Hemiergis is a distinctive limb-reduced clade of skinks of the Australian Sphenomorphus group that occur throughout much of southern Australia. Mitochondrial 12S and 16S rRNA gene-sequence data and Bayesian inference (relaxed clock and time-free models) are used to infer the phylogenetic relationships within Hemiergis, as well as test the monophyly of this clade with respect to Glaphyromorphus gracilipes, a southwestern Australia species of the polyphyletic “Glaphyromorphus” assemblage. Hemiergis monophyly is not supported by the mtDNA data, with G. gracilipes being placed as the sister lineage to H. decresiensis sensu lato. Using the Bayes factor, comparison of an alternative hypothesis of Hemiergis monophyly to the preferred hypothesis (i.e., the mtDNA inferred hypothesis with the highest posterior probability) indicates positive support (BF = 3.9–4.1) for the preferred hypothesis demonstrating Hemiergis paraphyly; thus, G. gracilipes is transferred to Hemiergis. Whereas these data strongly support the placement of the two-toed H. quadrilineatum as being closely related to the three- and four-toed populations of H. peronii, the interrelationships among these three limb-reduced phenotypes is unresolved. All other interspecific relationships within Hemiergis are weakly supported by the mtDNA. Within H. decresiensis sensu lato, there is strong support for two divergent lineages that are allopatric. The eastern lineage occurring in Victoria, New South Wales, and extreme southern Queensland is elevated to full species (=H. talbingoensis), with H. decresiensis sensu stricto restricted to the western lineage of South Australia. While many of the interspecific relationships within Hemiergis are weakly supported, these mtDNA data do very strongly favor our preferred hypothesis over an alternative phylogenetic hypothesis implied by a previously proposed parsimonious transformation series of limb reduction; this result implies more independent limb reduction events during the evolution of Hemiergis.

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