The Phylogeny of Lizard Families

In this chapter, we will summarize our current knowledge of higher-level lizard phylogeny, focusing on relationships among extant families. Despite recent suggestions that lizard phylogeny is unresolved due to conflicts between molecular and morphological data (e.g., Gauthier et al. 2012; Losos et al. 2012), we will argue that the phylogeny of extant lizard families is actually becoming increasingly well resolved and well supported. We will first argue that simply pointing out differences between molecular and morphological trees does not help us resolve phylogeny. Instead, the best way to resolve these conflicts is through combined analysis and identification of misleading signals. We will argue that combined analyses of large-scale molecular and morphological datasets clearly support the estimate of higher-level phylogeny from molecular datasets, and that there is strongly misleading signal in the morphological data. We will then review our current knowledge of higher-level squamate phylogeny, emphasizing those aspects that are now agreed upon by large-scale datasets, and those aspects that are still uncertain. We will also present a new time-calibrated phylogeny for squamate reptile families.