Despite the importance of treefall gaps in tropical forest dynamics, few studies have followed gap-phase processes for more than 2 y. We monitored, for five years, the growth and survival of many seedlings of Tetragastris panamensis (Engler) O. Kuntze, Protium panamense (Rose) I. M. Johnston, and Desmopsis panamensis (Rob.) Saff. (three common tree species of the Panamanian tropical moist forest) in artificially created treefall gaps and under intact-canopy control plots. On these same plots, we also monitored light levels using hemispherical photographs taken over an 8-y period. Seedling height growth was faster in gaps than under intact canopies during the first 42 mo of regrowth, then declined to rates similar to those under intact canopies. Light levels in gaps similarly rose and fell, returning to pre-gap levels by month 48. Only Tetragastris panamensis showed higher survival in gaps, contrary to the general assumption that seedling survival is enhanced by gap creation. Our results document important transition points that mark the conclusion of the gap phase, suggesting an estimate of 4y for the duration of the gap phase in this tropical forest.

Aechmea magdalenae is a terrestrial bromeliad that dominates areas of forest understorey on Barro Colorado Island, Panama. Nocturnal CO2 uptake via crassulacean acid metabolism was the primary means of carbon gain under well-watered conditions and all light regimes. The ability to maintain a positive carbon balance under conditions of very low light was demonstrated by laboratory measurements of photosynthesis and forest measurements of growth. Low-light-grown juvenile rosettes had the same daily net assimilation whether tested at photon flux densities of 15 or 300 μmol m−2 s−1 Growth rates of rosettes in treefall gaps were similar to those of plants in closed canopy forest. Growth rates of forest plants were increasingly correlated with canopy openness as the wet season progressed due to increased growth by gap plants, suggesting that water availability rather than light may limit growth during the annual dry season.

The Atlantic forest of Brazil is considered to be a high priority for conservation in South America. Despite its importance, few phenological and ecophysiological data are available for plants of this area. In this study the seasonal changes in the water potentials (Ψ) and the phenological behaviour of three woody legumes are related to environmental conditions, particularly air vapour pressure deficit (VPD). The values of Ψ at predawn were greater than −0.75 MPa for all species even during the dry season (May–September). The minimal daily value of Ψ was −3.8 MPa. The maximum daily amplitude of Ψ (Δ parameter) was correlated with the air vapour pressure deficit, showing high correlation coefficients in linear equations. A high recovery rate of Ψ after rain (greater than 0.80) was registered for all species, suggesting a high hydraulic conductivity. The high values of Ψ at predawn during the year and the strong relationship between the daily amplitude of Ψ and VPD suggested that the changes in the canopy cover are related more to atmospheric drought than to soil water deficit.

We studied the effects of savanna fires on the structure of local ungulate communities in a West African woodland savanna. The distribution of 11 ungulate species over 9−15 burned sites (the number of which increased as burning activity continued during the dry season) and 7−13 unburned sites was compared with a variety of null models or randomized ‘virtual communities’. Five different parameters of community structure were examined: body mass distribution, co-occurrence patterns, species richness, species density and guild dominance. Overall, ungulate species were not randomly distributed over burned and unburned sites. The regular spacing of body masses in the set of species recorded on burned and unburned sites indicated competition, since species similar in body mass are more likely to compete than species of different size. However, co-occurrence patterns on burned sites were random, indicating absence of competition at fine spatial scales due to differential habitat use within the burned landscape. Although the attractiveness of the regrowth on burned sites resulted in higher numbers of ungulates compared with unburned sites, species richness was not different. Grazers were the dominant guild on burned sites, but there were no differences in species richness or species density between grazers and browsers on unburned sites.

