Different phylogenomic methods support monophyly of enigmatic ‘Mesozoa’ (Dicyemida + Orthonectida, Lophotrochozoa)

The structure of the muscular and nervous systems of the orthonectid Rhopalura litoralis (Orthonectida) or what parasitism can do to an annelid

(2021) George S. Slyusarev et al.   ORGANISMS DIVERSITY & EVOLUTION

Phylogenetic tree building in the genomic age

(2020) Paschalia Kapli et al.   NATURE REVIEWS GENETICS

Conservative route to genome compaction in a miniature annelid

(2020) José M. Martín-Durán et al.   Nature Ecology & Evolution

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

(2019) Ferdinand Marlétaz et al.   CURRENT BIOLOGY

A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error

(2019) Jesús A Ballesteros et al.   SYSTEMATIC BIOLOGY

Comparative analysis of the mitochondrial genomes of Orthonectida: insights into the evolution of an invertebrate parasite species

(2019) N. Bondarenko et al.   MOLECULAR GENETICS AND GENOMICS

Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

(2019) Oleg A. Zverkov et al.   Frontiers in Genetics

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recent progress in reconstructing lophotrochozoan (spiralian) phylogeny

(2019) Christoph Bleidorn   ORGANISMS DIVERSITY & EVOLUTION

Orthonectids Are Highly Degenerate Annelid Worms

(2018) Philipp H. Schiffer et al.   CURRENT BIOLOGY

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

(2018) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Current Understanding of Ecdysozoa and its Internal Phylogenetic Relationships

(2017) Gonzalo Giribet et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution

(2017) Tsai-Ming Lu et al.   Zoological Letters

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

(2016) Kirill V. Mikhailov et al.   CURRENT BIOLOGY

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

(2016) Xing-Xing Shen et al.   Genome Biology and Evolution

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Twenty years into the “new animal phylogeny”: Changes and challenges

(2016) Andreas Wanninger   ORGANISMS DIVERSITY & EVOLUTION

How our view of animal phylogeny was reshaped by molecular approaches: lessons learned

(2016) Kenneth M. Halanych   ORGANISMS DIVERSITY & EVOLUTION

On 20 years of Lophotrochozoa

(2016) Kevin M. Kocot   ORGANISMS DIVERSITY & EVOLUTION

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Detailed reconstruction of the nervous and muscular system of Lobatocerebridae with an evaluation of its annelid affinity

(2015) Alexandra Kerbl et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomic Insights into Animal Evolution

(2015) Maximilian J. Telford et al.   CURRENT BIOLOGY

Ecological innovations in the Cambrian and the origins of the crown group phyla

(2015) Graham E. Budd et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Animal Phylogeny and Its Evolutionary Implications

(2014) Casey W. Dunn et al.   Annual Review of Ecology Evolution and Systematics

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

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

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

Phylogenetic Analysis of Dicyemid Mesozoans (Phylum Dicyemida) From Innexin Amino Acid Sequences: Dicyemids Are Not Related to Platyhelminthes

(2010) Takahito G. Suzuki et al.   JOURNAL OF PARASITOLOGY

Compositional Heterogeneity and Phylogenomic Inference of Metazoan Relationships

(2010) M. P. Nesnidal et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates

(2010) Jessica A. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS