Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships

► Phylogenetic signal dissection is a powerful tool for addressing rapid radiations in deep geologic time. ► Divergence of asteroids, echinoids and ophiuroids occurred rapidly in deep time. ► miRNA genes are phylogenetically uninformative. ► Standard phylogenetic analysis gives misleading results. ► Echinoids and ophiuroids are sister taxa with respect to asteroids.