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

TITLE Tree and habitat structure data from rainforest fragments and coffee plantations in the Anamalai Hills, Western Ghats, India DESCRIPTION This 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). Publications Specific portions of the dataset have been used in the following publications: Mudappa, D. 2001. Ecology of the brown palm civet Paradoxurus jerdoni in the tropical rainforests of the Western Ghats, India. Ph. D. thesis, Bharathiar University, Coimbatore. https://hdl.handle.net/10603/101890 Raman, T. R. S. 2001. Community ecology and conservation of mid-elevation tropical rainforest bird communities in the southern Western Ghats, India. PhD thesis, Indian Institute of Science, Bangalore. https://archive.org/details/raman-2001-ph-d-thesis-iisc Raman, T.R.S. 2006. Effects of Habitat Structure and Adjacent Habitats on Birds in Tropical Rainforest Fragments and Shaded Plantations in the Western Ghats, India. Biodiversity and Conservation 15: 1577–1607. https://doi.org/10.1007/s10531-005-2352-5 Sridhar, H., & Sankar, K. 2008. Effects of habitat degradation on mixed-species bird flocks in Indian rain forests. Journal of Tropical Ecology 24: 135-147. https://doi.org/10.1017/S0266467408004823 Surendra, A. & Raman, T. R. S. 2022. Forest bird decline and community change over 19 years in long-isolated South Asian tropical rainforest fragments. Preprint. BioRxiv 2022.10.22.513365. https://doi.org/10.1101/2022.10.22.513365 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 corrections Data 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. Acknowledgements We 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: [phone]. Email address: [e-mail] 5. ORCID: https://orcid.org/0000-0002-1347-3953 CONTACT #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: [phone]. Email address: [e-mail] 5. ORCID: https://orcid.org/0000-0001-9708-4826 CONTACT #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: [phone]. Email address: [e-mail] 5. ORCID: https://orcid.org/0000-0003-3286-0120 CONTACT #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: [phone]. Email address: [e-mail] 5. ORCID: https://orcid.org/0000-0003-2719-7432 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: 2000-01-01 (Year, Month, Day) 2. Ends: 2019-12-31 (Year, Month, Day) METHODS Methods 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 2 In sites.csv, changed habitat from "Rainforest" to "Tropical rainforest fragment" for Puthuthottam Added the anampcqs4gbif.rmd file with R code