Find research datasets worth reusing

Fig. 7 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 7. Ariamnes columnaceus sp. nov., holotype male. A. Pedipalpus, prolateral view; B. Pedipalpus, retrolateral view. Scale bar = 0.10 mm.

Fig. 2 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 2. Allothymoites repandus sp. nov., holotype male. A. Pedipalpus, ventral view; B. Conductor, ventral view; C. TTA, ventral view; D. Embolus, ventral view. Scale bars = 0.05 mm.

Fig. 6 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 6. Allothymoites sculptilis sp. nov., holotype male. A. Pedipalpus (cymbium removed), ventral view; B. Pedipalpus, ventral view; C. Pedipalpus, prolateral view; D. Pedipalpus, retrolateral view. Scale bars = 0.05 mm.

Fig. 5 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 5. Allothymoites sculptilis sp. nov., holotype male. A. Pedipalpus, ventral view; B. MA and conductor, ventral view; C. Embolus, ventral view. Scale bars = 0.10 mm.

Fig. 1 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 1. Allothymoites repandus sp. nov., holotype male. A. Pedipalpus, prolateral view; B. Pedipalpus, retrolateral view; Scale bar = 0.05 mm.

Fig. 13 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 13. Carniella foliosa sp. nov., holotype male. A. Pedipalpus, prolateral view; B. Pedipalpus, retrolateral view. Scale bar = 0.10 mm.

Fig. 9 in Comb-footed spiders (Araneae: Theridiidae) in the tropical rainforest of Xishuangbanna, Southwest China

Fig. 9. Ariamnes columnaceus sp. nov., holotype male. A. Pedipalpus (cymbium removed), ventral view; B. Pedipalpus, ventral view; C. Pedipalpus, prolateral view; D. Pedipalpus, retrolateral view. Scale bars = 0.10 mm.

opencc-zeroJan 2023View details →

High-resolution tropical rain-forest canopy climate data

Canopy habitats challenge researchers with their intrinsically difficult access. The current scarcity of climatic data from forest canopies limits our understanding of the conditions and environmental variability of these diverse and dynamic habitats. We present 307 days of climate records collected between 2019 and 2020 in the tropical rainforest canopy of the Yasuní National Park, Ecuador. We monitored climate with a 10-minute temporal resolution in the middle crowns of eight canopy trees. The distance between canopy climate stations ranged from 700 m to 10 km. Apart from air temperature, relative humidity, leaf wetness, and photosynthetically active radiation (PAR), measured in each canopy climate station, global radiation, rainfall, and wind speed were measured in different subsets of them. We processed the eight data series to omit erroneous records resulting from sensor failures or lack of the solar-based power supply. In addition to the eight original data series, we present three derived data series, two aggregating canopy climate for valleys or for ridges (from four stations each), and one overall average (from the eight stations). This last derived data series contains 306 days, while the shortest of the original data series covers 22 days and the longest 296 days. In addition to the data, two open-source tools, developed in RStudio, are presented that facilitate data visualization (a dashboard) and data exploration (a filtering app) of the original and aggregated records.

Tropical cyclones facilitate recovery of forest leaf area from dry spells in East Asia

This online repository copies the source code and the download link of the input data for the research work of analyzing forest leaf area change due to the TC activities in the west pacific ocean basin.  TC Track data, mask, climate reanalysis, leaf area, ERA5 (wind speed, surface pressure data), and SPEI dataset:  <a href="http://YYCdb.synology.me:5833/sharing/YizTR8HPR">http://YYCdb.synology.me:5833/sharing/YizTR8HPR</a> password:bg-2022-115 File size: 373G The path for downloading the source code/script for analyzing the LAI changes: <a href="http://YYCdb.synology.me:5833/sharing/JC2AGt9Kh">http://YYCdb.synology.me:5833/sharing/JC2AGt9Kh</a> password:bg-2022-115 File size: 880M Data table for all events used in this study: <a href="http://YYCdb.synology.me:5833/sharing/MqA4YFBHk">http://YYCdb.synology.me:5833/sharing/MqA4YFBHk</a> password:bg-2022-115 Filesize:824K

