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zenodo52/100

Fruit, seed dispersal, and life history traits of tropical rainforest trees of the Anamalai Hills, Western Ghats, India

This dataset contains compiled Fruit, seed dispersal, and life history traits of tropical rainforest trees of the Anamalai Hills, Western Ghats, India. The list of species included are mainly from the following two related publications: - Muthuramkumar, S., Ayyappan, N., Parthasarathy, N., Mudappa, D., Raman, T.R.S., Selwyn, M.A. and Pragasan, L.A. (2006), <a href="https://doi.org/10.1111/j.1744-7429.2006.00118.x">Plant Community Structure in Tropical Rain Forest Fragments of the Western Ghats, India</a>. Biotropica, 38: 143-160. https://doi.org/10.1111/j.1744-7429.2006.00118.x - Osuri, A., Chakravarthy, D., Mudappa, D., Raman, T., Ayyappan, N., Muthuramkumar, S., & Parthasarathy, N. (2017). <a href="http://httpd//doi.org/10.1017/S0266467417000219">Successional status, seed dispersal mode and overstorey species influence tree regeneration in tropical rain-forest fragments in Western Ghats, India</a>. Journal of Tropical Ecology, 33(4), 270-284. doi:10.1017/S0266467417000219 The present dataset is an expanded and updated version of the related dataset available at <a href="https://doi.org/10.5061/dryad.vd0nn">https://doi.org/10.5061/dryad.vd0nn</a>   Species traits information was collated from <a href="http://www.biotik.org/">BIOTIK (http://www.biotik.org/</a>), <a href="http://www.flowersofindia.net/">Flowers of India (http://www.flowersofindia.net/)</a>, India Biodiversity Portal (http://indiabiodiversity.org/), <a href="https://doi.org/10.5061/dryad.234/1">Global wood density database (https://doi.org/10.5061/dryad.234/1)</a> and <a href="https://doi.org/10.1017/S0266467417000219">Osuri et al. (2014): https://doi.org/10.1017/S0266467417000219</a>. We also referred to the following previous studies that provided information on the successional status of rain-forest species in the Western Ghats (Chetana 2013, Pascal 1988, Raman et al. 2009, Sreejith 2005). References: CHETANA, H. C. 2013. Assessing the ecological processes in abandoned tea plantations and its implication for ecological restoration in the Western Ghats, India. PhD thesis, Manipal University. OSURI, A. M., KUMAR, V. S. & SANKARAN, M. 2014. Altered stand structure and tree allometry reduce carbon storage in evergreen forest fragments in India’s Western Ghats. Forest Ecology and Management 329: 375–383. PASCAL, J. P. 1988. Wet evergreen forests of the Western Ghats of India: Ecology, structure, floristic composition and succession. Institut Français de Pondichéry, Pondicherry. RAMAN, T. R. S., MUDAPPA, D. & KAPOOR, V. 2009. Restoring rainforest fragments: survival of mixed-native species seedlings under contrasting site conditions in the Western Ghats, India. Restoration Ecology 17:137–147. SREEJITH, K. A. 2005. Ecological and ecophysiological studies on the successional status of tree seedlings in tropical wet evergreen and semi-evergreen forests of Kerala. PhD thesis, Forest Research Institute, Dehradun. Geographic Coverage: 1. Location/Study Area: Valparai Plateau, Tamil Nadu, India; Anamalai Tiger Reserve, Tamil Nadu, India 2. GPS coordinates: Valparai Plateau (10°15'- 10°22'N, 76°52' - 76°59'E); Anamalai Tiger Reserve (10°12' - 10°35'N, 76°49' - 77°24'E) Temporal Coverage: 1. Begins: 2003-03-01 (Year, Month, Day) 2. Ends: 2024-02-10 (Year, Month, Day) Besides the README.txt file, the dataset includes the following comma-delimited text (csv) file with the data in columns as explained below: Anamalai_tree_traits_2024.csv spec_name_ORIG: Scientific name of the species used during the data collection genus: Genus of the taxon specificEpithet: Specific epithet of the taxon in the Latin binomial name Accept_name_WFO: Updated scientific name of the species as in Plants of the World Online (POWO, https://powo.science.kew.org/) Habit: life form of the species(tree/shrub/cane/palm) Distribution: Distribution of the species in the study area (Native/Endemic/Introduced) IUCN_status: IUCN status of the species (CR-Critically Endangered,DD-Data deficient,EN-Endangered,LC-Least Concern,NT-Near Threatened,VU-Vulnerable,NA-Unknown) Wden_final: Wood density value assigned for the species (g cm^-3); NA - not available; sourced from Global wood density database (https://doi.org/10.5061/dryad.234/1) wd_level: Level in which the wood density value belongs (Species - wood density value is from species level; genus - wood density value assigned is the genus level average value) fruit_type: Morphological type of fruit fleshy_dry: Whether fruit is a dry fruit or fleshy, with aril or other parts  seed_size: Species seed size: L = Large (>3 cm); M = Medium (1-3 cm); S = Small (<1 cm) disperser: Categories indicating seed dispersal mode: Bird, mammal, bird and mammal (Mammal_bird), gravity, wind, or unknown habitat: Habitat affinity category: EG_edg - evergreen forest edge; EG_for - evergreen forest; Dec_for - deciduous forest; Int – Introduced species; Unknown – Unknown habt_new: Habitat affinity new category: Mature – mature forest; Secondary – secondary forest, NA - unknown/Introduced species ad_ht: Species maximum adult height (m)

opencc-by-4.0Feb 2024View details →

zenodo44/100

Tree and habitat structure data from rainforest fragments and coffee plantations in the Anamalai Hills, Western Ghats, India

