Ferns (Polypodiophyta) are an abundant floral element of the tropics with high sensitivity to environmental conditions and good indicators of overall biodiversity. Here, we set out to identify which geochemical factors determine fern diversity in a low-montane tropical rainforest in Eastern Ecuador. We conducted a field survey of high-spatial resolution completing a comprehensive fern inventory across two elevational ranges, combined with biochemical characterisation of the underlying soils. While α-diversity was negatively correlated with cation exchange capacity (CEC) and with elevation, β-diversity increased with elevation and with geographic distance, as predicted. Our results confirm that ferns have a high sensitivity to both elevational and environmental gradients, where the latter in this study was derived from enhanced aluminium, iron and calcium contents in some of the studied soils. Further monitoring of fern communities could therefore help to better understand and predict how environmental change may impact biodiversity, with a particular focus on threats potentially arising from toxic elements being released in tropical soils through modified soil CEC.

Small mammals can be used as environmental indicators and have been intensively studied in fragmented landscapes of Atlantic Forest, with a wide range of field methods. Our aim in this study was two-fold: we tested for the effects of methods and for the effects of the main environmental variables on observed small mammal richness in fragments of Atlantic Forest. We gathered information on small mammal richness, methods and environmental variables from 122 fragments of Atlantic Forest through literature review. These data were analysed using linear models and model selection based on AIC values along with a regression tree analysis. We found that studies will record more species with bigger trapping effort, using pitfall traps and sampling all forest strata. We also confirmed two important ecological assumptions: fragments at lower latitudes and bigger fragments were the ones with higher species richness. Methodological and environmental variables were analysed together on a regression tree, where trapping effort was the most important variable, surpassing any environmental effect. Considering that a significant number of the studies on Atlantic Forest fragments did not use pitfall traps or sample all forest strata, their results on forest fragmentation were affected by sampling bias.

Habitat loss and fragmentation are major threats to biodiversity worldwide, and little is known about their effects on bats in Africa. We investigated effects of forest fragmentation on bat assemblages at Kakamega Forest, western Kenya, examining captures at edge and interior locations in three forest fragments (Buyangu, 3950 ha; Kisere, 400 ha; and Malava, 100 ha) varying in forest area and human-use regimes. Basal area, canopy cover, tree density and intensity of human use were used as predictors of bat abundance and species richness. A total of 3456 mist-net hours and 3168 harp-trap hours resulted in the capture of 4983 bats representing 26 species, eight families and four foraging ensembles (frugivores, forest-interior insectivores, forest-edge insectivores and open-space insectivores). Frugivores were frequently captured at the edges of the larger, better-protected forests, but also in the interior of the smaller, more open fragment. Forest-interior insectivores and narrow-space foragers predominated in the interiors of larger fragments but avoided the smallest one. Forest specialists showed positive associations with forest variables (canopy cover, basal area and tree density), whereas frugivores responded positively to the human-use indicators. On these bases, specialist species appear to be especially vulnerable to forest fragmentation.

In 2000, we established a 24-ha plot in Peninsular Thailand to investigate how forest composition, structure and dynamics vary with spatial heterogeneity in resource availability. Detailed soil and topographic surveys were used to describe four edaphic habitats in the plot. Disturbance history was inferred from historical records and floristic analysis. The plot included >119 000 trees ≥1 cm dbh in 578 species, and was recensused in 2010. Species distributions, floristic turnover, stand structure, demographic rates and biomass dynamics were strongly influenced by heterogeneity in soils, topography and disturbance history. Over 75% of species were aggregated on specific edaphic habitats leading to strong compositional turnover across the plot. Soil chemistry more strongly affected species turnover than topography. Forest with high biomass and slow dynamics occurred on well-drained, low fertility ridges. The distribution and size structure of pioneer species reflected habitat-specific differences in disturbance history. Overall, above-ground biomass (AGB) increased by 0.64 Mg ha−1 y−1, from 385 to 392 Mg ha−1, an increase that was entirely attributable to recovery after natural disturbance. Forest composition and stand structure, by reflecting local disturbance history, provide insights into the likely drivers of AGB change in forests. Predicting future changes in tropical forests requires improved understanding of how soils and disturbance regulate forest dynamics.

