A phylogeny for 21 species of spatangoid sea urchins is constructed using data from three
genes and results compared with morphology-based phylogenies derived for the same taxa
and for a much larger sample of 88 Recent and fossil taxa. Different data sets and methods of
analysis generate different phylogenetic hypotheses, although congruence tests show that all
molecular approaches produce trees that are congruent with each other. By contrast, the trees
generated from morphological data differ significantly according to taxon sampling density
and only those with dense sampling (after a posteriori weighting) are congruent with molecular
estimates. With limited taxon sampling, secondary reversals in deep-water taxa are interpreted
as plesiomorphies, pulling them to a basal position. The addition of fossil taxa with their
unique character combinations reveals hidden homoplasy and generates a phylogeny that is
compatible with molecular estimates. As homoplasy levels were found to be broadly similar
across different anatomical structures in the echinoid test, no one suite of morphological
characters can be considered to provide more reliable phylogenetic information. Some traditional
groupings are supported, including the grouping of Loveniidae, Brissidae and Spatangidae
within the Micrasterina, but the Asterostomatidae is shown to be polyphyletic with members
scattered amongst at least five different clades. As these are mostly deep-sea taxa, this finding
implies multiple independent invasions into the deep sea.