TITLETree and habitat structure data from rainforest fragments and coffee plantations in the Anamalai Hills, Western Ghats, India  DESCRIPTIONThis dataset contains point-centred quarter (PCQ) data on trees and habitat structure measurements data from rainforest fragments and some coffee plantations in the Valparai Plateau and Anamalai Tiger Reserve, Tamil Nadu, India. The data were gathered to quantity habitat parameters for bird and small carnivorous mamm community studies. Data were gathered mainly by T. R. Shankar Raman and Divya Mudappa (2000 to 2003), Hari Sridhar (2005), and Akshay Surendra (2019).PublicationsSpecific portions of the dataset have been used in the following publications:<ul><li>Mudappa, D. 2001. <a href="https://hdl.handle.net/10603/101890">Ecology of the brown palm civet Paradoxurus jerdoni in the tropical rainforests of the Western Ghats, India</a>. Ph. D. thesis, Bharathiar University, Coimbatore. https://hdl.handle.net/10603/101890</li><li>Raman, T. R. S. 2001. <a href="https://archive.org/details/raman-2001-ph-d-thesis-iisc">Community ecology and conservation of mid-elevation tropical rainforest bird communities in the southern Western Ghats, India</a>. PhD thesis, Indian Institute of Science, Bangalore. https://archive.org/details/raman-2001-ph-d-thesis-iisc</li><li>Raman, T.R.S. 2006. <a href="https://doi.org/10.1007/s10531-005-2352-5">Effects of Habitat Structure and Adjacent Habitats on Birds in Tropical Rainforest Fragments and Shaded Plantations in the Western Ghats, India</a>. Biodiversity and Conservation 15: 1577–1607. https://doi.org/10.1007/s10531-005-2352-5</li><li>Sridhar, H., & Sankar, K. 2008. <a href="https://doi.org/10.1017/S0266467408004823">Effects of habitat degradation on mixed-species bird flocks in Indian rain forests</a>. Journal of Tropical Ecology 24: 135-147. https://doi.org/10.1017/S0266467408004823</li><li>Surendra, A. & Raman, T. R. S. 2022. <a href="https://doi.org/10.1101/2022.10.22.513365">Forest bird decline and community change over 19 years in long-isolated South Asian tropical rainforest fragments</a>. Preprint. BioRxiv 2022.10.22.513365. https://doi.org/10.1101/2022.10.22.513365  </li></ul>A related dataset is the following: Raman, T. R. S. (2020). Data from: Effects of Habitat Structure and Adjacent Habitats on Birds in Tropical Rainforest Fragments and Shaded Plantations in the Western Ghats, India. Dryad Dataset. https://doi.org/10.5061/dryad.4mw6m907q  Curation and correctionsData were collated, curated, and corrected before this upload. Besides addition of new columns, explanations of metadata, and other corrections included few related to canopy measurements, effective girth of multi-stem trees, and species identification.AcknowledgementsWe are grateful to P. Jeganathan and P. R. Shankar for assistance with data collection in 2000. Others who assisted with field research, and funding agencies related to the specific studies, are acknowledged in the above publications. The data compilation and publication was carried out as part of a grant from Fondation Franklinia to NCF. CONTACTS  CONTACT #1 1. Name: T. R. Shankar Raman 2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India 3. Work Phone: +91 821 2515601 4. Email address: trsr@ncf-india.org 5. ORCID: https://orcid.org/0000-0002-1347-3953CONTACT #2 1. Name: Divya Mudappa 2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India 3. Work Phone: +91 821 2515601 4. Email address: divya@ncf-india.org 5. ORCID: https://orcid.org/0000-0001-9708-4826CONTACT #3 1. Name: Hari Sridhar 2. Work Address: Wildlife Institute of India, Post Bag #18, Chandrabani, Dehradun – 248001, Uttarakhand, India; Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India 3. Work Phone: +91 821 2515601 4. Email address: harisridhar1982@gmail.com 5. ORCID: https://orcid.org/0000-0003-3286-0120CONTACT #4 1. Name:  Akshay Surendra 2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India; School of the Environment, Yale University, New Haven, CT – 06511, USA; New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458 3. Work Phone: +91 821 2515601 4. Email address: akshaysurendra1@gmail.com 5. ORCID: https://orcid.org/0000-0003-2719-7432   GEOGRAPHIC COVERAGE1. Location/Study Area: Valparai Plateau, Tamil Nadu, India; Anamalai Tiger Reserve, Tamil Nadu, India2. GPS coordinates: Valparai Plateau (10°15'- 10°22'N, 76°52' - 76°59'E); Anamalai Tiger Reserve (10°12' - 10°35'N, 76°49' - 77°24'E) TEMPORAL COVERAGE1. Begins: 2000-01-01 (Year, Month, Day) 2. Ends: 2019-12-31 (Year, Month, Day) METHODSMethods involved are described in the publications listed above. The vegetation sampling methods are briefly described below.PCQ data: Trees ≥30cm girth at breast height (gbh, at 1.3 m) were sampled in replicate point-centred quarter (PCQ) points in each of the sites (fragments or coffee plantations).All trees in the PCQ plots were identified to species, or in a few cases to genus, using available field guides. Using a tape measure, distance from plot centre to the middle of the bole and GBH were recorded for each tree. At each of the PCQ plots, circular plots were laid to enumerate shrubs and cut trees and record presence or absence of lianas, cane, Lantana etc as described in the metadata. Canopy and leaf litter variables were measured at replicate points, spaced 25  to 50 m apart, in each site. Elevation readings were also taken at these points using an altimeter or handheld GPS. Canopy height was measured using a rangefinder. Percentage canopy cover was measured using a spherical densiometer at each of the 25 points in each site. Vertical stratification was assessed by noting presence or absence of foliage in the following height intervals (in metres): 0–1, 1–2, 2–4, 4–8, 8–16, 16–24, 24–32, and > 32, directly above and in a 0.5 m radius around each point. Leaf litter depth on the forest floor was measured using a calibrated wooden probe at each point. Where ground vegetation and litter were disturbed along trails, the samples were taken away from trails in the forest floor. FILES INCLUDED Besides the 00_README.txt file that contains this metadata, the dataset includes the following 7 files, whose details and contents are explained below. (Wherever used in the various files, NA implies not available.)  