TreeGhatsData: Western Ghats tree database
In frmunoz/TreeGhats: Taxonomic name resolution and phylogeny generator for Western Ghats trees

TreeGhatsData

R Documentation

Western Ghats tree database

Description

A comprehensive database Western Ghats (WG) tree taxa with up-to-date taxonomic reference. It contains taxon names that have been commonly used in forest ecology research on Western Ghats. It also considers infrataxon level. The database is dynamic and will be updated.

Usage

data("TreeGhatsData")

Details

The database is a compilation of different taxa lists : taxa for which the word "tree" appears in habit/growth form in the Flowering plants of the Western Ghats, book edited by the Tropical Botanic Garden Research Institute (TBGRI), including planted or cultivated taxa and in the Indian Biodiversity Portail (http://indiabiodiversity.org/); taxa described after 2014; taxon names used in studies done in different parts of the Western Ghats by the French institut of Pondicherry (IFP) or from 2000 with published lists of taxa. As most of studies did not distinguish the infraspecific level, for each infra species (sub-species, variety or form), we automatically add the species level as an entry in our taxonomic database. The database includes also basic ecological and biogeographical informormation and the conservation status according to IUCN. The version of the database available in TreeGhats package has been published on Zenodo on August 21st (https://zenodo.org/record/846291).

Value

A data frame including the following information:

`Name`	Taxon names without authority.
`Spelling_variants`	Other spelling found for taxon names.
`Family_TBGRI`	Family names according to the Tropical Botanic Garden Research Institute (TBGRI).
`Family_APGIII`	Family names according to APGIII.
`Genus`	Genus of taxon names.
`Species`	Specific epithet of taxon names.
`InfraTaxonRank`	Intraspecific rank of taxon names, either 'f.', 'subsp.', 'var.' or `NA`.
`InfraTaxonName`	Intraspecific epithet of taxon names.
`Authority_InitialDatabases`	Names of the author(s) who first published the taxon name presented in the reference lists to build TreeGhatsData.
`Authority_TPL`	Names of the author(s) who first published the taxon name, according to TPL. 'Absent' indicates taxon names not found in TPL.
`Authority_IPNI`	Names of the author(s) who first published the taxon name, according to IPNI. 'Absent' indicates taxon names not found in IPNI.
`Full_name`	Taxon names with authority.
`ID_Tropicos`	Tropicos record 'id'. 'Absent' indicates taxon names not found in Tropicos.
`ID_TPL`	The Plant List record 'id'. 'Absent' indicates taxon names not found in TPL.
`Status_TPL`	Taxonomic status found in TPL, either 'Absent', 'Accepted', 'Synonym' or 'Unresolved' (see http://www.theplantlist.org/1.1/about/#status). 'Absent' indicates taxon names not found in TPL.
`ReferenceName_TPL`	Reference taxon names, extracted from TPL. The field is filled with `NA` when taxon names are absent in TPL.
`ReferenceAuthority_TPL`	Names of the author(s) who first published the TPL reference taxon names. The field is filled with `NA` when taxon names are absent in TPL.
`Status_TBGRI`	Taxonomic status according to TBGRI, either 'Absent', 'Accepted' or 'Synonym'. 'Absent' designs names not found in TBGRI.
`ReferenceName_TBGRI`	Taxa names, according to TBGRI. The field is filled with `NA` when the name is absent in TBGRI.
`ReferenceAuthorithy_TBGRI`	Names of the author(s) who first published the TBGRI reference taxon names. The field is filled with `NA` when the name is absent in TBGRI.
`Status_proposed`	Taxonomic status proposed, either 'Accepted', 'Synonym' or 'Unresolved'.
`ReferenceName_proposed`	Reference names proposed.
`ReferenceAuthorithy_proposed`	Names of the author(s) who first published the reference names proposed.
`Origin`	Biogeographic origin according to TBGRI or IFP expertise, either 'exotic', 'endemic India', 'endemic WG' for endemic of Western Ghats, or 'native' for taxon with broader distribution than India.
`Habit`	Habit according to TBGRI or IFP expertise, either 'climbing shrub', 'liana', 'shrub', 'straggling shrub', 'straggling tree', 'tree', 'twining shrub', 'unknown' or any combination of these terms.
`Phenology`	Leaf phenology of plants according to IFP expertise, either 'evergreen' or 'deciduous'. The field is filled with `NA` when the leaf phenology is unknown.
`IUCN`	IUCN status of plants, either 'CR', 'DD', 'EN', 'EX', 'LC', 'LR/cd', 'LR/lc', 'LR/nt', 'NE', 'VU'. `NA` correspond to the non evaluated taxa.

Note

The database is not exhaustive but will be updated and completed regularly. The priority has been to include the most commonly used taxon names, so the database does not content all the known synonyms for a taxon. The attribution of 'tree' as a growth form to a taxon depends on the criteria used in the study and/or on the environmental conditions of the study area. It can explain missing taxa in the database and the inclusion of some shrubs or lianas according to TBGRI flora, as they have been reported in forest plots with a GBH larger than 10 cm.

Author(s)

V. Raevel & F. Munoz

Source

Nayar, T., Rasiya Beegam, A. & Sibi, M. 2015. Flowering plants of the Western Ghats, India, Volume 1 Dicots; Volume 2 Monocots. Jawaharlal Nehru Tropical Botanic Garden and Research Insitute.

Ramesh, B.R., and Jean-Pierre Pascal. 1997. Atlas of Endemics of the Western Ghats (India): Distribution of Tree Species in the Evergreen and Semi-Evergreen Forests. French Institute of Pondicherry.

The International taxon names Index. http://www.ipni.org.

Tropicos.org. Missouri Botanical Garden. http://www.tropicos.org.

India biodiversity Portal. http://indiabiodiversity.org/

The Plant List. http://www.theplantlist.org/

References

Raevel, V., Ayyappan, N., Balachandran, N., Aravajy, S., Barathan, N., Ramesh, B. R. & Munoz, F. (2017) Taxonomic and ecological database of trees of Western Ghats - TreeGhatsData (ed Zenodo), https://zenodo.org/record/846291