Altitudinal gradients provide tractable, replicated systems in which to study changes in species richness and community composition over relatively short distances. Previously, richness was often assumed to follow a monotonic decline with altitude, but recent meta-analyses show that more complex patterns, including mid-altitude richness peaks, are also prevalent in birds. In this study, we used point counts to survey birds at multiple altitudes on three mountains on the island of Borneo in Sundaland, an area for which quantitative analyses of avian altitudinal distribution are unavailable. In total we conducted 1088 point counts and collected associated habitat data at 527 locations to estimate species richness by altitude on Mt Mulu (2376 m), Mt Pueh (1550 m) and Mt Topap Oso (1450 m). On Mulu, the only mountain with an intact habitat gradient, bird species richness peaks at 600 m. Richness appeared to peak at 600 m on Totap Oso as well, but on Pueh it peaked several hundred metres higher. The richness peak on Mulu differs from that predicted by null models and is instead caused by the overlap of distinct lowland and montane avifaunas, supporting the faunal overlap hypothesis. This finding provides further evidence that a lack of coincidence between peak turnover and peak richness is not sufficient evidence to rule out faunal overlap as a causal factor.

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.

The main phases of plant dispersal into, and out of the South-East Asian region are discussed in relation to plate tectonics and changing climates. The South-East Asian area was a backwater of angiosperm evolution until the collision of the Indian Plate with Asia during the early Cenozoic. The Late Cretaceous remains poorly understood, but the Paleocene topography was mountainous, and the climate was probably seasonally dry, with the result that frost-tolerant conifers were common in upland areas and a low-diversity East Asian aspect flora occurred at low altitudes. India's drift into the perhumid low latitudes during the Eocene brought opportunities for the dispersal into South-East Asia of diverse groups of megathermal angiosperms which originated in West Gondwana. They successfully dispersed and became established across the South-East Asian region, initially carried by wind or birds, beginning at about 49 Ma, and with a terrestrial connection after about 41 Ma. Many Paleocene lineages probably went extinct, but a few dispersed in the opposite direction into India. The Oligocene was a time of seasonally dry climates except along the eastern and southern seaboard of Sundaland, but with the collision of the Australian Plate with Sunda at the end of the Oligocene widespread perhumid conditions became established across the region. The uplift of the Himalaya, coinciding with the middle Miocene thermal maximum, created opportunities for South-East Asian evergreen taxa to disperse into north India, and then with the late Miocene strengthening of the Indian monsoon, seasonally dry conditions expanded across India and Indochina, resulting eventually in the disappearance of closed forest over much of the Indian peninsula. This drying affected Sunda, but it is thought unlikely that a ‘savanna’ corridor was present across Sunda during the Pleistocene. Some dispersals from Australasia occurred following its collision with Sunda and following the uplift of New Guinea and the islands of Wallacea, Gondwanan montane taxa also found their way into the region. Phases of uplift across the Sunda region created opportunities for allopatric speciation and further dispersal opportunities. There is abundant evidence to suggest that the Pleistocene refuge theory applies to the South-East Asian region.

Long-term forest dynamics plots in the tropics tend to be situated on stable terrain. This study investigated forest dynamics on the north coast of New Guinea where active subduction zones are uplifting lowland basins and exposing relatively young sediments to rapid weathering. We examined forest dynamics in relation to disturbance history, topography and soil nutrients based on partial re-census of the 50-ha Wanang Forest Dynamics Plot in Papua New Guinea. The plot is relatively high in cations and phosphorus but low in nitrogen. Soil nutrients and topography accounted for 29% of variation in species composition but only 4% of variation in basal area. There were few areas of high biomass and most of the forest was comprised of small-diameter stems. Approximately 18% of the forest was less than 30 y old and the annual tree mortality rate of nearly 4% was higher than in other tropical forests in South-East Asia and the neotropics. These results support the reputation of New Guinea's forests as highly dynamic, with frequent natural disturbance. Empirical documentation of this hypothesis expands our understanding of tropical forest dynamics and suggests that geomorphology might be incorporated in models of global carbon storage especially in regions of unstable terrain.

