Pruning Phylogenetic Trees and Bootstrap Values

Question

[Zeng Hao]

Hi everyone,

I am pruning a phylogenetic tree (gene tree) to create a simplified figure with a smaller number of taxa represented. This process will involve collapsing and deleting numerous nodes (both terminal and internal). As a result, my pruned tree contain branches with multiple bootstrap values corresponding to those internal nodes that have been deleted.

Question: Should I show only the bootstrap value at the terminal end (leading to the taxon) and can I ignore bootstrap values belonging to internal nodes (that no longer exist as the other taxa are already pruned)?

Alternatively, should I just create a separate phylogenetic tree using this smaller, more representative set of taxa? I am only worried that this method might lead to sampling issues which can affect the bootstrap values.

For reference I am using iTOL for pruning and my trees are constructed by maximum likelihood.

Answer 1

[Klaus S]

Dear Zeng,

you have to also prune the bootstrap trees and and reassign the bootstrap values to your small tree given the now smaller bootstrap trees.

Kind regards,

Klaus

[Zeng Hao]

Dear Klaus,

Thank you for the reply. If I could clarify with an example: With this tree,

B0----------------- A
-|    B1----------- B
  ---- |    B2----- C
        -----|
              ----- D

And I want to prune it such that only taxa A and C are kept, I would represent the pruned tree with bootstraps B0 and B2, while omitting B1?

Thank you again for your help.

Best,

ZH

[Klaus S]

The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values might be higher than in the original tree afterwards. In R (with packages ape & phangorn) the code could look like:

library(phangorn)
tree <- drop.tip(tree, c("B", "C"))
tree$node.label <- NULL # delete node labels
bs_trees <-  drop.tip(bs_trees, c("B", "C"))
tree <- plotBS(tree, bs_trees) # assign nodelabels and plot the tree
write.tree(tree)