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