classifications: Classifications of species
In daijiang/rtrees: Deriving Phylogenies from Synthesis Trees

classifications

R Documentation

Classifications of species

Description

Genus and family information of different groups of taxon.

Plant classification information. Its sources include: + based on V.PhyloMaker::nodes.info.1 + based on The Plant List + taxonlookup + Plants of the World online
Fish classification information was based on FishBase. There are 4,825 genus in this file. https://fishtreeoflife.org/downloads/PFC_taxonomy.csv.xz
Bee classification information was from Bee Tree of Life. Note that we used 'Subfamily' in their nomenclature file as "family" here. If a genus' Subfamily is missing, we used its Family.
Bird classification information was based on BirdLife, which resulted in 2,391 genus. http://datazone.birdlife.org/species/taxonomy However, based on the taxonomy file of the Jetz et al. 2012 phylogeny, there are additional 117 genus that are not in the file of BirdLife. Both are combined here, which leads to 2,508 genus.
Mammal classification information was based on PHYLACINE, which has 1,400 genus. https://github.com/MegaPast2Future/PHYLACINE_1.2/blob/master/Data/Taxonomy/Synonymy_table_valid_species_only.csv Additional genus from Vertlife were added too. For the same genus from both PHYLACINE and Vertlife that have different family information, I used the family from Vertlife as I found that they are mostly more accurate.
Amphibian classification information was from VertLife.
Reptile classification information was largely from wikipedia.
Shark and Ray classification information was largely from NCBI.
Butterfly classification information was from Kawahara et al. 2023, using the tip labels of their phylogeny.

Usage

classifications

Format

A data frame with three columns: genus, family, and taxon (plant, fish, bird, mammal, amphibian, reptile, shark_ray, bee, butterfly).