Cirripede phylogeny using a novel approach: Molecular morphometrics

We present a new method using nucleic acid secondary structure to assess ph ylogenetic relationships among species. In this method, which we term "mole cular morphometrics," the measurable structural parameters of the molecules (geometrical features, bond energies, base composition, etc.) are used as specific characters to construct a phylogenetic tree. This method relies bo th on traditional morphological comparison and on molecular sequence compar ison. Applied to the phylogenetic analysis of Cirripedia. molecular morphom etrics supports the most recent morphological analyses arguing for the mono phyly of Cirripedia sensu stricto (Thoracica + Rhizocephala + Acrothoracica ). As a proof, a classical multiple alignment was also performed, either us ing or not using the structural information to realign the sequence segment s considered in the molecular morphometrics analysis. These methods yielded the same tree topology as the direct use of structural characters as a phy logenetic signal. By taking into account the secondary structure of nucleic acids, the new method allows investigators to use the regions in which mul tiple alignments are barely reliable because of a large number of insertion s and deletions. It thus appears to be complementary to classical primary s equence analysis in phylogenetic studies.