TROVA outputs for the extratropical transition of tropical cyclones in the North Atlantic basin

Output data from the TRansport Of water Vapor (TROVA) tool for the research paper "Evaluating changes in the moisture sources for tropical cyclones precipitation in the North Atlantic that underwent extratropical transition".

opencc-by-4.0Nov 2022View details →

Data and code from paper: The carbon sink of secondary and degraded humid tropical forests

This repository contains the data and code produced for the following paper: Title: The carbon sink of recovering secondary and degraded humid tropical forests Contact: Viola Heinrich (viola.heinrich@bristol.ac.uk) Please note: <ul> <li> throughout repository where files include reference to: <...congo_basin...> this refers to the Central Africa region as it is termed in the main paper.</li> <li>the code has not been amended for wider use and still contains set working directories for use with University of Bristol systems, you will need to change these for the scripts to run. </li> </ul> The data produced in this project were produced using a combination of programming languages due to differences in the author's preferences and expertise. Overall, the initial data analysis was carried out in (i) Google Earth Engine, and (ii) Arcpy (Python3.6.10). Most of the post-processing of the initial data was then carried out in R (v3.6) for which the code and output datasets are available here. To access the code used in Google Earth Engine that was used to produce and export data from the Tropical Moist Forest dataset (e.g. Years Since Last Disturbance of secondary/degraded forest), please follow the link: https://code.earthengine.google.com/d303fc21e7b57a8fc259e0ee2b58bfb4  This repository contains the following zipped folders: <ul> <li>data_folder: this folder contains further folders with all the data produced for this paper.</li> </ul> <ol> <li>Fig1_data_models: All data needed to produce Figure 1 of the main paper, including an .RDS version of the 6 main regrowth models produced for this paper (secondary and degraded forests in the three regions). These are the files beginning with "regrowthModel_..RDS. Additionally, the folder includes the dataframe files originally from GeoTiff files that were used to extract the Aboveground Biomass in old-growth (undisturbed forests) > e.g. the subfolder "amazon_basin_oldG_AGB" contains the .dbf files representing the AGB in old-growth forest pixels. There are 4 files as the Amazon was split up into 4 sections for computational reasons. Similarly, the Central Africa region (here referred to as congo_basin) was split up into 2 regions.</li> <li>Fig2_data_models_plus_exFig3_to_5: The data needed to produce Figure 2 in the main paper as well as the Extended Data Figures 3 to 5. This includes .RDS versions of the regrowth models for secondary and degraded forests in the three regions for the different variables considered (files beginning with "regrowthModel_..RDS) e.g. "regrowtModel_borneo_deg_MaxTemo_low.rds", refers to the regrowth model shown in Figure 2c - the regrowth model for Bornean degraded forests for the variable "Maximum Temperature", where "low" refers to the lowest temperature range considered in the study. As before, files are provided giving information on the AGB in old-growth forests for each region within different conditions of each driving variable. </li> <li>Fig4: All the data needed to produce Figure 4 (and Supplementary Figure 18) of the main paper. This includes the file "regrowth_in_all_basins_by_country_input_data.csv", which contains data on the total number of cells for each forest type for each Years Since Last Disturbance (YSLD) in each region.</li> <li>Extended_dataFig1_input: The input for Extended Data Figure 1, including the values derived from other studies used in this comparison as well as additional notes/comments on how the data were assessed.</li> <li>Extended_dataFig2_input: the input data used to determine the standardised coefficients seen in the Extended Data Figure 2.</li> <li>Extended_data_table_inputs: The inputs for the Extended Data Tables 1 and 2. Inputs include the dataframe files (.dbf), of key variables that were extracted from the GeoTiff files. Only the .dbf files have been included here to limit excessively large data being uploaded. </li> </ol> <ul> <li>code_folder.zip: The code in this folder was used to produce the main figures and results for the extended data tables shown in the paper. <ul> <li>this folder also contains a file "example_code_read_in_models.R" which provides an example of how best to read in the regrowth models for each region and forest type to extract important information such as the: (i) average growth rate in the first 20 years of analysis, (ii) all AGCs as a function of YSLD, and (iii) the estimated time it takes to reach the asymptote. </li> </ul> </li> </ul> Data and Code usage: When using any code or data in this repository or another related to this study please cite Heinrich et al. and the original paper as well as the DOI of this repository.  Further source data in .xlsx format were also submitted with the main manuscript. If you need anything else, please contact the corresponding author: Viola Heinrich (viola.heinrich@bristol.ac.uk)

opencc-by-4.0Dec 2021View details →

A population in perpetual motion: highly dynamic roosting behaviour of a tropical island endemic bat

