Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes.

It is commonly acknowledged that cartilaginous fishes, Chondrichthyes, have a basal position among the Gnathostomata (jawed vertebrates). In order to explore this relationship we have sequenced the complete mitochondrial genome of the spiny dogfish, Squalus acanthias, and included it in a phylogenetic analysis together with a number of bony fishes and amniotes. The phylogenetic reconstructions placed the dogfish among the bony fishes. Thus, and contrary to the common view, the analyses have shown that the position of the sharks is not basal among the gnathostomes. The presently recognized phylogenetic position of the dogfish was identified irrespective of the outgroup used, echinoderms or agnathan fishes. The lungfish was the most basal gnathostome fish, while the teleosteans had an apical position in the piscine tree. A basal position of the dogfish among the gnathostomes was statistically rejected, but the phylogenetic relationship among the coelacanth, spiny dogfish, and teleosts was not conclusively resolved. The findings challenge the current theory that sharks and other chondrichthyans, if monophyletic, are the sister group to all other extant gnathostomes. The results open to question the status of several morphological characters commonly used in piscine phylogenetic reconstruction, most notably the presence versus absence of endochondral bone in the endoskeleton, the macromeric versus micromeric structure of the exoskeleton, and the presence/absence of swimbladder and/or lung. The study also confirmed recent findings demonstrating that the origin of the amniotes is deeper than the diversification of extant bony fishes.