Find research datasets worth reusing

opencc-zeroDec 2017View details →

Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?

Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understory, however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understory and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly occurrences in the canopy were largely uncorrelated with occurrences in the understory at both localities, indicating independent demographic patterns in the two habitats. We also documented modest, significant genome-level differentiation at both localities. Genetic differentiation between habitat types (approximately 20m in elevation) were comparable to levels of differentiation between sampling locations (approximately 1500km). We conclude that canopy and understory populations of A. demophon represent incipient independent evolutionary units. These findings support the hypothesis that divergence between canopy and understory-associated populations might be a mechanism generating insect diversity in the tropics.

opencc-zeroSep 2015View details →

Supporting data: The biogeographic origin of a radiation of trees in Madagascar: Implications for the assembly of a tropical forest biome

This directory contains xml files (which in turn contain concatenated alignments), newick, and phylip formatted tree files. Code and scripts used for generating figures, phylogenies and biogeographic models is available on request. ~/trees/ contains tree files and maximum clade credibility trees from the three phylogenetic inferences: 1) Canarieae with a fossil tip; 2) Canarieae with fossil nodes; and 3) Canarieae with fossil nodes, but without the Canarieae fossil node calibration. See the paper and supplemental text for more information. ~/trees/RAxML/ contains the RAXML starter trees used   ~/xml_files/ contains the xml files used for Bayesian phylogenetic inference in BEAST for all three phylogenetic inferences (see above). Concatenated alignments of molecular data can be found within the xml files.

opencc-by-4.0Dec 2022View details →

Dataset from paper: "Mind the Gap: Reconciling tropical forest carbon flux estimates from Earth Observation and National Reporting requires transparency"

This repository contains the processed data used in the publication of Heinrich et al., 2023 (Mind the Gap: Reconciling tropical forest carbon flux estimates from Earth Observation and National Reporting requires transparency). Carbon Balance and Management: https://cbmjournal.biomedcentral.com/articles/10.1186/s13021-023-00240-2 When using this data, full reference to the raw data publications and the publication Heinrich et al., 2023 must be made.The raw datasets used in this study are all available from their original sources.

opencc-zeroOct 2023View details →

Data from: Both the selection and complementarity effects underpin the effect of structural diversity on aboveground biomass in tropical forests

Aim: Despite mounting empirical evidence regarding the positive effects of forest structural diversity (STRDIV) on forest functioning, the underlying biotic mechanisms and controlling abiotic factors remain poorly understood. This study provides the first assessment of the interactive effects of STRDIV and diversity in species and functional traits on aboveground biomass (AGB) in natural forests in West and East Africa. Location: West and East Africa Time period: 2014-2020 Major taxa studied: Woody plants Methods: Using data from 276 plots and 7993 trees of 207 species distributed across various types of natural forests and major climatic zones of Africa, linear mixed-effects and structural equation models, we have evaluated how alternative causal relationships between STRDIV and taxonomic and functional diversity attributes influence AGB, while accounting for the effects of environmental covariates. We also assessed the consistency of these relationships across floristically and environmentally homogenous forest types. Results: We found that the positive effects of STRDIV on AGB were underpinned by both the community-weighted mean (CWM) of trait values (selection effects) and species richness (niche complementarity), but the relative importance of these effects varied depending on forest types. Across the forest types, STRDIV primarily mediated the effects of CWM of traits and species richness on AGB. We also found that STRDIV–AGB relationships were constrained by resource (water and nutrient) availability. Main conclusions: Our findings provide novel insights into the role of functional traits as key determinants of the effects of STRDIV on AGB in tropical forests. We suggest that forest management and climate change mitigation strategies aimed at conserving biodiversity and fostering biomass storage through increased STRDIV should focus on maintaining high levels of functionally dominant species while also increasing tree species diversity.

Fig. 2 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest

Fig. 2. Two pairs of females with infants drink the seepage water at a natural-lick.

Fig. 6 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest

Fig. 6. Visitation time of each orangutan class to the naturallicks.

Fig. 4 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest

Fig. 4. Visiting proportion of each orangutan class: flanged male, female with infant, and others.

Fig. 3 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest

Fig. 3. Proportion of visitation frequency of top 3 species among the natural-licks.