Dataset and R script for the manuscript "A population in perpetual motion: highly dynamic roosting behaviour of a tropical island endemic bat". During the embargo period, data is available upon request from the authors (muriel.dietrich@ird.fr).

opencc-zeroJan 2023View details →

Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)

Premise: Island systems have long served as a model for evolutionary processes due to their unique species interactions. Many studies of the evolution of species interactions on islands have focused on endemic taxa. Fewer studies have focused on how antagonistic and mutualistic interactions shape the phenotypic divergence of widespread non-endemic species living on island populations. Methods: We used the widespread plant Tribulus cistoides (Zygophyllaceae) to test phenotypic divergence in traits that mediate antagonistic interactions with vertebrate granivores (birds) and mutualistic interactions with pollinators and how this is explained by bioclimatic variables. We used both herbarium specimens and field-collected samples to compare phenotypic divergence between continental and island populations. Results: Fruits from island populations were larger than on continents, but the presence of lower spines on mericarps was lower on islands. The presence of spines was largely explained by environmental variation among islands. Petal length was on average 9% smaller on island than continental populations, an effect that was especially accentuated on the Galápagos Islands. Conclusions: Tribulus cistoides exhibits phenotypic divergence between island and continental habitats for antagonistic traits (seed defence) and mutualistic traits (floral traits). Further, the evolution of phenotypic traits that mediate antagonistic and mutualistic interactions depended on the abiotic characteristics of specific islands. This study shows the potential of using a combination of herbarium and field samples for comparative studies on a globally distributed species to test phenotypic divergence on island habitats.

Nudging the tropical Indian Ocean Applied to the IPSL-CM6A-LR model - Control Experiments

This experiment applies monthly nudging of -2, -1, +1, and +2 degree C to the tropical Indian Ocean region in the IPSL-CM6A-LR pre-industrial control run. The methods of nudging are defined in Ferster et al. (2021), where we apply a constant nudging and refer to the experiments as TIOxC, where "x" is the monthly nudging value (as in Ferster et al., 2021). Additional experiments were simulated for a paper within the submission process (to be included and updated within future versions) including the "TIOc" and "C0C" experiments, where the TIOC nudges towards towards the time-mean climatology and the C0C nudges at each monthly time step towards the pre-industrial control's corresponding monthly value (similar to adding white noise at each time step). The datasets are included from the experiments to help share our results and reproducibility of the figures within our manuscripts, the original model output is stored on the TGCC computing machine Irene. All datasets are saved on this data repository are saved as annual means! These datasets represent the C0C (TIO=0C) and TIOc control experiments. Please use the additional thredds link to access the full IPSL output for the experiments: https://thredds-su.ipsl.fr/thredds/catalog/tgcc_thredds/store/fersterb/IPSLCM6/DEVT/TIO-Experiment/Control-0C-TIO/1950-01-01/Control-0C-TIO1950-01/catalog.html https://thredds-su.ipsl.fr/thredds/catalog/tgcc_thredds/store/fersterb/IPSLCM6/DEVT/TIO-Experiment/TIOc/1950-01-01/TIOc1950-01/catalog.html The pre-industrial control from IPSL can be found on the CMIP6-ESGF servers and the TGCC computing machine Irene. Please contact us for additional explanations, datasets, or collaboration. *The datasets are created from the IPSL-CM6A-LR output files **This version serves as a preliminary version of the dataset for publication purposes, additional output is available and the experiment output exceeds the 50gb of storage offered through this platform (TGCC Irene). ***Contact: brady.ferster@locean.ipsl.fr or brady.ferster@yale.edu

Nudging the tropical Indian Ocean Applied to the IPSL-CM6A-LR model - Cooling Experiments

