phytools: findMRCA – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

findMRCA

Get the MRCA of a set of taxa

Description

This function returns node number of the most recent common ancestor of a set of taxa. If tips=NULL the function is redundant with mrca (for type="node") or vcv.phylo, but much slower (for type="height").

Usage

findMRCA(tree, tips=NULL, type=c("node","height"))

Arguments

`tree`	a phylogenetic tree as an object of class `"phylo"`.
`tips`	a vector containing a set of tip labels.
`type`	either `"node"` to return the node of the MRCA; or `"height"` to return the height above the root of the MRCA of `tips`.

Details

If tips==NULL and type="node" (the default) it will return the result of a normal function call to mrca.

If tips=NULL and type="height" it will return a matrix equal to that produced by vcv.phylo.

From phytools 0.5-66 forward findMRCA uses getMRCA in the ape package internally, which results in a big speed-up. Even though the two functions are thus totally redundant I have left findMRCA in the package to ensure backward compatibility.

Value

The node number of the MRCA, or a matrix of node numbers (if tips==NULL) - for type="node"; or the height of the MRCA, or a matrix of heights (if tips==NULL) - for type="height".

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Examples

data(anoletree)
anc<-findMRCA(anoletree,c("cristatellus","cooki",
    "gundlachi"))
plotTree(anoletree,type="fan",fsize=0.7,lwd=1)
nodelabels(node=anc,frame="circle",pch=21,cex=1.5,
    bg="blue")
legend("topleft","common ancestor of\nPuerto Rican TG anoles",
	pch=21,pt.cex=1.5,pt.bg="blue",cex=0.7,bty="n")
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margin to default

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19