Fig. 5 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest

Fig. 5. Duration of the visit of each orangutan class to the naturallicks.

opencc-by-4.0Oct 2023View details →

Fig. 2 in Long-term changes in avian relative abundances in relation to human disturbance in a tropical dry forest in central Myanmar

Fig. 2. Annual rainfall measured adjacent to Chatthin Wildlife Sanctuary 1999–2020.

opencc-by-4.0Oct 2023View details →

Fig. 3. Forest cover within 300 in Long-term changes in avian relative abundances in relation to human disturbance in a tropical dry forest in central Myanmar

Fig. 3. Forest cover within 300 meters of bird survey points in 1999 and 2020.

opencc-zeroDec 2023View details →

Contrasting responses of fine root biomass and traits to large-scale nitrogen and phosphorus addition in tropical forests in the Guiana shield

Fine roots mediate plant nutrient acquisition and growth. Depending on soil nutrient availability, plants can regulate fine root biomass and morphological traits to optimise nutrient acquisition. Little is known, however, about the importance of these parameters influencing forest functioning. In this study, we measured root responses to nutrient additions to gain a mechanistic understanding of plant adaptations to nutrient limitation in two tropical forests in French Guiana, differing two-fold in their soil nutrient statuses. We analysed the responses of root biomass, mean root diameter (RD), specific root length (SRL), specific root area (SRA), root tissue density (RTD) and carbon (C), nitrogen (N) and phosphorus (P) concentrations in roots down to 15 cm soil depth after three years of N and P additions. At the lower-fertility site Paracou, no changes in root biomass or morphological traits were detected with either N or P addition, although P concentrations in roots increased with P addition. In the higher fertility site, Nouragues, root biomass and P concentrations in roots increased with P addition, with no changes in morphological traits. In contrast, N addition shifted root traits from acquisitive to more conservative by increasing RTD. A significant interaction between N and P in Nouragues pointed to stronger responses to P addition in the absence of N. Our results suggest that the magnitude and direction of root biomass and trait expression were regulated by soil fertility, corroborated by the response to N or P additions. At low fertility sites, we found lower plasticity in root trait expression compared to more fertile conditions, where N and P additions caused stronger and antagonistic responses. Identifying the exact role of mechanisms affecting root nutrient uptake in Amazon forests growing in different soils will be crucial to foresee if and how rapid global changes can affect their carbon allocation.

opencc-zeroDec 2023View details →

Diversity patterns along ecological succession in tropical dry forests: A multi-taxonomic approach

Evaluating the diversity of multiple taxa is fundamental to understand community assembly and to assess the integrity and functionality of tropical secondary forests. In this study, we analyzed the natural regeneration of tropical dry forests (TDFs) in three regions of Brazil using Hill-Simpson diversity, abundance and β-diversity of trees and five groups of insects (herbivores, fruit-feeding butterflies, ants, culicid mosquitoes and dung beetles). Sampling was conducted in 39 0.1 ha plots using a chronosequence approach (13 plots in early, intermediate and old-growth forests). We evaluated the contribution of three different levels to γ-diversity: α (within plots), β¹ (among plots) and β² (among successional stages), and further determined the relative importance of turnover (species replacement) and nestedness (differences in species number among sites) to β². Our results showed that, unexpectedly, the Hill-Simpson diversity was consistently higher in early than old-growth stages for all regions, but varied more widely in the intermediate stages. For each group separately, the same trend was observed for butterflies, ants, dung beetles and herbivores and did not differ among stages for mosquitoes. Successional differences in abundance were only detected for trees (increasing along the gradient) and for mosquitoes (decreasing). According to our expectations, the additive partitioning analysis showed that β2-diversity contributed more to γ-diversity than β1-diversity, when all taxa were considered together and for most of them separately (except for butterflies and dung beetles). Most of the β²-diversity was due to species turnover, but this contribution varied among groups and regions, with the highest turnover for herbivores and the lowest for dung beetles. Our results suggest that the Hill-Simpson diversity and changes in species composition (as given by β²-diversity) are better indicators of forest natural regeneration than raw species richness, corroborating previous studies with plants and animals.

opencc-zeroJan 2024View details →

Pattern and driver of the compositional variations in a tropical cloud forest: Comparing vascular epiphytes with terrestrial woody plants

