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 support the morphological phylogenetic hypothesis of Iguania being sister to all remaining squamates. Here, we map molecular data onto additional phylogenetic hypotheses and show that the conclusions of McMahan and colleagues are flawed for three key reasons: 1) they misinterpreted a measure of branch length as a measure of branch support; 2) they considered only two phylogenetic hypotheses; and 3) their counts of molecular apomorphies are severely biased by their decision to collapse clades into large polytomies. We demonstrate that counting the molecular apomorphies along a given branch is a poor measure of support for a clade and that the molecular data do not provide support for the morphology-based squamate phylogeny as the optimal topology.