Diversity changes can be evaluated at various spatial scales, and the relationship between changes in diversity at the local, landscape and regional scales is not evident. The overall patterns of functional and beta diversity of bird assemblages were evaluated along a five-stage urbanization gradient, censused over the months of January to April in the years 2010–2013, in and around Amravati city, Deccan Plateau, Central India. We expected the abundance of large and predatory species to decline along the gradient, and urbanization to homogenize species richness at the landscape level. Overall, 112,829 birds belonging to 89 species were identified in the region, and species richness decreased from the rural forest (73 species) to more urbanized areas (lowest at the centre of Amravaty city with 29 species). Along the urbanization gradient, bird assemblages contained more small species, and the share of frugivorous and omnivorous species also increased, while that of insectivorous species decreased. Diversity partitioning indicated that of the overall pattern, local (alpha) diversity accounted for 50.1% of the total (gamma) diversity, and urbanization stages another 36.2%; the contribution of within-stage, local diversity was rather small (2.7%), indicating fairly homogeneous assemblages.

Tropical bamboos persist in a wide range of light conditions and quickly respond to changes in light availability. However, the mechanisms underpinning this ability remain unknown. In order to test the hypothesis that the modular and hollow culm architecture of bamboos explains their performance in a wide range of light environments, we determined the allometric relationships of two dominant bamboo species of the upper hill dipterocarp forests of Malaysia, Gigantochloa ligulata (n = 29) and Schizostachyum grande (n = 25), via destructive sampling. We also monitored biomass turnover of bamboos and woody trees in 24 permanent plots (1.92 ha in total) over a one-year period. Compared with woody trees, bamboo culms attained 1.5 times the height and their clumps supported four times as much total leaf area at the same above-ground biomass. In addition, at a given height, bamboo clumps had six times larger crown projection area than trees while having a similar amount of total leaf area per unit of crown projection area. Finally, bamboos’ biomass turnover rate was three times higher than trees, and G. ligulata increased its specific rate of biomass increase after canopy disturbance, while trees decreased. We conclude that the unique architecture of bamboos allows them to persist under closed forest canopy light conditions and to respond to gap formation via high biomass turnover rate.

Soil has been proposed as a driver explaining the development of monodominant forests in the tropics, for example, Gilbertiodendron dewevrei forests (GDF) in central Africa. The aim of this study was to compare the physical and chemical properties of soils under GDF with those under an adjacent mixed forest (AMF), while controlling for topography. To this end, we set up sixteen 0.25-ha plots according to forest type and topography (plateau vs. bottomland), in the Yoko forest reserve, Democratic Republic of Congo. In each plot, we measured litter thickness and collected a total of 80 soil samples at depths of 0–5, 5–10, 10–20, 20–40 and 120–150 cm, for standard physical and chemical analyses. When controlling for topography and soil texture, we found that most of the chemical properties of soils under GDF did not differ from those of soils under AMF, particularly acidity, cation concentration, total N and the C:N ratio. The litter layer was 2.3 times thicker under GDF than under AMF stands, and, for a given texture, soils under GDF had a slightly higher organic C concentration in the 0–5 cm soil layer. This study suggests that G. dewevrei stands modify organic matter dynamics, which may be important in maintaining its monodominance.

Phenology is a key ecosystem process that reflects climate–vegetation functioning, and is an indicator of global environmental changes. Recently, it has been suggested that land-use change and timber extraction promote differences in forest phenology. We use remote-sensing data to describe regional leaf phenological patterns in combination with field data from 131 plots in old-growth and disturbed forests distributed over subtropical forests of Argentina (54–65°W). We assessed how climate is related to phenological patterns, and analysed how changes in forest structural characteristics such as stock of above-ground biomass relate to the observed phenological signals across the gradient. We found that the first three axes of a principal component analysis explained 85% of the variation in phenological metrics across subtropical forests, ordering plots mainly along indicators of seasonality and productivity. At the regional scale, the relative importance of forest biomass in explaining variation in phenological patterns was about 15%. Climate showed the highest relative importance, with temperature and rainfall explaining Enhanced Vegetation Index metrics related to seasonality and productivity patterns (27% and 47%, respectively). Within forest types, climate explains the major fraction of variation in phenological patterns, suggesting that forest function may be particularly sensitive to climate change. We found that forest biomass contributed to explaining a proportion of leaf phenological variation within three of the five forest types studied, and this may be related to changes in species composition, probably as a result of forest use.

