18S RIBOSOMAL-RNA ALIGNMENTS DERIVED FROM DIFFERENT SECONDARY STRUCTURE MODELS CAN PRODUCE ALTERNATIVE PHYLOGENIES

Molecular sequence data are often aligned on the basis of secondary an d/or tertiary structure models. However, these models are regularly up dated and sometimes differ depending on the way in which they were con structed. We examined whether the choice of a particular 18S rRNA seco ndary structure model as alignment basis influences phylogeny inferenc e. We therefore compared 188 rRNA phylogenies derived from alignments based on different;models. We used: 1. Maximum parsimony; 2. The neigh bour-joining method; 3. The maximum-likelihood approach; and 4. Evolut ionary parsimony. This demonstrated that the secondary structure model on which an alignment is based may influence: 1. The tree topologies found by these four methods; 2. The numbers of most parsimonious trees found; and 3. The statistical values calculated by the evolutionary p arsimony method.