Squamate phylogenetics, molecular branch lengths, and molecular apomorphies: a response to McMahan et al. (2015)

Morphology-based studies of squamate phylogenetics recover very different topologies from studies that use molecular or combined molecular and morphological data. This has led to some stimulating dialogue regarding the respective merits of the alternative hypotheses, with the primary point of disagreement being the placement of Iguania. Molecular phylogenetic studies place Iguania in a highly nested position as a member of the clade Toxicofera, additionally containing Anguimorpha and Serpentes, whereas morphology-only studies have traditionally placed Iguania as sister to all remaining squamates. McMahan and colleagues recently posited that the molecular phylogenetic hypothesis of the placement of Iguania is a result of incorrect root placement. These authors mapped molecular data (i.e., DNA sequence data) onto phylogenetic hypotheses and identified more molecular apomorphies on the basal branches of the morphology-based phylogeny. They concluded from this result that the molecular data...