The evolution of body size in tetrapods is assessed using a database that includes 107 early stegocephalian species ranging in time from the Frasnian (Upper Devonian) to the Tatarian (Upper Permian). All analyses use methods that incorporate phylogenetic information (topology and branch lengths). In all tests, the impact of alternative topologies and branch lengths are assessed. Previous reports that raised doubts about the accuracy of squared-change parsimony assessment of ancestral character value appear to have used datasets in which there was no phylogenetic signal. Hence, squared-change parsimony may be more reliable than suggested in recent studies, at least when a phylogenetic signal is present in the datasets of interest. Analysis using random taxon reshuffling on three reference phylogenies shows that cranial and presacral length include a strong phylogenetic signal. Character optimization of body size in stegocephalians using squared-change parsimony on a time-calibrated phylogeny incorporating branch length information is used to test a previously published scenario on the origin of amniotes and of the amniotic egg that implies that the ancestors of amniotes were small (no more than 10 cm in snout-vent length), and that their size increased subsequent to the appearance of the amniotic egg. The optimization suggests that first amniotes were somewhat larger than previously hypothesized; the estimated snout-vent length is about 24 cm, and the lower end of the 95% confidence interval of the phylogeny that yields the smallest inferred size suggests that no ancestor of amniotes measured less than 12 cm in snout-vent length. Character optimization, permutational multiple linear regressions, and independent contrast analyses show that Cope's rule of phyletic size increase applies to early reptiliomorphs but that it does not apply to early stegocephalians globally.

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A review of the paleontological literature shows that the early dates of appearance of Lissamphibia recently inferred from molecular data do not favor an origin of extant amphibians from temnospondyls, contrary to recent claims. A supertree is assembled using new Mesquite modules that allow extinct taxa to be incorporated into a time-calibrated phylogeny with a user-defined geological time scale. The supertree incorporates 223 extinct species of lissamphibians and has a highly significant stratigraphic fit. Some divergences can even be dated with sufficient precision to serve as calibration points in molecular divergence date analyses. Fourteen combinations of minimal branch length settings and 10 random resolutions for each polytomy give much more recent minimal origination times of lissamphibian taxa than recent studies based on a phylogenetic analyses of molecular sequences. Attempts to replicate recent molecular date estimates show that these estimates depend strongly on the choice of calibration points, on the dating method, and on the chosen model of evolution; for instance, the estimate for the date of the origin of Lissamphibia can lie between 351 and 266 Mya. This range of values is generally compatible with our time-calibrated supertree and indicates that there is no unbridgeable gap between dates obtained using the fossil record and those using molecular evidence, contrary to previous suggestions.