[9][15] Recent molecular work has helped to clarify phylogeny that was historically based primarily on morphological traits, justifying the monophyly of Diplodactylidae, revising intergeneric relationships between several genera, and uncovering significant cryptic diversity within the family.
[16][17][3][18][19][20][21][22][23] However, the current understanding of the systematics and evolution of diplodactylid geckos remains limited, with certain genera and taxa still largely unstudied and significant underestimates in diversity at the species level left to resolve.
[19][6] Underwood completed the first comprehensive systematics analysis of geckos in 1954,[1] using morphological features like pupil shape and inferences around biogeography to establish three major families within Gekkota (or Gekkonoidea as it was also known): the Eublepharidae, the Sphaerodactylidae, and the Gekkonidae.
[22] Kluge disputed Underwood's classification, instead recognizing a single family, Gekkonidae (later equivalent to Gekkota) with four subfamilies that included the Eublepharinae, Sphaerodactylinae, Gekkoninae and Diplodactylinae.
However, Kluge's subfamilial allocations—including his subdivision of Diplodactylinae—and his apparent assumptions around their respective monophyly proved problematic for some (e.g., Moffatt 1973, Hecht 1976), who suggested alternative or expanded hypotheses.
[25][22] This grouping also made more sense biogeographically, as Kluge modified his earlier assumptions of gekkotan origins from fixed continents, landbridges, and oceanic dispersal, to lie more in line with the emerging plate-tectonics Gondwanan hypothesis.
[26][13][22] While these revisions helped advance systematics closer to the contemporary understanding of Diplodactylidae, inconsistencies around how Carphodactylini were then defined and how they fit within the Australia-New Zealand vicariance left questions that required more sophisticated genetic analyses to answer.
C-mos loci and 12S rRNA gene sequences to construct a molecular phylogeny helped to confirm the pygopods’ placement as a monophyletic sister lineage to the Diplodactylinae.
[27][6] These new pairings led Han et al. (2004) to reorder membership within the Diplodactylini and Carphodactylini and to propose a new taxonomy of geckos at the family level to reflect their findings.
[7][15] Due to their closer divergence, the New Zealand and Australian endemics (without Pseudothecadactylus) form a sister clade, while the New Caledonian diplodactylids show evidence of their more recent and rapid radiation in short branch lengths.
[7][15][6] Because the quick succession of genera can complicate phylogenetic reconstruction, it may remain difficult to produce well-supported intergeneric relationships for the eight New Caledonian diplodactylids in spite of a growing number of studies investigating them.
Most molecular divergence studies agree that diplodactylids were likely present prior to the final breakup of Australia and Antarctica[27][20] with diversification of crown diplodactyloids occurring between the late Cretaceous or the earliest Paleogene periods.
[30][15][27][18][29][7] A recent phylogenomic analysis suggests independent colonization events to New Zealand and New Caledonia after the K-T extinction in the late Paleogene and early Neogene, respectively.