A well-supported phylogeny of echinoderm classes has eluded morphological,
embryological, molecular, and combined analyses. From this body of work it
is apparent that (i) echinoids (sea urchins) and holothuroids (sea cucumber
s) are related, and (ii) crinoids (sea lilies) are the sister taxon to exta
nt eleutherozoan classes (asteroids, ophiuroids, echinoids, and holothuroid
s). However, the relationships of asteroids and ophiuroids to other echinod
erm classes have been difficult to recover. To address relationships betwee
n the asteroids and ophiuroids and other echinoderms, I have sequenced addi
tional nuclear loci and taxa and used novel computational approaches for co
-optimizing morphological with molecular evidence at the level of sequence
alignment. Support for the monophyly of each class is strong. Support for a
monophyletic Asteroidea + Xyloplax is as strong as for Asteroidea. Support
for Asterozoa (Asteroidea + Ophiuroidea) is apparent, albeit not as strong
as for other clades (e.g., Echinozoa, Eleutherozoa, and Echinodermata). I
also present detailed sensitivity analyses to provide (i) a test of the mon
ophyly of groups under a variety of evolutionary models and (ii) a statemen
t of the evidential value of various character systems.