Parachute geckos free fall into synonymy:Gekkophylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements
Authors: Wood Perry L. , Guo Xianguang , Travers Scott L. , Su Yong-Chao , Olson Karen V. , Bauer Aaron M. , Grismer L. Lee , Siler Cameron D. , Moyle Robert G. , Andersen Michael J. , Brown Rafe M. 
Published: July 2019

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread “generalist” clades. This is especially true in the Australasia, where the monophyly ofGekkoproper has been questioned with respect to phenotypically ornate flap-legged geckos of the genusLuperosaurus, the Philippine false geckos of the genusPseudogekko, and even the elaborately “derived” parachute geckos of the genusPtychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme was designed to address four persistent systematic questions in this group: (1) AreLuperosaurusandPtychozoonmonophyletic and are any of these named species truly nested withinGekko? (2) Are prior phylogenetic estimates of Sulawesi’sL. iskandarias sister to MelanesianG. vittatussupported by our genome-scale dataset? (3) Is the high elevationL. gulatof Palawan Island correctly placed withinGekko? (4) And, finally, where do the enigmatic taxaP. rhacophorusandL. brownifall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement ofPtychozoontaxa withinGekko;the sister relationship betweenL. iskandariandG. vittatus); resolve the systematic position of unplaced taxa (L. gulat, andL. browni); and transferL. iskandari, L. gulat, L. browni, and all members of the genusPtychozoonto the genusGekko. Our unexpected and novel systematic inference of the placement ofPtychozoon rhacophorussuggests that this species is not related toPtychozoonor evenLuperosaurus(as previously expected) but may, in fact, be most closely related to several Indochinese species ofGekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate ∼60 species within the more broadly defined and maximally-inclusive Australasian genusGekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genusGekkoas a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition ofGekko, containing multiple phylogenetically-defined subgenera, is that this practice has the potential to alleviate taxonomic vandalism, if widely adopted, by creating formally available, supraspecific taxa, accompanied by character-based diagnoses and properly assigned type species, such that future, more atomized classifications would necessarily be required to adopt today’s subgenera as tomorrow’s genera under the guidelines of The Code of Zoological Nomenclature. Not only does this simple practice effectively eliminate the nefarious motivation behind taxonomic vandalism, but it also ensures that supraspecific names are created only when accompanied by data, that they are coined with reference to a phylogenetic estimate, and that they explicitly involve appropriate specifiers in the form of type species and, ultimately, type specimens.