DOI: 10.5061/dryad.25j6h
title: Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia

description: In resolving the vertebrate tree of life, two fundamental questions
 remain: 1) what is the phylogenetic position of turtles within amniotes,
 and 2) what are the relationships between the three major lissamphibian
 (extant amphibian) groups? These relationships have historically been
 difficult to resolve, with five different hypotheses proposed for turtle
 placement, and four proposed branching patterns within Lissamphibia. We
 compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa)
 to address these outstanding questions. Gene-specific phylogenetic
 analyses revealed a great deal of variation in preferred topology,
 resulting in topologically ambiguous conclusions from the combined
 dataset. Due to consistent preferences for the same divergent topologies
 across genes, we suspected systematic phylogenetic error as a cause of
 some variation. Accordingly, we developed and tested a novel statistical
 method that identifies sites that have a high probability of containing
 biased signal for a specific phylogenetic relationship. After removing
 putatively biased sites, support emerged for a sister relationship between
 turtles and either crocodilians or archosaurs, as well as for a
 caecilian-salamander sister relationship within Lissamphibia, with
 Lissamphibia potentially paraphyletic.
description: 129
 taxaZip file of full
 datasets. Included are 8 files corresponding to 4 datasets 1)NUCL
 (nucleotide) based dataset and partition file (partitioned by codon n12
 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by
 gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1
 (nucleotide-based accounting for codon degeneracy) based dataset with
 partition file. Note, no taxa are excluded, although in final analyses
 rogue taxa are removed.129tax.zip16 taxaZip file of reduced taxon datasets (16 exemplar taxa). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.16tax.zipIndividual Genes75 individual gene datasets. All datasets start with the first codon position.IndividualGenes.zip31 genesZip file of reduced gene datasets (corresponding to turtle question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, taxon sampling has been reduced by removing rogue taxa.31genes.zip26 genesZip file of reduced gene datasets (corresponding to Lissamphibia question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, taxon sampling has been reduced by removing rogue taxa.26genes.zip16taxa 31genesZip file of reduced gene and 16 taxa datasets (corresponding to turtle question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.16tax-31genes.zip16taxa 26genesZip file of reduced gene and 16 taxa datasets (corresponding to Lissamphibia question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.16tax-26genes.zipSimulated DataTwo simulated datasets used in studySimulatedData.zipSlow GenesData and partition file for the reduced gene dataset, removing the 19 most quickly evolving genes. Partition is by gene.SlowGenes.zip