The potential effect of forest type on the structuring of animal communities in western Amazonia remains poorly understood. In this study, we tested the hypothesis that amphibian species richness, composition and abundance differ across forest types in the lowland rain forest of south-eastern Peru. By using 320 individual transects, we compared the amphibian assemblages across four major forest types (floodplain, terra firme, bamboo and palm swamp) at each of four sites separated by 3.5–105 km. We identified 1967 individuals of 65 species in 11 families and found that a large proportion of the amphibian diversity in this region is attributed to habitat-related beta diversity. Overall, we found that forest type is more important than site in predicting both species composition and abundance. We also found that, when analyses are conducted separately for each forest type and include species abundance data, similarity between assemblages decreases with increasing geographic distance. In contrast to studies that considered species presence/absence but ignored species abundances, our results highlight the importance of including abundance data in the assessment of animal diversity patterns in western Amazonia. We conclude that evaluating community structure across forest types can improve our understanding of diversity patterns in this region.

A fire-mediated recruitment bottleneck provides a possible explanation for the coexistence of trees and grasses in mesic savannas. The key element of this hypothesis is that saplings are particularly vulnerable to fire because they are small enough to be top-killed by grass fires, but unlike juveniles, they take several years to recover their original size. This limits the number of recruits into the adult size classes. Thus savanna vegetation may be maintained by a feedback whereby fire restricts the density of adult trees and allows a grass layer to develop, which provides fuel for subsequent fires. Here, we use results from a landscape-scale fire experiment in tropical Australia, to explore the possible existence of a recruitment bottleneck. This experiment compared tree recruitment and survival over 4 y under regimes of no fire, annual early and annual late dry-season fire. Stem mortality decreased with increasing stem height in the fire treatments but not in the unburnt treatment. Tree recruitment was 76–84% lower in the fire treatments than the unburnt treatment. Such fire-induced stem loss of saplings and reduced recruitment to the canopy layer in this eucalypt savanna are consistent with the predictions of the fire-mediated recruitment bottleneck hypothesis.

This study tested whether the reduction in the number of large-bodied seed dispersers is correlated with shifts in the taxonomic and functional (e.g. dispersal mode and seed size) traits of the seeding communities within small fragments of semi-deciduous forest, southern Mexico. In five fragments (2.3–640 ha) and one continuous forest site we sampled tree and seedling species in 40 (20 × 20 m) and 120 (3 × 3 m) plots respectively, and recorded the incidence (presence/absence) of the disperser fauna (three common large-birds and >500-g mammals). Tree and seedling species were categorized according to dispersal mode, seed size and whether they originated from local (i.e. from dropped) or immigrant (i.e. from actively dispersed) seeds. Fragment size negatively correlated with number of species of medium to large vertebrate seed-dispersers and number of seedlings of large-seeded species, but had no influence on functional traits of the adult-tree community. Between 41% and 61% of all seedlings were considered as immigrants and the proportion of immigrant seedlings of large-seeded tree species was negatively correlated with forest size. The results suggest that biased defaunation in small forest fragments may seriously reduce recruitment of large-seeded tree species (>1.4 cm length) dispersed by vertebrates, negatively affecting successional trajectories of small forest fragments.

As a proven food resource generalist, Meyer's parrot (Poicephalus meyeri) was expected to track the availability of all significant food resources in its diet over time. Here we recorded all feeding activity during 366 standardized road transects for correlation with an index of relative food resource abundance over 18 mo. As expected, Meyer's parrot made food resource decisions according to relative abundance at landscape level. Feeding activity on food resources available throughout the year (e.g. ripe Kigelia africana fruit) or not visible from the air (e.g. unripe Diospyros lycoides fruit), however, did not correlate significantly with fluctuations in their relative resource abundance. In addition, over 70% of all feeding bouts were in the high canopy and over 70% of all food items consumed formed bi-coloured displays. The influence of estimated protein and energy acquisition rates from different food resources was insignificant. Therefore, important selection criteria for utilization by Meyer's parrot include relative abundance and visibility from the air (i.e. food resources with the highest probability of encounter when dispersing from a central roost). Sensitivity to fluctuations in resource abundance at landscape level demonstrates the relative importance of maximizing net gain per unit foraging time by minimizing foraging flight distance.