The rain forests of South-East Asia represent a biodiversity hotspot of terrestrial leeches, but we have only fragmentary and often anecdotal information on this component of tropical communities. To address the foraging tactics of terrestrial leeches, we studied the vertical distribution of Haemadipsa picta on foliage in a Bornean tropical rain forest. We investigated the links between leech body length and the above-ground height of their ambush positions under natural conditions and in a choice experiment performed under semi-natural conditions. We studied 167 leeches, which varied considerably with respect to body length (4–29 mm). On average, the leeches ambushed at lower heights under natural conditions than under experimental conditions (47.7 cm vs. 67.5 cm), though the heights of ambush positions overlapped considerably. Leeches that chose higher ambush positions under natural conditions consistently chose higher ambush positions in the experiment (Pearson r = 0.29). Under both natural and experimental conditions, leech body length was positively correlated with the height of ambush positions (Pearson r = 0.48); on average, a 1-mm increase in body length corresponded to a 2–3 cm higher ambush position. Our findings suggest that H. picta individuals actively choose hunting locations according to their above-ground height, shifting their ambush sites over ontogeny to higher foliage. We hypothesize that growing leeches might target different prey following ontogenetic shifts in the foraging optima, ultimately decreasing intraspecific competition.

The upper canopy of some rain forests in New Caledonia is dominated by single species. These monodominants are commonly secondary species, their dominance not persisting without disturbance. We tested whether dominance is associated with efficient uptake and use of nutrients (N, P and K), comparing between seedlings of monodominants (Nothofagus spp., Arillastrum gummiferum and Cerberiopsis candelabra) and 14 subordinates, grown in a nursery house. We also tested whether this trend applies more broadly to shade-intolerant trees that regenerate episodically (ER species) versus shade-tolerant trees that regenerate continuously (CR species). In the sun treatment, monodominants had higher photosynthetic nutrient-use efficiency and productivity for N and K, and uptake efficiency for N, P and K, than subordinates; ER species had higher photosynthetic nutrient-use efficiency for N, P and K, and uptake efficiency for N and P, than CR species. Uptake efficiency and productivity per nutrient mass were uncorrelated across species, yet Nothofagus spp., A. gummiferum and C. candelabra combined high levels of both traits for N, and Nothofagus spp. and A. gummiferum combined moderate to high levels for P, in sun-grown seedlings. This trait combination may contribute substantially to competitiveness and post-disturbance dominance on these nutrient-poor soils.

Certain forestry and agricultural practices are known to affect arbuscular mycorrhizal (AM) fungal communities, but the effects of deforestation – including slash-and-burn management and other more severe disturbances – in tropical rain forests are poorly understood. We addressed the effects of anthropogenic disturbance on rain-forest AM fungal communities in French Guiana, by comparing mature tropical rain forest, slash-and-burn (5 y old) and clearcut areas (8 y old). A total of 36 soil samples were collected in six plots and sequenced using a high throughput 454-pyrosequencing platform. A total of 32649 sequences from 103 AM fungal virtual taxa (VT) were recorded. Whereas alpha diversity of AM fungi did not decrease due to land-use intensification, with average richness ranging from 17 to 21 taxa per plot, beta diversity (average distance to multivariate centroid) dropped by 28% from 0.46 in rain forest to 0.33 under clearcutting. AM fungal community composition was correlated with land use and soil chemical properties. Clearcut areas were characterized by the more frequent occurrence of specialist AM fungi, compared with mature forest or slash-and-burn areas. Specifically, clearcuts contained the highest proportions of VT that were geographic (21%), habitat (31%), abundance (97%) or host (97%) specialists based on VT metadata contained in the MaarjAM database. This suggests that certain AM fungi with narrow ecological niches have traits that allow them to exploit conditions of severe disturbance. In conclusion, slash-and-burn management appears to allow diverse AM fungal communities to persist, and may favour regeneration of tropical rain forest after abandonment. More severe disturbance in the form of clearcutting resulted in marked changes in AM fungal communities.

