Evolution and development at the origin of a phylum

Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible enabling continued evolutionary innovation throughout the clades’ history.

Methods
We constructed a novel character matrix comprising 413 characters incorporating the range of morphologies in early Paleozoic echinoderms . This character suite was constructed hierarchically and attempted to avoid overt phylogenetic signal by including autapomorphies and obviously homoplastic characters. This character suite was used to code 366 early Paleozoic echinoderm genera, including a nearly comprehensive sampling of Cambrian and Ordovician echinoderms along with representatives from groups in which definitive articulated body fossils are first recorded from the middle Paleozoic (Dataset S1).

In addition, this dataset was recoded based on an alternative interpretation of homoalozoan morphology (Dataset S2). 

Scripts are included for reconstructing ancestral character states and constructing a theorectical morphospace.