Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships.

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Molecular Phylogenetics and Evolution

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.ympev.2011.08.028PMID 21945533
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

  2011influential reference
• Molecular paleobiological insights into the origin of the Brachiopoda

  2011cited by this paper
• Echinoderm phylogeny including Xyloplax, a progenetic asteroid.

  2011cited by this paper
• Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

  2011cited by this paper
• microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

  2010cited by this paper
• Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm

  2010cited by this paper
• Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

  2010cited by this paper
• Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction.

  2010cited by this paper
• Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata.

  2010cited by this paper
• Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200‐Myr missing Precambrian fossil record of siliceous sponge spicules

  2010cited by this paper
• POY version 4: phylogenetic analysis using dynamic homologies

  2010cited by this paper
• MicroRNAs and metazoan phylogeny: big trees from little genes

  2009cited by this paper
• Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.

  2009cited by this paper
• Assessing the root of bilaterian animals with scalable phylogenomic methods

  2009cited by this paper
• TRACER v1.5

  2009cited by this paper
• The deep evolution of metazoan microRNAs

  2009cited by this paper
• A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics.

  2008cited by this paper
• Broad phylogenomic sampling improves resolution of the animal tree of life

  2008cited by this paper
• Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

  2008cited by this paper
• Detecting and overcoming systematic errors in genome-scale phylogenies.

  2007cited by this paper
• Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star.

  2007cited by this paper
• Phylogenomics: the beginning of incongruence?

  2006cited by this paper
• Computing Bayes factors using thermodynamic integration.

  2006cited by this paper
• RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

  2006cited by this paper
• Skeletal homologies, phylogeny and classification of the earliest asterozoan echinoderms

  2005cited by this paper
• Assembling the tree of life

  2004cited by this paper
• Estimating metazoan divergence times with a molecular clock.

  2004cited by this paper
• A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.

  2004cited by this paper
• Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda.

  2004cited by this paper
• PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

  2004cited by this paper
• From bilateral symmetry to pentaradiality: the phylogeny of hemichordates and echinoderms

  2004cited by this paper
• Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.

  2003cited by this paper
• POY version 3.0.11 (Wheeler, Gladstein and De Laet, May 6 2003). Command line documentation

  2003cited by this paper
• Matrix representation with parsimony, taxonomic congruence, and total evidence.

  2002cited by this paper
• PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10

  2002cited by this paper
• Phylogenetic relationships of extant echinoderm classes

  2001cited by this paper
• Bromidechinus, a new Ordovician echinozoan (Echinodermata), and its bearing on the early history of echinoids

  2001cited by this paper
• MRBAYES : Bayesian inference of phylogeny

  2001cited by this paper
• MRBAYES: Bayesian inference of phylogenetic trees

  2001cited by this paper
• Brain Evolution and Cognition

  2000cited by this paper
• What a New Model of Skeletal Homologies Tells Us About Asteroid Evolution1

  2000cited by this paper
• Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes.

  1999cited by this paper
• Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.

  1999cited by this paper
• The interrelationships of the echinoderm classes: morphological and molecular evidence

  1997cited by this paper
• Molecular phylogeny of the animal kingdom.

  1988cited by this paper
• Echinoderm phylogeny and evolutionary biology

  1988cited by this paper
• Cases in which Parsimony or Compatibility Methods will be Positively Misleading

  1978cited by this paper

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  2020cites this paper
• Supermatrix analyses and molecular clock rooting of Fabales: Exploring the effects of outgroup choice and long branch attraction on topology

  2020cites this paper
• Taxonomic identification of isolated theropod teeth: The case of the shed tooth crown associated with Aerosteon (Theropoda: Megaraptora) and the dentition of Abelisauridae

  2020cites this paper
• Genome-scale profiling reveals higher proportions of phylogenetic signal in non-coding data

  2019cites this paper
• Larval and Adult Body Axes in Echinoderms

  2018cites this paper
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  2018cites this paper
• The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

  2018cites this paper
• Regeneration in Stellate Echinoderms: Crinoidea, Asteroidea and Ophiuroidea.

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• Uzgoj trpova roda Holothuria

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• Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data.

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• Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

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• A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians

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• IL17 factors are early regulators in the gut epithelium during inflammatory response to Vibrio in the sea urchin larva

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• Phylogenetic taxonomy and classification of the Crinoidea (Echinodermata)

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• Echinobase: an expanding resource for echinoderm genomic information

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• A Conserved Role for VEGF Signaling in Specification of Homologous Mesenchymal Cell Types Positioned at Spatially Distinct Developmental Addresses in Early Development of Sea Urchins

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• Echinoderm development and evolution in the post-genomic era.

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• Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks

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• Application of multigene phylogenetics and site‐stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta)

  2016cites this paper
• Taxonomic status of the three color variants in sea cucumber (Apostichopus japonicus): evidence from mitochondrial phylogenomic analyses

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• The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas

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• Phylogenetic Signal Dissection Identifies the Root of Starfishes

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• Do echinoderm genomes measure up?

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• Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa

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• Evolution of voltage-gated ion channels at the emergence of Metazoa

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• The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

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• The Root of Flowering Plants and Total Evidence.

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• Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development.

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• Identification and comparative analysis of complement C3-associated microRNAs in immune response of Apostichopus japonicus by high-throughput sequencing

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• Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme.

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• Evolution of DNA Recognition in a Tbrain Transcription Factor and Its Impact on Larval Neurogenesis in Echinoderms

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• Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms

  2014cites this paper
• Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks

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• Branching out: Origins of the sea urchin larval skeleton in development and evolution

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• Les cténophores : de leur position dans l'arbre des métazoaires (approche phylogénomique) à leur diversité taxonomique (phylogénie moléculaire et anatomie comparée)

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• Neuropeptides and polypeptide hormones in echinoderms: new insights from analysis of the transcriptome of the sea cucumber Apostichopus japonicus.

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• Phylogenomic resolution of the hemichordate and echinoderm clade.

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• Deep metazoan phylogeny : the backbone of the tree of life : new insights from analyses of molecules, morphology, and theory of data analysis

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• Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci

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• SALMFamide salmagundi: the biology of a neuropeptide family in echinoderms.

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• Discovery of a novel neurophysin-associated neuropeptide that triggers cardiac stomach contraction and retraction in starfish

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  2013cites this paper
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