Eutherian phylogeny as inferred from mitochondrial DNA sequence data.

The phylogenetic relationships among Primates, Artiodactyla, Cetacea, Carnivora, and Rodentia were estimated from the amino acid sequences of proteins encoded by the mitochondrial genomes, for which entire nucleotide sequence data are available, using Marsupialia, Aves, and Amphibia as outgroups. The overall evidence of the maximum likelihood, as well as maximum parsimony, analyses strongly suggests that Rodentia is an outgroup to the other four eutherian orders, and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon, consistently with the molecular phylogenetic studies of previous authors. However, analyses of individual proteins do not necessarily conform to this conclusion, and some of the proteins reject the putatively correct tree with nearly 5% significance. Furthermore, the 12S mitochondrial ribosomal RNA sequences do not give the putatively correct tree irrespective of the alignments and of the phylogenetic methods, although the tree is not rejected with a statistical significance. The 16S ribosomal RNA sequences give the putatively correct tree with our sequence alignment when the ML method is used, but the result depends on the alignment and on the choice of outgroup species. These results illustrate the limitation of the ribosomal RNA data alone in phylogenetic inference, and suggest that we must analyze as many genes as possible and synthesize the results to draw a reliable conclusion.