findMRCA | R Documentation |
Finds the most recent common ancestor (MRCA) of a set of tips.
findMRCA(tree, tips=NULL, type=c("node","height"))
tree |
a phylogenetic tree as an object of class |
tips |
a vector containing a set of tip labels. |
type |
either |
This function returns node number of the most recent common ancestor of a set of taxa.
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 namespace to ensure backward compatibility.
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"
.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
findMRCA
, mrca
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","most recent common ancestor\nof Puerto 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
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