Data from: Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological datasets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and a few studies have combined morphological and molecular data to estimate combined-evidence phylogenies containing both fossil and extant taxa. However, to date, few if any studies have attempted to infer divergence time estimates using phylogenies containing both extinct and living taxa, sampled for both molecular and morphological data. Here, I infer both the phylogeny and time of origin for Lissamphibia using Bayesian methods, based on a dataset containing morphological data for extinct taxa, molecular data for a number of extant species, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post-hoc age constraints on internal nodes, and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined-evidence analyses whenever possible.