Bornean rain forests on phosphorus (P)-poor soils exhibit a high P-use efficiency in the production of reproductive organs (i.e. the inverse of P concentration in reproductive-organ litter). The mechanism underpinning this high P-use efficiency is not known, but is hypothesized to result from dilution of P in a given type of reproductive organ and/or a shift of the community composition of flower/fruit types with decreasing P availability. These hypotheses were tested using eight forests with different soil P availabilities on Mount Kinabalu, Borneo. Mean P concentration per forest by genus in inflorescences was significantly positively correlated with P availability, while that in seeds or pericarps was not significantly correlated. This trend was consistent across 21 genera that we analysed, suggesting that P concentration in seeds is maintained in exchange with the dilution of P in inflorescences. The composition of fruit types in tree community was estimated based on the relative abundances of genera in each forest. The relative abundance of capsulate species, which required less P in pericarps, tended to increase in tree community with decreasing P availability. Therefore, both mechanisms were involved in P-use efficiency. This work provides an insight into the reproductive adaptation of trees to P deficiency.

Seed dispersal effectiveness (SDE) is related to the role of seed dispersal agents in realizing the reproductive potential of plants through seed dispersal and subsequent plant recruitment. The SDE of a given seed disperser may vary spatially and temporally, with important implications for our understanding of the mutualistic relationships involving plants and frugivores. Here we observed 22 frugivorous bird species visiting an individual tree (Cabralea canjerana) over a 9-y period in a fragment of Atlantic forest in south-eastern Brazil to document the temporal variation in SDE. The quantitative (that takes into account the frequency of feeding visits to the focal plant and the number of fruits removed per visit) and qualitative (that considers the probability of seed deposition on a suitable site for plant recruitment) components of SDE varied in two and one order of magnitude both among bird species and among years within bird species, respectively. As a result, the SDE of bird species fluctuates over the years, especially for a migratory species that is the main seed disperser of C. canjerana (Chivi vireo Vireo chivi) whose quantitative component (i.e. the product of visit and fruit intake rates) varied from 3.0 to 7.1. This study illustrates the dynamic nature of the seed-dispersal environment to which a plant is subjected to over the course of its life, which has important consequences for the plant's individual fitness.

Plant–animal mutualistic interactions through ecological network systems and the environmental conditions in which they occur, allow us to understand patterns of species composition and the structure and dynamics of communities. We evaluated whether flower morphologies with different pollination syndromes (ornithophilous and non-ornithophilous) are used by hummingbirds and whether these characteristics affect the structure (core-peripheral species) of hummingbird networks. Observations were made in flowering patches, where plant–hummingbird interactions were recorded at three altitudes (300–2500 m) during three seasons (dry, rainy and post-rainy) from 2015 to 2016 at El Triunfo Biosphere Reserve, Chiapas, Mexico. We recorded 15 hummingbird species interacting with 58 plant species, and the greatest number of interacting hummingbird species (11; 14) and plant species (28; 40) were found at middle altitudes and during the dry season, respectively. In all study sites, most of the plant species visited by hummingbirds had an ornithophilous syndrome (67%) at high altitudes (22 plant species) and during the dry season (26 plant species), but more individual hummingbirds visited non-ornithophilous plant species. The hummingbird species at high altitudes exhibited the greatest level of specialization towards plants (H2′ = 0.74), but the networks of plant-hummingbird interactions were generalist (H2′ = 0.25); i.e. visiting plants with both syndromes, at low altitudes. The core generalist hummingbird species remained constant with altitude and season, but the core generalist plant species varied between different altitudes and seasons according to the phenology of the species.

Animals often select for habitats that increase their chance of survival by balancing the need to acquire food, reproduce and avoid predation. Perennial blooms of golden jellyfish (Mastigias papua etpisoni) are present in Jellyfish Lake, Palau, a popular tourist destination. Based on the species’ economic importance and unusual behavioural complexity, increased understanding of jellyfish habitat selection is necessary. We used a novel approach, a REMUS autonomous underwater vehicle, to quantify jellyfish distribution, abundance and habitat, and compared these findings to traditional methods. Midday acoustic surveys showed jellyfish distribution was patchy and the population resided mainly on the eastern side of the lake, as it is known that jellyfish migrate eastward towards the sun. Highest vertical densities of jellyfish were at 6–7 m, potentially to mitigate UV damage or photoinhibition of their photosymbionts, suggesting a coupling exists between their vertical distribution and water properties. Abundance estimates of jellyfish were ~2.75 and ~7.1 million (~2 million excluding bell diameters <1 cm) from acoustic and net samples, suggesting the methodology employed underestimated the population's smaller size fraction and non-synoptic surveys could impact estimates due to unresolved patchiness. Our approach could investigate population dynamics, behaviour or habitat associations on fine scales.

