School of Earth and Environmental Sciences, The University of Adelaide, SA 5005, Australia.
Mol Phylogenet Evol. 2013 Dec;69(3):906-18. doi: 10.1016/j.ympev.2013.06.014. Epub 2013 Jun 28.
The Australian Sphenomorphus group is a diverse clade (c. 250 species) of scincid lizards (skinks) incorporating more than half of the Australian scincid fauna. Previous phylogenetic analyses of mitochondrial and nuclear gene sequence data for selected Australian Sphenomorphus group scincids have provided support for several morphologically- and ecologically-distinct clades; however, the relationships among these clades are only incompletely resolved. This paper presents a new phylogenetic analysis of the Australian Sphenomorphus group, based on nucleotide sequences for three regions of the mitochondrial genome and four nuclear genes (5645 aligned sites in total). Phylogenies generated using standard concatenation and multi-species coalescent approaches are generally similar, and nearly all conflicting nodes are weakly supported. Monophyly of a number of genera and other (informal) supra-specific taxa, including Calyptotis, Ctenotus, Eremiascincus, Hemiergis, Lerista, Notoscincus, the 'Eulamprus' quoyii group, and the 'Glaphyromorphus' crassicaudis group is well supported in all analyses. There is significant support for a clade including the 'Eulamprus' tenuis group, Gnypetoscincus, and Nangura, and a clade comprising Coeranoscincus, Coggeria, Ophioscincus, and Saiphos receives at least marginal support (posterior probabilities above 0.93). All analyses indicate that Anomalopus is polyphyletic, although topology tests suggest that support for this result is equivocal. Divergence times inferred using relaxed molecular clock methods are consistent with an Oligocene origin of the Australian Sphenomorphus group following trans-oceanic dispersal from Asia. Age estimates for clades distributed primarily in arid habitats (c. 9-17 million years) are generally younger than those for clades occurring in mesic environments (c. 15-22 million years); however, arid-zone clades are substantially more diverse, including nearly 80% of all Australian Sphenomorphus group scincids. This pattern conforms well with reconstructions of Australian palaeo-environments during the Cenozoic, which indicate a progressive shift from widespread mesic habitats in the Early Miocene (prior to 16 Mya) to predominantly arid environments 4-2 Mya.
澳大利亚 Sphenomorphus 组是一个多样化的蜥蜴类群（约 250 种），包含了澳大利亚蜥蜴类群的一半以上物种。以前对选定的澳大利亚 Sphenomorphus 组蜥蜴的线粒体和核基因序列数据的系统发育分析为几个形态和生态上不同的分支提供了支持；然而，这些分支之间的关系仅部分解决。本文提出了一个基于线粒体基因组三个区域和四个核基因核苷酸序列的澳大利亚 Sphenomorphus 组新的系统发育分析（总共有 5645 个对齐位点）。使用标准的串联和多物种合并方法生成的系统发育树通常是相似的，几乎所有冲突的节点都只有微弱的支持。许多属和其他（非正式）超种分类群的单系性，包括 Calyptotis、Ctenotus、Eremiascincus、Hemiergis、Lerista、Notoscincus、'Eulamprus' quoyii 组和 'Glaphyromorphus' crassicaudis 组，在所有分析中都得到了很好的支持。有一个包括 'Eulamprus' tenuis 组、Gnypetoscincus 和 Nangura 的分支，以及一个包括 Coeranoscincus、Coggeria、Ophioscincus 和 Saiphos 的分支得到了显著支持（后验概率高于 0.93）。所有分析表明，Anomalopus 是多系的，尽管拓扑测试表明，这一结果的支持是不确定的。使用松弛分子钟方法推断的分歧时间与澳大利亚 Sphenomorphus 组的起源相一致，该组是在与亚洲的跨洋扩散后从中始新世起源的。主要分布在干旱生境中的分支（约 9-1700 万年）的年龄估计值通常比主要分布在湿润生境中的分支（约 15-2200 万年）的年龄估计值年轻；然而，干旱区分支的多样性要大得多，包括近 80%的所有澳大利亚 Sphenomorphus 组蜥蜴。这一模式与新生代澳大利亚古环境的重建非常吻合，重建表明从中始新世（1600 万年前）广泛的湿润生境向 4-200 万年前主要的干旱环境逐渐转变。
