Morphological (and not anatomical or reproductive) features define early vascular plant phylogenetic relationships.

Premise: Perhaps the most rapid period of vascular plant evolution occurred during the Silurian-Devonian time interval. Yet, few quantitative analyses have established the extent to which anatomical, morphological, or reproductive features contributed to this episode of tracheophyte diversification.

Methods: Phylogenetic analyses were performed using a newly revised matrix of 54 characters (with 158 character states) of 37 of the best-preserved Paleozoic (predominantly Devonian) plants. Equisetum was included to determine whether it aligns with fossil sphenopsids or taxa collectively considered "ferns". The topology of the 54-character consensus tree was then compared to the topologies generated using only reproductive features (18 characters; 47 character states), only anatomical features (14 characters; 54 character states), only morphological features (22 characters; 57 character states), and the three pairwise combinations (e.g., anatomical and morphological characters).

Results: The new 54-character tree topology continued to identify a trimerophyte-euphyllophyte clade and a zosterophyllophyte-lycophyte clade emerging from a Cooksonia-rhyniophyte plexus. Equisetum aligned with fossil sphenopsids rather than fern-like fossil taxa. Reproductive characters or anatomical characters analyzed in isolation resulted in nearly complete polytomy. Among the various permutations of the three categories, anatomical and morphological characters when combined provided the best restoration of the 54-character tree topology.

Conclusions: The phylogenetic relationships among the canonical fossil taxa used in this analysis predominantly reflect morphological trends. Reproductive and anatomical features taken in isolation appear to be evolutionarily conservative characters, i.e., natural selection "sees" the external phenotype.