300 Foxes and a Donkey's Jawbone
Despite the rigorous application of philosophical ploys to guard against circular reasoning in cladistic analysis it's a poster boy for circular reasoning because it's based in a paradigm which is the result of personal bias.
In 1991 we (me and the Holy Spirit) scared the faculty at Duke by demonstrating a flaw in the use of cladistic phylogenetic analysis to study the Devonian fossil Archaeopteris.
Evolution, naturally, goes back to Sir Charles Darwin and his infamous book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.