[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

-- 
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
http://www.mpi.nl/research/research-projects/evolutionary-processes



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