Conditionally neutral phylogenetic markers of major taxa: a new aspect of the evolution of macromolecules

摘要

The current phase of molecular phylogenetics can be named as the 18S rRNA gene era which is now approaching its end. To date, almost all phyla of metazoans and many taxa of protists are represented in databases of 18S rRNA gene sequences. The element of the phylogenetic tree of Metazoa from the 18S rRNA genes are characterized by unequal validity: some are well grounded; others are not adequately supported and probably will be revised later. Validity of phylogenetic reconstruction is influenced bytwo main factors: (1) erroneous grouping of long branches that occur because of abnormally high evolution rate; and (2) deficit of phylogenetically informative characters. A method for overcoming these difficulties is suggested in addition to known toolsusing phylogenetic markers that are stable within individual taxa and evolve by punctuated equilibrium. These markers are least influenced by the convergence caused by a high evolution rate of the entire gene. The nature of ancient taxa markers, paradoxical from the perspective of neutral evolution, is discussed as well as its importance for establishing monophyly of both new large-scale taxonomic groups of invertebrates (Bilateria+Rhombozoa+Orthonectida+Myxozoa+Cnidaria+Placozoa and Echinodermata+Hemichordata) and some major taxa of Nematoda.