Prior to the molecular phylogenetic revolution in squamate systematics, the traditional classification divided squamates into Iguania (considered basal) and Scleroglossa (all other squamates), with Scleroglossa further subdivided into Gekkota and Autarchoglossa.[1][5] Autarchoglossa (meaning "free-tongued") roughly corresponded in content to what would become Unidentata, but excluded the Iguania, which were thought to be primitive.[1]
Molecular analyses by Vidal and Hedges (2005), using DNA sequences from nine nuclear protein-coding genes, dramatically altered this picture. Iguanians were found to be nested deep within the squamate tree, forming part of the derived clade Toxicofera together with Anguimorpha and snakes, rather than being basal.[1] This rendered both Scleroglossa and Autarchoglossa paraphyletic in the molecular topology. Because redefining Autarchoglossa to include Iguania would have conflicted with the etymological meaning of the name ("free-tongued", a characteristic not shared by iguanians), Vidal and Hedges erected the new name Unidentata, which refers to a morphological character - the single egg tooth - that is shared by all members of the group, including iguanians.[1]
The monophyly of Unidentata has been broadly supported by subsequent large-scale molecular studies. Pyron and colleagues (2013) included 4,161 squamate species in a phylogenetic analysis based on 12 genes and confirmed the higher-level topology in which gekkotans are placed outside Unidentata.[6] Zheng and Wiens (2016) combined phylogenomic and supermatrix data for 52 genes and 4,162 species, further corroborating these relationships.[7] A genomic-scale anchored phylogenomics study by Burbrink and colleagues (2020), sampling 289 species and hundreds of loci, found unambiguous support (posterior probability of 1.0) for the major groups within this arrangement, including Unidentata, Episquamata, Toxicofera, and Laterata.[8]
Unidentata contains two principal subgroups:[1][5]