Collapse monophyletic groups in a phylogenetic tree — collapse

Identifies groups of symbiont tips that are monophyletic (all descended from the same host) and reduces each such group to a single representative tip. Used during codiversification analysis to remove within-host variation and focus on between-host branching patterns.

Usage

collapse_monophyletic(symbiont_subtree, Host_to_Symbiont_df)

Arguments

symbiont_subtree: A phylo object representing a subtree of the symbiont phylogeny
Host_to_Symbiont_df: A data frame with "Host" and "Symbiont" columns linking symbionts to their source hosts

Value

A phylo object in which every monophyletic group of tips from a single host has been reduced to one representative tip. Tips from a host that do not form a single monophyletic group (polyphyly) are kept, one per monophyletic group. When a group carries branch lengths the tip furthest from the group's root is kept; otherwise the first tip is kept.

Details

Collapsing does not depend on branch lengths. A monophyletic group of tips from one host is reduced to a single tip whether its members sit on long branches, on branches of equal length, on zero-length branches (identical sequences), or on a tree with no branch lengths at all.

Examples

host_tree <- ape::rtree(5)
symbiont_tree <- ape::rtree(30)
hs_df <- data.frame(
  Host = rep(host_tree$tip.label, 6),
  Symbiont = symbiont_tree$tip.label
)
collapsed <- collapse_monophyletic(symbiont_tree, hs_df)