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.