ABSTRACT
The phylogenetic relationships among the main lineages of vertebrates (mammals, birds, reptiles, amphibians, and fishes) were analysed using nuclear 28S rDNA, and mitochondrial (combined tRNA genes and concatenated protein-coding genes) sequence data. The comparatively slowly-evolving nuclear 28S rRNA gene was able to recover a vertebrate phylogeny which is in agreement with palaeontological and morphological evidence. Cartilaginous fishes were placed basal to a clade including bony fishes and tetrapods with a high bootstrap support. Lobe-finned fishes showed an unusually high rate of evolution for the 28S rRNA gene. The mitochondrial tRNA data set showed an extensive among-site rate variation, and a limited number of sites containing phylogenetic signal, unable to resolve the short nodes on the base of the vertebrate tree. As a result, the recovered tRNA tree, although congruent with the morphology-based vertebrate phylogeny, remained largely unresolved. The phylogenetic analyses of the protein data set at the amino acid level using hagfish and lamprey as outgroups arrived at rather unorthodox topologies in which bizarre vertebrate groupings were found such as e.g. snake+hagfish, amphibians+bony fishes, teleosts+cartilaginous fishes. The biologically incorrect phylogenetic estimates were identified to be artefacts stemming from non-random misleading noise in the protein data set. The adverse phylogenetic signal/noise ratio of the protein mitochondrial data set was likely due to several causes including saturation, heterogeneous rates of evolution among different vertebrate lineages, among-site rate variation, and the selection of distant taxa as outgroups.
