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Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

View ORCID ProfilePerry L. Wood Jr., Xianguang Guo, Scott L. Travers, Yong-Chao Su, Karen V. Olson, Aaron M. Bauer, L. Lee Grismer, Cameron D. Siler, Robert G. Moyle, Michael J. Andersen, Rafe M. Brown
doi: https://doi.org/10.1101/717520
Perry L. Wood Jr.
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
bDepartment of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA
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  • ORCID record for Perry L. Wood Jr.
  • For correspondence: perryleewoodjr@gmail.com
Xianguang Guo
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
cChengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
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Scott L. Travers
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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Yong-Chao Su
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
dDepartment of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
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Karen V. Olson
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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Aaron M. Bauer
eDepartment of Biology, 147 Mendel Hall, Villanova University, Villanova, PA 19085, USA
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L. Lee Grismer
fHerpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, 92515, USA
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Cameron D. Siler
gDepartment of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA
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Robert G. Moyle
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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Michael J. Andersen
hDepartment of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Rafe M. Brown
aBiodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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ABSTRACT

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 of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately “derived” parachute geckos of the genus Ptychozoon. 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) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesi’s L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. 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 genus Gekko. 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 genus Gekko as 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 of Gekko, 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.

Footnotes

  • Email addresses: guoxg{at}cib.ac.cn (Xianguang Guo), stravers{at}ku.edu (Scott L. Travers), ycsu527{at}kmu.edu.tw (Yong-Chao Su), olson{at}ku.edu (Karen V. Olson), aaron.bauer{at}villanova.edu (Aaron M. Bauer), lgrismer{at}lasierra.edu (L. Lee Grismer), camsiler{at}ou.edu (Cameron D. Siler), moyle{at}ku.edu (Robert G. Moyle), mjandersen{at}unm.edu (Michael J. Andersen), rafe{at}ku.edu (Rafe M. Brown).

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements
Perry L. Wood Jr., Xianguang Guo, Scott L. Travers, Yong-Chao Su, Karen V. Olson, Aaron M. Bauer, L. Lee Grismer, Cameron D. Siler, Robert G. Moyle, Michael J. Andersen, Rafe M. Brown
bioRxiv 717520; doi: https://doi.org/10.1101/717520
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Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements
Perry L. Wood Jr., Xianguang Guo, Scott L. Travers, Yong-Chao Su, Karen V. Olson, Aaron M. Bauer, L. Lee Grismer, Cameron D. Siler, Robert G. Moyle, Michael J. Andersen, Rafe M. Brown
bioRxiv 717520; doi: https://doi.org/10.1101/717520

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