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.
Students showed significant improvements in three skill-based items: inferring ancestral traits when provided with information about the traits of extant taxa (Q.6), mapping character state changes while constructing trees (Q.7c), and aligning extant taxa at branch tips while constructing trees (Q.7d; Table 3 and Figure 3).
In the third and fourth exercises, students learned two different techniques to construct phylogenetic trees by hand ("base-to-tips" and "tips-to-base"), using the information contained in character-by-taxon matrices and extant outgroups as reference taxa.
River dolphin paraphyly/polyphyly implies several possible evolutionary explanations for morphological characters shared by extant river dolphins and Pontoporia: 1) the characters are convergent, 2) the similarities are symplesiomorphic, 3) similarities are due to reversals, or 4) various combinations of these effects.
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).
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.
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.
