The Tree of Knowledge is a well-known concept, and the tree can indeed be used to arrange information. One possible use is to describe the relationships of derivative products (ie. the chemical derivatives of other substances). Indeed, these can be viewed as having a "phylogeny", since the processing follows a time sequence.
The U.S. Geological Survey (in the U.S. Department of the Interior) has provided one such example in Geological Survey Circular 1143 Coal — a Complex Natural Resource. The centerfold of that publication shows:
Coal byproducts in tree form showing basic chemicals as branches and derivative substances as twigs and leaves. [Modified from an undated public domain illustration provided by the Virginia Surface Mining and Reclamation Association.]
However, a tree is a simplification of a network, and the network can thus show more information. In this case, the same information has previously been illustrated using a reticulating network, not a tree.
In the 7th edition (1924) of Joseph Meyer's Große Conversations-lexikon für gebildete Stände (first edition 1840-1855) there is a Steintohle: Stammbaum der Steintohlenerzeugnisse [Coal: family tree of coal products]:
This has three reticulations, showing coal products produced as a result of combining two different processing routes. This is thus a hybridization network.
Thanks to the Trees of Knowledge page (by Paul Michel) of the "Encyclopedias as Indicators of Change in the Social Importance of Knowledge, Education and Information" web site, for pointing out this unexpected use of trees of knowledge.