Isotopic composition of leaf carbon (δ13C) and nitrogen (δ15N) is determined by biotic and abiotic factors. In order to determine the influence of leaf habit and site on leaf δ13C and δ15N in the understorey of two Atlantic forests in Brazil that differ in annual precipitation (1200 and 1900 mm), we measured these isotopes in the shaded understorey of 38 tropical tree species (20 in the 1200-mm site and 18 in the 1900-mm site). Mean site values for δ15N were significantly lower at the 1200-mm site (−1.4‰) compared with the 1900-mm site (+3.0‰), and δ13C was significantly greater in the 1200-mm site (−30.4‰) than in the 1900-mm site (−31.6‰). Leaf C concentration was greater and leaf N concentration was lower at 1200-mm than at 1900-mm. Leaf δ15N was negatively correlated with δ13C across the two sites. Leaf δ13C and δ15N of evergreen and deciduous species were not significantly different within a site. No significant phylogenetic signal for any traits among the study species was found. Overall, site differences were the main factor distinguishing traits among species, suggesting strong functional convergence to local climate and soils within each site for individuals in the shaded understorey.

A high-resolution pollen record from a 5-m-long sediment core from the closed-lake basin Laguna Piusbi in the southern Colombian Pacific lowlands of Chocó, dated by 11 AMS14C dates that range from ca. 7670 to 22014C yr B.P., represents the first Holocene record from the Chocó rain forest area. The interval between 7600 and 610014C yr B.P. (500–265 cm), composed of sandy clays that accumulated during the initial phase of lake formation, is almost barren of pollen. Fungal spores and the presence of herbs and disturbance taxa suggest the basin was at least temporarily inundated and the vegetation was open. The closed lake basin might have formed during an earthquake, probably about 440014C yr B.P. From the interval of about 600014C yr B.P. onwards, 200 different pollen and spore types were identified in the core, illustrating a diverse floristic composition of the local rain forest. Main taxa are Moraceae/Urticaceae, Cecropia,Melastomataceae/Combretaceae, Acalypha, Alchornea,Fabaceae, Mimosa, Piper, Protium, Sloanea, Euterpe/Geonoma, Socratea,and Wettinia.Little change took place during that time interval. Compared to the pollen records from the rain forests of the Colombian Amazon basin and adjacent savannas, the Chocó rain forest ecosystem has been very stable during the late Holocene. Paleoindians probably lived there at least since 346014C yr B.P. Evidence of agricultural activity, shown by cultivation of Zea maissurrounding the lake, spans the last 1710 yr. Past and present very moist climate and little human influence are important factors in maintaining the stable ecosystem and high biodiversity of the Chocó rain forest.

Some species-rich secondary forests in New Caledonia have a monodominant canopy. Here we investigate growth and biomass allocation traits that might explain single-species’ dominance of these post-disturbance stands, and their later decline in the absence of large-scale disturbance. Seedlings of 20 rain-forest trees were grown in two light treatments in a nursery house. In the sun treatment, monodominants grew faster (56.7 ± 1.4 mg g−1 wk−1) than subordinates (40.2 ± 2.6 mg g−1 wk−1). However, some episodically regenerating (ER) subordinates had high growth rates similar to those of monodominants. In the shade treatment, monodominants and subordinates had similar growth rates (33.7 ± 2.6 and 34.0 ± 1.9 mg g−1 wk−1 respectively). Notably, monodominants in both sun and shade treatments had lower root mass fraction (0.29 ± 0.02 and 0.27 ± 0.02 g g−1 respectively) than subordinates (0.39 ± 0.02 and 0.37 ± 0.02 g g−1). Fast growth in sunny conditions is probably imperative for these relatively shade-intolerant ER monodominants. In field conditions, high shoot mass fraction combined with efficient root performance may facilitate faster growth in monodominants competing with other ER species in sunlit sites. Slower growth in shade may contribute to loss of dominance over time in undisturbed forests.

