Extracting and working with subtrees using ape can be executed using the following steps:

1. Load the ape library and then load the tree:

library(ape)
newick <-read.tree(file.path(getwd(), "datasets", "ch4", "mammal_tree.nwk"))

2. Get a list of all of the subtrees:

l <- subtrees(newick)
plot(newick)
plot(l[[4]], sub = "Node 4")

3. Extract a specific subtree:

small_tree <- extract.clade(newick, 9)

4. Combine two trees:

new_tree <- bind.tree(newick, small_tree, 3)
plot(new_tree)