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Data from: Effect of distance to edge and edge interaction on seedling regeneration and biotic damage in tropical rainforest fragments: a long‐term experiment

In forest fragments, edge effects can influence forest regeneration, but little is known about how edge effects influence seedling performance and the interaction between seedlings and their natural enemies over time. In central Amazonia, we recorded survival and growth (in height and leaf number) and damage by insect herbivores and leaf‐fungal pathogens of Chrysophyllum pomiferum (Sapotaceae) seedlings that were exposed to different numbers of edges and to different distances from the forest edge. Grown seedlings were transplanted into one‐square‐metre plots within 1‐ha blocks located in the centre (no edge), the edge (one edge), and the corner (two edges), and at different distances from the edge towards the interior (i.e., 20, 40, 60, 80, and 100 m) of two rectangular fragments (10‐ and 100‐ha in size). Plots were visited once every 2 months for 1 year (1992–1993) and thereafter every 2 years for almost 8 years (1993–2001). Overall, results showed that seedling survival, height, leaf number, and biotic damage varied over time with the presence of nearby edges and with the distance from the edge. Survival was lower in fragment edges and corners than in centres. Increase in height was similar for all positions within the 100‐ha fragment, whereas in the 10‐ha fragment seedling height had a greater increase at the edge and corner than in the centre. Furthermore, survival increased with distance from the edge as did leaf number, whereas height showed a lower increase closer to the edge than farther away. Regarding biotic damage, for both fragments herbivory was greater at the centres and decreased with edge proximity over time, whereas leaf‐fungal damage was greater at the corners than in the edges and increased significantly over time. Biotic damage was correlated with seedling size. Small seedlings were more susceptible to fungal attack, whereas larger seedlings were so to herbivores. Synthesis. This study demonstrated that despite stochastic environmental factors seedling survival, growth, and biotic damage by herbivores and fungal pathogens varied with the level of edge exposure and proximity, which may threaten forest regeneration in the long term.

opencc-zeroDec 2015View details →

Data from: Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.

opencc-zeroDec 2011View details →

Data from: Diversity partitioning confirms the importance of beta components in tropical rainforest Lepidoptera

Tropical beta diversity, and particularly that of herbivorous insects in rainforests, is often considered enormous, but this notion has recently been challenged. As tropical beta diversity is highly relevant to our view on biodiversity, it is important to gain more insights and resolve methodological problems that may lead to the contradictions in different studies. We used data on two ecologically distinct moth families from Southeast-Asia and analyzed separately the contribution of beta components to overall species richness at three spatial scales. Observed diversity partitions were compared under different types of null models. We found that alpha diversity was lower than expected from null models, whereas hierarchical beta components were larger than expected. Beta components played a significant role in shaping gamma diversity, and their contribution can be high (multiplicative beta >5). We found a reduction of beta components when comparing primary forests and agricultural sites (cf. "biotic homogenization"), but even in these habitats beta components were still substantial. Our analyses show that beta components do play an important role in our data on tropical herbivorous insects, and that these results are not due to lumping different habitats when sampling environmental gradients.

Data from: The effects of rainforest fragment area on the strength of plant-pathogen interactions

Pathogenic interactions between fungi and plants facilitate plant species coexistence and tropical rainforest diversity. Such interactions, however, may be affected by forest fragmentation as fungi are susceptible to anthropogenic disturbance. To examine how fragmentation affects fungus-induced seed and seedling mortality, we sowed seeds of six plant species in soils collected from 21 forest fragments. We compared seedling establishment in unmanipulated soils to soils treated with fungicides. Fungicides increased germination of Toona ciliata seeds and decreased mortality of Syzygium rubicundum and Olea dioica seedlings. The fungus-induced mortality of one of these species, S. rubicundum, decreased with decreasing fragment size, indicating that its interactions with pathogenic fungi may weaken as fragments become smaller. We provide evidence that a potential diversity-maintaining plant-fungus interaction weakens in small forest fragments and suggest that such disruptions may have important long-term consequences for plant diversity. We, however, emphasize the need for further research across rainforest plant communities to better understand the future of diversity in fragmented rainforest landscapes.

