A molecular phylogeny was reconstructed for 26 recognized genera of the Gymnophthalmidae using a total of 2379 bp of mitochondrial (12S, 16s and ND4) and nuclear (18s and c-mos) DNA sequences. We performed maximum parsimony (MP) and maximum likelihood (ML) analyses, and data partitions were analysed separately and in combination under MP. ML analyses were carried out only on the combined sequences for computational simplicity. Robustness for the recovered nodes was assessed with bootstrap and partitioned Bremer support (PBS) analyses. The total molecular evidence provided a better-resolved hypothesis than did separate analysis of individual partitions, and the PBS analysis indicates congruence among independent partitions for support of some internal nodes. Based on this hypothesis, a new classification for the family is proposed. Alopoglossus, the sister group of all the other Gymnophthalmidae was allocated to a new subfamily Alopoglossinae, and Rhachisaums (a new genus for Anotosaura brachylepis) to the new Rhachisaurinae. Two tribes are recognized within the subfamily Gymnophthalminae: Heterodactylini and Gymnophthalmini, and two others within Cercosaurinae (Ecpleopini and Cercosaurini). Some ecological and evolutionary implications of the phylogenetic hypothesis are considered, including the independent occurrence of limb reduction, body elongation, and other characters associated with fossoriality.

Phylogenetic analyses based on mtDNA cytochrome b were performed in 42 lizards of the Gymnodactylus darwinii complex from three regions within Brazil's Atlantic Forest. Mainland regions and continental shelf islands in the south-eastern range and mainland areas from the north-east were sampled. The criteria of maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods were explored, with the robustness for nodes assessed by bootstrapping (MP and ML) and posterior probabilities (Bayesian searches). By all methods, three distinctive phylogroups were recovered: a south-eastern clade (SE) and two clades from northern regions (NE 1 and NE 2 ). The pattern of genetic structure of the major clades coincided with the presence of river systems in the Atlantic Forest, and based on corrected genetic distances between those clades, divergence times were tentatively estimated using mtDNA rates calibrated for squamate reptiles. The putative role of Atlantic Forest rivers in generating differentiation is discussed. We present a hypothesis of species limits for G. darwinii , based on concordant lines of evidence including cytogenetic and mtDNA analyses. Two chromosome races (cytotype A, 2n = 38; and cytotype B, 2n = 40) had distributions concordant with clades SE and NE 1 + NE 2 , respectively. These races are interpreted to be full species on the basis of a number of empirical criteria.

A molecular phylogeny was reconstructed for 26 recognized genera of the Gymnophthalmidae using a total of 2379 bp of mitochondrial (12S, 16s and ND4) and nuclear (18s and c-mos) DNA sequences. We performed maximum parsimony (MP) and maximum likelihood (ML) analyses, and data partitions were analysed separately and in combination under MP. ML analyses were carried out only on the combined sequences for computational simplicity. Robustness for the recovered nodes was assessed with bootstrap and partitioned Bremer support (PBS) analyses. The total molecular evidence provided a better-resolved hypothesis than did separate analysis of individual partitions, and the PBS analysis indicates congruence among independent partitions for support of some internal nodes. Based on this hypothesis, a new classification for the family is proposed. Alopoglossus, the sister group of all the other Gymnophthalmidae was allocated to a new subfamily Alopoglossinae, and Rhachisaums (a new genus for Anotosaura brachylepis) to the new Rhachisaurinae. Two tribes are recognized within the subfamily Gymnophthalminae: Heterodactylini and Gymnophthalmini, and two others within Cercosaurinae (Ecpleopini and Cercosaurini). Some ecological and evolutionary implications of the phylogenetic hypothesis are considered, including the independent occurrence of limb reduction, body elongation, and other characters associated with fossoriality.

We infer phylogenetic relationships within Teioidea, a superfamily of Nearctic and Neotropical lizards, using nucleotide sequences. Phylogenetic analyses relied on parsimony under tree‐alignment and similarity‐alignment, with length variation (i.e. gaps) treated as evidence and as absence of evidence, and maximum‐likelihood under similarity‐alignment with gaps as absence of evidence. All analyses produced almost completely resolved trees despite 86% of missing data. Tree‐alignment produced the shortest trees, the strict consensus of which is more similar to the maximum‐likelihood tree than to any of the other parsimony trees, in terms of both number of clades shared, parsimony cost and likelihood scores. Comparisons of tree costs suggest that the pattern of indels inferred by similarity‐alignment drove parsimony analyses on similarity‐aligned sequences away from more optimal solutions. All analyses agree in a majority of clades, although they differ from each other in unique ways, suggesting that neither the criterion of optimality, alignment nor treatment of indels alone can explain all differences. Parsimony rejects the monophyly of Gymnophthalmidae due to the position of Alopoglossinae relative to Teiidae, whereas support of Gymnophthalmidae by maximum‐likelihood was low. We address various nomenclatural issues, including Gymnophthalmidae Fitzinger, 1826 being an older name than Teiidae Gray, 1827. We recognize three families in the arrangement Alopoglossidae + (Teiidae + Gymnophthalmidae). Within Gymnophthalmidae we recognize Cercosaurinae, Gymnophthalminae, Rhachisaurinae and Riolaminae in the relationship Cercosaurinae + (Rhachisaurinae + (Riolaminae + Gymnophthalminae)). Cercosaurinae is composed of three tribes—Bachiini, Cercosaurini and Ecpleopodini—and Gymnophthalminae is composed of three—Gymnophthalmini, Heterodactylini and Iphisini. Within Teiidae we retain the currently recognized three subfamilies in the arrangement: Callopistinae + (Tupinambinae + Teiinae). We also propose several genus‐level changes to restore the monophyly of taxa.