Abstract
Evolutionary models of molecular structures must incorporate molecular information at different levels of structural complexity and must be phrased within a phylogenetic perspective. In this regard, phylogenetic trees of substructures that are reconstructed from molecular features that contribute to order and thermodynamic stability show that a gradual model of evolution of 5S rRNA structure is more parsimonious than models that invoke large segmental duplications of the molecule. The search for trees of substructures that are most parsimonious, by their very nature, defines an objective strategy to select models of molecular change that best fit structural data. When combined with additional data, such as the age of protein domains that interact with RNA substructures, these trees can be used to falsify unlikely hypotheses.
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