This experiment applies monthly nudging of -2, -1, +1, and +2 degree C to the tropical Indian Ocean region in the IPSL-CM6A-LR pre-industrial control run. The methods of nudging are defined in Ferster et al. (2021), where we apply a constant nudging and refer to the experiments as TIOxC, where "x" is the monthly nudging value (as in Ferster et al., 2021). Additional experiments were simulated for a paper within the submission process (to be included and updated within future versions) including the "TIOc" and "C0C" experiments, where the TIOC nudges towards towards the time-mean climatology and the C0C nudges at each monthly time step towards the pre-industrial control's corresponding monthly value (similar to adding white noise at each time step). The datasets are included from the experiments to help share our results and reproducibility of the figures within our manuscripts, the original model output is stored on the TGCC computing machine Irene. All datasets are saved on this data repository are saved as annual means! These datasets represent the -2 and -1 degree C experiments.   Please use the additional thredds link to access the full IPSL output for the experiments: https://thredds-su.ipsl.fr/thredds/catalog/tgcc_thredds/store/fersterb/IPSLCM6/DEVT/TIO-Experiment/M1C-TIO/1950-01-01/M1C-TIO1950-01/catalog.html https://thredds-su.ipsl.fr/thredds/catalog/tgcc_thredds/store/fersterb/IPSLCM6/DEVT/TIO-Experiment/M2C-TIO/1950-01-01/M2C-TIO1950-01/catalog.html The pre-industrial control from IPSL can be found on the CMIP6-ESGF servers and the TGCC computing machine Irene. Please contact us for additional explanations, datasets, or collaboration. *The datasets are created from the IPSL-CM6A-LR output files **This version serves as a preliminary version of the dataset for publication purposes, additional output is available and the experiment output exceeds the 50gb of storage offered through this platform (TGCC Irene). ***Contact: brady.ferster@locean.ipsl.fr or brady.ferster@yale.edu

opencc-zeroFeb 2023View details →

The relationship between plant diversity and facilitation during tropical dry forest restoration

Restoration programs that promote the functioning of restored ecosystems are in urgent demand. Although several biodiversity and ecosystem functioning (BEF) experiments have demonstrated the importance of functional complementarity enhancing plant community performance, no BEF study has yet experimentally manipulated facilitation testing its contribution to how the complementarity effect modulates community performance. We built a restoration experiment manipulating diversity and facilitation in a tropical semiarid forest. We planted 4704 seedlings of 16 native tree species to assemble 147 experimental communities with 45 different compositions comprising 1, 2, 4, 8 or 16 species. Facilitation was included in the experimental design by creating a gradient of communities from low to high facilitation potential (based on prior research). We measured functional diversity and functional identity using species above and below-ground traits to investigate how they modulate the effects of species diversity and facilitation on leaf biomass production, and its additive partition biodiversity effects (NE, CE & SE). The joint influence of diversity and facilitation was tested separately for leaf biomass production and Net Biodiversity Effect using Linear Mixed Models (LMMs). We subsequently ran LMMs including functional diversity and functional identity. We hypothesised that facilitation would increase community productivity and functioning and that functional dispersion and functional identity related to above and below-ground traits would explain facilitation performance. Facilitation positively influenced leaf biomass production as predicted, but unexpectedly, neither of the functional traits were important for modulating the facilitation process. Positive values for Complementarity Effect (CE) showed that plants performed better in mixtures in comparison to monocultures. Selection Effect (SE) negative values, showed that species with below-average performance in monocultures, performed better in mixtures. Unexpectedly, CE did not increase as species diversity or facilitation increased. SE was influenced negatively by facilitation leading to a more equal distribution of biomass production between species in mixtures. Synthesis: Facilitation improves biomass production in restored communities and increases biomass equitability among plant species and thus ecosystem reliability. To improve restoration success, plant communities should be built using facilitating plants.

opencc-by-4.0Feb 2023View details →

Data - Krieg et al. (2023) Functional Traits and Trait Co-ordination Change Over the Life of a Leaf in a Tropical Fern Species. AJB.

