Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

(2014) Alexandra R. Wey-Fabrizius et al.   PLoS One

New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

(2013) Maximilian P Nesnidal et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics of Annelida revisited: a cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data

(2013) Sebastian Kvist et al.   CLADISTICS

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny

(2013) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

(2013) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

(2013) Torsten H. Struck   PLoS One

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

Opsins in Onychophora (Velvet Worms) Suggest a Single Origin and Subsequent Diversification of Visual Pigments in Arthropods

(2012) Lars Hering et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model

(2012) Patrick Kück et al.   PLoS One

Evolution of centralized nervous systems: Two schools of evolutionary thought

(2012) R. G. Northcutt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay between a Wnt-dependent organiser and the Notch segmentation clock regulates posterior development in Periplaneta americana

(2012) J. E. Chesebro et al.   Biology Open

Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids

(2011) Min Zhong et al.   BMC EVOLUTIONARY BIOLOGY

Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

(2011) Mark P. Simmons   CLADISTICS

Spurious 99% bootstrap and jackknife support for unsupported clades

(2011) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data

(2011) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

Higher-level metazoan relationships: recent progress and remaining questions

(2011) Gregory D. Edgecombe et al.   ORGANISMS DIVERSITY & EVOLUTION

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Profiling by Image Registration Reveals Common Origin of Annelid Mushroom Bodies and Vertebrate Pallium

(2010) Raju Tomer et al.   CELL

Comparative neuroanatomy suggests repeated reduction of neuroarchitectural complexity in Annelida

(2010) Carsten M Heuer et al.   Frontiers in Zoology

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

(2010) Patrick Kück et al.   Frontiers in Zoology

Plathelminthes and Plathelminthomorpha - paraphyletic taxa

(2010) G. Haszprunar   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida)

(2010) Bernhard Hausdorf et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Parallel evolution of segmentation by co-option of ancestral gene regulatory networks

(2009) Ariel D. Chipman   BIOESSAYS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Segmentation, metamerism and the Cambrian explosion

(2009) Juan Pablo Couso   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal Acoelomorpha

(2009) J. Paps et al.   MOLECULAR BIOLOGY AND EVOLUTION

Support for the monophyletic origin of Gnathifera from phylogenomics

(2009) Alexander Witek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes

(2009) J. Paps et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades

(2008) G. Alexe et al.   JOURNAL OF MOLECULAR EVOLUTION

Phylogenetic Position of Nemertea Derived from Phylogenomic Data

(2008) T. H. Struck et al.   MOLECULAR BIOLOGY AND EVOLUTION

A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics

(2008) Omar Rota-Stabelli et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Assembling the lophotrochozoan (=spiralian) tree of life

(2008) G. Giribet   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The molecular ancestry of segmentation mechanisms

(2008) E. M. De Robertis   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel implications for the basal internal relationships of Gastrotricha revealed by an analysis of morphological characters

(2008) Alexander Kieneke et al.   ZOOLOGICA SCRIPTA

Architecture of the nervous system in two Dactylopodola species (Gastrotricha, Macrodasyida)

(2008) Birgen H. Rothe et al.   ZOOMORPHOLOGY