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Gene Sequencing Reveals New Gecko Clade

NEW YORK (GenomeWeb News) – Using gene sequencing and phylogenetics, researchers from the University of Minnesota and Villanova University have uncovered a new clade of geckos — previously misclassified because of their physical resemblance to members of other taxonomic groups.
The team did phylogenetic analysis on dozens of gecko species based on sequence data from five different protein-coding genes. Their results, which will appear in an upcoming issue of the journal Zoologica Scripta, suggest that scientists have overlooked a family of geckos containing eight genera and more than 100 species. Until now, the clade has been a “cryptic” group of species, lumped in with several other taxonomic groups based on their morphology.
In a statement released yesterday, lead author Tony Gamble, a graduate student in the conservation biology program at the University of Minnesota, noted that the new analysis will provide the basis for new insights into gecko evolution.
Geckos are a family of lizards found around the world that are known for their sticky toes and species diversity. Classifying geckos taxonomically can be tricky, though, because of this diversity and extensive geographical distribution. In addition, some species may share certain physical features through convergent evolution that masks their underlying genetic differences.
In the past, gecko classifications were based largely on the animals’ foot structure — a categorization that was useful but that missed other, more subtle differences between different gecko groups. “A classification based solely on foot structure will track selective pressure on the feet and not represent actual evolutionary history,” Gamble said.
In an effort to clarify gecko taxonomy and better understand evolutionary relationships between geckos, Gamble and his colleagues took a phylogenetic approach, classifying more than fifty gecko specimens collected around the world based on gene sequencing.
To do this, they extracted genomic DNA from muscle, liver, or tail tissue and amplified regions of five different protein-coding genes by PCR. They then sequenced purified PCR products at the University of Minnesota’s Advanced Genetic Analysis Center on an ABI 3730x1 sequencer or at Villanova University on an ABI 3700 sequencer. Using maximum parsimony, maximum likelihood, and Bayesian analyses, they then looked for phylogenetic relationships between the geckos tested.
Based on this analysis, they proposed an entirely new group of geckos containing 103 species from eight genera. The team also predicted that members of three other genera, not yet tested, would also fall into this group.
Members of the clade — which the team called Phyllodactylidae because it contains some “leaf-toed” geckos — live in semiarid and tropical regions across the world, from North Africa and the Middle East to the Americas and the Caribbean.
“The existence of this clade is unexpected, as no other phylogenetic or taxonomic hypotheses have proposed linking taxa represented in Phyllodactylidae,” Gamble and his co-authors wrote. “[P]revious authorities have consistently grouped constituent taxa with other genera outside of the Phyllodactylidae or in separate higher-level categories.”
The study illustrates the usefulness of genetics for classifying species-rich groups of animals. In contrast, the authors noted, relying on just a few morphological features for classification — such as toe shape or number — can be deceptive.
And, they added, as more and more genetic information is added and analyzed, researchers will likely get a much clearer picture of molecular relationships between different species as well as the evolution of morphological traits.
“It stands to reason that as large-scale phylogenetic research progresses through so-called ‘tree of life’ projects that additional novel, higher-level taxa will be identified from genetic data,” the authors wrote.

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