As the destruction and severe disturbance of primary tropical forest continues, it is important to understand how these forests may recover from perturbations. Considerable work has been done on above-ground recovery but below-ground processes are less well understood. To determine changes in root mass during tropical secondary succession in lowland forests of Central Borneo, samples were taken from stands of increasing ages since abandonment of agriculture (1, 3, 14 and 31 y) with a primary forest control (six plots from 1-y-old stands and three from all other ages). Root mass and elemental concentrations were determined and soils were chemically analysed. There was no increase in root mass with stand age for fine-root (< 2 mm diameter) or small-root (< 5 mm diameter) mass but there was a trend for coarse-root mass (5–10 mm diameter) to increase with stand age. Negative correlations were shown between root mass and soil nutrient status. Fine-root C concentrations increased with stand age but there was no clear effect of stand age on fine-root N or P. Fine-root mass did not increase significantly with stand age suggesting a rapid recovery; instead, soil nutrient status appeared to be the most important factor controlling root mass. Of the soil nutrients measured in this study, N had a stronger control over root mass than P suggesting that this element may be limiting during secondary succession in tropical lowland forests of Borneo.

The relationship between leaf longevity and other leaf traits was compared among different life-form categories (trees, herbs, climbers and epiphytes) of 101 plant species in a tropical montane forest on Mt. Halimun, West Java, Indonesia. We applied the Cox proportional hazards regression to estimate the leaf longevity of each species from 30 mo of census data. We examined whether estimated longevity was explained by either species life-form categories, taxonomic groupings (eudicots, monocots, magnoliids and chloranthales, and ferns) or such leaf traits as leaf area, leaf mass per area (LMA), mass-based leaf nitrogen, penetrometer reading, condensed-tannin-free total phenolics and condensed tannin. There was a wide-ranged interspecific variation in leaf longevity, mostly 10–50 mo, similarly across life-form categories. LMA showed a strong positive influence on leaf longevity. We found that relationships between leaf longevity and some leaf traits were different among various life forms. Trees tended to have high LMA, while climbers tended to have low LMA at the same leaf longevity. We hypothesize that such difference among life forms reflects shoot architecture characteristics. Multi-shoot trees with branching architecture need to have self-supporting leaves, whereas semi-epiphytic climbers can maintain relatively low biomass investment to leaves hanging or relying upon the mechanical support from host plants.

One component of the high organismal diversity of tropical lowland rain forests is the existence of series of closely related, sympatric species. For example, the six distinct tree species of the monophyletic Polyalthia hypoleuca complex regularly grow sympatrically in various combinations throughout the rain forests of Malesia. Theoretical and empirical evidence has been presented indicating that the members of such series either (1) are well differentiated with respect to at least one major niche component; or (2) may lack differentiated niches. In this study, certain sympatric members of the complex are shown to have clearly diverged in autecological characteristics that affect their distribution including: (1) P. glauca, P. hypoleuca, and P. sumatrana differ in growth characteristics, height at maturity, seedling germination requirements, and are found on soils with differing degrees of hydration; (2) P. discolor grows to a different height and on different substrate types than does P. multinervis; and (3) P. glauca and P. hypoleuca seedlings differ in transpiration characteristics and response to flooding and drought.

Several studies have evaluated the short-term effects of tropical forest fragmentation on plant taxonomic diversity, while only a few have evaluated its effects on functional or phylogenetic diversity. To our knowledge no study has looked at the long-term consequences of tropical forest fragmentation on the three main components of plant diversity simultaneously: taxonomic, functional and phylogenetic diversity. We sampled the vascular flora using belt transects (50 × 4 m) in a continuous tropical semi-evergreen forest (16 transects) and in an adjacent naturally fragmented forest (fragments of 1.7-My-old semi-evergreen forest immersed in a mangrove/sedge matrix) (18 transects), and compared their taxonomic, functional and phylogenetic plant diversity. There were 36 species in the continuous forest and 28 in the fragmented forest. Continuous forest was taxonomically more diverse (25%) than the fragmented forest. All functional diversity metrics were greater (6–33%) in the continuous than in the fragmented forest. Phylogenetic diversity was 19% greater and phylogenetically more overdispersed in the continuous forest than in the fragmented forest. The results suggest that in the fragmented forest not only is taxonomic plant diversity lower, but functional and phylogenetic diversity are as well. The negative effects of forest fragmentation on plant diversity seem to be chronic.

