The Brazilian Amazon rain forest has lost c. 17% of its originally forested portion, due to deforestation and selective logging. Forest degradation caused by logging contributes to loss of animal species that require specialized habitats to survive, such as woodcreepers that inhabit understorey areas. Habitat associations of woodcreeper species can be important for identifying species that have restricted distribution and/or habitat specialization. Our study investigates the effects of spatial variation in forest structure and some landscape features (canopy openness, altitude, distance to stream and exploited basal area) on the abundance and composition of woodcreeper assemblage in selectively logged tropical forests in Southern Amazonia. We used mist-nets and points count to quantify the composition and abundance of woodcreepers in 32 plots in three sites. Plots were spatially arranged in PPBio LTER sites (long-term ecological research plots, systematically spaced at 1-km intervals) in Southern Amazonia. A total of 240 individuals (captured, observed and/or heard) belonging to 11 woodcreeper species were detected. Mantel tests showed that there is no spatial autocorrelation among woodcreeper assemblage and distance between plots. Altitude and canopy openness were significantly associated with the composition of the woodcreeper assemblage. Altitude was negatively associated with species richness, and the abundance of the two dominant species (Glyphorynchus spirurus and Xiphorhynchus elegans). The negative relationship with canopy openness suggests that woodcreeper assemblages that inhabit understorey are likely to be indirectly affected by selective logging which reduces canopy cover. The selective logging indirectly changes bird species assemblages, and depending on the intensity, may result in the local extinction of some insectivorous species. Short- and long-term studies addressing different intensities of selective logging are needed to determine the impacts on the bird species and forest structure.

Few studies have been conducted to investigate ecological roles of litter amphibians in forest ecosystems. In this study, ten field enclosures (3 m × 2 m × 0.4 m) were used to evaluate effects of the toad Bufo bankorensis on the abundance of litter invertebrates (microbivores, fragmenters and predatory arthropods) and litter decomposition rates in a subtropical forest of southern Taiwan. Litterbags collected from toad and control (toad-excluded) enclosures were analysed for the communities and abundances of litter invertebrates and decay loss during this decomposition study from September to December 2001. The presence of B. bankorensis significantly changed phosphorus concentrations in the litter, but not the densities of litter invertebrates (microbivores, fragmenters and predatory arthropods) or rates of litter decomposition. These results were not consistent with previous studies, which have shown that Plethodon cenereus in a temperate forest of north-east USA and Eleutherodactylus coqui in a tropical rain forest of Puerto Rico significantly changed decomposition rates. We suggest that ecological roles of ground-dwelling amphibians may be species-specific and vary with different terrestrial ecosystems.

Freshwater migratory shrimps, an important component of tropical aquatic ecosystems, are vulnerable to land-use change during their upstream and downstream migrations. At La Selva Biological Station in the Sarapiquí region of Costa Rica, shrimp population data were collected between 1988 and 1989, before massive land-use change occurred downstream that could potentially affect shrimp recruitment upstream. Using generalized linear models and a Bayesian inference framework, the relative abundance of Macrobrachium olfersi between recent (2008–2011) and historical time periods (1988–1989) was compared in three stream reaches. Shrimp relative abundance in two stream reaches within the protected area of La Selva was relatively constant yearly and between recent post-disturbance (2008–2011) and historical pre-disturbance (1988–89) time periods. In contrast, a stream reach bordered by pasture accessible to fishermen, showed an 87% decrease in relative abundance between recent and historical time periods suggesting site-level disturbance, possibly from fishing. The lack of change between historical and contemporary sampling periods within interior-forest stream reaches suggests that shrimp populations in protected forested reaches are resistant or resilient to certain land-use changes occurring downstream.

