveground biomass and canopy structure across the degradation landscape. The maps reveal considerable spatial variation in the impacts of previous logging, a pattern that was less clear when considering field data alone. Up-scaled maps revealed a pronounced decline in aboveground live tree biomass with increasing disturbance, impacts which are also clearly visible in the field data even a decade after logging. Field data demonstrate a rapid recovery in forest canopy structure with the canopy recovering to pre-disturbance levels a decade after logging. Yet, up-scaled maps show that both LAI and FCover are still reduced in logged compared to primary forest stands and markedly lower in oil palm stands. While uncertainties remain, these maps can now be utilised to identify conservation win–wins, especially when combining them with ongoing biodiversity surveys and measurements of carbon sequestration, hydrological cycles and microclimate.

Epiphytic vascular plants are common species in humid tropical forests. Epiphytes are influenced by abiotic and biotic variables, but little is known about the relative importance of direct and indirect effects on epiphyte distribution. We surveyed 70 transects (10 m × 50 m) along an elevation gradient (180 m–1521 m) and sampled all vascular epiphytes and trees in a typical tropical forest on Hainan Island, south China. The direct and indirect effects of abiotic factors (climatic and edaphic) and tree community characteristics on epiphytes species diversity were examined. The abundance and richness of vascular epiphytes generally showed a unimodal curve with elevation and reached maximum value at ca. 1300 m. The species composition in transects from high elevation (above 1200 m) showed a more similar assemblage. Climate explained the most variation in epiphytes species diversity followed by tree community characteristics and soil features. Overall, climate (relative humidity) and tree community characteristics (tree size represented by basal area) had the strongest direct effects on epiphyte diversity while soil variables (soil water content and available phosphorus) mainly had indirect effects. Our study suggests that air humidity is the most important abiotic while stand basal area is the most important biotic determinants of epiphyte diversity along the tropical elevational gradient.

Understanding of mechanisms underlying carbon flux dynamics in the Eastern Arc Mountains and their catchment areas is lacking, due to data shortage (e.g. biome specific canopy structure) and spatial heterogeneity of tropical ecosystems. This study focuses on documenting leaf area index (LAI) for the main biomes in the Eastern Arc Mountains and their surroundings. In situ optical instruments, i.e. hemispherical photography and a SunScan device, were used to acquire ground LAI measurements. Spectral vegetation indices (VIs) extracted from Landsat Enhanced Thematic Mapper (ETM +) and Systeme Probatoire d'Observation de la Terre (SPOT) reflectance data were used, along with mean annual precipitation (MAP), as explanatory variables of LAI variation. The results indicate that LAI significantly increases with increasing MAP for woody biomes. Implementing long-term MAP as a second predictor variable into the VI–LAI models significantly improved LAI predictions by up to 10% using the normalised difference vegetation index (NDVI), modified soil adjusted vegetation index (MSAVI 2) and 2-band enhanced vegetation index (EVI 2). Varying forest disturbances and agricultural management practises may have contributed to observed discrepancies of LAI with MAP across biomes. The importance of altitudinal gradients is yet to be explained fully with more study required. However, LAI appears to be higher in low-altitude forests compared to forests at higher altitudes. Our results indicate that SPOT and Landsat-derived VIs, in combination with long-term MAP, may be a suitable tool to develop landscape maps of LAI in Eastern Africa. This study also presents the in situ LAI measurements for further validation of global products for areas that are currently under-represented in Earth Observation (EO) global validation networks.

Growth defense tradeoff theory predicts that plants in low-resource habitats invest more energy in defense mechanisms against natural enemies than growth, whereas plants in high-resource habitats can afford higher leaf loss rates. A less-studied defense against herbivores involves the synchrony of leaf production, which can be an effective defense strategy if leaf biomass production exceeds the capacity of consumption by insects. The aim of this study was to determine whether leaf synchrony varied across habitats with different available resources and whether insects were able to track young leaf production among tree habitat specialists in a tropical forest of French Guiana. We predicted that high-resource habitats would exhibit more synchrony in leaf production due to the low cost and investment to replace leaf tissue. We also expected closer patterns of leaf synchrony and herbivory within related species, assuming that they shared herbivores. We simultaneously monitored leaf production and herbivory rates of five pairs of tree species, each composed of a specialist of terra firme or white-sand forests within the same lineage. Our prediction was not supported by the strong interaction of habitat and lineage for leaf synchrony within individuals of the same species; although habitat specialists differed in leaf synchrony within four of five lineages, the direction of the effect was variable. All species showed short time lags for the correlation between leaf production and herbivory, suggesting that insects are tightly tracking leaf production, especially for the most synchronous species. Leaf synchrony may provide an important escape defense against herbivores, and its expression appears to be constrained by both evolutionary history and environmental factors.

Monitoring protected areas and their surrounds at local to regional scales is essential given their vulnerability to anthropogenic pressures, including those associated with climatic fluctuation, and important for management and fulfilment of national and international directives and agreements. Whilst monitoring has commonly revolved around field data, remote sensing can play a key role in establishing baselines of the extent and condition of habitats and associated species diversity as well as quantifying losses, degradation or recovery associated with specific events or processes. Landsat images constitute a major data source for habitat monitoring, capturing broad scale information on changes in habitat extent and spatial patterns of fragmentation that allow disturbances in protected areas to be identified. These data are, however, less able to provide information on changes in habitat quality, species distribution and fine-scale disturbances, and hence data from other spaceborne optical sensors are increasingly being considered. Very High Resolution (VHR) optical datasets have been exploited to a lesser extent, partly because of the relative recency of spaceborne observations and challenges associated with obtaining and routinely extracting information from airborne multi-spectral and hyperspectral datasets. The lack of a shortwave infrared band in many VHR datasets and provision of too much detail (e.g., shadows within and from landscape objects) also present challenges in some cases. Light Detection and Ranging (LiDAR) and Synthetic Aperture Radar (SAR) data, particularly when used synergistically with optical data, have benefited the detection of changes in the three-dimensional structure of habitats. This review shows that remote sensing has a strong, yet underexploited potential to assist in the monitoring of protected areas. However, the data generated need to be utilized more effectively to enable better management of the condition of protected areas and their surrounds, prepare for climate change, and assist planning for future landscape management. (C) 2012 Elsevier Ltd. All rights reserved.