DOI: 10.5061/dryad.8120
title: Data from: Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

description: 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.
description: morph.nexMorphological character matrix from Vallin and Laurin (2004). Used to estimate morphology-only tree of stegocephalian relationships (Fig. 1).morph.treFIGURE 1. Phylogeny of the lissamphibians and related tetrapods based on BI analysis of 161 morphological characters in MrBayes. Numbers above nodes represent Pp values based on 45 million post-burnin generations. From MrBayes analysis of morph.nextmDNA.nexMorphological character matrix of Vallin and Laurin (2004), supplemented with DNA sequences from the RAG-1 gene. Analyzed using MrBayes to produce Fig. 2.tmDNA.treFIGURE 2. Bayesian phylogeny of the lissamphibians and related tetrapods based on 161 morphological characters, supplemented with molecular data (RAG-1, 2652bp) for the eight extant taxa. Numbers above nodes represent Pp values based on 45 million post-burnin generations from MrBayes from analysis of tmDNA.nex.tma.nexMorphological character matrix from Vallin and Laurin (2004) combined with DNA sequence data from the RAG-1 gene for additional lissamphibian taxa. Analyzed in MrBayes to produce Fig. 3.tma.treFIGURE 3. Bayesian phylogeny of the lissamphibians and related tetrapods based on 161 morphological characters for 41 fossil taxa, combined with molecular data (RAG-1, 2652bp) for 34 extant taxa, 8 of which also had morphological data. Numbers above nodes represent Pp values based on 45 million post-burnin generations from MrBayes analysis of tma.nex.TMA_1Clock.xmlXML file from BEAST analysis of the combined molecular and morphological data, resulting in Fig. 4.TMA_1Clock.treFIGURE 4. Dated chronogram with branch lengths equal to time in millions of years (Ma), produced using the combined morphological and molecular dataset (Fig. 3) under the 1-clock model in the program BEAST. Blue bars at nodes represent the 95% HPD for the mean estimate of the age of that node, based on 90 million post-burnin generations. Nodes without bars are supported at Pp&lt;0.50. Nodes supported at Pp&gt;0.95 are indicated with an asterisk (*). Taxa present at time zero are extant, while non-contemporaneous tips are extinct species. Tip dates taken from Benton (1993) and Laurin (2004) and are given in Online Appendix A. Produced in BEAST through analysis of TMA_1Clock.xml.TMA_2Clock.xmlXML file for 2-clock analsyis of combined molecular and morphological data in BEAST. Results described in manuscript but tree not shown.TMA_2Clock.treTree resulting from 2-clock analysis of combined molecular and morphological analysis in BEAST, from file TMA_2Clock.xml.