01) sites.csv -- Details of study sites verbatimLocality: Name of locality as originally used Fragment: Name of rainforest fragment or coffee plantation decimalLongitude: Longitude in decimal degrees North (WGS 84 datum) decimalLatitude: Latitude in decimal degrees East (WGS 84 datum) habitat: Habitat type as mature tropical rainforest, tropical rainforest fragment, or coffee plantation Description: Description of the place  02) allpcqdata.csv -- Tree data from point-centred quarter (PCQ) surveys Year: Year of survey for  bird and vegetation study verbatimLocality: Name of locality as originally used Fragment: Name of rainforest fragment or coffee plantation Point_name: Name ID of point-centred quarter (PCQ) point as used within a survey year pointID: Unique ID of point-centred quarter (PCQ) point including year of survey Tree_no: Tree number ID given to the four trees in each PCQ plot (T1 to T4) verbatimIdentification: Scientific name of tree species as originally written or identified scientificName: Scientific name as currently identified under updated taxonomy nativeAlien: Category indicating whether species is native or alien to the region/country kingdom: Taxonomic Kingdom phylum: Taxonomic Phylum Distance_eff: Distance in metres from centre of PCQ plot to centre of tree trunk Girth_eff: Girth in centimetres (cm) at breast height (1.3 m) of the tree after correction (using appropriate formula) in the case of multi-stemmed individuals locationRemarks: Code for site name as originally used SpCode: Species code as originally used during data entry TreeHeight: Tree height in metres (only  available in 2019 survey) identificationRemarks: Notes related to identification if available occurrenceRemarks: Notes related to multi-stemmed individuals (girths in cm) if available and note on one possibly errorneous girth  03) pcqlocations.csv -- Locations of sample PCQ points pointID: Unique ID of point-centred quarter (PCQ) point including year of survey note: Site name code decimalLatitude: Latitude in decimal degrees East (WGS 84 datum) decimalLongitude: Longitude in decimal degrees North (WGS 84 datum) coordinateUncertaintyInMeters: Approximate uncertainty of the location in metres  04) allhabitat.csv -- Data on habitat structure variables Year: Year of survey for  bird and vegetation study verbatimLocality: Name of locality as originally used Fragment: Name of rainforest fragment or coffee plantation Point: ID of replicate survey point within the Fragment 0-1m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 0-1 m above ground 1-2m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 1-2 m above ground 2-4m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 2-4 m above ground 4-8m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 4-8 m above ground 8-16m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 8-16 m above ground 16-24m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 16-24 m above ground 24-32m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 24-32 m above ground over32m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band greater than 32 m above ground VertStrata: Number of vertical strata with foliage (sum of preceding 8 columns) CanopyHeight: Canopy height in metres CanopyOpenness: Canopy openness in percentage as measured using a spherical densiometer CanopyCover: Canopy cover (closure) in percentage as measured using a spherical densiometer CanopyOverlap: Canopy overlap rank: 0-open sky above; 1-branches above barely touching; 2-overlapping branches above, sky visible; 3-overlapping branches, sky not visible UC: Canopy overlap rank as above, for understorey vegetation only MC: Canopy overlap rank as above, for the midstorey only CC: Canopy overlap rank as above, for the upper canopy only Altitude: Altitude above sea leavel in metres, measued from hand-held altimeter or GPS device RfShrub: Number of shrubs (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of point Coffee: Number of coffee bushes (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of point Maesopsis: Number of alien Maesopsis eminii stems (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of point Strobilanthes: Number of Strobilanthes shrubs (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of point TotalShrub: Total number of shrubs within 2 m radius of point Liana: Presence (1) or absence (0) of woody lianas within 5 m radius of point Cane: Presence (1) or absence (0) of cane (Calamus sp.) within 2 m radius of point Lantana: Presence (1) or absence (0) of Lantana camara shrubs within 2 m radius of point Bamboo: Presence (1) or absence (0) of bamboo culms within 2 m radius of point LeafLitter: Depth of leaf litter in cm (to 0.5 cm accuracy) measured using a calibrated wooden probe CutTrees: Number of cut trees within 5 m radius of point  05) gbifnames.csv -- Results of GBIF name matching tool sno: Serial number verbatimScientificName: Scientific name of tree species as originally written or identified scientificName: Scientific name after matching with Global Biodiversity Information Facility (GBIF) database to lowest taxonomic level sciNameWithAuthor: Scientific name with author as provided by GBIF name matching tool key: GBIF key as provided by GBIF name matching tool matchType: Type of match as provided by GBIF name matching tool confidence: Confidence as provided by GBIF name matching tool status: Status as accepted name or synonym as provided by GBIF name matching tool rank: Taxonomic rank as provided by GBIF name matching tool kingdom: Kingdom as provided by GBIF name matching tool phylum: Phylum as provided by GBIF name matching tool class: Class as provided by GBIF name matching tool order: Order as provided by GBIF name matching tool family: Family as provided by GBIF name matching tool genus: Genus as provided by GBIF name matching tool species: Species as provided by GBIF name matching tool canonicalName: Canonical name as provided by GBIF name matching tool authorship: Author of name as provided by GBIF name matching tool  06) plots2000.csv -- Data from 5 m radius circular plots in select sites verbatimLocality: Name of locality as originally used Fragment: Name of rainforest fragment or coffee plantation PlotID: ID of 5 m radius plot Treeno: Serial number of tree in the plot verbatimIdentification: Scientific name of tree species as originally written or identified scientificName: Scientific name as currently identified under updated taxonomy Girth_eff: Girth in centimetres (cm) at breast height (1.3 m) of the tree after correction (using appropriate formula) in the case of multi-stemmed individuals nativeAlien: Category indicating whether species is native or alien to the region/country kingdom: Kingdom as provided by GBIF name matching tool phylum: Phylum as provided by GBIF name matching tool occurrenceRemarks: Notes related to multi-stemmed individuals (girths in cm) if available and identification 07) anampcqs4gbif.rmd -- Text file with code in the R statistical and programming language This R code was used for converting data in this Zenodo dataset into Darwin Core occurrence dataset for upload to the Global Biodiversity Information Facility (GBIF, https://www.gbif.org). The published dataset can now be accessed at: https://doi.org/10.15468/cmsveh Changes in Version 2In sites.csv, changed habitat from "Rainforest" to "Tropical rainforest fragment" for PuthuthottamAdded the anampcqs4gbif.rmd file with R code