The plant vigour hypothesis proposes that herbivores should favour feeding on more vigorously growing plants or plant modules. Similarly, we would expect herbivores to favour plants that regrow vigorously after herbivory. Larger animals, like elephants, may also select plant species relative to their availability and prefer species with larger growth forms in order to meet their intake requirements. The food preferences of the Bornean elephant (Elephas maximus borneensis) in the Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia, were investigated along 12 transects in areas where elephants were recently sighted feeding. One hundred and eighty-two plants were eaten and 185 plants were measured for species availability along transects. Species vigour was determined by the monthly regrowth in new shoot length after elephant feeding and the number of new shoots produced on each plant. Measurements were carried out on each plant for 9 mo or until the new shoot was eaten. Plant sizes were determined from their basal diameter. The Bornean elephant did not prefer more vigorous species or species with larger growth forms. New shoots did not grow longer on preferred than avoided species. Additionally, unlike other elephants that live in a forest environment, the Bornean elephant preferred species from the Poaceae (specifically Phragmites karka and Dinochloa scabrida) over other plant types including gingers, palms, lianas and woody trees.

The distribution of the giraffe (Giraffa camelopardalis peralta Thomas 1898) has greatly diminished in West Africa, and now the last remaining population, reduced to less than 100 individuals, is found in Niger. These giraffes of West Africa are seriously threatened by extensive deforestation and clearing of their habitat. They live peacefully with humans and cattle and participate in an essential way in the dynamics of vegetation. Their disappearance would represent another step towards the impoverishment of the inheritance of Africa, a process already too far advanced. To save them, a fundamental rethinking of the connection between the environment and development on the one hand, and on the responsibilities of rural communities for the management of their natural resources on the other, has to be undertaken.

In the Neotropics, crops that are grown in agroforestry systems with shade trees support high levels of bird diversity compared with crops grown without shade (Estrada & Coates-Estrada 2005, Faria et al. 2006). Several experiments in shaded coffee farms have explored how insectivorous birds reduce herbivore numbers and their damage to plants and have simultaneously approached ecological questions that are applied (e.g. biological control) and basic (e.g. tri-trophic interactions) (Borkhataria et al. 2006, Greenberg et al., Perfecto et al. 2004). Here we used exclosures to test whether birds lower the densities of herbivorous insects and reduce insect damage to cocoa (Theobroma cacao L., Sterculiaceae) foliage in shaded farms of western Panama. Although bird predation has been shown to reduce insect damage to crops in other systems (Mols & Visser 2002), we provide the first test for shade-grown cocoa.

Termites play a critical role in the regulation of soil processes, for example, water retention, nutrient cycling, and the formation and maintenance of soil structure. There is a consensus that mound-building termites modify physical and chemical soil properties in clay soils, but there is limited investigation into their influence for sandy soils in the Brazilian Atlantic rain forest. We tested the hypotheses that the termitosphere effectively improves properties of sandy soil, and that the role of termite soil particle selection is of greater importance in soils with higher sand concentration and lower nutrient status. The work was conducted in three vegetation physiognomies: woodland, savanna and grassland. In the woodland physiognomy we sampled in the border and in the interior, totalling four studied areas. We described a soil profile and collected five samples of termitaria and surface soil in each area. Also, in three 100-m2 plots allotted in each area, termite-mound density and volume were estimated, and termites were collected for taxonomic identification. Soil samples were submitted to physical and chemical analysis, and regression models were employed to analyse termite particle selection ability in different soil conditions. In most areas, the concentrations of nutrients, organic carbon and clay-size particles were significantly higher in termite mounds than in surface soils. On a weight basis, termite mounds had up to 32 times more nutrients, 12 times more organic carbon, and five times more clay than surrounding soils, however, aluminium toxicity was lower in termite mounds. Regression models demonstrated that the role of termites in soil particle selection is of greater ecological importance with decreasing soil nutrient status and increasing sand concentration. Therefore, termites greatly improve soil properties, representing truly ecosystem engineers in sandy soils, with an average soil turnover by mound-building activity reaching 10.5 m3 ha−1.

A method of assessing rain forest structure by ranking relative abundance of 41 habitat variables was used to describe habitat differences among six trapping sites (324 subsites). Variables included aspects of all vegetation layers but concentrated on those considered to be important to small mammal distribution. Ordination and classification methods resulted in similar analyses of the data. Differences in habitat structure were primarily related to the moisture conditions of the trapping sites and secondarily to their successional age (regenerating versus primary forest). The most important habitat variables for differentiating between sites were LITTER, CLEARING, SOILS, PIG DAMAGE, FLOODING, FAN PALM, EMERGENTS, CANOPY SURFACE and SEEDLINGS. Habitat structure also varied within sites with some suggestion of small-scale patterning.