Maintenance of biodiversity in tropical agrarian landscapes is challenging in the face of anthropomorphic simplification of habitats. As part of an experiment testing influences of planting treatment on tree recruitment in southern Mexico, counts of bird species were made over 10 years in twenty-four 30 × 30-m fenced plots in over-grazed pasture. Plots were planted with native tree species or left as unplanted controls in 2006. Annual censuses of birds in the plots from 2007–2016 indicated statistically significant increases in the number of fruit-eating species and individuals as vegetation matured, but increases in non-frugivorous species and individuals over the decade were not significant. Among four species of planted animal-dispersed trees that bore fruit during this time, Cecropia obtusifolia consistently produced substantial crops after 2009. In 2015, all 53 planted or passively recruited female trees of mature size of this species bore fruit. The summed body masses of fruit-eating birds in each of 24 plots were significantly correlated with rank order of available fruit per plot. Differential use of habitat patches in an agrarian landscape suggested substantial value to frugivores, but less to non-frugivorous birds than expected.

Deforestation and forest fragmentation are contributing to declines in crop pollinator populations worldwide. Several studies have examined the impact of forest proximity on plant pollination ecology, but concentrated on single crop species. However, it can be more informative to investigate multiple crop and pollinator species in a community, because different pollinator groups may respond differently to forest distance. We evaluated flower visitor diversity, visitation frequency, and fruit set for three crop species (rambutan, durian and mango) in 10 pairs of mixed fruit orchards. Each pair consisted of one orchard near to (< 1 km) and one orchard far from (> 7 km) the forest edge. Rambutan fruit set was significantly influenced by distance to forest. The main visitors of rambutan flowers were stingless bees. In contrast, the dominant visitors to durian and mango flowers were nectarivorous bats and flies, respectively, and the fruit set of these crops were not significantly influenced by distance to forest. However, durian fruit set was negatively affected by distance to the nearest cave inhabited by nectarivorous bats. This study demonstrates that both caves and forests can be important pollinator sources for agricultural crops, and that the dispersal success of pollinators is related to isolation from source habitats. Maintaining forest patches and limestone karsts may provide stepping stones across fragmented landscapes, and attract greater numbers of pollinators to agricultural areas.

In equatorial regions, where tree rings are less distinct or even absent, the response of forests to high-frequency climate variability is poorly understood. We measured stable carbon and oxygen isotopes in anatomically distinct, annual growth rings of four Pericopsis elata trees from a plantation in the Congo Basin, to assess their sensitivity to recorded changes in precipitation over the last 50 y. Our results suggest that oxygen isotopes have high common signal strength (EPS = 0.74), and respond to multi-annual precipitation variability at the regional scale, with low δ18O values (28–29‰) during wetter conditions (1960–1970). Conversely, δ13C are mostly related to growth variation, which in a light-demanding species are driven by competition for light. Differences in δ13C values between fast- and slow-growing trees (c. 2‰), result in low common signal strength (EPS = 0.37) and are driven by micro-site conditions rather than by climate. This study highlights the potential for understanding the causes of growth variation in P. elata as well as past hydroclimatic changes, in a climatically complex region characterized by a bimodal distribution in precipitation.