β-diversity patterns (the compositional variations across sites) and their drivers are the major concerns of biodiversity research and conservation practices, whereas such information remains scarce for vascular epiphytes, especially in tropical forest communities. This study aimed to reveal the pattern and driving process of the compositional variations of vascular epiphytes in a tropical cloud forest on Hainan island, southern China, and their differences from those of terrestrial woody plants. To this end, we quantified their between-habitat compositional variations and distinguished the underlying components of β-diversity (nestedness and turnover). We then examined the relative roles of niche-based and neutral processes in driving the compositional variations by using a null model approach. Our results showed that the between-habitat compositional variations were significant for both plant assemblages and stronger in vascular epiphytes than in terrestrial woody plants. The turnover component of β-diversity was significantly stronger in terrestrial woody plants, accounting for 73.16%–80.08% of the variations. By contrast, the nestedness component was significantly stronger in vascular epiphytes and characterized 46.82%–67.5% of the variations. Besides, the compositional variations of both plant assemblages, especially terrestrial woody plants, were generally poorly fitted by the simulated niche-based scenarios but well fitted by the simulated neutral scenarios. Overall, the compositional variations of both plant assemblages were significant and mainly due to dispersal limitation, albeit to varying degrees. Hence, further studies of these plant assemblages at local scales should not be ideologically limited to the niche-based framework. Moreover, the stronger nestedness observed in vascular epiphytes suggests the greater importance of prioritizing conservation efforts in the species-rich habitats for these plants.

opencc-zeroFeb 2024View details →

Data on arthropod abundance in tropical forest restoration plots with high or low plant phylogenetic diversity

Consideration of plant phylogenetic diversity in ecological restoration carries substantial potential, as communities with a greater diversity of lineages with older evolutionary histories can increase the diversity of niches and thus are likely to recover larger species networks than communities clustered in specific clades with reduced variation in functional traits. In this study, we experimentally assessed how arthropod communities were affected by the phylogenetic diversity of a set of tropical tree species. We established 12 experimental restoration plots with either high or low plant phylogenetic diversity, while maintaining constant the number of plant species. After one and three years, arthropods with different feeding habits (herbivores, predators, pollinators, and detritivores) were collected and identified as morphospecies or operational taxonomic units using metabarcoding techniques. We provide insights on the influence of plant phylogenetic diversity on arthropod abundance and species diversity, particularly among predator, pollinator, and detritivore common and dominant species, which increased with plant phylogenetic diversity. The trend, however, was the opposite for the diversity of herbivore common and dominant species, which decreased as plant phylogenetic diversity increased. These findings highlight the importance of considering plant species richness when designing restoration strategies, but also their evolutionary histories, as the same number of plant species can produce different outcomes for higher trophic levels, as a function of their phylogenetic relationships.

opencc-by-4.0Dec 2021View details →

Tropical forest seedling census data from Danum Valley, Sabah, Malaysia (2019-2021)

