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.

The origins of the extant amphibians (frogs, salamanders, caecilians) remain controversial after over a century of debate. Three groups of hypotheses persist in the current literature: the "temnospondyl hypothesis" (TH) which roots Lissamphibia Haeckel, 1866 (the smallest clade composed of the extant amphibians) within the Paleozoic temnospondyls, the "lepospondyl hypothesis" (LH) which postulates a monophyletic Lissamphibia nested within the Paleozoic lepospondyls, and the "polyphyly hypothesis" (PH), according to which the frogs and the salamanders are temnospondyls while the caecilians are lepospondyls. The discovery of the Middle Jurassic to Pliocene albanerpetontids, which are very similar to the extant amphibians, has complicated rather than resolved this situation. We present a review of recent publications and theses in this field, several of which show more support for the LH than for the TH and considerably more than for the PH. In addition, we show that there is no particular attraction between long-bodied lissamphibians (caecilians) and long-bodied lepospondyls (such as the lysorophians): when they are removed from two published matrices, reanalyses nonetheless find the LH. In one case the LH is found even when all salamanders are removed as well. We furthermore propose that the complex of characters called the salamander mode of autopodium development is (in its less extreme forms) plesiomorphic for limbed vertebrates, so the apparent presence of this mode of development in temnospondyls cannot support the TH or the PH. Still, a consensus will not be reached soon, despite the increasing

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH)—though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved—we document and justify all changes to the matrix—but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the “polyphyly hypothesis” (PH—R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid “nectrideans” and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious—but not difficult.

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The origin of frogs, salamanders and caecilians is controversial. McGowan published an original hypothesis on lissamphibian origins in 2002 (McGowan, 2002, Zoological Journal of the Linnean Society, 135: 1-32), stating that Gymnophiona was nested inside the ‘microsaurian’ lepospondyls, this clade was the sister-group of a caudate-salientian-albanerpetontid clade, and both were nested inside the dissorophoid temnospondyls. We have investigated McGowan’s data matrix and disagree with the scoring of 35% of the cells. All taxa and all but two characters are affected. In some cases, we have a different interpretation about correspondence between morphology and character states, or we delimit states differently (or use information that was unknown in 2002). In others, we report probable typographic errors. When these cells and characters are revised, the most parsimonious trees – now longer by almost 64% – support one of the three commonly advocated hypotheses, namely a monophyletic Lissamphibia nested, together with its sister-group Albanerpetontidae, within the temnospondyls (next to Doleserpeton) – even though we did not add any characters or taxa to the very small data matrix. This exemplifies the impact of errors in data matrices on the results of phylogenetic analyses. Adding the lysorophian Brachydectes, however, results in the Lissamphibia-Albanerpetontidae clade becoming the sister-group of Brachydectes and settling within the lepospondyls rather than the temnospondyls, thus supporting another of the previously published three hypotheses. This latter finding does not change if the recently described Gerobatrachus is also added. Finally, when Doleserpeton is interpreted as morphologically immature (which means scoring three characters as unknown instead of known), Lissamphibia and Albanerpetontidae are again nested within the ‘microsaurian’ lepospondyls, even though Brachydectes is not included in this analysis. This, too, does not change if Gerobatrachus is added and likewise treated as morphologically immature. Bootstrap supports are rather low under all assumptions. Such lability was to be expected from the small size of the data matrix.

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