Data from: Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

Burbrink F, Grazziotin F, Pyron R, Cundall D, Donnellan S, Irish F, Keogh S, Kraus F, Murphy R, Noonan B, Raxworthy C, Ruane S, Lemmon A, Lemmon E, Zaher H

Date Published: September 13, 2019

DOI: https://doi.org/10.5061/dryad.sm6jb0p

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Title Data_S1_Aligned_AHA genomic_data_for tree_order
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Description Anchored hybrid enrichment genomic-scale data for squamata
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Title Data_S2_Concatenated_Squam_Concatenated
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Description Concatenated loci
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Title Data_S3_Concatenated_partitioned_models
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Description Partitions and models for the concatenated data
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Title Data_S4_Tree_1_Squamate_ASTRAL_IQ_BS_Tree
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Description ASTRAL III phylogeny using IQTree gene trees with bootstrap support
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Title Data_S5_Tree_2_SQ_IQ_ASTRAL_Full_Annotations
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Description ASTRAL III Phylogeny using IQ gene trees with full ASTRAL annotations on quadripartitions
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Title Data_S6_Tree_3_Squamata_IQ_ASTRAL_ASTRAL_Support
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Description ASTRAL III phylogeny with ASTRAL quadripartion support
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Title Data_S7_Tree_4_Squam_IQ_Concat_Part_BS_SH
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Description Concatenated and partitioned IQTree with bootstrap and SH support (BS/SH)
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Title Data_S8_Dated_ASTRAL_IQ_Point_Tree
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Description Dated phylogeny where concatenated sequence data were fit to the topology of ASTRAL III tree and dates were estimated using TreePL
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Title Data_S9_Dated_IQ_UF_Bootstraps_with_error
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Description Dated phylogeny with error using 1000 IQ trees and UFBoots (Fast bootstrap) function and estimated with TreePL
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Title Data_S10_Dated_Combined_Slow_bootstraps_RAXML_with_error
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Description Dated phylogeny with error using 100 RAxML bootstraps and phylogenies estimates using IQTree and estimated with TreePL (slow bootstraps)
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Title Data_S11_Tree_PL_control
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Description Control file for running TreePL
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Title Data_S12_All_Code_Squamate_Monophyly-Multicolinearity_STATS
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Description Code for running Neural Network for gene interrogation and other functions
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Title Data_S13_gene_support_species_tree_by_date
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Description Dated nodes from the species tree showing the number of genes that support or do not support that node
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Title Data_S14_Support_by_node_table
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Description Nodes from species tree showing if each locus supports (1) or does not support (0) that node
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Title Data_S15. NN_Table_All_Stats
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Description Table of all stats for each locus for testing predictions of RFgt-st differences using NN code for regression predictions.
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Title Data_S16_Gene_Trees_Dib_Gekkota_not_mono_ASTRAL_tree
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Description ASTRAL III tree generated from IQ Trees not showing Dibamidae and Gekkota as monophyletic
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Title Data_S17_Gene_Trees_Not_Supporting_Anilius_ASTRAL_tree
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Description ASTRAL III tree generated from IQ Trees not showing Dibamidae and Gekkota as monophyletic
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Title Data_S18_Gene_Trees_Not_Supporting_Toxicofera_ASTRAL_Tree
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Description ASTRAL III tree generated from IQ Trees not showing Toxicofera as monophyletic
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Title Data_S19_NN_Test_Data_Anil_Dib_Tox
Downloaded 12 times
Description Data table for use with NN code (Data_S12) to make classification prediction for why genes do or do not find Toxicofera, Amerophidia, Dibamia/Gekkota.
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Title Fig_S1_Phylogenetic Informativeness
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Description Phylogenetic informativeness for each locus ranked by the length of time. The length of time colored for each locus is associated with strong phylogenetic informativeness over that time period. Loci at the top of the graph are informative over a larger range of time than those at the bottom
Download Fig_S1_Phylogenetic Informativeness.docx (126.0 Kb)
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Title Fig_S2_NN_Model
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Description An artificial NN model showing input neurons characterizing each AHE locus, the single hidden neuron layer (H1), and the output variable predicting RF distances between each gene tree and the species tree (RFgtst). This diagram shows both intercept terms (bias), B1 and B2, which increases NN efficiency, and synaptic weights indicated by the thickness and bolding of lines connecting the neurons
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Title Table_S1_SquamateAssemblySummary
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Description Excel list of Squamata species sequenced and corresponding summary statistics of capture and sequencing success.
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Title Table_S2_Calibration_points_for_Squamata_phylogeny
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Description Calibration points for Squamata phylogeny
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Burbrink F, Grazziotin F, Pyron R, Cundall D, Donnellan S, Irish F, Keogh S, Kraus F, Murphy R, Noonan B, Raxworthy C, Ruane S, Lemmon A, Lemmon E, Zaher H (2019) Data from: Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Dryad Digital Repository. https://doi.org/10.5061/dryad.sm6jb0p
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