MALLATT, Jon M ; WINCHELL , Christopher J: Use of combined large-subunit and small-subunit ribosomal RNA sequences to classify the protostomes and deuterostomes

The small-subunit ribosomal RNA gene (SSU rRNA) is most widely used for molecular systematics, but we have added large-subunit (LSU) rRNA sequences from about forty taxa of protostome and deuterostome animals. The combined SSU and LSU sequences, when analyzed by the methods of maximum parsimony, maximum likelihood, and minimum evolution of LogDet-transformed distances, support the division of metazoan animals into protostomes and deuterostomes, and of protostomes into ecdysozoans (moulting animals) and lophotrochozoans. In deuterostomes, a grouping of hemichordates with echinoderms into Ambulacraria is supported, as is a cephalochordate-plus-vertebrate clade. However, tunicate sequences are unusual and group with those of other chordates only under certain analytical conditions (namely, spectral analysis of LogDet-transformed distances). Overall, combined LSU and SSU sequences give more-robust phylogenies than does SSU rRNA alone.