Nitrogen-fixing plants provide critical nitrogen inputs that support the high productivity of tropical forests, but our understanding of the ecology of nitrogen fixers – and especially their interactions with herbivores – remains incomplete. Herbivores may interact differently with nitrogen fixers vs. non-fixers due to differences in leaf nitrogen content and herbivore defence strategies. To examine these potential differences, our study compared leaf carbon, nitrogen, toughness, chemical defence and herbivory for four nitrogen-fixing tree species (Inga oerstediana, Inga sapindoides, Inga thibaudiana and Pentaclethra macroloba) and three non-fixing species (Anaxagorea crassipetala, Casearia arborea and Dipteryx panamensis) in a lowland tropical rain forest. Leaf chemical defence, not nutritional content, was the primary driver of herbivore damage among our species. Even though nitrogen fixers exhibited 21.1% higher leaf nitrogen content, 20.1% lower C:N ratios and 15.4% lower leaf toughness than non-fixers, we found no differences in herbivory or chemical defence between these two plant groups. Our results do not support the common hypotheses that nitrogen fixers experience preferential herbivory or that they produce more nitrogen-rich defensive compounds than non-fixers. Rather, these findings suggest strong species-specific differences in plant–herbivore relationships among both nitrogen-fixing and non-fixing tropical trees.

The variation in CO2 flux from the forest floor is important in understanding the role of mangrove forests as a carbon sink. To clarify the effects of soil temperature and tidal conditions on variation in CO2 flux, sediment–atmosphere CO2 fluxes were measured between June 2012 and May 2013. We used the closed chamber method for two plots, with a 0.5 m difference in elevation (B, high elevation; R-B, low elevation), in a mangrove forest in south-western Japan. CO2 fluxes were highest in the warm season and showed a weak positive correlation with soil temperature in both forests. Estimated monthly CO2 flux showed moderate seasonal variation in accordance with the exposure duration of the soil surface under tidal fluctuation. Additionally, measured CO2 flux and soil temperature were slightly higher in the R-B plot than the B plot, although estimated annual CO2 flux was higher in the B plot than the R-B plot due to different exposure durations. These results suggest that variation in the exposure duration of the forest floor, which changes seasonally and microgeographically, is important in evaluating the annual CO2 flux at a local scale and understanding the role of mangrove ecosystems as regulators of atmospheric CO2.

Earthworm populations in grassland and plantations in the area of Bulolo, Papua New Guinea were compared with populations in nearby undisturbed rain forest. The grasslands had been maintained by burning for many years. The Pinus plantation had been developed on a burned grassland site and the Araucaria plantation on a site which had been cleared of secondary forest.

The grasslands and the Pinus plantation supported moderate populations of exotic earthworms including Pontoscolex corethrurus, but no indigenous species. The Araucaria site supported a native species, Amynthas zebrus only, which was also found together with two other native species at very low density in rain forest.

Exotic earthworm species widespread throughout the tropics, were present in disturbed soils and formed moderately high density populations in burned grasslands. There was no evidence that they displaced native Megascolecidae in rain forest.

Although what drives the abundance and habitat selection of ungulates is a long-standing question, coherent datasets investigating the influences of rainfall, competition and fire on ungulates are unusual. Over 4 y we carried out extensive monthly road transects in Ithala Game Reserve, South Africa, to determine the demographics and habitat occupancy of the region's prevalent grazer (wildebeest) and mixed-feeder (impala). Habitat occupancy was determined using a GIS-based approach. We obtained 8742 sighting records, encompassing 8400 wildebeest and 10071 impala. Annual rainfall did not significantly correlate with population sizes of either species. Fecundity of wildebeest, but not of impala, showed a significant positive relationship with rainfall specifically over the perinatal period (November–December), whilst no significant relationships were found for either species between fecundity and rainfall over the previous year, 2 y, rut (February–April) or height of the dry season (June–August). Impala unexpectedly favoured browse habitats to grassland year round, probably consequent on competition for grass with wildebeest. Dry-season grass flushes attracted both wildebeest and impala. The study emphasized how rainfall, competition and fire regimes may affect differently grazers compared with mixed-feeders.