Data from: Diversity change during the rise of tetrapods and the impact of the 'Carboniferous rainforest collapse'

The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the 'Carboniferous rainforest collapse' (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling. Here, we reassess early tetrapod diversity and biogeography with a new global species-level dataset using sampling standardization and network biogeography methods. Our results support a tight relationship between observed richness and sampling, particularly during the Carboniferous. We found that subsampled species richness initially increased into the late Carboniferous, then decreased substantially across the Carboniferous/Permian boundary before slowly recovering in the early Permian. Our analysis of biogeography does not support the hypothesis that the CRC drove endemism; instead, we found evidence for increased cosmopolitanism in the early Permian. While a changing environment may have played a role in reducing diversity in the earliest Permian, our results suggest that the CRC was followed by increased global connectivity between communities, possibly reflecting both reduced barriers to dispersal and the diversification of amniotes.

Data from: Contrasting patterns of local richness of seedlings, saplings and trees may have implications for regeneration in rainforest remnants

Remnants of lowland rainforest remain following deforestation, but the longer-term effects of fragmentation remain poorly understood, partly due to the long generation times of trees. We study rainforest trees in three size classes: seedlings (<1 cm dbh), saplings (1-5 cm dbh) and trees (>5 cm), that broadly reflect pre- and post-fragmentation communities, and we examine the impacts of fragmentation on forest regeneration in Sabah, Malaysian Borneo. We found that seedling richness (measured as the number of genera per plot) in fragments was about 30 percent lower than in plots in undisturbed forest, and about 20 percent lower than in an extensive tract of selectively logged forest, providing evidence of recruitment declines in fragments. Seedling richness was lowest in small, isolated, and disturbed fragments, potentially signalling an extinction debt given that these fragmentation impacts were not observed in trees. Unlike seedlings, saplings showed no declines in richness in fragments, suggesting that density dependent mortality (where rare individuals have a higher survival rate) and/or year-to-year variation in which species are recruiting could potentially compensate for the reductions in seedling richness we observed. Longer-term studies are required to determine whether sporadic or failed recruitment in small fragments will eventually translate into reduced richness of mature trees, or whether the processes that currently retain high sapling richness will continue in fragments.

opencc-zeroDec 2013View details →

Data from: Strong coupling of plant and fungal community structure across western Amazonian rainforests

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant–fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.

opencc-zeroOct 2019View details →

Data from: Soil carbon, nitrogen and phosphorus stoichiometry (C:N:P) in relation to conifer species productivity and nutrition across British Columbia perhumid rainforests

Temperate rainforest soils of the Pacific Northwest are often carbon (C) rich and encompass a wide range in fertility reflecting varying nitrogen (N) and phosphorus (P) availability. Soil resource stoichiometry (C:N:P) may provide an effective measure of site nutrient status and help refine species-dependent patterns in forest productivity across edaphic gradients. We described the nature of soil organic matter for mineral soil and forest floor substrates across very wet (perhumid) rainforest sites of southwestern Vancouver Island (Canada), and employed soil element ratios as covariates in a long-term planting density trial to test their utility in defining basal area growth response of four conifer species. There were strong positive correlations in mineral soil C, N and organic P (Po) concentrations, and close alignment in C:N and C:Po both among and between substrates. Stand basal area after five decades was best reflected by soil C:N but included a significant species-soil interaction. The conifers with ectomycorrhizal fungi had diverging growth responses displaying either competitive (Picea sitchensis) or stress-tolerant (Tsuga heterophylla, Pseudotsuga menziesii) attributes, in contrast to a more generalist response by an arbuscular mycorrhizal tree (Thuja plicata). Despite the consistent patterns in organic matter quality we found no evidence via foliar nutrition for increased P availability with declining element ratios as we did for N. The often high C:Po ratios (as much as 3000) of these soils may reflect a stronger immobilization sink for P than N, which, along with ongoing sorption of PO4-, could limit the utility of C:Po or N:Po to adequately reflect P supply. The dynamics and availability of soil P to trees, particularly as Po, deserves greater attention as many perhumid rainforests were co-limited by N and P, or, in some stands, possibly P alone.