opencc-by-4.0Oct 2023View details →

edi44/100

canopy herbivory and leaf traits of tree communities in tropical montane rainforests of southern Ecuador

This dataset contains herbivory data estimated as leaf area loss [cm²] and [%] and several leaf traits measured either conventionally or via spectral sensing-based techniques from canopies of tree communities in tropical montane rainforests of the Andes in southern Ecuador between February and March in 2019. The data were used by Schön et al. (in prep) to evaluate whether leaf traits are valuable indicators of canopy herbivory mainly caused by arthropods and further, whether chemical leaf traits estimated via spectral sensing-based techniques have similar strong relations to herbivory as leaf traits measured conventionally. Herbivory was estimated with the software WinFOLIA ™ 2019a from scanned mature and sun-exposed leaves of tree canopies. Spectral sensing-based leaf traits comprising secondary plant metabolites and both structural and nutritional cell components were estimated from leaves with an OceanOptics spectrometer HDX. Conventionally measured leaf traits comprising morphological and nutritional traits were derived by applying both elemental and morphometrical analyses (e.g., ICP analysis, a digital micrometer and penetrometer). For detailed descriptions of the methodology see Schön et al. (in prep), Homeier et al. (2021), and Limberger et al. (2021). Research was conducted by the subprojects A1, B1, and B4 within the framework of the RESPECT project (Environmental changes in biodiversity hotspot ecosystems of South Ecuador: RESPonse and feedback effECTs) funded by the DFG with the grant numbers: BE1780/51-1, BE1780/51-2, Ho3296/6-1, FA 925/11-1, FA 925/11-2, FA 925/16-1, BR1293/17-1.

openCC (other)Aug 2024View details →

dryad40/100

Secondary Amazon rainforest partially recovers tree cavities suitable for nesting birds in 18–34 years