We performed a pot experiment in which 540 seedlings of nine non-pioneer light-demanding tree species were grown for 12 months in shade houses at three light levels, 46% daylight, 13% daylight and 2% daylight, to examine the mechanisms contributing to the coexistence of seedlings of non-pioneer light-demanding tree species in secondary successional tropical rain forest in Hainan, China. Growth and survival of tree seedlings were compared at different light levels, and the morphological and physiological correlates of high-light seedling growth and low-light survival across species were determined. For all species, mortality was very low in the 46% daylight and 13% daylight treatment but increased significantly in the 2% daylight treatment. Seedling survival in 2% daylight treatment was positively related to seed mass. Trade-off between high-light growth and low-light survival was more evident in the relationship with 2% daylight treatment as compared with 13% daylight treatment. Relative growth rate in the 2% daylight treatment was not significantly related to relative growth rate in the 13% daylight or 46% daylight treatment; although a slight negative correlation was apparent. Interspecific variation in RGRm was only closely correlated with net assimilation rate (NAR). The results provide some support for the niche-partitioning hypothesis.

Population structure and dynamics of the black-cheeked gnateater (Conopophaga melanops) were studied at Salto Morato Nature Reserve, in Paraná, southern Brazil, from October 2006 to September 2007. Territory size and population density, breeding season (timing and length), reproductive success and annual survival rates were estimated from sightings of 18 marked adult birds and the success of 18 nesting attempts. The black-cheeked gnateater is socially monogamous and territorial, with a breeding-season length of approximately 3 mo beginning in early October. Predation caused most nest failures, nest survival was 0.96 d−1 and apparent annual nesting success was 22%, resulting in annual productivity of 0.36 individuals per adult. Apparent adult annual survival was ~0.44 y−1. Seventy-five per cent of fledglings survived at least 2 mo after fledging. Two methods of estimating population growth rate suggest very different rates: r = −0.04 (~ stable), or λ varies between 0.475–0.616 (declining). Yet, low apparent adult survival suggests that territories are not permanent, perhaps abandoned after nest failure. We find that by estimating population growth, even in short-term studies, testable hypotheses can be generated that will allow better understanding of population dynamics.

We analysed thirty-five 400-m2 plots encompassing forest, savanna and intermediate vegetation types in an ecotonal area in Ghana, West Africa. Across all plots, fire frequency was over a period of 15 years relatively uniform (once in 2–4 years). Although woodlands were dominated by species typically associated with savanna-type formations, and with forest formations dominated by species usually associated with closed canopies, these associations were non-obligatory and with a discrete non-specialized species grouping also identified. Across all plots, crown area index, stem basal area and above-ground biomass were positively associated with higher soil exchangeable potassium and silt contents: this supporting recent suggestions of interplays between potassium and soil water storage potential as a significant influence on tropical vegetation structure. We also found an average NDVI cover increase of ~0.15% year−1 (1984–2011) with plots dominated by non-specialized species increasing more than those dominated by either forest- or savanna-affiliated species. Our results challenge the traditional view of a simple forest vs. savanna dichotomy controlled by fire, and with our newly identified third non-specialized species grouping also potentially important in understanding ecotonal responses to climate change.

Land-use change in tropical forests can affect the micro-environment for decomposition under modified canopies. In turn, decomposition may have consequences for soil fertility and ecosystem sustainability. The effects of the conversion from primary forest to pastures on leaf-litter decomposition and its recovery in secondary forests 20 y after pasture abandonment were evaluated using litterbags and a general mixed model approach. Litterbags containing leaf-litter of two contrasting qualities were placed in those three ecosystems and the mass remaining after 90 d was quantified. The mass remaining was 50% lower in high- than in low-quality leaves. The effects of the decomposition environment depended on the substrate quality. Although differences among ecosystems were not significant for low-quality leaves, high-quality leaves decomposed more slowly in pastures than in forests (mean dry mass remaining was 38% in pastures, 14% in secondary and 12% in primary forest). The decomposition of common substrates did not differ among forests. Results show that the conversion of primary forest to pasture may produce conditions for slower decomposition; however, these conditions appear be restored to a great extent in 20-y-old secondary forests.

