DOI: 10.5281/zenodo.10077040
title: Tree and habitat structure data from rainforest fragments and coffee plantations in the Anamalai Hills, Western Ghats, India

description: 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 #11. Name: T. R. Shankar Raman2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India3. Work Phone: +91 821 25156014. Email address: trsr@ncf-india.org5. ORCID: https://orcid.org/0000-0002-1347-3953
CONTACT #21. Name: Divya Mudappa2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India3. Work Phone: +91 821 25156014. Email address: divya@ncf-india.org5. ORCID: https://orcid.org/0000-0001-9708-4826
CONTACT #31. Name: Hari Sridhar2. 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, India3. Work Phone: +91 821 25156014. Email address: harisridhar1982@gmail.com5. ORCID: https://orcid.org/0000-0003-3286-0120
CONTACT #41. Name:  Akshay Surendra2. 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 104583. Work Phone: +91 821 25156014. Email address: akshaysurendra1@gmail.com5. 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 INCLUDEDBesides 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 sitesverbatimLocality: Name of locality as originally usedFragment: Name of rainforest fragment or coffee plantationdecimalLongitude: 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 plantationDescription: Description of the place 
02) allpcqdata.csv -- Tree data from point-centred quarter (PCQ) surveysYear: Year of survey for  bird and vegetation studyverbatimLocality: Name of locality as originally usedFragment: Name of rainforest fragment or coffee plantationPoint_name: Name ID of point-centred quarter (PCQ) point as used within a survey yearpointID: Unique ID of point-centred quarter (PCQ) point including year of surveyTree_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 identifiedscientificName: Scientific name as currently identified under updated taxonomynativeAlien: Category indicating whether species is native or alien to the region/countrykingdom: Taxonomic Kingdomphylum: Taxonomic PhylumDistance_eff: Distance in metres from centre of PCQ plot to centre of tree trunkGirth_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 individualslocationRemarks: Code for site name as originally usedSpCode: Species code as originally used during data entryTreeHeight: Tree height in metres (only  available in 2019 survey)identificationRemarks: Notes related to identification if availableoccurrenceRemarks: 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 pointspointID: Unique ID of point-centred quarter (PCQ) point including year of surveynote: Site name codedecimalLatitude: 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 variablesYear: Year of survey for  bird and vegetation studyverbatimLocality: Name of locality as originally usedFragment: Name of rainforest fragment or coffee plantationPoint: ID of replicate survey point within the Fragment0-1m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 0-1 m above ground1-2m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 1-2 m above ground2-4m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 2-4 m above ground4-8m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 4-8 m above ground8-16m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 8-16 m above ground16-24m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 16-24 m above ground24-32m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band 24-32 m above groundover32m: Presence (1) or absence (0) of foliage within 0.5 m of point in the vertical band greater than 32 m above groundVertStrata: Number of vertical strata with foliage (sum of preceding 8 columns)CanopyHeight: Canopy height in metresCanopyOpenness: Canopy openness in percentage as measured using a spherical densiometerCanopyCover: Canopy cover (closure) in percentage as measured using a spherical densiometerCanopyOverlap: Canopy overlap rank: 0-open sky above; 1-branches above barely touching; 2-overlapping branches above, sky visible; 3-overlapping branches, sky not visibleUC: Canopy overlap rank as above, for understorey vegetation onlyMC: Canopy overlap rank as above, for the midstorey onlyCC: Canopy overlap rank as above, for the upper canopy onlyAltitude: Altitude above sea leavel in metres, measued from hand-held altimeter or GPS deviceRfShrub: Number of shrubs (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of pointCoffee: Number of coffee bushes (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of pointMaesopsis: Number of alien Maesopsis eminii stems (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of pointStrobilanthes: Number of Strobilanthes shrubs (woody stems at least 1 m in height, GBH < 30 cm) within 2 m radius of pointTotalShrub: Total number of shrubs within 2 m radius of pointLiana: Presence (1) or absence (0) of woody lianas within 5 m radius of pointCane: Presence (1) or absence (0) of cane (Calamus sp.) within 2 m radius of pointLantana: Presence (1) or absence (0) of Lantana camara shrubs within 2 m radius of pointBamboo: Presence (1) or absence (0) of bamboo culms within 2 m radius of pointLeafLitter: Depth of leaf litter in cm (to 0.5 cm accuracy) measured using a calibrated wooden probeCutTrees: Number of cut trees within 5 m radius of point 
05) gbifnames.csv -- Results of GBIF name matching toolsno: Serial numberverbatimScientificName: Scientific name of tree species as originally written or identifiedscientificName: Scientific name after matching with Global Biodiversity Information Facility (GBIF) database to lowest taxonomic levelsciNameWithAuthor: Scientific name with author as provided by GBIF name matching toolkey: GBIF key as provided by GBIF name matching toolmatchType: Type of match as provided by GBIF name matching toolconfidence: Confidence as provided by GBIF name matching toolstatus: Status as accepted name or synonym as provided by GBIF name matching toolrank: Taxonomic rank as provided by GBIF name matching toolkingdom: Kingdom as provided by GBIF name matching toolphylum: Phylum as provided by GBIF name matching toolclass: Class as provided by GBIF name matching toolorder: Order as provided by GBIF name matching toolfamily: Family as provided by GBIF name matching toolgenus: Genus as provided by GBIF name matching toolspecies: Species as provided by GBIF name matching toolcanonicalName: Canonical name as provided by GBIF name matching toolauthorship: Author of name as provided by GBIF name matching tool 
06) plots2000.csv -- Data from 5 m radius circular plots in select sitesverbatimLocality: Name of locality as originally usedFragment: Name of rainforest fragment or coffee plantationPlotID: ID of 5 m radius plotTreeno: Serial number of tree in the plotverbatimIdentification: Scientific name of tree species as originally written or identifiedscientificName: Scientific name as currently identified under updated taxonomyGirth_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 individualsnativeAlien: Category indicating whether species is native or alien to the region/countrykingdom: Kingdom as provided by GBIF name matching toolphylum: Phylum as provided by GBIF name matching tooloccurrenceRemarks: 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