The river zonation hypothesis predicts that abiotic and biotic conditions along riparian gradients drive variation in animal communities. Glass frogs are a diverse group of Neotropical anurans that use riparian habitats exclusively for oviposition and larval development, but little is known about how glass frog communities are distributed across riparian gradients. Here, we measured glass frog community assembly across a gradient of riparian habitats from first- to fifth-order streams at La Selva Biological Station, Costa Rica. We performed repeated nocturnal frog calling surveys and built occupancy and N-mixture abundance models to test for varying patterns of species occupancy, community assembly, species richness (α-diversity) and species turnover (ß-diversity). We observed significant differences in patterns of species occupancy and community assembly across a stream-order gradient: occupancy of two species increased with stream order (Teratohyla pulverata, Hyalinobatrachium fleischmanni), one species decreased (Teratohyla spinosa), and one species did not vary (Espadarana prosoblepon). We evaluated four a priori hypotheses describing how α- and ß-diversity of centrolenids are shaped across the riparian gradient; our data were most consistent with a pattern of nested assemblages and increasing species richness along the riparian gradient. Species-specific patterns of occupancy and abundance resulted in assemblage-level differences consistent with theoretical predictions for highly aquatic organisms along riparian gradients.

Forest fires pose an important threat to tropical rain-forest biodiversity. In the present study, we assessed ground layer (herb and shrub) communities in six differentially disturbed landscape plots in East Kalimantan, Indonesia, including primary and logged forest and once-, twice- and frequently-burnt forest. Overall, we recorded 175 species of herbs and shrubs; richness was highest in twice-burnt forest and lowest in logged forest. Vegetation and topographical variables including the percentage of the plot burnt and tree abundance were significant predictors of variation in composition. The main compositional gradient showed a clear distinction between subplots in unburnt versus burnt forest. A subset of subplots in burnt forest, however, clustered together with subplots from unburnt forest. These plots were located in a network of relatively unscathed forest along floodplains that persisted in the burnt-forest matrix. Small plant species associated with unburnt forest included several species of Dryopteridaceae, Marantaceae and Rubiaceae. Species associated with once- and twice-burnt forest included Mikania scandens (Compositae), Microlepia speluncae (Dennstaedtiaceae), Nephrolepis cf. biserrata (Nephrolepidaceae), Lygodium microphyllum (Schizaeaceae) and Hornstedtia cf. reticulata (Zingiberaceae). The frequently-burnt landscape plot was characterized by a high cover of the grass species Imperata cylindrica and the invasive exotic shrub Chromolaena odorata. Importantly, these species and other exotics had also invaded the once- and twice-burnt forest and represent a potential threat to forest recovery.

The mechanisms underlying occupancy patterns of species in modified tropical landscapes are poorly understood. The presence of adults in a modified habitat may not necessarily indicate the quality of the habitat for sub-adult stages. These issues were addressed by examining patterns in breeding-site use by adult frogs and tadpole performance across a pasture-forest gradient in the Osa Peninsula, Costa Rica. The use of artificial pools by adult frogs for breeding activity was quantified along three transects, with a pool located at the edge (0 m) and 10, 30 and 50 m into forest and pasture. Next, survival, size at metamorphosis and time to metamorphosis were quantified for tadpoles of Engyptomops pustulosus and Dendrobates auratus in artificial pools at the edge, pasture and forest. Adult frogs used breeding pools non-randomly; two species used pools only in pasture, whereas three species used pools only in forest. In addition, Smilisca phaeota used pools in pasture and at the edge while E. pustulosus used pools across the pasture-forest gradient. The habitat where adults used breeding pools generally also yielded high performance of their tadpoles, with some exceptions. Tadpole survival to metamorphosis was low in pastures (<5%) and higher in edge and forest (>18%) for D. auratus; in contrast, survival of E. pustulosus was over 80% in each habitat. Metamorphs of D. auratus were largest in edges but larval period did not differ among habitats. Metamorphs of E. pustulosus were 18% larger and larval period was 27% shorter in pastures compared with forest. These results suggest that modified habitats represent an ecological jackpot for some species, such that offspring performance is enhanced compared with that in forest habitat. Populations of other species may be restricted to forest habitat because of intolerable abiotic conditions in modified habitats. The results of this study indicate that adult breeding site use and tadpole performance contribute to mechanisms that underlie patterns of species occupancy in modified tropical landscapes.