The proliferation of disturbance-adapted species in human-modified landscapes may change the structure of plant communities, but the response of biodiversity to human disturbances remains poorly understood. We examine the proliferation of the palm, Syagrus coronata, in disturbed forest stands and its impacts on the structure of vascular epiphyte assemblages in a human-modified landscape of Brazilian Caatinga dry forest. First, we compared S. coronata density between old-growth and regenerating forest stands. We then surveyed vascular epiphytes on 680 phorophytes (S. coronata and non-palm/control species) across five habitat types with different disturbance levels. There was an eight-fold increase in S. coronata density in regenerating areas compared with in old-growth forest. Syagrus coronota supported richer epiphyte assemblages at local (i.e. per palm) and landscape (i.e. pooling all palms) scale than control phorophytes, supporting more than 11 times the number of species of control phorophytes at both scales. Epiphyte assemblages were more abundant, species-rich and dominated by abiotically dispersed species in forest sites with intermediate disturbance levels (regenerating forest stands). More than simply operating as an exclusive phorophyte for more than 90% of the epiphyte species we recorded here, S. coronata favours epiphyte persistence and structures their assemblages across human-modified landscapes of the Caatinga forest.

Occurrence data for Julbernardia globiflora and J. paniculata at 617 sites in the miombo woodland region of central, eastern and southern Africa and forest inventory data for 512 woodland plots in Zambia were used to determine species distribution and dominance. Distribution of the two Julbernardia species overlaps in the central region of the miombo woodland range while the eastern and western range regions are exclusively for only one of the two species. In the region of co-occurrence, there is a clear spatial separation in the dominance of the two species. In old-growth woodland a significant proportion of the variation in the dominance of J. globiflora was explained by the dominance of J. paniculata while mean annual maximum temperature and tree species richness negatively affect the dominance of J. paniculata. Old-growth woodland clearing changes the local climatic conditions and alters the way Julbernardia species in re-growth stands respond to potential evapo-transpiration (PET). Climate change, especially global warming, may further reinforce the impacts of PET to differentially favour J. globiflora. Because of this altered response of Julbernardia species in re-growth miombo, preserving old-growth miombo and preventing present human disturbances in designated areas, such as forest reserves and national parks, may be a useful climate adaptation strategy for these species.

The pollination ecology and breeding system of Trochetia granulata (Malvaceae), an endemic tree species from Réunion were studied. In 2010–2011, compatibility studies were conducted on a total of 154 flowers from 35 different individuals using three different hand pollination treatments: (a) autofertility, (b) self-pollination and (c) cross-pollination. During the period, we also studied the pollination ecology of T. granulata. During 48 h of video recordings, we tracked flower visits to T. granulata in six different sites and studied the behaviour of the visitors. The results from the hand-cross experiments show that T. granulata is self-compatible (60.8% fruit set) but cannot produce fruit (5.4% fruit set) without the visit of a pollen vector. During surveys, four different visitors were reported: the introduced honey bee (Apis mellifera), two endemic species of white-eye (Zosterops borbonicus borbonicus and Z. olivaceus) and the endemic Réunion day gecko (Phelsuma borbonica). This study documented a new case of vertebrate-pollination by lizard and birds in an insular context. These interactions might be linked to several uncommon floral traits of Trochetia species.

Avian predators may represent an important selective pressure favouring the evolution of aposematic colouration in millipedes that present chemical defences. However, the role of their warning colouration in predator avoidance remains poorly explored under field conditions, especially in Neotropical forests. Thus, to evaluate the hypothesis of the predator avoidance, we conducted a factorial experiment utilizing artificial replicas of millipedes constructed from plasticine and placed in the natural habitat of Odontopeltis aleijadinho (Polydesmida, Chelodesmidae), an Atlantic Forest endemic aposematic millipede. We assessed patterns of attack to aposematic and non-aposematic replicas applied with repugnant fluid extracted from living millipedes and two control treatments, distributed as a total of 300 replicas exposed for 48 h on the forest floor. The average percentage of replicas attacked was nearly 10-fold higher on those non-aposematic control replicas (13.3% ± 3.3%) than on aposematic replicas (1.3% ± 0.9%). In 24 replicas attacked by avian predators, no effect of millipede repugnant fluid was found, but the effect of colouration pattern was statistically significant. Our data support the hypothesis that a warning colouration pattern involving yellow spots symmetrically distributed along the millipede body can mediate avian predator avoidance.

