DOI: 10.5061/dryad.855
title: Data from: Systematics of the lizard family Pygopodidae with implications for the diversification of Australian temperate biotas

description: 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 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 than expected
 rates of speciation; (3) our findings support earlier studies showing that
 speciation of mesic-adapted biotas in the southeastern and southwestern
 corners of Australia largely occurred within each of these regions between
 12 and 23 million years ago as opposed to repeated dispersal between these
 regions; and (4) we have identified for the first time the existence of
 several pairs of sympatric sister species of lizards living in arid and
 semiarid ecosystems. These sympatric sister species seem to be younger
 than allopatric or parapatric sister-species pairs, which is not
 consistent with previous beliefs.
description: Substitution Models and
 Parameter Estimates