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dc.contributor.author Fong, Jonathan J.
dc.contributor.author Brown, Jeremy M.
dc.contributor.author Fujita, Matthew K.
dc.contributor.author Boussau, Bastien
dc.date.accessioned 2012-11-12T18:19:57Z
dc.date.available 2012-11-12T18:19:57Z
dc.date.issued 2012-11-07
dc.identifier doi:10.5061/dryad.25j6h
dc.identifier.citation Fong JJ, Brown JM, Fujita MK, Boussau B (2012) A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. PLoS ONE 7(11): e48990.
dc.identifier.uri http://hdl.handle.net/10255/dryad.42992
dc.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.
dc.relation.haspart doi:10.5061/dryad.25j6h/1
dc.relation.haspart doi:10.5061/dryad.25j6h/2
dc.relation.haspart doi:10.5061/dryad.25j6h/3
dc.relation.haspart doi:10.5061/dryad.25j6h/4
dc.relation.haspart doi:10.5061/dryad.25j6h/5
dc.relation.haspart doi:10.5061/dryad.25j6h/6
dc.relation.haspart doi:10.5061/dryad.25j6h/7
dc.relation.haspart doi:10.5061/dryad.25j6h/8
dc.relation.haspart doi:10.5061/dryad.25j6h/9
dc.relation.isreferencedby doi:10.1371/journal.pone.0048990
dc.relation.isreferencedby PMID:23145043
dc.subject tree of life
dc.subject higher-level systematics
dc.subject non-phylogenetic signal
dc.subject systematic error
dc.subject data filtering
dc.subject discriminant function analysis
dc.title Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia
dc.type Article *
dwc.ScientificName Testudines
dwc.ScientificName Lissamphibia
dc.contributor.correspondingAuthor Fong, Jonathan J.
prism.publicationName PLoS ONE

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Title 129 taxa
Downloaded 46 times
Description Zip 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.
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Title 16 taxa
Downloaded 42 times
Description Zip 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.
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Title Individual Genes
Downloaded 43 times
Description 75 individual gene datasets. All datasets start with the first codon position.
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Title 31 genes
Downloaded 32 times
Description Zip 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.
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Title 26 genes
Downloaded 40 times
Description Zip 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.
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Title 16taxa 31genes
Downloaded 37 times
Description Zip 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.
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Title 16taxa 26genes
Downloaded 39 times
Description Zip 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.
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Title Simulated Data
Downloaded 35 times
Description Two simulated datasets used in study
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Title Slow Genes
Downloaded 45 times
Description Data and partition file for the reduced gene dataset, removing the 19 most quickly evolving genes. Partition is by gene.
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