Small mammal captures were more likely in drier sites and subsites, but there was no difference in trap success between regenerating sites and primary forest sites. Greater numbers of species were captured in sites containing a variety of habitats, a discrete layering of vegetation and an extensive understorey. Small mammal captures were positively associated with five habitat variables (EMERGENTS, LITTER, ROTTING LOGS, SEEDLINGS, ROUGH BARK) and negatively associated with five others (LAYERS, BERTAM, SEDGES, PIG DAMAGE, FLOODING). The destruction caused by pigs is thought to be a major factor since it reduces litter and food availability over wide areas. Leopoldamys sabanus was the most abundant small mammal captured (40/68 individuals) and trap success differences among sites (0.4–1.9%) reflect its preference for higher, well-drained habitats.

The study demonstrates the usefulness of a simple method of ranking habitat features according to importance/abundance thus eliminating the all but impossible task of direct measurements in this complex system. This simple method of habitat description provides a basis for studying variables influencing faunal distribution patterns.

Conversion of natural habitats to anthropogenic land uses is a primary cause of amphibian declines in species-rich tropical regions. However, agricultural lands are frequently used by a subset of forest-associated species, and the habitat value of a given land use is likely modified by the presence and characteristics of remnant trees. Here we used mark–recapture methods to examine abundances and movement probability of the poison frog, Oophaga pumilio, at individual trees in forest-fragment edges and adjacent pastures in north-eastern Costa Rica. One hundred and forty-seven trees were surveyed at three replicate sites that each included a forest fragment and adjacent pasture. Trees were sampled at distances of ≤30 m into forest and ≤150 m into pastures for Oophaga pumilio, and local environmental characteristics were measured at each tree. We also measured indices of physical condition (size and endurance) of frogs captured in forest edges and in nearby pastures. Analyses of 167 marked individuals showed no difference in per-tree abundances or sex ratios between pasture and forest edges. We found significant interactions between habitat type and leaf-litter cover, tree dbh and number of logs, indicating greater influence of local variables on abundances in pastures. Movement among trees was infrequent and not predicted by sex, size, habitat type or environmental variables. While results of endurance tests did not differ for individuals from the two habitats, frogs captured in pastures were, on average, larger than frogs captured in forest edges. These data indicate that remnant trees are important habitat features for O. pumilio in pastures and corroborate research in other systems that suggests that large relictual trees should be retained to maximize the potential for altered landscapes to provide habitat for native species.

Elephants (Loxodonta africana (Blumenbach 1797)) can have a major transforming effect on savanna structure through felling, debarking or uprooting trees (Dublin et al. 1990, Laws 1970, Mapaure & Campbell 2002). However, it is difficult to separate their influence from that of other causes of tree mortality, including wind storms (Spinage & Guinness 1971), drought (Lewis 1991, van de Vijver et al. 1999), fire (Higgins et al. 2000), and in some situations frost (Childes & Walker 1987, Holdo 2006), especially when interactions among them may occur (de Beer et al. 2006, Laws et al. 1975, Pienaar et al. 1966). Furthermore, the consequences for woodland dynamics depend on the size classes of the trees affected, as well as on how the disturbance is concentrated in time and space. Mortality of canopy trees has a much greater and longer-lasting impact than losses among the regenerating stages of these trees. However, the consequences may be less adverse for ecosystem function and biodiversity if the disturbing effects are locally concentrated, generating a patch mosaic of stands at different stages of regeneration (Remmert 1991).

