Data from: Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction

Harrington SM, Reeder TW

Date Published: November 28, 2016

DOI: http://dx.doi.org/10.5061/dryad.cm603

 

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Title Fig. S1. Limb reconstruction on uniform clock phylogeny
Downloaded 45 times
Description Fig. S1. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the uniform clock phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
Download Fig_S1_limbs_uniform_clock.pdf (94.19 Kb)
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Title Fig. S2. Macrostomatan phenotype reconstruction on uniform clock phylogeny
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Description Fig. S2. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the uniform clock phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
Download Fig_S2_Gape_uniform_clock.pdf (78.85 Kb)
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Title Fig. S3. Limb reconstruction on constrained, fossil tip FBD phylogeny
Downloaded 85 times
Description Fig. S3. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, fossil tip FBD phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
Download Fig_S3_limbs_constrained_foss_tip_FBD.pdf.pdf (96.20 Kb)
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Title Fig. S4. Macrostomatan phenotype reconstruction on constrained, fossil tip FBD phylogeny
Downloaded 31 times
Description Fig. S4. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, fossil tip FBD phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
Download Fig_S4_Gape_constrained_foss_tip_FBD.pdf (81.00 Kb)
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Title Fig. S5. Limb reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogeny.
Downloaded 32 times
Description Fig. S5. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. The phylogeny is plotted without Diablophis or Portugalophis because of issues visualizing branch lengths when these taxa were included, but they were included in the trees used for ancestral state reconstruction.
Download Fig_S5_Limbs_no_Tetrapodophis.pdf (83.49 Kb)
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Title Fig. S6. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogeny
Downloaded 50 times
Description Fig. S6. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. The phylogeny is plotted without Diablophis or Portugalophis because of issues visualizing branch lengths when these taxa were included, but they were included in the trees used for ancestral state reconstruction.
Download Fig_S6_Gape_no_Tetrapodophis.pdf (70.89 Kb)
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Title Fig. S7. Limb reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny
Downloaded 40 times
Description Fig. S7. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
Download Fig_S7_Limbs_no_Tetrapodophis_or_Caldwell...15.pdf (78.04 Kb)
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Title Fig. S8. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny
Downloaded 16 times
Description Fig. S8. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
Download Fig_S8_Gape_no_Tetrapodophis_or_Caldwell_...15.pdf (65.42 Kb)
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Title Fig. S9. Macrostomatan phenotype reconstruction on constrained, diversified FBD phylogeny with madstoiids coded uncertain
Downloaded 27 times
Description Fig. S9. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. Madstoiids were coded as uncertain in this analysis and the analysis was performed on the phylogeny from the constrained, diversified FBD analysis.
Download Fig_S9_Gape_reconstruction_Madtsoiidae_un...in.pdf (83.74 Kb)
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Title Files S1-S17. Supplemental tree files.
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Description Files S1-S17. This zip file contains all of the supplemental tree files. Individual tree files are described in the ReadMe file and in a text file within the zip file.
Download README.txt (4.977 Kb)
Download Files_S1-S17_tree_files.zip (237.8 Kb)
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Title Files S18-S23. Zip file containing data matrices and MrBayes blocks
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Description Files S18-S23. This zip file contains all of the data matrices and MrBayes blocks used for analyses. Individual files are described in the ReadMe file and in a text file within the zip file.
Download README.txt (1.001 Kb)
Download Files_S18-S23_matrices_MrBayes_blocks.zip (1.806 Mb)
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Title Table S1. Node calibrations included in divergence dating analyses.
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Download Table_S1_calibrations.xlsx (10.57 Kb)
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When using this data, please cite the original publication:

Harrington SM, Reeder TW (2017) Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction. Biological Journal of the Linnean Society 121(2): 379-394. http://dx.doi.org/10.1093/biolinnean/blw039

Additionally, please cite the Dryad data package:

Harrington SM, Reeder TW (2017) Data from: Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cm603
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