A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

(2019) Arnaud Di Franco et al.   BMC EVOLUTIONARY BIOLOGY

Molecular mechanisms underpinning transgenerational plasticity in the green sea urchin Psammechinus miliaris

(2019) Melody S. Clark et al.   Scientific Reports

The phylogenomic revolution and its conceptual innovations: a text mining approach

(2019) Nicolás Mongiardino Koch   ORGANISMS DIVERSITY & EVOLUTION

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix

(2019) Seraina Klopfstein et al.   PLoS One

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

(2019) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Homoplasy and extinction: the phylogeny of cassidulid echinoids (Echinodermata)

(2019) Camilla Souto et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida)

(2019) Jih-Pai Lin et al.   GENOMICS

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

(2018) Paul Simion et al.   BMC BIOLOGY

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

Structural stress response of segmented natural shells: a numerical case study on the clypeasteroid echinoid Echinocyamus pusillus

(2018) Tobias B. Grun et al.   Journal of the Royal Society Interface

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

A new stem group echinoid from the Triassic of China leads to a revised macroevolutionary history of echinoids during the end-Permian mass extinction

(2018) Jeffrey R. Thompson et al.   Royal Society Open Science

The youngest ophiocistioid: a first Palaeozoic-type echinoderm group representative from the Mesozoic

(2018) Mike Reich et al.   PALAEONTOLOGY

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata

(2018) Nicolás Mongiardino Koch et al.   PLoS One

ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes

(2018) Benoit Morel et al.   BIOINFORMATICS

A phylogenomic resolution of the sea urchin tree of life

(2018) Nicolás Mongiardino Koch et al.   BMC EVOLUTIONARY BIOLOGY

Paleozoic echinoderm hangovers: Waking up in the Triassic

(2017) Ben Thuy et al.   GEOLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of extant Holothuroidea (Echinodermata)

(2017) Allison K. Miller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

(2017) Jeffrey R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

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

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

Echinobase: an expanding resource for echinoderm genomic information

(2017) Parul Kudtarkar et al.   Database-The Journal of Biological Databases and Curation

Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

(2016) Joseph E. O'Reilly et al.   Biology Letters

Inferring node dates from tip dates in fossil Canidae: the importance of tree priors

(2016) Nicholas J. Matzke et al.   Biology Letters

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms

(2016) Daniel A. Janies et al.   BMC BIOINFORMATICS

TNT version 1.5, including a full implementation of phylogenetic morphometrics

(2016) Pablo A. Goloboff et al.   CLADISTICS

Facies distribution and taphonomy of echinoids from the Fort Payne Formation (late Osagean, early Viséan, Mississippian) of Kentucky

(2016) Jeffrey R. Thompson et al.   JOURNAL OF PALEONTOLOGY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biases of tree-independent-character-subsampling methods

(2016) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

(2016) Rosa Fernández et al.   SYSTEMATIC BIOLOGY

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

(2016) Juan Diego Gaitán-Espitia et al.   Scientific Reports

Forked Tongues Revisited: Molecular Apomorphies Support Morphological Hypotheses of Squamate Evolution

(2015) Caleb D. McMahan et al.   COPEIA

Morphological Phylogenetics in the Genomic Age

(2015) Michael S.Y. Lee et al.   CURRENT BIOLOGY

Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchinArbacia lixulausing RNA-seq

(2015) R. Pérez-Portela et al.   Molecular Ecology Resources

An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

(2015) Dahiana Arcila et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution

(2015) Melanie J. Hopkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

Post-molecular systematics and the future of phylogenetics

(2015) R. Alexander Pyron   TRENDS IN ECOLOGY & EVOLUTION

Dating Tips for Divergence-Time Estimation

(2015) Joseph E. O’Reilly et al.   TRENDS IN GENETICS

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

(2015) Adrian Reich et al.   PLoS One

Reorganization of sea urchin gene regulatory networks at least 268 million years ago as revealed by oldest fossil cidaroid echinoid

(2015) Jeffrey R. Thompson et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Torsten H. Struck et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Global regime shift dynamics of catastrophic sea urchin overgrazing

(2014) S. D. Ling et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Agalma: an automated phylogenomics workflow

(2013) Casey W Dunn et al.   BMC BIOINFORMATICS

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko 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

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

(2013) Michael D. Nowak et al.   PLoS One

Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution

(2013) Graham J. Slater et al.   Methods in Ecology and Evolution

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The phylogeny and classification of post-Palaeozoic echinoids

(2011) Andreas Kroh et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

(2011) Carla A. Cummins et al.   SYSTEMATIC BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Compositional Heterogeneity and Phylogenomic Inference of Metazoan Relationships

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

Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa

(2010) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Diversity dynamics: molecular phylogenies need the fossil record

(2010) Tiago B. Quental et al.   TRENDS IN ECOLOGY & EVOLUTION

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE