A phylogeny of tetrapods is inferred from nearly complete sequences of the nuclear RAG-1 gene sampled across 88 taxa encompassing all major clades, analyzed via parsimony and Bayesian methods. The phylogeny provides support for Lissamphibia, Theria, Lepidosauria, a turtle-archosaur clade, as well as most traditionally accepted groupings. This tree allows simultaneous molecular clock dating for all tetrapod groups using a set of well-corroborated calibrations. Relaxed clock (PLRS) methods, using the amniote = 315 Mya (million years ago) calibration or a set of consistent calibrations, recovers reasonable divergence dates for most groups. However, the analysis systematically underestimates divergence dates within archosaurs. The bird-crocodile split, robustly documented in the fossil record as being around approximately 245 Mya, is estimated at only approximately 190 Mya, and dates for other divergences within archosaurs are similarly underestimated. Archosaurs, and particulary turtles have slow apparent rates possibly confounding rate modeling, and inclusion of calibrations within archosaurs (despite their high deviances) not only improves divergence estimates within archosaurs, but also across other groups. Notably, the monotreme-therian split ( approximately 210 Mya) matches the fossil record; the squamate radiation ( approximately 190 Mya) is younger than suggested by some recent molecular studies and inconsistent with identification of approximately 220 and approximately 165 Myo (million-year-old) fossils as acrodont iguanians and approximately 95 Myo fossils colubroid snakes; the bird-lizard (reptile) split is considerably older than fossil estimates (< or = 285 Mya); and Sphenodon is a remarkable phylogenetic relic, being the sole survivor of a lineage more than a quarter of a billion years old. Comparison with other molecular clock studies of tetrapod divergences suggests that the common practice of enforcing most calibrations as minima, with a single liberal maximal constraint, will systematically overestimate divergence dates. Similarly, saturation of mitochondrial DNA sequences, and the resultant greater compression of basal branches means that using only external deep calibrations will also lead to inflated age estimates within the focal ingroup.

One of the most prolific radiations of venomous snakes, the Australo‐Melanesian Hydrophiinae includes ∼100 species of Australasian terrestrial elapids plus all ∼60 species of viviparous sea snakes. Here, we estimate hydrophiine relationships based on a large data set comprising 5800 bp drawn from seven genes (mitochondrial: ND4, cytb, 12S, 16S; nuclear: rag1, cmos, myh). These data were analysed using parsimony, likelihood and Bayesian methods to better resolve hydrophiine phylogeny and provide a timescale for the terrestrial and marine radiations. Among oviparous forms, Cacophis, Furina and Demansia are basal to other Australian elapids (core oxyuranines). The Melanesian Toxicocalamus and Aspidomorphus group with Demansia, indicating multiple dispersal events between New Guinea and Australia. Oxyuranus and Pseudonaja form a robust clade. The small burrowing taxa form two separate clades, one consisting of Vermicella and Neelaps calanotus, and the other including Simoselaps, Brachyurophis and Neelaps bimaculatus. The viviparous terrestrial elapids form three separate groups: Acanthophis, the Rhinoplocephalus group and the Notechis–Hemiaspis group. True sea snakes (Hydrophiini) are robustly united with the Notechis–Hemiaspis group. Many of the retrieved groupings are consistent with previous molecular and morphological analyses, but the polyphyly of the viviparous and burrowing groups, and of Neelaps, are novel results. Bayesian relaxed clock analyses indicate very recent divergences: the ∼160 species of the core Australian radiation (including sea snakes) arose within the last 10 Myr, with most inter‐generic splits dating to between 10 and 6 Ma. The Hydrophis sea snake lineage is an exceptionally rapid radiation, with > 40 species evolving within the last 5 Myr.

Recent mtDNA phylogenies of Australasian agamid lizards are highly incongruent with existing morphological views. To resolve this discrepancy we sequenced two nuclear gene regions, c-mos and brain-derived neurotrophic factor (BDNF). These were highly concordant with each other and the mtDNA phylogeny, but not the morphology. A combined molecular analysis reveals substantial hidden support (additional phylogenetic signal that emerges only when the data sets interact in a combined analysis). Bayesian posteriors, and a partitioned bootstrap procedure introduced here, indicate strong support for most nodes. The resultant tree implies extensive morphological homoplasy, with many genera emerging as non-monophyletic (Amphibolurus, Rankinia, Ctenophorus, Physignathus, Diporiphora). The water and forest dragons (Physignathus and Hypsilurus) form a paraphyletic basal assemblage to the more derived Australian forms such as Amphibolurus and Ctenophorus, which include almost all the xeric taxa. However, the thorny devil Moloch horridus is a basal lineage and not closely related to the other arid forms. Tree topology, inferred divergence dates, palaeogeographical and palaeoclimatic data are all consistent with Miocene immigration into Australia from the north by mesic forest ecomorphs, followed by initial diversification in mesic habitats before radiation into xeric habitats facilitated by increasing aridity.

The lizards of the Egernia group of Australia and Melanesia include some of the most distinctive members of the family Scincidae in morphology (including giant size, spinose scalation), ecology and behaviour. Social behaviour, including long-term recognition of individuals and kin, mate fidelity and home site fidelity, is amongst the most complex known in squamate reptiles and is the subject of an expanding number of studies. Lack of a sound phylogeny for the Egernia group has limited our ability to understand the evolution and patterns of variation in social behaviour within this group, and evidence for the monophyly of the largest genus, Egernia (64% of the species), has been lacking. We present data derived from nucleotide sequences that establish a phylogenetic framework for the Egernia group. We used two mitochondrial sequences, the protein-encoding ND4 gene and a ribosomal gene, 12s rRNA, and two nuclear sequences, the protein-encoding c-mos, and non-encoding intron 7 of b-fibrinogen. Our phylogenetic analyses show that Corucia of the Solomon Islands is the sister group of the rest of the Egernia group. The genus Egernia is paraphyletic, including four well-supported monophyletic units, one of which is the sister lineage of the Tiliqua lineage (Tiliqua plus Cyclodomorphus). We suggest a revised taxonomic scheme that recognizes the major monophyletic lineages in Egernia (s.l.) as distinct genera.

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