Ruben E. Valas and Philip E Bourne (2010. Save the tree of life or get lost in the woods. Biology Direct 5: 44) have an interesting discussion of the relationship between the Tree of Life and the Web of Life. They argue that:
Function follows more of a tree-like structure than genetic material, even in the presence of horizontal transfer ... We propose a duality where we must consider variation of genetic material in terms of networks and selection of cellular function in terms of trees. Otherwise one gets lost in the woods of neutral evolution.
As an aside, they also note:
We must keep in mind the humor of calling the central metaphor for evolution "the tree of life". The phrase first appears in Genesis 2:9 ... There is irony in using the name of a tree central to the creation story to argue against that very myth.
There is clearly a duality in Darwin's theory of descent with modification: the history of variation is well described by a network and the history of selection is well described by a tree.