All plant species face a fundamental reproductive trade-off: for a given investment in seed mass, they can produce either many small seeds or few large seeds. Whereas small seeds favour the germination of numerous seedlings, large seeds favour the survival of seedlings in the face of common stresses such as herbivory, drought or shade (Leishman et al. 2000). One mechanism explaining the better survival of large-seeded species is the seedling size effect (SSE) (Westoby et al. 1996): because seeds with large reserves result in bigger seedlings, seedlings from large-seeded species would have better access to light and/or to reliable water supply than seedlings from small-seeded species.

Arboreal earthworms are scarce in tropical rain forests, being confined to tree trunks or epiphytes (Fragoso & Rojas-Fernandez 1996). Their above-ground presence might be attributed to (1) temporary responses to flooding (Adis & Righi 1989), (2) permanent responses to acidity, flooding and anoxia of very wet forest soils (Lee 1983), (3) drought (Fragoso & Rojas-Fernandez 1996), (4) accidental events, e.g. mudslides (Picado 1911), or (5) anti-predation responses, e.g. escape from army ants (Gotwald 1995).

Light is a key environmental factor limiting growth and survival of trees in the subcanopy of wet tropical forests (Davies 2001, Thomas 1996). Light availability varies both vertically and horizontally and affects tree height, crown shape and tree architecture (Bongers & Sterck 1998, Sterck & Bongers 2001, Sterck et al. 1999) in addition to growth and survival (Clark & Clark 1992, 2001). Although many studies of tree seedlings and saplings have shown that growth varies significantly with light availability in tropical wet forests (Clark et al. 1993, Iriarte & Chazdon 2005, King 1991, Kohyama 1991, Montgomery & Chazdon 2002, Oberbauer et al. 1988, 1993; Poorter & Werger 1999, Sterck et al. 1999, Welden et al. 1991), few studies have examined these relationships in size classes above 5 cm dbh (Sterck 1999). King et al. (2005) found that annual increment growth of trees in the 8–20-cm dbh size class in two Asian forests was positively dependent on an index of crown light interception, but no direct measurements of light availability were taken in this study. Due to logistical challenges, few direct measurements of light environments above tree crowns have been made in tropical forests (Sterck & Bongers 2001). To our knowledge, no measurements have been made in second-growth forests.

Leaf phenology and leaf traits of the fern Oleandra pistillaris were examined in relation to canopy cover (open and understorey) and seasonal reduction in rainfall in a wet tropical montane forest, Indonesia. Although the annual rainfall is high, rainfall is relatively less in June and July. Stomatal density and diameter were greater in the open than in the understorey (229 versus 167 mm−2 for stomatal density and 33 versus 29 μm for stomatal diameter). The stable carbon isotope ratio (δ13C) of leaves, positively correlated with water use efficiency, was higher in the open than in the understorey (mean δ13C −30 versus −33‰). Therefore, it is considered that leaves have high gas-exchange capacities per leaf area in the open where water availability would be limited, compared with the understorey. In contrast, leaf mass per area (LMA) was lower and leaf life span was longer in the understorey than in the open (25 versus 34 g m−2 for LMA and 2.1 and 1.6 y for leaf life span). These thin leaves with a long life span in the understorey would contribute to efficient light capture and photosynthetic production per leaf mass. The number of leaves per stem decreased during the period with less rainfall in both the open and understorey conditions, which should reduce the water loss from plants, but increased again after the period with less rainfall. Stem growth rate was higher in the open than in the understorey, and the seasonal reduction in rainfall hardly affected stem growth rate in either open or understorey conditions. This study concludes that O. pistillaris responds to canopy cover and seasonal reduction in rainfall by adjusting leaf traits and leaf phenology, respectively.

We used stable isotope analysis (15N/14N) to characterize the trophic relationships of consumer communities of an aquatic food web (a permanent pond) and the adjacent terrestrial food web (secondary dry dipterocarp forest) from a seasonal tropical field site in north-eastern Thailand. In general, isotopic signatures of aquatic vertebrates were higher (δ15N range = 4.51–9.90‰) than those of invertebrates (δ15N range = 1.10–6.00‰). High 15N signatures identified water snakes and swamp eels as top predators in the pond food web. In the terrestrial food web 15N signatures of saprophagous litter invertebrates (diplopods, earthworms), termites, ants and beetle larvae were lower than in those of predatory invertebrates (scolopendrids, scorpions, whip spiders). Predatory terrestrial frogs and caecilians had lower 15N signatures than snakes, indicating that snakes are among the top predators in the terrestrial web. Based on the distribution of isotopic signatures, we estimated five trophic levels for both the aquatic and terrestrial food web. The food chains of a seasonal tropical site studied were rather short, which implies similarities to the structure of temperate food webs.