Summary of the data set used in Krieg et al. (2023) Functional Traits and Trait Co-ordination Change Over the Life of a Leaf in a Tropical Fern Species. AJB.

opencc-zeroFeb 2023View details →

Dataset from: The effects of crop type, landscape composition and agroecological practices on biodiversity and ecosystem services in tropical smallholder farms

1. In the tropics, smallholder farming characterizes some of the world's most biodiverse landscapes. Agroecology as a pathway to sustainable agriculture has been proposed and implemented in sub-Saharan Africa, but the effects of agricultural practices in smallholder agriculture on biodiversity and ecosystem services are understudied. Similarly, the contribution of different landscape elements, such as shrubland or grassland cover, on biodiversity and ecosystem services to fields remains unknown. 2. We selected 24 villages situated in landscapes with varying shrubland and grassland cover in Malawi. In each village, we assessed biodiversity of eight taxa and ecosystem services in relation to crop type, shrubland and grassland cover and the number of agroecological pest and soil management practices on smallholder's fields of different crop types (bean monoculture, maize-bean intercrop, and maize monoculture). 3. Increasing shrubland cover altered carabid and soil bacteria communities. Carabid abundance increased in maize but decreased in intercrop and bean fields with increasing shrubland cover. Carabid abundance and richness and wasp abundance increased with soil management practices. Carabid, spider, and parasitoid abundances were higher in bean monocultures, but this was modulated by surrounding shrubland cover. Natural enemy abundances in beans were especially high in landscapes with little shrubland, possibly leading to lower bean damage in monocultures compared to intercropped fields, whereas maize monocultures had higher damage. In maize, grassland cover and pest management practices were positively related to damage. Carabid abundance was higher in fields with high bean damage and increased carabid richness in fields with high maize damage. Parasitoid abundance was negatively associated with bean damage. 4. Synthesis and application: Our results suggest that maintaining biodiversity and ecosystem services on smallholder farms is not achievable with a "one size fits all" approach but should instead be adapted to the landscape context and the priorities of smallholders. Shrubland is important to maintain carabid and soil bacterial diversity, but legume cultivation beneficial to natural enemies could complement pest management in landscapes with a low shrubland cover. An increased number of agroecological soil management practices can lead to improved pest control whilst the effectiveness of agroecological pest management practices needs to be re-evaluated.

opencc-zeroFeb 2023View details →

Nutrient-based species selection is a prevalent driver of community assembly and functional trait space in tropical forests

1. Soil nutrient availability and functional traits interact in complex ways during the assembly of tree communities hindering our understanding of the implications that this may have for their phylogenetic and functional diversity. 2. We combined abundance, taxonomic, phylogenetic and functional trait data of 222 tree species distributed along nutrient concentration gradients at twenty-four plots in two tropical forest study sites. We analysed micro and macronutrient concentration in organic and topsoil horizons and tested for: (1) nutrient-based species sorting due to contrasting trait-environment relationships; (2) whether nutrient filtering has consequences for phylogenetic and functional diversity, and functional space size and occupancy; and (3) we mapped trait distributions across the phylogeny of tree species to track the evolutionary signature of nutrient availability. 3. We found that total nitrogen (N), available phosphorus and total potassium in soil accounted for 68% of the variation in tropical tree species community composition, with strong associations with nutrient concentration for 89% of the tree species included in the analysis. This nutrient-based species selection was mediated by interactions between the three soil nutrient concentrations with leaf nitrogen, leaf thickness and wood density. Soil N concentration was positively associated with the functional space at the site level. At a plot level soil N concentration positively correlated with functional evenness and it was negatively associated with the functional space not occupied by any species in the tree community. Despite the phylogenetic conservatism of leaf N across tree lineages even when not considering legumes, many sister-species pairs show contrasting values which match with their habitat preferences thus indicating the evolutionary lability of this trait, particularly within recently diversified clades. 4. Synthesis. Our results demonstrate that soil nutrient-based species selection is a prevalent driver of community assembly in tropical forests, a process mediated by key functional traits within the leaf and wood economics spectrum. Functional space size and its filling increase with soil nutrient concentration, whereas niche vacancy decreases. This selection process has likely influenced tropical tree species diversification patterns via habitat specialization.