The first analyses involving Nephelornis using molecular characters were based on DNA-DNA hybridization.
The molecular characters are completely congruent with anatomical data: all specimens without a venom apparatus are in the Acus clade, and all specimens with a venom apparatus are in the Terebra clade.
However, molecular characters are capable to reveal more definite relationships.
If morphological characters are well chosen and molecular characters are informative and substantial, homoplasy should be reduced, thus resulting in similar phylogenies.
All molecular characters were treated as unordered and equally weighted, offering a contrast with the Bayesian analyses (where complex models of molecular evolution were used).
In simultaneous analysis using direct optimization, morphological and molecular characters are co-optimized at the level of sequence alignment in search of a globally optimal solution.
To reconstruct the biogeographical history of this invasive form in the western Mediterranean, variation in spatial patterns of shell, genital and molecular characters was previously estimated by investigating more than hundred of populations representative of the aspersum range (western Mediterranean and European coastlines) (Fig 1).
However, defining the complexity (or simplicity) of its molecular features (characters) is problematic, as it often depends on the levels of molecular structure analyzed (e.g., molecular sequence, motifs in sequence, structural motifs, structural domains), the rooting of the tree of life, and the methods used for ancestral character state reconstruction.
That this study represents the minimal diversity of form is evident in the taxon sampling; although this phylogeny is by far the most comprehensive available (both in terms of taxa and molecular characters), it is limited to ~40%% of the known diversity of Zoanthidea species and the true diversity is likely to be much greater (as newly discovered taxa have recently and rapidly proliferated).
The present study strongly underscores the well-known but still often neglected problem of defining groups based on overall morphological similarity (although also molecular characters have been suggested to be essentially "phenetic"; e.g. [ 36], and comments in [ 37]).
