Data from: 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 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.