Chordate phylogeny and evolution: a not so simple three-taxon problem

Traditional concepts of chordate phylogeny have recently been in turmoil: in a large-scale molecular study, the traditional hypothesis that cephalochordates are sister taxon to craniates was replaced by the hypothesis of a sister group relationship between tunicates and craniates. It was claimed that the morphological evidence that supported traditional phylogeny was weak and that morphological characters at least equally strong could be mustered in support of the 'new phylogeny.' In the present review, it is shown that the uncritical use of published codings of morphological characters in recent phylogenetic analyses is responsible for this perception. To ameliorate this situation, the main focus of the present publication is a review of the morphological evidence that has been deemed relevant in chordate phylogeny. Characters are presented in enough detail to allow readers to make self-reliant informed decisions on character coding. I then analyze these characters cladistically, and it is demonstrated that support of the traditional hypothesis is substantial. I briefly evaluate molecular systematic studies and criticize 'evo-devo' studies for lack of cladistic rigor in the evolutionary interpretations of their data by (1) failing to formally code their characters (2) failing to subject their data to the congruence test with other characters, the crucial test in phylogenetic analyses. Finally, a short and by necessity eclectic discussion of suggested evolutionary scenarios is presented.