Passive restoration of secondary forests can partially offset loss of biodiversity following tropical deforestation. Tree cavities, an essential resource for cavity-nesting birds, are usually associated with old forest. We investigated the restoration time for tree cavities suitable for cavity-nesting birds in secondary forest at the Biological Dynamics of Forest Fragments Project (BDFFP) in central Amazonian Brazil. We hypothesized that cavity abundance would increase with forest age, but more rapidly in areas exposed to cutting only, compared to areas where forest was cut and burned. We also hypothesized that cavities would be lower, smaller, and less variable in secondary forest than in old-growth forest, which at the BDFFP is part of a vast lowland forest with no recent history of human disturbance. We used pole-mounted cameras and tree-climbing to survey cavities in 39 plots (each 200 × 40 m) across old-growth forests and 11–34 year-old secondary forests. We used generalized linear models to examine how cavity supply was related to forest age and land-use history (cut only vs cut-and-burn), and principal components analysis to compare cavity characteristics between old-growth and secondary forest. Cavity availability increased with secondary forest age, regardless of land-use history, but the oldest secondary forest (31–34 years) still had fewer cavities (mean ± SE = 9.8 ± 2.2 cavities/ha) than old-growth forest (20.5 ± 4.2 cavities/ha). Moreover, secondary forests lacked cavities that were high and deep, with large entrances – characteristics likely to be important for many species of cavity-nesting birds. Several decades may be necessary to restore cavity supply in secondary Amazonian forests, especially for the largest birds (e.g, forest-falcons and parrots > 190 g). Retention of legacy trees as forest is cleared might help maintain a supply of cavities that could allow earlier recolonization by some species of cavity-nesting birds when cleared areas are abandoned.

opencc-zeroFeb 2024View details →

zenodo40/100

Ficus trees with upregulated or downregulated defence did not impact predation on their neighbours in a tropical rainforest

Trees can emit volatile organic compounds (VOCs) when under attack by herbivores, and these signals can also be detected by natural enemies and neighbouring trees. There is still limited knowledge of intra- and inter-specific communication in diverse habitats. We studied the effects of induced VOC emissions by three Ficus species on predation on the focal Ficus trees in a lowland tropical rainforest in Papua New Guinea. Further we assessed predation across a phylogenetically diverse set of neighbouring tree species. Two of the focal tree species, Ficus pachyrrhachis and F. hispidioides, have strong alkaloid-based constitutive defences while the third one, F. wassa, is lower in constitutive chemical defences. We experimentally manipulated the jasmonic acid signalling pathway by spraying the focal individuals with either methyl jasmonate (MeJA) or diethyldithiocarbamic acid (DIECA). These treatments induce increases or decreases in VOC emissions, respectively. We tested the possible effects of VOC emissions on each focal Ficus tree and two of its neighbours by measuring the predation rate of plasticine caterpillars. We found that predation increased after the MeJA application in only one focal tree species, F. wassa, while the DIECA application had no effect on any of the three focal species. Further, we did not detect an effect of our treatments on predation rates across neighbouring trees. Neither the phylogenetic distance of the neighbouring tree from the focal tree nor the physical distance from the focal tree had any effect on predation rates for any of the three focal Ficus species. These results suggest that even congeneric tree species vary in their response to the MeJA and DIECA treatment and subsequent response to VOC emissions by predators. Our results also suggest that MeJA effects did not spill over to neighbouring trees in highly diverse tropical rainforest vegetation.

opencc-by-4.0Mar 2022View details →

dryad40/100

Data from: Impact of human foraging on tree diversity, composition and abundance in a tropical rainforest

These are summarised plot data from fifteen 40 m by 40 m sample plots established in Oban Division of Cross River National Park, Nigeria, between 23rd August 2019 and 9th September 2019. We have also included data summaries and RStudio codes used for analysis and generating results for the manuscript entitled: "Impact of human foraging on tree diversity, composition and abundance in a tropical rainforest", submitted for publication as an original research article in Biotropica. All data and R code required to generate the results as shown in the manuscript have been included. Complete tree species and plot data can be accessed at https://forestplots.net/.

opencc-zeroOct 2022View details →

dryad40/100

Admixture may be extensive among hyperdominant Amazon rainforest tree species

Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We assembled target loci from raw sequence reads, conducted tree-based paralog trimming, and estimated species trees using maximum likelihood approaches. In addition, we called single nucleotide polymorphisms for members of the Parvifolia clade and used a Bayesian clustering approach to estimate the ancestry of individuals. We distinguished between population structure and evidence of admixture using a test based on rooted gene trees. We also investigated overlap in geographical range, phenology, and morphology of species, including those we found to admix. We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.

opencc-zeroSep 2021View details →

dryad40/100

Data from: Cavities and the demographic performance of tropical rainforest trees

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publicFeb 2025View details →

dryad40/100

Admixture may be extensive among hyperdominant Amazon rainforest tree species

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publicSep 2021View details →

dryad40/100

Data from: Impact of human foraging on tree diversity, composition and abundance in a tropical rainforest

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publicOct 2022View details →

dryad40/100

Secondary Amazon rainforest partially recovers tree cavities suitable for nesting birds in 18–34 years

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publicFeb 2024View details →

edi40/100

Growth and survival of seedlings of 14 species of lowland rainforest trees planted in the La Guaria Annex (Canada Plot) of La Selva Biological Station, Costa Rica, in 1986 and measured every six months or every year until 1992 (Part 1 of 2)

