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

Pyron RA, Pyron RA

Date Published: December 17, 2010

DOI: http://dx.doi.org/10.5061/dryad.8120

 

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Title morph.nex
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Description Morphological character matrix from Vallin and Laurin (2004). Used to estimate morphology-only tree of stegocephalian relationships (Fig. 1).
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Title morph.tre
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Description FIGURE 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.nex
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Title tmDNA.nex
Downloaded 78 times
Description Morphological character matrix of Vallin and Laurin (2004), supplemented with DNA sequences from the RAG-1 gene. Analyzed using MrBayes to produce Fig. 2.
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Title tmDNA.tre
Downloaded 46 times
Description FIGURE 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.
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Title tma.nex
Downloaded 85 times
Description Morphological 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.
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Title tma.tre
Downloaded 59 times
Description FIGURE 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.
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Title TMA_1Clock.xml
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Description XML file from BEAST analysis of the combined molecular and morphological data, resulting in Fig. 4.
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Title TMA_1Clock.tre
Downloaded 83 times
Description FIGURE 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<0.50. Nodes supported at Pp>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.
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Title TMA_2Clock.xml
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Description XML file for 2-clock analsyis of combined molecular and morphological data in BEAST. Results described in manuscript but tree not shown.
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Title TMA_2Clock.tre
Downloaded 60 times
Description Tree resulting from 2-clock analysis of combined molecular and morphological analysis in BEAST, from file TMA_2Clock.xml.
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When using this data, please cite the original publication:

Pyron RA (2011) Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology 60(4): 466-481. http://dx.doi.org/10.1093/sysbio/syr047

Additionally, please cite the Dryad data package:

Pyron RA, Pyron RA (2011) Data from: Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8120
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