opencc-zeroDec 2014View details →

Data from: From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly

Seed dispersal is a key process in plant spatial dynamics. However, consistently applicable generalisations about dispersal across scales are mostly absent because of the constraints on measuring propagule dispersal distances for many species. Here, we focus on fleshy-fruited taxa, specifically taxa with large fleshy fruits and their dispersers across an entire continental rainforest biome. We compare species-level results of whole-chloroplast DNA analyses in sister taxa with large and small fruits, to regional plot-based samples (310 plots), and whole of continent patterns for the distribution of woody species with either large (>30mm) or smaller fleshy fruits (1093 taxa). The pairwise genomic comparison found higher genetic distances between populations and between regions in the large-fruited species (Endiandra globosa), but higher overall diversity within the small-fruited species (Endiandra discolor). Floristic comparisons among plots confirmed lower numbers of large-fruited species in areas where more extreme rainforest contraction occurred, and re-colonisation by small-fruited species readily dispersed by the available fauna. Species distribution patterns showed that larger-fruited species had smaller geographic ranges than smaller-fruited species and locations with stable refugia (and high endemism) aligned with concentrations of large fleshy-fruited taxa, making them a potentially valuable conservation-planning indicator.

opencc-zeroDec 2014View details →

Data from: Spatial structure of above-ground biomass limits accuracy of carbon mapping in rainforest but large scale forest inventories can help to overcome

Precise mapping of above-ground biomass (AGB) is a major challenge for the success of REDD+ processes in tropical rainforest. The usual mapping methods are based on two hypotheses: a large and long-ranged spatial autocorrelation and a strong environment influence at the regional scale. However, there are no studies of the spatial structure of AGB at the landscapes scale to support these assumptions. We studied spatial variation in AGB at various scales using two large forest inventories conducted in French Guiana. The dataset comprised 2507 plots (0.4 to 0.5 ha) of undisturbed rainforest distributed over the whole region. After checking the uncertainties of estimates obtained from these data, we used half of the dataset to develop explicit predictive models including spatial and environmental effects and tested the accuracy of the resulting maps according to their resolution using the rest of the data. Forest inventories provided accurate AGB estimates at the plot scale, for a mean of 325 Mg.ha-1. They revealed high local variability combined with a weak autocorrelation up to distances of no more than10 km. Environmental variables accounted for a minor part of spatial variation. Accuracy of the best model including spatial effects was 90 Mg.ha-1 at plot scale but coarse graining up to 2-km resolution allowed mapping AGB with accuracy lower than 50 Mg.ha-1. Whatever the resolution, no agreement was found with available pan-tropical reference maps at all resolutions. We concluded that the combined weak autocorrelation and weak environmental effect limit AGB maps accuracy in rainforest, and that a trade-off has to be found between spatial resolution and effective accuracy until adequate "wall-to-wall" remote sensing signals provide reliable AGB predictions. Waiting for this, using large forest inventories with low sampling rate (<0.5%) may be an efficient way to increase the global coverage of AGB maps with acceptable accuracy at kilometric resolution.

opencc-zeroDec 2015View details →

Data from: Fine partitioning of epiphyte habitat within Johansson zones in tropical Australian rainforest trees

For over three decades, the Johansson zones have been widely used in epiphyte studies as a way of stratifying the host tree into habitat zones, however, the usefulness of this system has been questioned. We test the effectiveness of the Johansson zones by grouping epiphyte species by the substrate and microclimatic attributes of their individual occurrences and assessing the fidelity of these groups to the Johansson zones. Habitat characteristics were recorded for every individual epiphyte on 30 trees in the lower montane rainforests of north-eastern Australia. Twenty-four epiphyte species were agglomerated into four groups using Ward's method. Group 4 was highly distinct and included shade loving species and nomadic vines from the lower zones of the host trees. Group 3 contained species from the most exposed habitats. Group 1 had higher light levels and lower substrate thickness than Group 2, yet both groups had close to identical distributions over the Johansson zones. This suggests that groups of epiphyte species may utilise different micro-sites within the same zone. While the Johansson zones are a useful tool in epiphyte studies, finer partitioning of habitat within the host tree may be missed.

