Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae

(2014) Maria D. Mikkelsen et al.   ANNALS OF BOTANY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets

(2014) Rosa Fernández et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Genome-wide probabilistic reconciliation analysis across vertebrates

(2013) Owais Mahmudi et al.   BMC BIOINFORMATICS

Evolution: Out of the Ocean

(2013) Casey W. Dunn   CURRENT BIOLOGY

Molecular Timetrees Reveal a Cambrian Colonization of Land and a New Scenario for Ecdysozoan Evolution

(2013) Omar Rota-Stabelli et al.   CURRENT BIOLOGY

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

(2013) Timothy Y. James et al.   CURRENT BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Did Terrestrial Diversification of Amoebas (Amoebozoa) Occur in Synchrony with Land Plants?

(2013) Omar Fiz-Palacios et al.   PLoS One

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

(2013) E. Tisserant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Capsaspora genome reveals a complex unicellular prehistory of animals

(2013) Hiroshi Suga et al.   Nature Communications

DLRS: gene tree evolution in light of a species tree

(2012) Joel Sjöstrand et al.   BIOINFORMATICS

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin

(2012) Isabelle Benoit et al.   BMC GENOMICS

First plants cooled the Ordovician

(2012) Timothy M. Lenton et al.   Nature Geoscience

A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic

(2012) P. Kenrick et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda

(2012) Christopher W. Wheat et al.   SYSTEMATIC BIOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants

(2011) Zoë A. Popper et al.   Annual Review of Plant Biology

Fungal enzyme sets for plant polysaccharide degradation

(2011) Joost van den Brink et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

A multigene phylogeny of Olpidium and its implications for early fungal evolution

(2011) Satoshi Sekimoto et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary analysis of glycosyl hydrolase family 28 (GH28) suggests lineage-specific expansions in necrotrophic fungal pathogens

(2011) Daniel D. Sprockett et al.   GENE

Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

(2011) Apurva Narechania et al.   Genome Biology and Evolution

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

(2011) G. Torruella et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Possible evolution of mobile animals in association with microbial mats

(2011) Murray Gingras et al.   Nature Geoscience

The charophycean green algae provide insights into the early origins of plant cell walls

(2011) Iben Sørensen et al.   PLANT JOURNAL

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

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

Arthropod colonization of land – Linking molecules and fossils in oribatid mites (Acari, Oribatida)

(2010) Ina Schaefer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FASconCAT: Convenient handling of data matrices

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

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)

(2010) C. V. Rubinstein et al.   NEW PHYTOLOGIST

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

(2009) Yu Liu et al.   BMC EVOLUTIONARY BIOLOGY

The Fungi

(2009) Jason E. Stajich et al.   CURRENT BIOLOGY

Fungi evolved right on track

(2009) Robert Lücking et al.   MYCOLOGIA

Origin and Radiation of the Earliest Vascular Land Plants

(2009) P. Steemans et al.   SCIENCE

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

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

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

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

(2009) Li-Jun Ma et al.   PLoS Genetics

Identification, biochemical characterization, and evolution of the Rhizopus oryzae 99–880 polygalacturonase gene family

(2008) Jeffrey A. Mertens et al.   FUNGAL GENETICS AND BIOLOGY

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY