Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates

The evolutionary relationships of gnathostomes (jawed vertebrates), which c omprise chondrichthyans (cartilaginous fishes), lobe-finned fishes (coelaca nths and lungfishes), tetrapods, and actinopterygians (ray-finned fishes), have been debated for almost a century. Phylogenetic analyses based on foss ils, morphology, and molecular sequences have generated different models of relationships that remain unresolved. We identified 13 derived shared mole cular markers (synapomorphies) that define clades in the vertebrate lineage and used them to resolve the phylogenetic relationships of extant jawed ve rtebrates. Our markers include the presence or absence of insertions and de letions in coding sequences, nuclear introns, and alternatively spliced tra nscripts. The synapomorphies identified by us are congruent with each other and give rise to a single phylogenetic tree. This tree confirms that chond richthyans are basal to all living gnathostomes, that lungfishes (Dipnoi) a re the closest living relatives of tetrapods, and that bichirs (Cladistia) are the living members of the most ancient family of ray-finned fishes. Our study also provides molecular evidence to support the monophyly of living tetrapods and teleosts.