Patterns of evolutionary change in the marginal musculature were assessed by mapping extant character states onto the composite phylogeny of Zoanthidea, followed by phylogenetic analysis with Mesquite 2.75 [ 50] and MorphoJ 1.06c [ 51].
The tree was used to trace and visualize extant and ancestral character states of TAP gene family evolution in Plantae.
The molecular dataset (60,851 characters; 29 extant taxa) was merged with the morphology dataset (304 characters; 29 extant taxa and 45 extinct taxa) into a single, concatenated supermatrix.
3) Only molecular, behavioral, and "soft anatomical" characters for extant taxa; this run shows the pattern supported by information that generally can only be coded from extant taxa.
Additionally, students have difficulty inferring the characters of extant species given evolutionary transitions marked on a tree (Fig. 2) both before and after the exercises (Perry et al. 2008).
In addition, classical developmental and morphological characters in extant taxa (such as the fate of the blastopore, cleavage patterns, mesoderm and coelomic cavities) are by no means easy to recognize (or simply unavailable) in many fossils, including the material under consideration here.
However, it is plausible that ephippial characters from extant subgenera are non-diagnostic in Mesozoic taxa.
This is the simplest possible explanation for the extant distribution of the characters if no assumptions are made with regards to the branching order of that tree.
Taxonomic descriptions and systematic classifications were exclusively based on morphological (anatomical and conchological) characters while extant species show a mosaic pattern of plesiomorphic and apomorphic features resulting from convergent evolution [ 6, 7, 9, 10].
Most gnetalean fossils are ephedroid, but none of them possesses defining characters of extant Ephedra and most of them have been assigned to various species of the extinct genus Liaoxia.
Unweighted parsimony applied to all DNA sequences and insertion-deletion (indel) characters of extant taxa alone support a placental root at murid rodents; combined with morphology this shifts to Afrotheria.