The lowland rain-forest ecosystem in Sundaland (Borneo, Sumatra, Java, the Malay Peninsula south of 10°N, and associated islands) has been recognized as a biodiversity hotspot (Myers et al. 2000). However, it is suffering from huge amounts of disturbance, and it is predicted that South-East Asia will lose three-quarters of its rain forest by the turn of next century (Sodhi et al. 2004).

Hemi-epiphytic figs (Moraceae; Ficus subgenus Urostigma) are a distinctive component of the canopy of tropical rain forests. The hemi-epiphytic habit has risen independently several times, and is recorded in over 20 plant families today, but with approximately 350 species globally figs are by far the most important (Berg & Corner 2005, Putz & Holbrook 1986). They are ubiquitously diverse in tropical lowland rain forests and are represented by independent radiations in each region (Harrison 2005, Jousselin et al. 2003). Moreover, their abundant production of fruit at all times of the year makes them functionally important as food for wildlife, especially during periods of general fruit shortage (Shanahan et al. 2001a). However, hemi-epiphytic fig populations occur at very low densities and this, combined with the difficulties of access to the canopy, has meant that study of their biology lags behind that of other rain forest plants (Harrison et al. 2003). Here, I present the first estimates of mortality and recruitment for any community of hemi-epiphytic figs.

In Hawaii, where there are no native reptiles or amphibians, 27 species of reptiles and amphibians have established (Kraus 2003); however, few have been studied to determine their ecological impacts. For example, little is known about the impacts of the Puerto Rican frog, Eleutherodactylus coqui Thomas, that recently invaded (late 1980s) (Kraus et al. 1999), and has established on all four main Hawaiian Islands (Kraus & Campbell 2002). However, there are likely to be consequences because E. coqui can attain high densities (20 570 frogs ha−1 on average in Puerto Rico) and consume large quantities of invertebrates (114 000 prey items ha−1 per night on average in Puerto Rico) (Stewart & Woolbright 1996).

Over the last few decades a rapid and extensive conversion of tropical forests to agricultural land has taken place resulting in mosaics of fragmented forest patches, pastures and farmland. While the effects of forest fragmentation on biodiversity have been intensively studied within the remaining forests, relatively little is known about the biodiversity in tropical farmland (Daily et al. 2001, Pimentel et al. 1992). Frugivorous birds are an important group of species in tropical farmland ecosystems. Frugivorous birds are significant seed dispersers and can play a prominent role in transporting seeds into disturbed areas and setting the stage for the regeneration of these systems. Isolated fleshy-fruited trees in agricultural landscapes have been shown to attract birds, leading to an increased seed rain and seedling establishment under their canopies (Carrière et al. 2002, Duncan & Chapman 1999, Guevara et al. 1986, 2004; Slocum & Horvitz 2000).

The crab-eating fox (Cerdocyon thous (Linnaeus, 1766)) and the raccoon (Procyon cancrivorus (Cuvier, 1798)) are medium-sized nocturnal carnivores (3–8 kg) belonging, respectively, to families Canidae and Procyonidae (Berta 1982, Langguth 1975, Yanosky & Mercolli 1993). Both are widely distributed over the Neotropical Region (Colombia, Venezuela, Guyana, Surinam, French Guiana, Paraguay, Uruguay, northern Argentina and the greater part of Brazil) (Berta 1982, Brady 1979, Langguth 1975, Santos & Hartz 1999), being sympatric over most of their range. In Brazil both species are found in various different habitats, including the coastal plains (restingas) (Berta 1987, Langguth 1975, Motta-Junior et al. 1994, Novaes 2002, Santos & Hartz 1999, Wang & Sampaio 2001).

To be able to make accurate estimates of the carbon stocks present in the world's tropical forests, there is a growing need for accurate tree biomass estimations on large spatial scales (Chave et al. 2004, Cummings et al. 2002, Nascimento & Laurance 2004). Wood-specific gravity forms an important component of these biomass estimations (Baker et al. 2004, Magcale-Macandog 2004, Nogueira et al. 2005). Even though Chave et al. (2004) found that the most important source of error in above-ground biomass estimation (AGB) is currently related to the choice of allometric model, Baker et al. (2004) show that for two estimates of AGB in Amazonian forests derived using different allometric equations, stand-level specific wood gravity still explained 45.4% and 29.7% of the total variation in AGB.

A prominent hypothesis to account for the maintenance of the woody species diversity in tropical forests is niche differentiation with respect to resources (Ashton 1969, Connell 1978). According to the hypothesis, species can coexist when each species is specialized for a specific set of growth conditions. Spatial and temporal variations in the forest understorey light conditions can be an important niche gradient. If species are adapted to a certain light condition for optimizing growth and share different optimal light conditions with each other, they can coexist by reducing direct competition; i.e. the regeneration niche differentiation sensu Grubb (1977). Species difference in rate of exclusion of trees in suboptimal light conditions due to mortality also contributes to species coexistence. Many scientists have emphasized the importance of the spatial and temporal variations in understorey light conditions on species coexistence in tropical forests (Clark & Clark 1992, Kohyama & Hotta 1990, Poorter & Arets 2003).

