Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista

(2015) Thomas Cavalier-Smith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic perspectives on the birth and spread of plastids: Fig. 1.

(2015) John M. Archibald   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial proteins pinpoint a single eukaryotic root

(2015) Romain Derelle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?

(2015) Tereza Ševčíková et al.   Scientific Reports

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Endosymbiotic theory for organelle origins

(2014) Verena Zimorski et al.   CURRENT OPINION IN MICROBIOLOGY

Chromera velia, Endosymbioses and the Rhodoplex Hypothesis—Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles, and Haptophytes (CASH Lineages)

(2014) Jörn Petersen et al.   Genome Biology and Evolution

An Amino Acid Substitution-Selection Model Adjusts Residue Fitness to Improve Phylogenetic Estimation

(2014) H.-C. Wang 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

Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites

(2014) Laura A. Katz et al.   SYSTEMATIC BIOLOGY

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

(2014) F. Burki   Cold Spring Harbor Perspectives in Biology

The evolution of photosynthesis in chromist algae through serial endosymbioses

(2014) John W. Stiller et al.   Nature Communications

Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista

(2014) Akinori Yabuki et al.   Scientific Reports

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Symbiogenesis: Mechanisms, Evolutionary Consequences, and Systematic Implications

(2013) Thomas Cavalier-Smith   Annual Review of Ecology Evolution and Systematics

The Number, Speed, and Impact of Plastid Endosymbioses in Eukaryotic Evolution

(2013) Patrick J. Keeling   Annual Review of Plant Biology

Phylogenomics of the Intracellular Parasite Mikrocytos mackini Reveals Evidence for a Mitosome in Rhizaria

(2013) Fabien Burki et al.   CURRENT BIOLOGY

Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates

(2013) Fabien Burki et al.   EUKARYOTIC CELL

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as ‘Picobiliphytes’

(2013) Ramkumar Seenivasan et al.   PLoS One

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

(2013) M. W. Brown et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distribution of the SELMA Translocon in Secondary Plastids of Red Algal Origin and Predicted Uncoupling of Ubiquitin-Dependent Translocation from Degradation

(2012) Simone Stork et al.   EUKARYOTIC CELL

Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin

(2012) Fabien Burki et al.   Genome Biology and Evolution

Reevaluating the Green Contribution to Diatom Genomes

(2012) Philippe Deschamps et al.   Genome Biology and Evolution

Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny

(2012) Huan Qiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

(2012) Julien Soubrier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

(2012) Bruce A. Curtis et al.   NATURE

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

(2012) F. Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

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

Dinoflagellate Genome Evolution

(2010) Jennifer H. Wisecaver et al.   Annual Review of Microbiology

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations

(2010) Jon Bråte et al.   BMC MICROBIOLOGY

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

(2010) D. Baurain et al.   MOLECULAR BIOLOGY AND EVOLUTION

The endosymbiotic origin, diversification and fate of plastids

(2010) P. J. Keeling   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

(2010) J. Janouskovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The Puzzle of Plastid Evolution

(2009) John M. Archibald   CURRENT BIOLOGY

Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates

(2009) Fabien Burki et al.   Genome Biology and Evolution

Protein Targeting into Secondary Plastids

(2009) KATHRIN BOLTE et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov

(2009) Noriko Okamoto et al.   PLoS One

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromalveolate plastids: direct descent or multiple endosymbioses?

(2009) Andrzej Bodył et al.   TRENDS IN ECOLOGY & EVOLUTION

A HYPOTHESIS FOR PLASTID EVOLUTION IN CHROMALVEOLATES1

(2008) M. Virginia Sanchez-Puerta et al.   JOURNAL OF PHYCOLOGY

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

(2008) N. Lartillot et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata

(2008) Eunsoo Kim et al.   PLoS One