During the 1960s, 1970s, and 1980s, Costa Rica’s old growth forests were being cut to clear land for cattle pastures and large-scale agriculture. Timber concessions were also growing pine, gmelina, and other non-native trees for harvesting. The Costa Rican government was developing plans for a reforestation program and for a Payment for Environmental Services program to combat forest loss. At this time there were no data available on the growth of native trees species. The TRIALS project (starting with the CANADA Plot) was designed by OTS (Organization for Tropical Studies) and the DGF (Dirección General Forestal) to measure the growth and survival of native tree seedlings planted on abandoned pasture lands at the La Selva Biological Station. Data from these seedlings formed the basis of the reforestation law and the Payments of Ecosystem Services (PES) plan and this model was replicated in many other areas of Costa Rica.

openCC0Apr 2021View details →

edi40/100

Growth and survival of seedlings of 14 species of lowland rainforest trees planted in the La Guaria Annex (Canada Plot) of La Selva Biological Station, Costa Rica, in 1986 and measured every six months or every year until 1992 (Part 2 of 2)

openCC0Apr 2021View details →

dryad36/100

Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part II)

Forest fragmentation and habitat loss are major disruptors of plant–frugivore interactions, affecting seed dispersal and altering recruitment patterns of tree species dependent on vertebrate dispersers. In a heterogeneous production landscape (primarily tea and coffee plantations) in the southern Western Ghats, India, we examined effects of surrounding forest cover and fruit crop size on frugivory of four rainforest bird-dispersed tree species (N = 131 trees, ≥ 30 trees per species, observed for 623 h). Frugivore composition differed among the four tree species with the large-seeded Canarium strictum and Myristica dactyloides exclusively dependent on large-bodied avian frugivores, whereas, medium-seeded Persea macrantha and Heynea trijuga were predominantlyvisited by small-bodied and large-bodied avian frugivores, respectively. Using the seed-dispersal-effectiveness framework, we identified effective frugivores and examined their response to forest cover and fruit crop size. Results were idiosyncratic and governed by plant and frugivore traits. Visitations to medium-seeded Persea had a positive relationship with forest cover but the relationship was negative for the large-seeded Myristica. In addition, two of the three effective frugivores for Persea responded to the interactive effect of forest cover and fruit crop size. Frugivore visitations to Hyenea were not related to forest cover or fruit crop and there were too few visitations to Canarium to discern any trends. These results highlight the context-specific response of plant-frugivore interactions to forest cover and fruit crop size influenced by the plant and frugivore traits.

opencc-zeroMay 2020View details →

dryad36/100

Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part I)

Forest fragmentation and habitat loss are major disruptors of plant–frugivore interactions, affecting seed dispersal and altering recruitment patterns of tree species dependent on vertebrate dispersers. In a heterogeneous production landscape (primarily tea and coffee plantations) in the southern Western Ghats, India, we examined effects of surrounding forest cover and fruit crop size on frugivory of four rainforest bird-dispersed tree species (N = 131 trees, ≥ 30 trees per species, observed for 623 h). Frugivore composition differed among the four tree species with the large-seeded Canarium strictum and Myristica dactyloides exclusively dependent on large-bodied avian frugivores, whereas, medium-seeded Persea macrantha and Heynea trijuga were predominantly visited by small-bodied and large-bodied avian frugivores, respectively. Using the seed-dispersal-effectiveness framework, we identified effective frugivores and examined their response to forest cover and fruit crop size. Results were idiosyncratic and governed by plant and frugivore traits. Visitations to medium-seeded Persea had a positive relationship with forest cover but the relationship was negativefor the large-seeded Myristica. In addition, two of the three effective frugivores for Persea responded to the interactive effect of forest cover and fruit crop size. Frugivore visitations to Hyenea were not related to forest cover or fruit crop and there were too few visitations to Canarium to discern any trends. These results highlight the context-specific response of plant-frugivore interactions to forest cover and fruit crop size influenced by the plant and frugivore traits.

opencc-zeroJun 2020View details →

dryad36/100

Data from: Effects of restoration on tree communities and carbon storage in rainforest fragments of the Western Ghats, India

Ecological restoration is a leading strategy for reversing biodiversity losses and enhancing terrestrial carbon sequestration in degraded tropical forests. There have been few comprehensive assessments of recovery following restoration in fragmented forest landscapes, and the efficacy of active versus passive (i.e., natural regeneration) restoration remains unclear. We examined 11 indicators of forest structure, tree diversity and composition (adult and sapling), and aboveground carbon storage in 25 pairs of actively restored (AR; 7–15 yr after weed removal and mixed-native tree species planting) and naturally regenerating (NR) plots within degraded rainforest fragments, and in 17 less-disturbed benchmark (BM) rainforest plots in the Western Ghats, India. We assessed the effects of active restoration on the 11 indicators and tested the hypothesis that active restoration effects increase with isolation from contiguous and relatively intact rainforests. Active restoration significantly increased canopy cover, adult tree and sapling density, adult and sapling species density (overall and late successional), compositional similarity to benchmarks, and aboveground carbon storage, which recovered 14–82% toward BM targets relative to NR baselines. By contrast, tree height–diameter ratios and the proportion of native saplings did not recover consistently in actively restored forests. The effects of active restoration on canopy cover, species density (adult), late successional species density (adult and sapling), and species composition, but not carbon storage, increased with isolation across the fragmented landscape. Our findings show that active restoration can promote recovery of forest structure, composition, and carbon storage within 7–15 yr of restoration in degraded tropical rainforest fragments, although the benefits of active over passive restoration across fragmented landscapes would depend on indicator type and may increase with site isolation. These findings on early stages of recovery suggest that active restoration in ubiquitous fragmented landscapes of the tropics could complement passive restoration of degraded forests in less fragmented landscapes, and protection of intact forests, as a key strategy for conserving biodiversity and mitigating climate change.