Some tree species exhibit large year-to-year variation in seed production, a phenomenon known as masting (Kelly 1994, Kelly & Sork 2002). Even in tropical rain forests, in which the climate is suitable for plant growth all year round with little seasonal variation (Whitmore 1998), there are many reports of masting (Appanah 1993, Hart 1995, Newbery et al. 1998, Newstrom et al. 1994, Wheelwright 1986). In particular, Dipterocarpaceae, the dominant family in lowland mixed dipterocarp forests in South-East Asia, undergo mast fruiting following mass-flowering with strong interspecific synchronization in aseasonal western Malesia (Appanah 1985, 1993; Ashton 1989, Ashton et al. 1988, Curran et al. 1999, Janzen 1974, Medway 1972, Sakai et al. 1999, Whitmore 1998, Wood 1956). In mixed-dipterocarp forests, dipterocarp species contribute more than 70% of the canopy biomass (Bruenig 1996, Curran & Leighton 2000). Masting of dipterocarp species is therefore likely to have a major impact on animal populations, and also on the nutrient cycle in such forest ecosystems by causing fluctuations in the availability of resources (Sakai 2002).

Several studies have shown that qualitative (binary) ant-plant networks are highly nested in tropical environments, in which specialist species (with fewer interactions) are connected with generalists (with the most interactions) in cohesive subgroups. Interactions occur in both qualitative and quantitative networks, however, how their frequency may structure the nestedness in ecological networks involving these organisms is, we believe, unknown. Based on this perspective, we used nestedness analysis to address the effect of interaction frequency on ant-plant networks (n = 14 networks). Unlike binary networks, quantitative networks are often significantly non-nested. In addition, species with a higher interaction frequency have a higher number of links, indicating that these species are possibly more abundant and/or competitive. Moreover, different biological parameters can change the nature of ant-plant interactions, as a plant can be a good resource for one ant and a ‘bad’ resource for another. Thus, this suggests a new perspective for the study of interaction networks in the tropics, since species with lower interaction frequency are not necessarily subsets of species with higher frequency, and consequently generate the non-nested pattern in quantitative networks.

Influence of habitat on physiological and structural characteristics was investigated for broad-leaved tropical monocotyledons in the genus Heliconia (Heliconiaceae). Seven species were selected from three different light regimes, enabling an analysis of the extent to which this genus has adapted its photosynthetic strategies and morphological characteristics to different daily photon flux densities (PFD). Predictably, light response curves showed a clear gradient with respect to light saturation and rates of maximum net assimilation (Amax). Heliconia latispatha, an open site species, showed saturation at higher PFD (1400 μmol m−2 s−1) and higher Amax (14–16 μmol m−2 s−1) than H. mathiasiae, a forest edge species (PFD 1000 μmol m−2 s−1; Amax 7.5–8.5 μmol m−2 s−1) and H. irrasa of deep-shade forest understorey (PFD 250 μmol m−2 s−1; Amax 3.5 mol m−2 s−1). Leaf blade areas were largest in open sites, and leaf specific mass was also significantly higher, but leaf support efficiency was highest in understorey species. Species in open sites had thicker leaves with more chlorenchyma, whereas deep-shade species had very thin leaves and low stomatal densities. These rapidly growing herbaceous perennials appear to allocate much of their above-ground biomass to leaf tissues and have a relatively low investment in support tissues. This contrasts with understorey palms, in which leaf form and structural investment has been interpreted as a trade-off between economy and protection against tissue loss from falling branches. Presence of below-ground rhizomes in Heliconia may provide the key to this difference.

Tropical montane cloud forests (TMCFs) are dynamic ecosystems defined by frequent, but intermittent, contact with fog. The resultant microclimate can vary considerably over short spatial and temporal scales, affecting the ecophysiology of TMCF plants. We synthesized research to date on TMCF carbon and water fluxes at the scale of the leaf, plant and ecosystem and then contextualized this synthesis with tropical lowland forest ecosystems. Mean light-saturated photosynthesis was lower than that of lowland forests, probably due to the effects of persistent reduced radiation leading to shade acclimation. Scaled to the ecosystem, measures of annual net primary productivity were also lower. Mean rates of transpiration, from the scale of the leaf to the ecosystem, were also lower than in lowland sites, likely due to lower atmospheric water demand, although there was considerable overlap in range. Lastly, although carbon use efficiency appears relatively invariant, limited evidence indicates that water use efficiency generally increases with altitude, perhaps due to increased cloudiness exerting a stronger effect on vapour pressure deficit than photosynthesis. The results reveal clear differences in carbon and water balance between TMCFs and their lowland counterparts and suggest many outstanding questions for understanding TMCF ecophysiology now and in the future.