Data Link This is a link to a dataset affiliated with SEARRP but that is stored in a different repository. Please find the link to the dataset below, and be sure to cite the data correctly via that repository. Correct Citation Burslem, D.F.R.P.; Banin, L.F.; Bartholomew, D.C.; Bin Suis, M.A.F.; Bittencourt, P.R.L.; Chapman, D.; Dent, D.H.; Hayward, R.M.; O’Brien, M.J.; Rowland, L.M. (2022). Tropical forest seedling census data from Danum Valley, Sabah, Malaysia, 2019-2021. NERC EDS Environmental Information Data Centre. (Dataset). https://doi.org/10.5285/c1813d0d-193f-4f23-82c6-333d5d099b42 Abstract Southeast Asian tropical forests have been subjected to recent intense pressure due to selective logging and widespread clearance for Oil Palm cultivation. Consequently there is an emerging interest in restoring degraded forests using either natural regeneration or active restoration treatments. However, the reproductive biology of Southeast Asian tropical forest trees limits research on the effectiveness of these approaches, because most large canopy trees only flower and fruit very rarely. These sporadic mass reproductive events are responsible for establishing new cohorts of seedlings that grow up to become the next generation of adult canopy trees, and it is critical to discover whether the success of these episodic attempts at regeneration is as great in forests that have been degraded by logging as they are in primary forests, and whether the processes leading to seedling recruitment are restored effectively in forests where treatments such as tree planting and climber cutting have been applied. However, because these regeneration events occur so infrequently and unpredictably it is very difficult to incorporate them into the conventional planning cycle for research, despite the critical importance of the events that occur early in the life cycle of trees to future forests. In this project we will rapidly establish sampling sites in Sabah, Malaysia, where we know that a mass flowering of canopy trees was initiated in May 2019, for the first time since 2010. We aim to compare the amount and diversity of fruits and seedlings produced during this masting event in primary (undisturbed, unlogged) forests, and in adjacent forests that have been logged and either left to regenerate naturally or restored by planting tree seedlings and maintaining them for five years by climber cutting. Because the restoration of logged forests began more than 20 years ago, the original cohort of planted seedlings are now, in some cases, large canopy trees that may contribute seeds and seedlings for the first time during the reproductive event this year. We will also measure the expression of traits that determine how plants capture and use resources such as light and nutrients for the most common species that occur in each of the three types of forest, which will determine whether the community of seedlings that establish in the restored forests functions in a more similar way to that in the undisturbed primary forest than in the forests left to regenerate naturally after logging. A key focus on this study will be on species of the dominant family of canopy and emergent trees, the Dipterocarpaceae, which are targeted for logging. Logged forests possess a lower density of large reproductively mature dipterocarp individuals, and a key aim of restoration is to re-establish the dominance and diversity of this family by planting and maintaining dipterocarp seedlings. Dipterocarps possess an unusual trait for the tree flora of tropical forests, which is that they form mutualistic associations with root-colonising ectomycorrhizal fungi (ECM), whereas most other species in the forest form a different type of root association with arbuscular mycorrhizas (AM). Our recent research has shown that ECM seedlings benefit from proximity to a high density of ECM adults, possibly because they exchange resources through a common below-ground fungal network and because ECM species suppress root pathogens. In contrast, AM seedlings have lower survival when located close to a high density of adults of the same species. A final aim of our project is to test whether the beneficial effects of high adult density for ECM species is reduced in logged forests where the density of ECM adults is much lower, and whether these effects are offset by restoration. This research will therefore contribute results that are vital to understanding how Southeast Asian forests regenerate during masting events, and whether the negative effects of logging can be mitigated by restoration. Link to project website: <a href="https://gtr.ukri.org/projects?ref=NE%2FT006560%2F1">GtR (ukri.org)</a> Link to data repository: <a href="https://doi.org/10.5285/c1813d0d-193f-4f23-82c6-333d5d099b42" target="_blank" rel="noopener">DOI</a>

opencc-by-4.0Dec 2021View details →

Tropical forest seedling trait data collected in Danum Valley, Sabah, Malaysia, in February 2020

opencc-zeroMar 2024View details →

Empirical data and model simulations of the effect of repeated hurricanes on soil carbon dynamics in a humid tropical forest

Increasing hurricane frequency and intensity with climate change is likely to affect soil organic carbon (C) stocks in tropical forests. We examined the cycling of C between soil pools and with depth at the Luquillo Experimental Forest in Puerto Rico in soils over a 30-year period that spanned repeated hurricanes. We used a non-linear matrix model of soil C pools and fluxes ("soilR") and constrained the parameters with soil and litter survey data. Soil chemistry and stable and radiocarbon isotopes were measured from three soil depths across a topographic gradient in 1988 and 2018. Our results suggest that pulses and subsequent reduction of inputs caused by severe hurricanes in 1989, 1998, and two in 2017 led to faster mean transit times and younger mean ages of soil C in the particulate, occluded, and mineral-associated soil organic matter pools at 0–10 cm and 35–60 cm depths relative to a modeled control soil with constant inputs over the thirty years. Between 1988 and 2018, the occluded C stock increased, and d13C in all pools decreased, while changes in particulate and mineral-associated C were undetectable. The differences between 1988 and 2018 suggest that hurricane disturbance results in a dilution of the occluded light C pool with an influx of young, debris-deposited C, and possible microbial scavenging of old and young C in the particulate and mineral-associated pools. These effects led to a younger total soil C pool with faster mean transit times. Our results suggest that increasing frequency of intense hurricanes will speed up rates of C cycling in tropical forests, and eventually lead to net losses of C from tropical forest soils.

opencc-by-4.0Aug 2023View details →

Novel climates are already widespread beneath the world's tropical forest canopies.

R code and data to accompany 'Novel climates are already widespread beneath the world’s tropical forest canopies'.