Cladistic analyses of molecular characters: The good, the bad and the ugly

Molecular cladistics is an emerging discipline in which any heritable molecular characteristic can be treated in the same way that a traditional cladist would treat a morphological character. Taxa that share specific derived molecular characters (synapomorphies) are recognized as more closely related to each other than they are to other taxa without these characters. Herein, I point out that molecular characters are susceptible to the same problems of homoplasy and uncertain polarity as morphological characters and illustrate these problems (and point towards a general solution) using examples from the Metazoa.