DOI: 10.5061/dryad.qt48h
title: Data from: Fossils, molecules, divergence times, and the origin of Lissamphibians

description: 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.
description: Marjanovic_&_Laurin_App_1Methods and sources used to compile the main phylogeny (Figs. 3–7) and to determine the stratigraphic distribution of various lissamphibian species, and of the fossiliferous localities.Marjanovic_&_Laurin_App_2Timetree in pdf format.Marjanovic_&_Laurin_App_3Comparison between the estimated minimal age of various taxa under our supertree and under the phylogeny of Frost et al. (2006).Marjanovic_&_Laurin_App_4Estimated date of appearance of selected taxa in the supertree under various assumptions of branch lengths.Marjanovic_&_Laurin_App_5Estimated date of appearance of selected taxa under various random resolutions of the polytomies in the supertree.Marjanovic_&_Laurin_App_6Biological nomenclature.Marjanovic_&_Laurin_App_7List of localities that have yielded lissamphibian fossils.Marjanovic_&_Laurin_App_8Marjanovic_&_Laurin_App_9Correlation and discrepancy between the predicted number of fossiliferous lissamphibian localities according to various models and the observed number of localities.Marjanovic_&_Laurin_App_10Lissamphibian biodiversity through time.Marjanovic_&_Laurin_App_11Model parameters chosen by Modeltest 3.7 using a neighbor joining (NJ) and the most parsimonious (MP) guide trees, compared to the model used by Zhang et al. (2005; pers. comm.) which was selected by Modeltest 3.06.Marjanovic_&_Laurin_App_12Quartets used for quartet-dating in QDate 1.11 (see Table 5).Marjanovic_&_Laurin_App_13Molecular divergence dates (rounded to Ma ago) calculated by quartet dating using QDate 1.11 using the evolution models from the three right columns of Appendix 11, compared to those reported (with confidence intervals) by Zhang et al. (2005) and to those from our supertree (Figs. 3–7).Marjanovic_&_Laurin_App_14Divergence dates calculated by penalized maximum likelihood using r8s 1.71 (TN algorithm) under different assumptions.Marjanovic_&_Laurin_App_15Molecular divergence dates calculated using PATHd8 1.0, rounded to the nearest Ma.