Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers

(2016) Kathryn A. Hodgins et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

The number of known plants species in the world and its annual increase

(2016) MAARTEN J.M. CHRISTENHUSZ et al.   Phytotaxa

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss

(2015) Tracey A Ruhlman et al.   BMC PLANT BIOLOGY

Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families

(2015) Amanda R. De La Torre et al.   Genome Biology and Evolution

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

(2015) René L. Warren et al.   PLANT JOURNAL

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads

(2014) Dayana E. Salas-Leiva et al.   Molecular Ecology Resources

Evolution and biogeography of gymnosperms

(2014) Xiao-Quan Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

Insights into Conifer Giga-Genomes

(2014) A. R. De La Torre et al.   PLANT PHYSIOLOGY

Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes

(2014) Ying Lu et al.   PLoS One

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

Transcriptome analysis in maritime pine using laser capture microdissection and 454 pyrosequencing

(2014) R. A. Canas et al.   TREE PHYSIOLOGY

Overly simplistic substitution models obscure green plant phylogeny

(2014) Endymion D. Cooper   TRENDS IN PLANT SCIENCE

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads

(2013) Chung-Shien Wu et al.   Genome Biology and Evolution

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

(2013) Manuel Gil et al.   MOLECULAR BIOLOGY AND EVOLUTION

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity inLolium perenne

(2013) Tom Ruttink et al.   PLANT BIOTECHNOLOGY JOURNAL

Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships

(2013) Zhenxiang Xi et al.   PLoS One

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

(2012) Jun Chen et al.   BMC GENOMICS

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

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

(2011) Diego Darriba et al.   BIOINFORMATICS

Diversification of land plants: insights from a family-level phylogenetic analysis

(2011) Omar Fiz-Palacios et al.   BMC EVOLUTIONARY BIOLOGY

Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

(2011) Chung-Shien Wu et al.   Genome Biology and Evolution

Systematic Error in Seed Plant Phylogenomics

(2011) Bojian Zhong et al.   Genome Biology and Evolution

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms

(2011) Michael D. Crisp et al.   NEW PHYTOLOGIST

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

Recent Synchronous Radiation of a Living Fossil

(2011) N. S. Nagalingum et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

(2010) Ching-Ping Lin et al.   Genome Biology and Evolution

Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

(2010) Angélica Cibrián-Jaramillo et al.   Genome Biology and Evolution

Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

(2010) Robert M. Waterhouse et al.   Genome Biology and Evolution

The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics

(2010) B. Zhong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Linear Angiosperm Phylogeny Group (LAPG) III: a linear sequence of the families in APG III

(2009) ELSPETH HASTON et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

A phylogenetic classification of the land plants to accompany APG III

(2009) MARK W. CHASE et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny

(2009) Thomas Werner Anthony Braukmann et al.   CURRENT GENETICS

Selection on Nuclear Genes in a Pinus Phylogeny

(2009) A.E. Palmé et al.   MOLECULAR BIOLOGY AND EVOLUTION

The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae)

(2009) Rachel A. Levin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy

(2009) Chung-Shien Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms

(2009) Jin-Hua Ran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data

(2009) Jose Eduardo de la Torre-Bárcena et al.   PLoS One

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

(2008) Sarah Mathews   AMERICAN JOURNAL OF BOTANY

A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)

(2008) Steven G Ralph et al.   BMC GENOMICS

Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins

(2008) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY