Data from: 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 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.本研究针对鳞脚蜥科蜥蜴（pygopodid lizards）开展系统发育学研究，该类群包含38个物种，特有分布于澳大利亚与新几内亚。本次研究包含两大核心目标：其一，重建该类群具备完整分类覆盖度且支持度稳健的系统发育树；其二，依托该系统发育框架，深入解析鳞脚蜥科辐射演化的节奏、模式与时间尺度。 研究分别基于线粒体DNA（mtDNA）、核DNA（nDNA）以及已发表的形态学数据，通过简约法、最大似然法与贝叶斯法，对独立数据集及三者合并数据集开展系统发育分析，所得树拓扑结构整体相似且内群拓扑高度稳定。不过，针对6个涵盖范围最广、支持度明确的演化支（Aprasia、Delma、Lialis、Ophidiocephalus、Pletholax及Pygopus），其内部亲缘关系会因所采用的数据集不同而出现差异。本研究借助参数自举法，尝试明确在本研究数据框架下，连接这6个属的三种分支拓扑结构中哪一种最具合理性。 基于研究结果，我们认为拓扑结构((((Delma, Lialis)Pygopus)Pletholax)(Aprasia, Ophidiocephalus))是属间亲缘关系的最优假说。本研究遇到的第二个关键问题在于，所选的两个外类群类群（Diplodactylus）无法实现系统发育树的正确定根，不同分析方法得到了三种不同的定根位置。该长枝吸引问题十分严重，甚至干扰了内群亲缘关系的推断。因此，我们采用分子钟法对鳞脚蜥科系统发育树进行定根。两项独立的分子钟分析（分别基于mtDNA与nDNA）得到了一致的定根位置，即指向Delma属的分支。我们有充分信心确定该定根位置的正确性：鳞脚蜥科系统发育树共存在65种可能的定根分支，两次分子钟分析结果偶然重合的概率极低（约为1/65）。 本研究同时发现，Delma fraseri并非单系群，该结果得到了参数自举检验的支持。鉴于无法用杂交与不完全谱系分选来解释该并系基因树的成因，且D. grayii与其姊妹种D. fraseri存在广泛的同域分布，我们将西澳亚种Delma f. petersoni提升为独立物种，即Delma petersoni。 此前有研究推测，过去2300万年间的气候变化——将澳大利亚从湿润翠绿的大陆转变为以干旱棕黄为主的大陆——在澳大利亚温带生物群的多样化进程中发挥了核心作用。我们针对鳞脚蜥科物种形成与生物地理学的系统发育分析得到了四项与该气候变化驱动多样化模型相符的重要结论：（1）经化石校准的系统发育树显示，尽管部分现存鳞脚蜥科支系的起源早于澳大利亚干旱化进程，但本研究纳入的33个鳞脚蜥科物种中，有28个的起源时间均不晚于过去2300万年；（2）相对分支发生速率检验结果表明，多个主要演化支的物种形成速率高于预期水平；（3）我们的研究结果支持前人结论：澳大利亚东南部与西南部的湿润生境适应类群的物种形成，主要发生在1200万至2300万年前的各自区域内，而非在两区域间反复扩散；（4）我们首次发现，在干旱与半干旱生态系统中存在多对同域分布的蜥蜴姊妹种。这些同域姊妹种的分化时间似乎晚于异域或邻域分布的姊妹种对，这与此前的学术认知相悖。