Successional state of forest and availability of pioneer plants are recognized factors affecting densities of leaf-cutting ants. However little is known about how abiotic factors can shape nest distributions. We investigated the effect of topography, soil, forest successional state and inundation risk on nest density and size of Atta cephalotes colonies along streams in a tropical wet forest in Costa Rica. In each forest type, we surveyed 12 sites, each site comprising five transects (10 × 100 m) varying in topography and proximity to streambeds. We found no difference regarding nest size or density between forest types or soil consociation. Nest density varied with topographic environment, with significantly higher nest density on slope tops (farther from streambeds) and without colonies in valley bottoms (closer to streambeds). Nests found in areas affected by the last great inundation before our study were scarcer and smaller than nests in non-flooded areas. We showed that inundation events favour an accumulation of Atta colonies towards higher sites, where they are also allowed to become larger and may survive longer. Inundation risk may be a strong force shaping the distribution of leaf-cutting ant nests in tropical floodplain forests, even concealing the relevance of successional state of forest.

We have studied a number of related processes of the nitrogen cycle in a Brazilian floodplain lake to identify the major pools and pathways over a short time period. The study was centred on the littoral zone dominated by the floating plant Eichhornia azurea, which has a large epiphyte algal community of which heterocystous cyanobacteria were the major components. The water column was continuously undersaturated with oxygen although some elevated values (to 60% saturation) were recorded in the macrophyte beds in the afternoon. Marked diel temperature changes were documented. NH4-N dominated the dissolved N component in the water with maximal values (60 mg m−3) at lowest O2, concentrations early in the morning. Nitrogen fixation (acetylene reduction) of the epiphyte community showed marked diel changes with daily values of 5 mg N fixed m−2 day−1 (based on 3:1 C2H4:N2 ratio). Macrophyte NH4-N uptake rates (in situ incubations) were 93 mg N m−2 day−1. The activities of nitrifying bacteria could not be detected with the nitrapyrin block on dark CO2 fixation but denitrification (acetylene block technique) was recorded in the sediments when enhanced with NO-3. The major pathways of aquatic nitrogen involved macrophyte uptake and sediment release of NH4-N.

We tested the hypothesis that seed size influences which frugivores eat fruits, and the size and nature of disperser assemblages in Pakke Tiger Reserve, India. Four tree species had large seeds (> 18 mm width) that could be handled by birds with large gape widths, while two tree species had smaller seeds (< 7 mm width) falling within the gape size range of many frugivores. We tested whether (1) disperser assemblage and activity reflected seed size, and (2) large-gaped hornbills were more effective at fruit removal of tree species with large seeds, than of those with smaller seeds and many dispersers. Day-long watches were conducted in 2005 at trees of Dysoxylum binectariferum (three in 2005 and nine in 2006), Chisocheton cumingianus (nine), Aglaia spectabilis (seven), Polyalthia simiarum (nine), Litsea monopetala (four) and Cinnamomum bejolghota (two in 2005 and six in 2006) to determine which frugivores visited trees and ate fruit. Disperser visitation and species diversity per tree to species with medium-sized seeds averaged 85 visits and 10 species d−1, contrasted with five visits by one frugivore species to large-seeded tree species. Seed removal rates per tree averaged 486 seeds d−1 from medium-seeded tree species, but 10 seeds d−1 from large-seeded species. Hornbills (Bucerotidae) and Ducula badia (Columbidae) removed large seeds from capsules of Aglaia spectabilis, Chisocheton cumingianus and Dysoxylum binectariferum (Meliaceae). Primates, civets and bats also consumed drupes of large-seeded Polyalthia simiarum (Annonaceae). Anthracoceros albirostris hornbills were important dispersers of Litsea monopetala (Lauraceae), a medium-seeded tree with a large disperser assemblage. Conversely, hornbills were quantitatively inconsequential for Cinnamomum bejolghota (Lauraceae), another medium-seeded tree species with several dispersers. Results suggest that the size and activity of disperser assemblages accurately reflects seed size. While hornbills were quantitatively important dispersers of large-seeded tree species, their effectiveness for trees with small- to medium-sized seeds depended on the tree species.

Given their difficulty of access, the canopies of tropical rain forests are considered a last frontier of biological/ecological research (Lowman & Nadkarni 1995). Climbing techniques are arduous and do not reach the tips of branches; towers, cranes and walkways limit the spatial exploration of the forest.