Where one or a few tree species reach local high abundance, different ecological factors may variously facilitate or hinder their regeneration. Plant pathogens are thought to be one of those possible agents which drive intraspecific density-dependent mortality of tree seedlings in tropical forests. Experimental evidence for this is scarce, however. In an African rain forest at Korup, we manipulated the density of recently established seedlings (~5–8 wk old; low vs. high-density) of two dominant species of contrasting recruitment potential, and altered their exposure to pathogens using a broad-spectrum fungicide. Seedling mortality of the abundantly recruiting subcanopy tree Oubanguia alata was strongly density-dependent after 7 mo, yet fungicide-treated seedlings had slightly higher mortality than controls. By contrast, seedling mortality of the poorly recruiting large canopy-emergent tree Microberlinia bisulcata was unaffected by density or fungicide. Ectomycorrhizal colonization of M. bisulcata was not affected by density or fungicide either. For O. alata, adverse effects of fungicide on its vesicular arbuscular mycorrhizas may have offset any possible benefit of pathogen removal. We tentatively conclude that fungal pathogens are not a likely major cause of density dependence in O. alata, or of early post-establishment mortality in M. bisulcata. They do not explain the latter's currently very low recruitment rate at Korup.

The ecological effects of logging in the tropics have been analysed largely in terms of its impacts on species diversity and abundance. However, information is very limited regarding the impact of logging on ecological processes such as species interactions. Here we hypothesize that timber extraction per se, that is, in the absence of hunting, affects the abundance of the frugivorous spider monkey, Ateles geoffroyi, and that this has indirect effects on the recruitment of a predominant tree species, Manilkara zapota, and the diversity of the understorey plant community. We compared logged and unlogged sites, using a paired design. In each management condition we conducted line transects and interviews to evaluate spider monkey abundance and game preferences, respectively. Impact on plant recruitment and understorey diversity were evaluated using 2 × 2-m plots (N = 320) established under 40 M. zapota tree crowns. No spider monkeys were recorded in logged sites whereas they were abundant (15 ± 8 individuals per man-km) in unlogged sites. Interviews showed that spider monkeys are not hunted by local inhabitants. Logging was correlated with a reduction of the number of M. zapota fruits used by A. geoffroyi; an increase in the number of sites dominated by M. zapota; and a reduction in understorey plant diversity. Our results suggest that the absence of A. geoffroyi in logged sites can indirectly impact plant recruitment and diversity via the disruption of plant–frugivore interactions. Further work is needed to assess if these effects persist over the long term, to define if logging operations affect the overall diversity of tropical forests.

Disentangling local and historical factors that determine species diversity patterns at multiple spatial scales is fundamental to elucidating processes that govern ecological communities. Here we investigated how environmental correlates may influence diversity at local and regional scales. Primarily utilizing published species lists, amphibian and reptile alpha and beta diversity were assessed at 17 well-surveyed sites distributed among ecoregions throughout Costa Rica. The degree to which regional species diversity patterns were related to environmental variables and geographic distance was determined using Canonical Correspondence Analysis and Mantel tests. Amphibian alpha diversity was highest in lowland Pacific sites (mean = 43.3 species) and lowest at the high elevation site (9 species). Reptile alpha diversity values were high for both lowland Atlantic (mean = 69.5 species) and lowland Pacific (mean = 67 species) sites and lowest for the high elevation site (8 species). We found high species turnover between local sites and ecoregions, demonstrating the importance of beta diversity in the determination of regional diversity. For both amphibians and reptiles, beta diversity was highest between the high-elevation site and all others, and lowest among lowland sites within the same ecoregion. The effect of geographic distance on beta diversity was minor. Ecologically significant climatic variables related to rain, temperature, sunshine and insolation were found to be important determinants of local and regional diversity for both amphibians and reptiles in Costa Rica.

Large seasonal variation in the rate of change in girth of tropical rain-forest tree species has been described, but its origin is still under debate. We tested whether this variation might be related to variation in atmospheric relative humidity through its influence on bark water content and thickness. Variation in trunk circumference of 182 adult trees was measured about twice a month in an undisturbed tropical rain forest over 18 mo using dendrometers. Furthermore, a laboratory experiment was conducted to test the direct influence of relative air humidity on bark water content and thickness. In the field, most trees displayed highly positive rates of change in girth at the onset of the wet season, while a quarter of the trees displayed negative changes during long dry seasons, whatever their total annual growth. This variation was correlated with environmental conditions, particularly with atmospheric relative humidity. Trees with high bark water content and thickness displayed a stronger decrease in girth during the dry season. In the chamber experiment, desiccation induced a decrease in the diameter of the trunk sections in tandem with a decrease in bark water content. As a result, seasonal variation in the rate of change in girth of tropical rain-forest trees reflects variation in trunk biophysical properties, through the influence of relative humidity on bark properties, but not directly variation in secondary growth.

