Mitogenomic analyses of deep gnathostome divergences: a fish is a fish.

It is commonly accepted that among recent fishes the lungfishes are the closest relatives of the tetrapods. According to this hypothesis, the tetrapods, lungfishes and coelacanths constitute a group of specialized fishes (Sarcopterygii) to the exclusion of other bony fishes. Here, we describe basal relationships among gnathostome (jawed) vertebrates as reconstructed by analysis of complete mitochondrial DNA sequences. The study includes all major extant groups of both tetrapods and fishes and uses agnathan (jawless) vertebrates as an outgroup to root the trees. The analyses split extant gnathostomes into two monophyletic groups: tetrapods and fishes (including cartilaginous fishes). Cladistia (bichirs, ropefish) is in a basal position on the piscine branch. Thus, contrary to the traditional view, the mitogenomic results suggest that among living gnathostomes a tetrapod is a tetrapod and a fish, a fish. Similarly, analyses of 18S and 28S rRNA genes (both nuclear) do not support the commonly accepted tree.