Recent Advances in the (molecular) Phylogeny of Vertebrates

■ Abstract The analysis of molecular phylogenetic data has advanced the knowledge of the relationships among the major groups of living vertebrates. Whereas the molecular hypotheses generally agree with traditional morphology-based systematics, they sometimes contradict them. We review the major controversies in vertebrate phylogenetics and the contribution of molecular phylogenetic data to their resolution: (a) the mono-paraphyly of cyclostomes, (b) the relationships among the major groups of rayfinned fish, (c) the identity of the living sistergroup of tetrapods, (d ) the relationships among the living orders of amphibians, (e) the phylogeny of amniotes with particular emphasis on the position of turtles as diapsids, (f ) ordinal relationships among birds, and (g) the radiation of mammals with specific attention to the phylogenetic relationships among the monotremes, marsupial, and placental mammals. We present a discussion of limitations of currently used molecular markers and phylogenetic methods as well as make recommendations for future approaches and sets of marker genes.