Natural licks are activity hotspots for frugivorous bats in the Peruvian Amazon. Large numbers of frugivorous bats congregate at licks to drink water. Because most Amazonian soils are relatively poor in nutrients, plants may contain low concentrations of some nutrients; consequently, frugivorous bats may face nutrient limitations. Accordingly, a potential explanation for lick visitation by bats is to obtain key limited resources. We assessed this hypothesis by comparing concentrations of cations (Ca, K, Mg, Na) in water at three licks and associated non-lick sites across years and seasons at Los Amigos Conservation Concession in south-eastern Peru. We also examined bat activity patterns between lick and non-lick sites. Regardless of the season, at licks >10 bats per net h−1 were captured compared with forest and gap sites where <1 bat per net h−1 was captured. At licks bats belonged primarily to the subfamily Stenodermatinae and over 70% were reproductive females. Although calcium, magnesium and potassium concentrations varied across water sources, sodium concentrations were consistently higher in lick water (>50 ppm) compared with creeks and oxbow lakes (<2 ppm) across seasons. Therefore, since sodium is one of the most limiting nutrients for vertebrates in the tropics, licks may function as sources of sodium (or other elements) for bats. In any case, licks are reliable potential sources of sodium in the south-eastern Peruvian Amazon, an otherwise mineral-poor landscape.

Measurements were conducted within a fence-exclosure between February 2008 and July 2009 to investigate the influence of soil moisture on ecosystem CO2 fluxes in a Themeda triandra-dominated grassland of a humid Kenyan savanna. Rainout shelters were constructed to reduce ambient rainfall by 0%, 10% and 20% respectively to attain variable soil water content (SWC) during plant growth. SWC within the top 30 cm layer, above-ground biomass, soil and plant nitrogen (N) concentrations were assessed monthly alongside CO2 fluxes. Net ecosystem CO2 exchange (NEE) and ecosystem respiration (Reco) were measured with closed chambers while carbon (C) partitioning during the wet and dry seasons were assessed through pulse 13C labelling. There were significant seasonal and between plot differences in SWC, above-ground biomass, canopy light utilization efficiency (α), CO2 fluxes and C allocation pattern resulting from differences in SWC. The ecosystem was a net C sink during the wet and C neutral during the dry seasons. The study showed strong seasonal fluctuations in ecosystem CO2 fluxes and underscores the significant role of the savanna grasslands in regional C balance due to its expansive nature. The savanna grassland is however vulnerable to low soil moisture, with significant reduction in CO2 uptake during drought.

Despite the potential importance of temporal separation for the coexistence of competing species, no study has found significant segregation at the circadian level between jaguar (Panthera onca) and puma (Puma concolor) in sympatry. Using data from camera trap surveys (wet and dry seasons), we have evaluated the activity patterns of both species and their potential prey at four areas in the dry forest of the Bolivian Chaco. We tested if temporal separation existed between these two species, and if their activity was related to that of a particular prey. At most sites, activity patterns of jaguar and puma did not vary significantly between seasons, except for puma at one site. There were no differences between sexes for any cat species at any site. At three sites we found statistically significant differences in the activity patterns of jaguar and puma, as they showed a clear temporal segregation. None of them followed the activity patterns of any particular prey species across sites. The latter suggests that segregation is influenced by avoidance behaviour between the two felid species. Therefore, temporal separation may be an important behavioural factor promoting the coexistence of jaguar and puma in some areas of this dry forest.

Dung beetles are a functionally important component of most terrestrial ecosystems, but communities change with habitat disturbance and deforestation. In this study, we tested if dung beetle ensembles on dung of introduced cattle and of the endemic anoa, a small buffalo, are affected differentially by habitat disturbance. Therefore, we exposed 10 pitfall traps, five baited with anoa and five baited with cattle dung, per site in six habitat types ranging from natural and selectively logged rain forest to three types of agroforestry system (characterized by different management intensity) and open areas (n = 4 replicate sites per habitat type) at the margin of Lore Lindu National Park, Central Sulawesi, Indonesia. We found 28 species, 43% of which were endemic to Sulawesi. Species richness, abundance and biomass declined from natural forest towards open area. Large-bodied species appeared to be more sensitive to habitat disturbance and the ratio of large to small-sized dung beetles declined with land-use intensity. Although selectively logged forest and cocoa agroforestry systems had lower species richness compared with natural forest, they appeared to maintain a high portion of species originally inhabiting forest sites. The similarity of dung beetle ensembles recorded at forest and agroforestry sites reflects the high similarity of some habitat variables (e.g. vegetation structure and microclimate) between both habitat types compared with open areas. Species richness and abundances as well as species composition, which was characterized by decreases in mean body size, changed with land-use intensity, indicating that dung type is less important than habitat type for determining ensemble structure of these Indonesian dung beetles.