Leaf traits of tropical tree species are known to operate as intrinsic determinants of insect herbivory. However, we know little about how habitat fragmentation affects these traits and what, if any, are the consequences of this process on herbivory. We tested the effects of forest fragmentation on the leaf traits of sapling of four light-demanding species: Acalypha diversifolia, Hampea nutricia, Myriocarpa longipes, Siparuna thecaphora, and two shade-tolerant species: Pseudolmedia glabrata and Garcinia intermedia, in Los Tuxtlas, Mexico. We also conducted an acceptability assay with a generalist herbivore Spodoptera frugiperda. Plant traits did not change with forest fragmentation, but did with plant regeneration mode and species identity. Light-demanding species had significantly higher water content, nitrogen concentration and specific leaf area than shade-tolerant species. The latter had significantly higher leaf strength, carbon concentration and carbon:nitrogen ratio. Acceptability was affected by fragmentation but only in P. glabrata; plant tissue from forest fragments was consumed 2.6 times more than that from continuous forest. We conclude that forest fragmentation did not affect leaf traits in this site.

Despite its high plant diversity, the Amazon forest is dominated by a limited number of highly abundant, oligarchic tree and liana species. The high diversity can be related to specific habitat requirements in many of the less common species, but fewer studies have investigated the characteristics of the dominant species. To test how environmental variation may contribute to the success of dominant species we investigated whether the vital rates of the abundant liana Machaerium cuspidatum is sensitive to canopy height, topographic steepness, vegetation density, soil components and floristic composition across an Ecuadorian Amazon forest. The population was inventoried in 1998 and in 2009. Plants were divided into seedling-sized individuals, non-climbers and climbers. Out of 448 seedling-sized plants 421 died, 539 of 732 non-climbers died, and 107 of 198 climbers died. There was weak positive effect of dense understorey on the relative growth rate of climbers. The mortality of seedling-sized plants was higher in areas with intermediate slope, but for larger plants mortality was not related to environmental variation. The limited sensitivity of the vital rates to environmental gradients in the area suggests that ecological generalism contributes to the success of this dominant Amazonian liana.

Several monodominant rain-forest trees in New Caledonia have population size structures suggesting establishment following large-scale disturbance, with eventual replacement by shade-tolerant species predicted in the absence of future disturbance. Links of dominance and population dynamics to leaf-level photosynthesis were investigated in seedlings of 20 tree species from these forests, grown in experimental sun and shade conditions. In particular, we tested whether episodically regenerating (ER) species, including monodominants, have higher assimilation rates at high irradiances and lower tolerance of shade than continuously regenerating species (CR). ER species had higher maximum net assimilation rates (Amax-area) in sun plants (9.6 ± 0.4 μmol m−2 s−1) than CR species (6.2 ± 0.3 μmol m−2 s−1) and high plasticity, typical of shade-intolerant species, but monodominant species did not differ from other ER species. CR species had leaf-level traits consistent with shade tolerance, including lower dark respiration rates (Rd-area = 0.47 ± 0.03μmol m−2 s−1; Rd-mass = 7 ± 1 nmol g−1 s−1) than ER species (Rd-area = 0.63 ± 0.06 μmol m−2 s−1; Rd-mass = 11 ± 2 nmol g−1 s−1) in shade plants. Hence leaf-level assimilation traits were largely consistent with regeneration patterns, but do not explain why some shade-intolerant species can achieve monodominance.

The identification of seed dispersers and predators is essential to understand the effect of anthropogenic disturbances, and the associated defaunation process, on tropical forest dynamics in Central Africa. In this study, the animals involved in seed predation and dispersal of Dacryodes normandii (Burseraceae), an endozoochorously dispersed tree species endemic to Gabonese forests, were identified in a site in south-east Gabon using two complementary methods: direct observation and camera-trap monitoring of fruit piles. The combined sampling effort (172 h of direct observations and 796 d of camera trapping) led to the identification of six disperser and eight predator species of D. normandii seeds. With high frequency of consumption (88% and 57% of their visits, respectively) and long visit duration (83 and 23 min, respectively), the western lowland gorilla and central chimpanzee were identified as the main dispersers of this species. Seeds passed through the gorilla gut exhibited high germination success (68%). Rodents were identified as predators of D. normandii seeds, potentially displaying rare secondary dispersal through scatter-hoarding. The results of this study highlight the importance of great apes in the seed dispersal of this tree species.

