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. Unfortunately, Nature does not cooperate.
Nature provides misleading and contradictory clues.
Cladistic analysis using parsimony and numerous similarities and differences. The difficult job for phylogenetic reconstruction, like that for classification, is deciding which way of choosing characters is most reliable in any particular case. Phylogenies are inferred from characters shared between species. This section introduces the idea of rooted and unrooted trees. An unrooted tree indicates relationships without specifying any direction for evolutionary change.