Trends in structural and chemical leaf traits along a chronosequence of semi-evergreen tropical forest and their correlation with litter production and decomposition and associated carbon (C) and nitrogen (N) fluxes were assessed. Leaves of 15 dominant species in each plot were collected to measure leaf area, specific leaf area (SLA), C and N concentration and C:N ratio. Litterfall was measured and litter decomposition experiments were set up in 16 experimental plots in a chronosequence of secondary and mature forest. All five leaf traits combined discriminated the secondary forests from mature forest. SLA, N and C:N were significantly correlated to litter decomposition rates. Litter decomposition was significantly slower in mature forest compared with secondary forests. The N concentration of litter was lowest during the dry season, when litterfall was highest. N concentration in fresh leaves was higher than in litter, indicating that N is re-absorbed before leaf abscission. Leaf dynamics and associated nutrient cycling differ significantly between secondary forests and mature forest. Ecosystem-level leaf structural and chemical traits are good predictors of the stage of the forest and explain well the differences in decomposition rates between secondary and primary forests.

We used all 167 typhoon warnings issued by the Taiwanese Central Weather Bureau from 1958–2006 to assess the long-term effect of cyclone disturbance on vascular epiphytes. Tracks and eyes of past typhoons were plotted as circles with radii of Beaufort scale 7 and 10, and the frequency of each cohort in 1-km2 grid cells was calculated. The presence of vascular epiphytes in the same grid cells was predicted using species distribution models (SDMs). First, we used herbarium specimens and other sources to compile a comprehensive georeferenced vascular epiphyte database that contained 39084 records in 331 species. Next, we assigned each epiphyte record to a cell in the same 1-km2 grid as above. Finally, we used SDMs (MaXent), based on 30 environmental variables except typhoon frequency, to predict the potential presence of each species in the grid cells. For our analysis we only considered cells east of the central mountain ridge where typhoons hit with full force. After elimination of rare species and species that could not be validated in the SDMs, we were left with 156 epiphyte species in 10725 1-km2 cells. The number of projected species in the cells was 36.5 on average, varying between two and 82 species. Correlation analyses showed that, over time, typhoons led to a decrease in epiphyte richness at Beaufort scale 7 and 10 (Pearson's r = −0.07 and −0.08 respectively). Ferns, orchids, hemiepiphytes and dicotyledons generally showed the same pattern, except hemiepiphytes that showed a positive correlation at B7 (Pearson's r = 0.15). A partial canonical correspondence ordination analysis showed that, independent of temperature- and rainfall-related variables, Beaufort scale 7 and 10 typhoons also had significant influence on the species composition of the vascular epiphyte communities in the landscape. We recommend in situ monitoring of epiphytes over a long period to corroborate the suggestion from this indirect study that typhoons have a long-term effect on the distribution of epiphytes in Taiwan.

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.

Although large herbivore habitat use has been extensively studied, more information is still required on the use of heterogeneous vegetation types. Over 3 y we carried out monthly road transects in the Zambezi National Park (ZNP), Zimbabwe, to determine the impala density in each of five vegetation types. In addition we determined grass and browse chemical composition to test if at the time the impala switches from grass to browse, grass nutritive quality had declined below that of browse. Furthermore, grass height was measured in the five vegetation types. The impala used mixed, acacia and terminalia vegetation types, which constituted 37% of the protected area and avoided grassland and the predominant Zambezi teak (60% of ZNP) vegetation types. At the time of the diet switch by the impala from grass to browse, woody plant leaf nutritive quality was higher than grass in terms of nitrogen, calcium and acid detergent fibre content. The three vegetation types used by the impala had short to medium grass height. We concluded that when the impala switched from grass to browse the grass nutritive quality was lower than that of the browse.

The movement of African ungulates between habitats is determined by diverse factors including forage composition, availability and quality, water availability, topography, the catenary level and the effect of fire on vegetation. We assessed how grass flushes, following dry-season fires, and availability of water influenced seasonal movements of hartebeest, impala, warthog, white rhino, wildebeest and zebra in Ithala Game Reserve, a fenced reserve in South Africa. Over a 6-d period each month for 4 y, road transects covering a representative sample of the reserve's different vegetation types, and 23% of the reserve's total area, were carried out. We recorded the species, number, sex and age class of herbivores, obtaining 8742 records (total herbivores sighted = 47055), and obtained positional data on sightings over the last 2 y of the study. Using a GIS-based approach, we determined that ruminant, but not non-ruminants, were significantly attracted to dry-season grass flushes, and that presence or absence of such flushes significantly affected their mean distance to water and hence seasonal movements on the catena.