opencc-zeroDec 2011View details →

Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria

An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. In order to test this hypothesis we assessed genetic diversity and structure in populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30 km. Almost all genetic variation was due to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5–10 m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.

opencc-zeroJan 2020View details →

Modifications of the rainforest frugivore community are associated with reduced seed removal at the community level

Tropical rainforests worldwide are under increasing pressure from human activities, which are altering key ecosystem processes such as plant-animal interactions. However, while the direct impact of anthropogenic disturbance on animal communities has been well studied, the consequences of such defaunation for mutualistic interactions such as seed dispersal remains chiefly understood at the plant species level. We asked whether communities of endozoochorous tree species had altered seed removal in forests affected by hunting and logging and if this could be related to modifications of the frugivore community. At two contrasting forest sites in French Guiana, Nouragues (protected) and Montagne de Kaw (hunted and partly logged), we focused on four families of animal-dispersed trees (Sapotaceae, Myristicaceae, Burseraceae and Fabaceae) which represent 88 % of all endozoochorous trees which were fruiting at the time and location of the study. We assessed the abundance of the seed dispersers and predators of these four focal families by conducting diurnal distance sampling along line transects. Densities of several key seed dispersers such as large-bodied primates were greatly reduced at Montagne de Kaw, where the specialist frugivore Ateles paniscus is probably extinct. In parallel, we estimated seed removal rates from fruit and seed counts conducted in one-square-meter quadrats placed on the ground beneath fruiting trees. Seed removal rates dropped from 77 % at Nouragues to 47 % at Montagne de Kaw, confirming that the loss of frugivores associated with human disturbance impacts seed removal at the community level. In contrast to Sapotaceae, whose seeds are dispersed by mammals only, weaker declines in seed removal for Burseraceae and Myristicaceae suggest that some compensation may occur for these bird- and mammal-dispersed families, possibly because of the high abundance of toucans at the disturbed site. The defaunation process currently occurring across many tropical forests could dramatically reduce the diversity of entire communities of animal-dispersed trees through seed removal limitation.

opencc-zeroDec 2018View details →

Data from: Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae)

Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tumors. We identify patterns of pollen-mediated gene flow within natural populations of F. picrosperma and estimate genetic parameters and genetic structure between adult and juvenile groups using microsatellite markers. Our results show pollination events occur over much shorter distances than reported for tropical canopy species. At least 63 % of seeds are sired by male trees located within 30 m of the mother. On average, 27 % of the local male population contributed to successful reproduction of F. picrosperma with most fathers siring a single seed, however, the contributions to reproduction were uneven. Larger male trees with more flowers had gre ater reproductive success than those with less flowers (P < 0.05). There were comparatively low levels of genetic variation across the species (HE = 0.405 for adult trees and 0.379 for juveniles) and we found no loss of genetic diversity between adult and juvenile trees. Short distance pollen flow and low genetic diversity is theoretically a prelude to genetic impoverishment, however F. picrosperma has persisted through multiple significant climatic oscillations. Nevertheless, the remaining low genetic diversity is of concern for domestication programs which require maximal genetic diversity to facilitate efficient selective breeding and genetic improvement of this commercially significant species.

opencc-zeroDec 2016View details →

Data from: Ants as ecological indicators of rainforest restoration: community convergence and the development of an Ant Forest Indicator Index in the Australian wet tropics