Although seed dispersal plays a critical role for plant regeneration, the long-term benefits of frugivores for recruitment success have been poorly explored. We evaluated the relative importance of tree species abundance and of frugivore-related factors for successful plant recruitment on 18 tree species in a lowland Colombian rain forest. We combined census data from four 1-ha plots of trees (>10 cm dbh), saplings (1–5 cm dbh) and seedlings (<1.7 m) with a dataset describing tree–frugivore interactions. Seedling abundance was higher for large-seeded species dispersed by the spider monkey, while sapling abundance was higher for large-seeded species dispersed by birds. The identity of the dispersal agent and its interaction with seed size explained 20–30% of the total variance in seedling and sapling abundance across scales. Seed size consistently influenced the species abundance of seedlings and saplings across scales, but in opposite ways. These developmental changes suggest that what is beneficial to seedlings is not necessarily beneficial to saplings. Species identity explained 10–50% of the total variance in seedling and sapling abundance among and within 1-ha plots. Overall, our findings suggest that recruitment success is context-dependent as the relative importance of the different variables addressed may shift along spatial and temporal scales.

A community of frugivorous weevils was studied by quantitative rearing of 57 weevil species represented by 10485 individuals from 326 woody plant species in lowland rain forest in Papua New Guinea. Only fruits from 35% of plant species were attacked by weevils. On average, weevils were reared from only 1 in 33 fruits and 1 kg of fruit was attacked by 2.51 individuals. Weevil host specificity was relatively high: 42% of weevil species fed on a single plant genus, 19% on a single plant family and only 16% were reared from more than one family. However, monophagous specialists represented only 23% of all reared individuals. The average 1 kg of fruits was infested by 1.84 individuals of generalist weevils (feeding on allogeneric or allofamilial host species), 0.52 individual of specialists (feeding on a single or several congeneric species), and 0.15 individual of unknown host specificity. Large-seeded fruits with thin mesocarp tended to host specialist species whereas those with thick, fleshy mesocarp were often infested with both specialists and generalists. Weevils tended to avoid small-seeded, fleshy fruits. The low incidence of seed damage (3% of seeds) suggests that weevils are unlikely to play a major role in regulating plant populations via density-dependent mortality processes outlined by the Janzen–Connell hypothesis.

Uncertainty about the H+ buffering capacity in tropical rain forest limits our ability to predict the future effect of anthropogenic deposition on the streamwater chemistry. Export of major ions to the stream and the ion-fluxes via rainfall, throughfall, litter-leachate and soil-water pathways were observed to examine the source of streamwater nutrients in a small catchment in Sabah, Malaysia. The streamwater and the ion-fluxes were measured for 3.75 and 2 y, respectively, by collecting water twice a month and setting ion-exchange-resin columns. Streamwater pH ranged from 6.5 to 7.6 and was not sensitive to water discharge controlling base cations. The NO3−-N, Ca2+ and Mg2+ fluxes were low in atmospheric depositions (0.6, 0.5 and 0.3 kg ha−1 y−1, respectively) and markedly increased in the litter layer. The NO3−-N flux decreased drastically from subsoil (70 kg ha−1 y−1) to the stream (1.4 kg ha−1 y−1) whereas the Ca2+ and Mg2+ fluxes were not different between subsoil (38 and 18 kg ha−1 y−1) and stream (30 and 15 kg ha−1 y−1). Neutral pH in tropical streams was mainly due to the base cation leaching with deep chemical weathering in deeper strata, and a rapid decrease in NO3− leaching from the subsoil to the stream.