Fire is a common feature of tropical savannas and it has an important role in the ecology and evolution of the flora. Many woody species in tropical savannas are well adapted to fire and have a vigorous resprouting ability that enables them to survive recurring fire (Frost & Robertson 1987, Hoffmann & Solbrig 2003, Meyer et al. 2005). Studies on the interaction between fire and woody plants in Mediterranean-climate regions have considerably increased our understanding of the subject but relationships between plant attributes (stem diameter and height) and post-fire resprouting ability of southern African savanna woody species are poorly understood. Resprouting is a widespread mechanism by which many plants regenerate after partial or total defoliation (Bellingham & Sparrow 2000, Bond & Midgley 2001).

Sessile organisms interact locally on the scale of their body sizes, and one of the great advances in population and community ecology is the use of individual-based models to examine species interactions (Biondini 2001, Bolker & Pacala 1999, Pacala & Deutschman 1995, Pacala & Silander 1985, 1987; Silander & Pacala 1985). Canopies are often taken as a proxy for body size in the plant literature, even though roots can make up substantial amounts of a plant's biomass, have productivity that equals or exceeds the above-ground parts, and are critical in both competition and mutualisms involving nutrient capture and water balance (Biondini 2001, Casper & Jackson 1997, Casper et al. 2003, Rajaniemi & Reynolds 2004, Robinson 2004). Root zones, however, are seldom incorporated in plant ecological studies because they are exceptionally difficult to measure, and the importance of intra- and interspecific root interactions is little known (Schenk & Jackson 2002).

Termites are dominant invertebrates in tropical soils (Wood & Sands 1978) and are important mediators of decomposition in terrestrial ecosystems (Abe & Matsumoto 1979, Lawton et al. 1996, Lee & Wood 1971, Matsumoto & Abe 1979, Wood & Sands 1978, Yamada et al. 2005). Furthermore, these processes, such as carbon mineralization and nitrogen fixation, are dependent on the species assemblage structure of the termite community (Lawton et al. 1996, Yamada et al. 2005, 2006). Feeding habits of termites reflect their metabolic processes. The three major isopteran groups – wood-feeders, fungus-growers (fungus-growing wood/litter feeders), soil-feeders – appear to play very different roles in the decomposition process (Tayasu et al. 1997, Wood 1976, Wood & Sands 1978, Yamada et al. 2005). Consequently, the relative abundance of each feeding group provides useful information on the function of the termite assemblage in an ecosystem.

The population biology and ecology of most members of the neotropical family Centrolenidae, or glass frogs, are unknown. Glass frogs deposit their eggs in a gelatinous mass on vegetation overhanging streams, the eggs hatch, and the tadpoles drop into the water, where they complete development (Savage 2002). This study will contribute to our limited understanding of centrolenid reproductive ecology by quantifying variation in clutch size, embryonic development and embryonic mortality in a population of Hyalinobatrachium pulveratum.

Among the hypotheses invoked to explain high species richness in tropical forests, the niche differentiation hypothesis has received observational and experimental support (Ashton 1969, Chesson 2000, Clark et al. 1999, Souza & Martins 2004, Svenning 2001, Terborgh & Mathews 1999). Habitat specialization with regard to edaphic factors and topography has been observed in several plant groups including trees, lianas, shrubs, ferns and palms (Clark et al. 1999, Ibarra-Manriquez & Martinez-Ramos 2002, Svenning 1999, Tuomisto & Ruokolainen 1993). Treefall gaps and light gradients have also been found to be important ecological factors affecting plant distribution and niche differentiation in the understory (Chazdon 1986, Poorter & Arets 2003, Terborgh & Mathews 1999). It is suggested that such habitat heterogeneity may not only maintain biodiversity but also may lead to the origin of new species through the process of parapatric speciation (Gentry 1989, Haffer 1997, Patton & Smith 1992).

Seed dispersal, predation, desiccation and seedling survival are strong bottlenecks that impede tropical forest recovery on abandoned agricultural lands (reviewed in Holl 2002). The ability to resprout after disturbances overcomes these barriers, as those individuals bypass the seed stage and have more vigorous shoots than seedlings (Bond & Midgley 2001, Kammesheidt 1999, Kennard et al. 2002). Resprouting is a particularly important recovery mechanism in tropical dry forests (reviewed in Vieira & Scariot 2006). There are a number of reasons why resprouting may be more important in dry forests than in rain forests, including slower decay rates of trunk bases (Ewel 1980), or adaptation of plants to drought (Bond & Midgley 2001, Sampaio et al. 1993).