DOI: 10.5061/dryad.cm603
title: 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

description: Bayesian divergence time analyses were used to simultaneously infer the
 phylogenetic relationships and date the major clades of snakes including
 several important fossils that have not previously been included in
 divergence dating analyses as terminal taxa. We also explored the effect
 of using fossilized birth–death (FBD) and uniform tree priors for
 divergence dating with terminal calibrations. Nonclock and relaxed clock
 analyses of the combined morphology and molecular data set supported
 previous molecular phylogenetic hypotheses for the major clades of snakes,
 including the paraphyly of the traditionally recognized Scolecophidia and
 Macrostomata. Tip-dating analyses using either a uniform tree prior or FBD
 prior that assume that all fossils are tips and that extant lineages are
 randomly sampled resulted in older ages than those inferred using a FBD
 prior assuming diversified sampling of extant lineages and those estimated
 by previous studies. We used Bayesian ancestral state reconstruction
 methods to map the evolution of the ability to consume large prey and the
 loss of limbs onto our inferred time-calibrated phylogeny. We found strong
 support for early evolution of the ability to consume large prey,
 indicating multiple independent losses of this ability. We also found
 strong support for retention of external hindlimbs until relatively late
 in snake evolution, indicating multiple independent losses of hindlimbs.
description: Fig. S1. Limb
 reconstruction on uniform clock phylogenyFig. 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.Fig_S1_limbs_uniform_clock.pdfFig. S2. Macrostomatan phenotype reconstruction on uniform clock phylogenyFig. 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.Fig_S2_Gape_uniform_clock.pdfFig. S3. Limb reconstruction on constrained, fossil tip FBD phylogenyFig. 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.Fig_S3_limbs_constrained_foss_tip_FBD.pdf.pdfFig. S4. Macrostomatan phenotype reconstruction on constrained, fossil tip FBD phylogenyFig. 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.Fig_S4_Gape_constrained_foss_tip_FBD.pdfFig. S5. Limb reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogeny.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.Fig_S5_Limbs_no_Tetrapodophis.pdfFig. S6. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogenyFig. 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.Fig_S6_Gape_no_Tetrapodophis.pdfFig. S7. Limb reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogenyFig. 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.Fig_S7_Limbs_no_Tetrapodophis_or_Caldwell_etal2015.pdfFig. S8. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogenyFig. 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.Fig_S8_Gape_no_Tetrapodophis_or_Caldwell_etal2015.pdfFig. S9. Macrostomatan phenotype reconstruction on constrained, diversified FBD phylogeny with madstoiids coded uncertainFig. 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.Fig_S9_Gape_reconstruction_Madtsoiidae_uncertain.pdfFiles S1-S17. Supplemental tree files.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.Files_S1-S17_tree_files.zipFiles S18-S23. Zip file containing data matrices and MrBayes blocksFiles 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.Files_S18-S23_matrices_MrBayes_blocks.zipTable S1. Node calibrations included in divergence dating analyses.Table_S1_calibrations.xlsx