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.

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Keywords molecular synapomorphy, phylogeny, rare genomic change, RGC, Metazoa, cladistics
Journal Contributions to Zoology
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Released under the CC-BY 4.0 ("Attribution") License

Citation
Telford, M. J. (2002). Cladistic analyses of molecular characters: The good, the bad and the ugly. Contributions to Zoology, 71(1/3), 93–100.