Logged forests form an increasingly large proportion of tropical landscapes but disproportionately few studies have studied the impact of forest disturbance, e.g. lightly vs. heavily logged, on tree and seedling communities simultaneously. We sampled all trees (on 1 ha) and all recently germinated seedlings (on 90 m2) in three lightly and three heavily logged sites in each of the following three East African tropical forests: Budongo Forest and Mabira Forest in Uganda and Kakamega Forest in Kenya. We analysed species richness, diversity, abundance and community composition of late- and early-successional trees and seedlings. We recorded no difference in species richness or diversity of late-successional or early-successional trees between lightly and heavily logged sites. However, the abundance of late-successional species was lower in heavily than lightly logged sites. Moreover, there was no difference in species richness or diversity of trees among the three forests. Yet, abundances of late-successional trees were higher in Budongo Forest than in Mabira Forest and Kakamega Forest. Species richness, diversity and abundance of seedlings did not differ between lightly and heavily logged sites. Only the abundance of seedlings of late-successional species differed among the forests with more individuals in Budongo Forest than in Mabira Forest. This was corroborated by non-metric multidimensional scaling (NMDS) showing clear differences in composition of tree and seedling communities among the three forests. Thus, both, the tree and seedling communities differed significantly among the three forests but not between lightly and heavily logged sites.

Avian hosts may either resist the negative effects of nestling ectoparasites by minimizing the number of parasites, or tolerate parasitism by increasing their fecundity via the reproductive compensation hypothesis. Little is known about the interactions between ectoparasites and their avian hosts in the tropics. We (1) examined nestling development rates, and tested whether (2) parasitism by a subcutaneous ectoparasitic botfly (Philornis sp.) had negative effects on the condition of nestlings, and (3) these negative effects were minimized in larger broods in a tropical cavity-nesting bird, the planalto woodcreeper (Dendrocolaptes platyrostris), in primary and secondary Atlantic forests in the northern province of Misiones, Argentina. Nestling mass and ectoparasite load per nestling reached maxima when nestlings (n = 50) were between 10 and 14 d old. General linear mixed models predicted that mass at fledging declined with increasing nestling parasite load, suggesting that botflies had a negative influence on fledging condition. Parasite load per nestling declined with increasing brood size indicating that woodcreepers that increase their reproductive output minimize the negative effects of parasitism. Overall we found evidence to support the tolerance via reproductive compensation hypothesis. Future tests of the reproductive compensation hypothesis may help determine the underlying mechanism of the observed negative correlation between parasite load of nestlings and brood size.

The concept of ecosystem engineering has catalysed novel approaches and models for non-trophic species interactions and ecosystem functions. Ecosystem engineers physically modify abiotic and biotic environments, thereby creating new habitats that can be colonized by a new suite of species. In the Peruvian Amazonas, we tested whether peccaries (Tayassuidae) function as ecosystem engineers by creating and maintaining wallows. Such wallows could be critical aquatic habitats and breeding sites for anuran species during dry seasons. We compared hydroperiods of 21 peccary wallows and 13 naturally formed ponds across three dry seasons and found that wallows had a consistently higher mean water surface area than ponds. We also examined the pH, dissolved oxygen and temperature, and found no significant differences in these parameters between water bodies. Wallows had a significantly higher density of tadpoles, metamorphs and adult anurans, as well as higher β-diversity and species richness than ponds. This study not only provides the first systematic evidence of the ecosystem engineering processes of peccaries, but also reveals the positive consequences of such for anuran species.

Differences in growth patterns between the sexes of the gracile mouse opossum Gracilinanus microtarsus and the consequences for home range size were investigated in a savanna habitat (cerrado) of south-eastern Brazil. A total of 51 juvenile individuals of Gracilinanus microtarsus was monitored using capture–mark–recapture from November 2005 to August 2006. The increase in body mass of gracile mouse opossums was described using the Gompertz growth model. Male gracile mouse opossums grew faster than females (dimorphic ratio of 1.5). Home range size, estimated with the minimum convex polygon method, was positively related to body mass. Model selection using Akaike's Information Criterion (AICc) and incorporating body mass, sex and season as independent variables showed that the best-supported model describing variance in home range sizes included only body mass. Our data suggest that a greater body mass gain in juvenile males is probably the proximate cause of sexual dimorphism in adult gracile mouse opossums and that energetic needs required for growth have a greater influence in home range size.

