ArticlePloS one2012
A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Unveiling the Evolutionary Lineages and Habitat Dynamics of the Monotypic Crowned River TurtleEcology and evolution · 2025Article
- MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses.Molecular biology and evolution · 2025Article
- Genomic and phylogenetic features of theVirus evolution · 2024Article
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- Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference.Systematic biology · 2022Article
- Morphology of the Cutaneous Poison and Mucous Glands in Amphibians with Particular Emphasis on Caecilians (Toxins · 2021Article
- Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree.Genome biology and evolution · 2021Article
- Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.Systematic biology · 2021Article
- Structural Variation of the Turtle Mitochondrial Control Region.Journal of molecular evolution · 2020Article
- Smooth Muscle in Cardiac Chambers is Common in Turtles and Extensive in the Emydid Turtle, Trachemys scripta.Anatomical record (Hoboken, N.J. : 2007) · 2020Article
- IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.Molecular biology and evolution · 2020Article
- Origin and Evolution of Two Independently Duplicated Genes Encoding UDP- Glucose: Glycoprotein Glucosyltransferases inG3 (Bethesda, Md.) · 2020Article
- Article
- The Prevalence and Impact of Model Violations in Phylogenetic Analysis.Genome biology and evolution · 2019Article
- Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.Molecular biology and evolution · 2019Article
- Structure and evolutionary implications of the earliest (Sinemurian, Early Jurassic) dinosaur eggs and eggshells.Scientific reports · 2019Article
- Postcranial heterochrony, modularity, integration and disparity in the prenatal ossification in bats (Chiroptera).BMC evolutionary biology · 2019Article
- Article
- Phylotranscriptomic consolidation of the jawed vertebrate timetree.Nature ecology & evolution · 2017Article
- Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.BMC evolutionary biology · 2017Article
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4 authors.
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Abstract
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.
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