[R-sig-phylo] adding a new taxa to an existing clade in a tree set

Annemarie Verkerk annemarie.verkerk at mpi.nl
Thu Feb 16 03:57:37 CET 2012

Hi all,

I have a question regarding the manual addition of a leaf to an existing 
clade in a set of trees. The reason I ask is because I want to test the 
influence of adding ancestral data to an ancestral state estimation. I 
have some ancestral data on the feature I want to investigate, and I 
know from other sources where the leaf is situated on the trees, but I 
don't have any data that I can use to actually build new trees which 
also incorporate this leaf at the moment. So I'm hoping to add it 
manually and see whether it makes a difference.

I know it is possible to add a leaf to any of the external edges (I 
mean, edges leading to the leaves) of a tree using bind.tree() in ape. 
However, if I wanted to add a leaf to a lower position in the tree, say 
on an branch that splits and leads to two other leaves, it becomes 
difficult: not all the trees in the sample might feature the grouping of 
those two leaves, and even if they do, the relevant edge to which I 
would want to add the new leaf will have a different number in each tree.

So I guess I have two questions:
1. Is there an easy way to select the trees that have a certain clade, 
so I can try to add a new leaf to only those trees? (I suspect a lot of 
error messages if I try to do it for the complete tree sample, as there 
will be trees that do not have the relevant clade.)
2. Is there a way (for those trees that have the clade I want to add the 
new leaf to) to define the relevant edge using only the leaf numbers and 
not the internal nodes/edge numbers? I.e., I want to add the leaf to the 
internal edge that leads to the leaves with number 5, 6, and 7, for 
instance, is there a way identify that internal edge?

Many thanks for any suggestions,

Annemarie Verkerk, MA
Evolutionary Processes in Language and Culture (PhD student)
Max Planck Institute for Psycholinguistics
P.O. Box 310, 6500AH Nijmegen, The Netherlands
+31 (0)24 3521 185

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