The direct removal of adult trees by logging affects tree recruitment in tropical rain forests. However, secondary effects of logging, such as loss of vertebrate seed dispersers may also affect tree recruitment. We studied the recruitment and spatial distribution of five tree species namely Balanites wilsoniana, Celtis zenkeri, Chrysophyllum albidum, Cordia millenii and Ricinodendron heudelotii in Kibale, Budongo and Mabira Forests in Uganda. These forests have been subjected to varying degrees of disturbance leading to changes in their vertebrate seed dispersers. Vertebrate frugivores of the five tree species were identified. Three 1-ha plots were established around adult trees of the same five species in each forest and the distance from the juveniles to the nearest adult conspecific was measured to generate a recruitment curve. Frugivore visitation rates were high in the less disturbed Budongo and Kibale (2.2 and 1.6 individuals h−1 respectively) compared with the highly disturbed Mabira (0.9 individuals h−1). In the frugivore-impoverished forest, 70–90% of juveniles established beneath adult conspecifics, whereas in the less-disturbed forests juveniles were established up to 80 m from adult conspecifics. Shade-tolerant species capable of recruiting beneath adult conspecifics appeared to maintain their populations without dispersal. Consequently, disturbances leading to significant loss of vertebrates may alter tree recruitment and spatial distribution with consequences for long-term population viability of shade-intolerant tropical trees.

Community structure and species’ abundances may be strongly correlated to patterns of forest cover, although such patterns are poorly known for tropical dry-forest birds, especially for those in Panamanian dry forests. Birds were distance-sampled during point counts in five dry-forest fragments in Panama. Distance from point count to forest edge and forest coverage at three spatial scales (500, 1000 and 2000-m radius) were compared as covariate predictors of the abundance of avian species and guilds. Each covariate was selected in at least two models of species or guild abundance. Abundance patterns were consistent with previously reported habitat associations for only two of seven open-habitat or forest-preferring species that showed forest cover-abundance relationships. Null models best described the abundance of all forest species and the subset of uncommon forest species. Thus many of these species appear insensitive to the forest-cover gradients studied. Total abundance of open-habitat-preferring species increased in dry forests with increasing forest coverage within 500 m, suggesting that the relationship between their abundance and vegetation structure are spatial-scale and habitat dependent. Nectarivores had lower abundance as forest cover within 1000 m increased, supporting previous claims that this group is tolerant of forest edges.

Environmental factors influencing grass establishment and performance in tropical savannas are poorly understood, particularly in relation to disturbance. We describe a seed sowing experiment that examined the effects of fire regime, canopy cover and litter cover on the emergence, establishment, height and fecundity (seed production) of the regionally dominant annual grass Sorghum intrans in northern Australia. Establishment was significantly lower under the woody canopy compared with canopy gaps, and where seeds were sown on a layer of litter compared with bare soil. However, variation in fire regime had no significant effect on establishment or seed production. Additionally, a shade-house experiment was conducted to test the effects of litter on seedling emergence of S. intrans and six other grass species representative of the local flora (Pseudopogonatherum contortum, Sorghum plumosum, Chrysopogon latifolius, Eriachne triseta, Heteropogon triticeus and Alloteropsis semialata). All species showed reduced emergence when sown either above or below litter, compared with bare soil. Our results demonstrate the importance of the overstorey as a determinant of S. intrans abundance and savanna grass composition more generally, through its effect on establishment. The aversion of savanna grasses to litter (and S. intrans to canopy shading) supports the notion of savanna species being highly adapted to disturbance.

Ecosystem pool of phosphorus (P) was determined as the sum of above-ground vegetation, roots, necromass and soils to 1 m deep in a tropical rain forest in Sabah, Malaysia. Relationships among soil P fractions, acid phosphatase activity and fine-root biomass across soil horizons were also determined to understand P availability. Ecosystem pools of P, and of simultaneously quantified nitrogen (N) and carbon (C) were 3.4, 12 and 370 Mg ha−1, respectively. Only 2.6% of the total ecosystem P was in the above-ground vegetation, contrasting to C (60%) and N (16%). Canopy foliage of dominant tree species showed an extremely high N to P ratio of 31.5, which implied the excessively short supply of P compared with ample N. Soil P primarily consisted of recalcitrant occluded fractions (78–91%) and only 4% was labile. Approximately three-quarters of labile soil P was an organic fraction (Po). The concentration of labile Po did not differ between soil horizons, while both phosphatase activity and fine-root density were the greatest in the topsoil (top 5 cm) and dramatically decreased with depth. This suggests that trees depend on the acquisition of P from the labile Po in the topsoil, despite a greater amount of labile P in the subsoil. Trees with a high foliar N/P ratio may invest N to acquire P from the topsoil by secreting phosphatase that consists of proteins, rather than investing C to extending roots to scavenge P in the subsoil.