clade
gets all species that are closest related to specified taxa
Contents
Syntax
[members, taxon] = clade (taxa, level, site)
Description
If taxa contains several members, clade gets all species in the add_my_pet collection that belong to the lowest common taxon of a group of taxa. To find this taxon, the lineages of all members of input taxa are obtained, then the taxon of lowest rank is found that is shared by all members of input taxa and all members of this taxon in the add_my_pet collection are selected. If a single taxon is specified, members are selected from a taxon that is a number of levels up in the classification, including the single taxon. If this single taxon is not present in AmP, it is searched in Catalog of Life and Taxonomicon, and the lowest taxon in these lineages that is present in AmP is selected as clade
Input:
- taxa: cell string with names of taxa or character string with a single name
- level: optional integer with number of nodes up, in the case of a single taxon (default: such that more than 2 members result with smallest number)
- site: 0 (default) Col only, 1 Taxonomicon only, 2 both CoL and Taxonomicon
Output:
- cell string with all species in the add_my_pet collection that belong to that taxon
- character string with the name of the lowest taxon to which all taxa belong
Remarks
The root is Animalia; If this is the lowest common taxon, the output contains all species in the collection. If the species is not in AmP, but the genus is, the AmP members of that genus are in the resulting clade, but this does not imply that the species is recognized and accepeted. The second input (i.e. level) only works for species that are in AmP. Print properties of related taxa with e.g. prtStat(clade('Lemmus_trimucronatus'), 'p_M');. Include the tree as well with e.g. [~, taxon]= clade('Lemmus_trimucronatus'); pedigree(taxon, 'p_M')
Example of use
members = clade({'Gorilla', 'Tupaia'}) or clade('Daphnia_magna') or clade('Homarus_gammarus',4) or clade('Daphnia_galeata') % while 'Daphnia_galeata' was not present in AmP at 2018/01/05