opencc-zeroSep 2020View details →

zenodo36/100

Destructive harvest data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã

Title ----- Destructive harvest data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã Authors -------  A. Burt M. Boni Vicari A. C. L. da Costa I. Coughlin P. Meir L. Rowland M. Disney Contact ------- a.burt@ucl.ac.uk License ------- These data are distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC BY 4.0) - see the LICENSE file for details. Overview -------- We harvested four large tropical rainforest trees (diameter range: 0.6-1.2m, height range: 30-46m) in a natural closed forest stand in Floresta Nacional de Caxiuanã, Pará, Brazil (approx. coordinates in the WGS-84 datum: -1.798, -51.435 degrees), during August/October 2018. The objective was to measure the green mass of each tree in its entirety, and to measure woody tissue green-to-dry mass and volume ratios, and basic/green/dry woody tissue density.  A complete description of the four trees, these data, and the companion terrestrial lidar data (collected pre-harvest) can be found in our paper entitled: ‘New insights into large tropical tree mass and structure from direct harvest and terrestrial lidar’. Acquisition ----------- Field measurements: Neighbouring vegetation surrounding each tree was removed, including complete clearing of the felling area. Stem diameter was measured using a circumference/diameter tape at either 1.3m above-ground, or 0.5m above-buttress. Each tree was felled onto tarpaulin using a STIHL MS 650 chainsaw with a 20” bar length and 13/64” chain loop. Tree height (incl. stump) was measured with a surveyor's tape measure, and GPS data were acquired from the centre of the stump using a Garmin GPSMAP 64st. The stem (incl. stump) and crown were cut into manageable sections, and the mass of each section was measured via weighing using two Adam LHS 500 crane scales. Mass measurements commenced immediately post-felling, requiring two, four, four and two days to complete measurement of CAX-H_T1 to CAX-H_T4 respectively. Multiple discs (approx. 50mm thick) were also collected from each tree: at 1.3m and 25%, 50% and 75% the length of the stem, and up to 3x discs were taken from the mid-points of 1st, 2nd and 3rd order branches (totalling a minimum of 11 discs per tree). Foliage/fruit samples were retained to confirm taxonomic identity at the Museu Paraense Emílio Goeldi, Belem, Pará, Brazil. Laboratory measurements: All discs were reduced to a set of subsamples using a consistent approach: for any particular disc, they were cut as guided by parallel chords straddling above and below the major axis, each with approximate dimensions of 150mm x 50mm x 50mm (i.e., each set included periderm, phloem, cambium, xylem and pith tissues). Mass and volume measurements were made on each subsample in a green and dry state. Subsamples were considered in a green state after soaking for 48 hours, and a dry state once a constant mass had been attained whilst drying in an oven at 105 degree Celsius. Mass was measured using an Adam NBL4602i Nimbus Precision balance, and volume measurements were made on the same balance via Archimedes’ principle. Processing ---------- Dry mass was estimated from measured green mass and an estimate of whole-tree woody tissue green-to-dry mass ratio.  Whole-tree woody tissue green-to-dry mass ratio was estimated by weighting the mean value from subsamples in each pool (stem and crown), by the green mass in each pool. This mass-weighted approach was also used for estimating whole-tree woody tissue green-to-dry volume ratio and whole-tree basic/green/dry woody tissue density.  File and directory naming convention ------------------------------------ The four trees are identified: CAX-H_T1, CAX-H_T2, CAX-H_T3 and CAX-H_T4. The various files and directories are described as follows:  ./CAXH-H/ ├───overview/ │   ├───cal_cert/                    (Directory: contains balance calibration certificates) │   ├───images/                        (Directory: various photographs illustrating the field and laboratory measurements) │   ├───sentinel-2                    (Directory: contains RGB and NDVI images from Sentinel-2 data over the harvest site during the campaign dates) │   ├───CAX-H.results.xlsx                    (File: top-level results) ├───CAX-H_T1/                        (Directory: tree-level directories) ├───CAX-H_T2/ ├───CAX-H_T3/ ├───CAX-H_T4/ │   ├───fieldsheets/ │   │   ├───CAX-H_T4.fieldsheets.pdf                (File: fieldsheets from the original campaign) │   │   ├───CAX-H_T4.remeasurement.fieldsheets.pdf        (File: fieldsheets from the remeasurement campaign) │   ├───gps/ │   │   ├───CAX-H_T4.gps.txt │   ├───media/                        (Directory: contains various photographs and videos of the field measurements, and the discs and subsamples) │   ├───CAX-H_T4.results.xlsx                    (File: tree-level results)

opencc-by-4.0Sep 2020View details →

dryad36/100

Data from: Three decades of annual growth, mortality, physical condition, and microsite for ten tropical rainforest tree species

