Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa

Squamate reptiles (lizards and snakes) are a pivotal group whose
relationships have become increasingly controversial. Squamates include
>9000 species, making them the second largest group of terrestrial
vertebrates. They are important medicinally and as model systems for
ecological and evolutionary research. However, studies of squamate biology
are hindered by uncertainty over their relationships, and some consider
squamate phylogeny unresolved, given recent conflicts between molecular
and morphological results. To resolve these conflicts, we expand existing
morphological and molecular datasets for squamates (691 morphological
characters and 46 genes, for 161 living and 49 fossil taxa, including a
new set of 81 morphological characters and adding two genes from published
studies) and perform integrated analyses. Our results resolve higher-level
relationships as indicated by molecular analyses, and reveal hidden
morphological support for the molecular hypothesis (but not vice-versa).
Furthermore, we find that integrating molecular, morphological, and
paleontological data leads to surprising placements for two major fossil
clades (Mosasauria and Polyglyphanodontia). These results further
demonstrate the importance of combining fossil and molecular information,
and the potential problems of estimating the placement of fossil taxa from
morphological data alone. Thus, our results caution against estimating
fossil relationships without considering relevant molecular data, and
against placing fossils into molecular trees (e.g. for dating analyses)
without considering the possible impact of molecular data on their
placement.