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

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 (~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 sus