Ecosystem restoration can help reverse biodiversity loss, but whether faunal communities of forests undergoing restoration converge with those of primary forest over time remains contentious. There is a need to develop faunal indicators of restoration success that more comprehensively reflect changes in biodiversity and ecosystem function. Ants are an ecologically dominant faunal group and are widely advocated as ecological indicators. We examine ant species and functional group responses on a chronosequence of rainforest restoration in northern Australia, and develop a novel method for selecting and using indicator species. Four sampling techniques were used to survey ants at 48 sites, from grassland, through various ages (1–24 years) of restoration plantings, to mature forest. From principal components analysis of seven vegetation metrics, we derived a Forest Development Index (FDI) of vegetation change along the chronosequence. A novel Ant Forest Indicator Index (AFII), based on the occurrences of ten key indicator species associated with either grassland or mature forest, was used to assess ant community change with forest restoration. Grasslands and mature forests supported compositionally distinct ant communities at both species and functional levels. The AFII was strongly correlated with forest development (FDI). At forest restoration sites older than 5–10 years that had a relatively closed canopy, ant communities converged on those of mature rainforest, indicating a promising restoration trajectory for fauna as well as plants. Our findings reinforce the utility of ants as ecological indicators and emphasize the importance of restoration methods that achieve rapid closed-canopy conditions. The novel AFII assessed restoration status from diverse and patchily distributed species, closely tracking ant community succession using comprehensive species-level data. It has wide applicability for assessing forest restoration in a way that is relatively independent of sampling methodology and intensity, and without a need for new comparative data from reference sites.

Data from: Dry-season decline in tree sapflux is correlated with leaf turgor loss point in a tropical rainforest

1. Water availability is a key determinant of forest ecosystem function and tree species distributions. While droughts are increasing in frequency in many ecosystems, including in the tropics, plant responses to water supply vary with species and drought intensity, and are therefore difficult to model. Based on physiological first principles, we hypothesized that trees with a lower turgor loss point (πtlp), i.e., a more negative leaf water potential at wilting, would maintain water transport for longer into a dry season. 2. We measured sapflux density of 22 mature trees of 10 species during a dry season in an Amazonian rainforest, quantified sapflux decline as soil water content decreased, and tested its relationship to tree πtlp, size, and leaf predawn and midday water potentials measured after the onset of the dry season. 3. The measured trees varied strongly in the response of water use to the seasonal drought, with sapflux at the end of the dry season ranging from 37 to 117% (on average 83 ± 5 %) of that at the beginning of the dry season. The decline of water transport as soil dried was correlated with tree πtlp (Spearman ρ≥0.63), but not with tree size or predawn and midday water potentials. Thus, trees with more drought-tolerant leaves better maintained water transport during the seasonal drought. 4. Our study provides an explicit correlation between a trait, measurable at the leaf level, and whole-plant performance under drying conditions. Physiological traits such as πtlp can be used to assess and model higher-scale processes in response to drying conditions.

FIGURE 3 in A third species of the rare frog genus Holoaden (Terrarana, Strabomantidae) from a montane rainforest area of southeastern Brazil

FIGURE 3. Holoaden pholeter sp. nov., holotype (MNRJ 51475). Dorsal and lateral views of head; ventral views of hand and foot; scale bars represent 5 mm.

FIGURE 4 in A third species of the rare frog genus Holoaden (Terrarana, Strabomantidae) from a montane rainforest area of southeastern Brazil

FIGURE 4. Distribution of the species of Holoaden. Holoaden pholeter sp. nov. (dot); H. luederwaldti (triangle); H. luerderwaldti and H. bradei (star); Holoaden sp. (square).

FIGURE 2 in A third species of the rare frog genus Holoaden (Terrarana, Strabomantidae) from a montane rainforest area of southeastern Brazil

FIGURE 2. Holoaden pholeter sp. nov., holotype (MNRJ 51475, adult female, SVL 44.6 mm), dorsal and ventral views.

FIGURE 3 in Two additional treefrogs of the Boophis ulftunni species group (Anura: Mantellidae) discovered in rainforests of northern and south-eastern Madagascar

FIGURE 3. Male holotype of Boophis lilianae sp. n. (ZSM 201/2006) in life. A. Dorsolateral view, B. Ventral view. SVL 18.3 mm.