Systematics of the Lizard Family Pygopodidae with Implications for the Diversification of Australian Temperate Biotas

Abstract

We conducted a phylogenetic study of pygopodid lizards, a group of 38 species endemic to Australia and New Guinea, with two major goals: to reconstruct a taxonomically complete and robustly supported phylogeny for the group and to use this information to gain insights into the tempo, mode, and timing of the pygopodid radiation. Phylogenetic analyses of mitochondrial DNA (mtDNA), nuclear DNA (nDNA), and previously published morphological data using parsimony, maximum likelihood, and Bayesian methods on the independent and combined three data sets yielded trees with similar and largely stable ingroup topologies. However, relationships among the six most inclusive and unambiguously supported clades (Aprasia, Delma, Lialis, Ophidiocephalus, Pletholax, and Pygopus) varied depending on data set analyzed. We used parametric bootstrapping to help us understand which of the three-branch schemes linking these six taxa was most plausible given our data. We conclude based on our results that the arrangement ((((Delma, Lialis)Pygopus)Pletholax)(Aprasia, Ophidiocephalus)) represents the best hypothesis of intergeneric relationships. A second major problem to arise in our study concerned the inability of our two outgroup taxa (Diplodactylus) to root trees properly; three different rooting locations were suggested depending upon analysis. This long-branch attraction problem was so severe that the outgroup branch also interfered with estimation of ingroup relationships. We therefore used the molecular clock method to root the pygopodid tree. Results of two independent molecular clock analyses (mtDNA and nDNA) converged upon the same root location (branch leading to Delma). We are confident that we have found the correct root because the possibility of our clock estimates agreeing by chance alone is remote given that there are 65 possible root locations (branches) on the pygopodid tree (approximately 1 in 65 odds). Our analysis also indicated that Delma fraseri is not monophyletic, a result supported by a parametric bootstrapping test. We elevated the Western Australian race, Delma f. petersoni, to species status (i.e., Delma petersoni) because hybridization and incomplete lineage sorting could be ruled out as potential causes of this paraphyletic gene tree and because D. grayii is broadly sympatric with its sister species D. fraseri. Climate changes over the past 23 million years, which transformed Australia from a wet, green continent to one that is largely dry and brown, have been suspected as playing a major role in the diversification of Australia's temperate biotas. Our phylogenetic analyses of pygopodid speciation and biogeography revealed four important findings consistent with this climate change diversification model: (1) our fossil-calibrated phylogeny shows that although some extant pygopodid lineages predate the onset of aridification, 28 of 33 pygopodid species included in our study seem to have originated in the last 23 million years; (2) relative cladogenesis tests suggest that several major clades underwent higher...

Two new species of the Delma tincta group (Squamata: Pygopodidae) from northwestern Australia

“…Since this revision, several additional species and subspecies have been recognized in Western Australia, including D. butleri Storr, 1987, D. haroldi Storr, 1987 andD. fraseri petersoni Shea, 1991. Shea (1991 advocated synonymy of D. haroldi and D. butleri and this view is supported in a recent phylogenetic study of pygopodid lizards by Jennings et al (2003). These authors also elevated D. f. petersoni to full species status and advocated transfer of Ac1ys eoncinna Kluge, 1974 to Delma [as suggested also by Kluge (1976)].…”

Systematics of stone geckos in the genus Diplodactylus (Reptilia: Diplodactylidae) from northwestern Australia, with a description of a new species from the Northwest Cape, Western Australia

“…An approximately 900-bp segment of coding region was amplified using the following primers; light strand 5'-GCC CAr ACC CCG AAA ATS TTG-3' (modified from Jennings et al 2(03) and heavy 5'-TTA GGG TRG TTA TTT GHC AY A TKC C-3' (Oliver et al 2007b). This fragment of the ND2 gene has been successfully used to examine intrageneric relationships in many diplodactyline gecko groups (Jennings et al 2003;Melville et al 2004;Pepper et al 2006;Bauer et al 2006;Oliver et al 2007a,b). PCR products were amplified using Hotmaster Taq (Eppendorf) using the following conditions: denaturing 94°C, annealling 55°C and for extension noc for 34 amplification cycles.…”

A new species of the Aprasia repens species-group (Squamata: Pygopodidae) from Western Australia

“…The A. repens species-group, originally defi ned by Storr et al (1990), now comprises seven species of very similar appearance and that to most fi eld biologists remain diffi cult to distinguish. However, the use of molecular techniques both herein and elsewhere (Jennings et al 2003) has shown that there are clear and distinct genetic divergences among species. These techniques combined with our morphological studies have also demonstrated that the current diversity within the A. repens species-group is underestimated with additional new species.…”

“…Smith and Henry (1999) described A. picturata from central inland Western Australia, the fi rst new species for over 20 years. Jennings et al (2003) published a molecular phylogeny for 32 species within the pygopodidae, including all but two of the described species of Aprasia. His study found the genus to be monophyletic when compared to other pygopodid genera and he provided a phylogenetic framework within Aprasia that was mostly concordant with relationships inferred using morphology (Kluge 1974).…”