Other data for computing trees. Molecular sequences and distance statistics. Molecular vs. paleontological evidence. 510 index page Introduction to Chapter 17. The basic logic of phylogenetic reconstruction is quite straightforward.
Nature provides species.
These species have a phylogenic history, but that history cannot be observed directly. There is only one true phylogeny. Inheritance from common ancestry produces similarity. Evolutionary divergence produces differences. We arrange the species according to similarities and differences.