In lowland tropical rainforest, hundreds of tree species typically occur within mesoscale landscapes (50-500 ha). There is no consensus ecological theory that accounts for the coexistence of so many species with similar morphologies and the same fundamental requirements of light, nutrients, water, and physical space. In part this is due to the limited understanding of post-establishment ecology for the vast majority of tropical tree species. Of even more concern is the lack of understanding of how these trees are responding to on-going atmospheric and climatic changes. Here we present long-term data on the post-establishment ecology of ten species of tropical rainforest trees that span a broad life-history spectrum. The study site was upland (non-swamp) old-growth tropical wet forest at the La Selva Biological Station (N.E. Costa Rica). Focal individuals from established seedlings to mature trees were assessed annually, with an emphasis on accuracy and long-term consistency of the observations. The annual time-step, rare for longterm studies in tropical rainforest, captures the typically abrupt changes in forest structure and light environments, the frequent instances of major physical damage, and the trees' responses to these events and to interannual and long-term climatic variation. With the completion of the study in 2016, the data for survivorship, growth, and microsite conditions span 4499 individuals and 34 years. The first ten years of these data were published as an Ecology/Ecological Archives data paper in 2000 (Clark and Clark 2000), with two subsequent update publications (Clark and Clark 2006, 2012). This final update adds the final six years of observations, digitized field comments, and histories of points of measurement on the trees. The metadata now include the scanned original field data-sheets for the entire study and a narrative detailing the annual qa/qc of the data. The data set is unique for its scope (years of continuous annual measurements, number of monitored individuals), the in-depth documentation, and the unrestricted data access. The data have been used to study life history patterns, tree ecology through ontogeny, and effects on tree performance from interannual and long-term climatic and atmospheric change. They have also contributed to numerous remote-sensing studies.

opencc-zeroDec 2017View details →

dryad36/100

Predictive mapping of tree species assemblages in an African montane rainforest

Conservation of mountain ecosystems can benefit from knowledge of habitats and their distribution patterns. This benefit is particularly true for diverse ecosystems with high conservation values such as the "Afromontane" rainforests. We mapped the vegetation of one such forest: the rugged Bwindi Impenetrable Forest, Uganda—a World Heritage Site known for its many restricted-range plants and animal taxa including several iconic species. Given variation in elevation, terrain and human impacts across Bwindi, we hypothesised that these factors influence the composition and distribution of tree species. To test this, detailed surveys were carried out using stratified random sampling. We established 289 georeferenced sample sites (each with 15 trees ≥20 cm dbh) ranging from 1,320 to 2,467 m a.s.l. and measured 4,335 trees comprising 89 species that occurred in four or more sample sites. These data were analysed against twenty-one digitally mapped biophysical variables using various analytical techniques including non-metric multidimensional scaling (NMDS) and random forests. We identified six tree species assemblages with distinct compositions. Among the biophysical variables, elevation had the strongest correlation with the ordination (r2=0.5; p<0.001). The "out-of-bag" (OOB) estimate of the error rate for the best final model was 50.7% meaning that nearly half of the variation was accounted for using a limited set of variables. We demonstrate that it is possible to predict the spatial pattern of such a forest based on sampling across a highly complex landscape. Such methods offer accurate mapping of composition that can guide conservation.

opencc-zeroDec 2023View details →

dryad36/100

Data from: Weak edge effects on trees in Bornean rainforest remnants bordering oil palm

Many tropical forests are dominated by edge habitat, with consequences for forest structure, carbon stocks and biodiversity. However, edge effects are highly variable and context-dependent, and are poorly quantified in oil palm landscapes. We studied edge effects in 10 lowland rainforest remnants bordering mature oil palm plantations on Borneo, by surveying 0.2 ha plots along transects running perpendicular to the forest edge (ten 1.6 km transects, 5-6 plots per transect; 57 plots in total). We examined how edge proximity affected plot-level forest structure (canopy cover, number and size of stems ⩾10 cm diameter), aboveground carbon stocks, microclimate (air temperature and light intensity), and tree community composition and richness. The largest trees were significantly smaller (up to 21% reduced diameter) in plots near edges, and plot-level carbon was up to 30% lower (model-fitted average = 64.7 Mg ha−1 at 50m from the edge, versus 92.3 Mg ha−1 at 1600 m), with the strongest effects within 300m of edges. However, these significant effects of edge proximity were relatively small in the context of existing variation, with distance-from-edge explaining <13% of the total variability in maximum tree size or carbon. Additionally, there were generally no effects of edge proximity on any other component of forest structure, composition or diversity, and only a weak effect on microclimate. We conclude that limited edge effects in this system may reflect low structural contrast between forest and mature oil palm, and limited invasion of pioneer trees from plantations, which diminished edge influence in highly heterogeneous forest remnants.

opencc-zeroMay 2022View details →

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record