Impact of recurrent gene duplication on adaptation of plant genomes

Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection

(2013) Zefeng Yang et al.   BMC PLANT BIOLOGY

Locally Duplicated Ohnologs Evolve Faster Than Nonlocally Duplicated Ohnologs in Arabidopsis and Rice

(2013) Yupeng Wang   Genome Biology and Evolution

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Genomic and Transcriptomic Analysis of Tandemly and Segmentally Duplicated Genes in Rice

(2013) Shu-Ye Jiang et al.   PLoS One

Plant F-Box Protein Evolution Is Determined by Lineage-Specific Timing of Major Gene Family Expansion Waves

(2013) Aura Navarro-Quezada et al.   PLoS One

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional Evolution of an Anthocyanin Pathway Enzyme during a Flower Color Transition

(2012) Stacey D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

(2012) A. R. Leitch et al.   NEW PHYTOLOGIST

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

(2012) Jonathan Romiguier et al.   PLoS One

Leucine-Rich repeat receptor kinases are sporadically distributed in eukaryotic genomes

(2011) Anne Diévart et al.   BMC EVOLUTIONARY BIOLOGY

Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

(2011) Lindsey K Tuominen et al.   BMC GENOMICS

Models, algorithms and programs for phylogeny reconciliation

(2011) J.-P. Doyon et al.   BRIEFINGS IN BIOINFORMATICS

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

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

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Divergent evolution of oxidosqualene cyclases in plants

(2011) Zheyong Xue et al.   NEW PHYTOLOGIST

An evolutionary view of functional diversity in family 1 glycosyltransferases

(2011) Keiko Yonekura-Sakakibara et al.   PLANT JOURNAL

Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift

(2011) Zhihua Hua et al.   PLoS One

Diversity in the Architecture of ATLs, a Family of Plant Ubiquitin-Ligases, Leads to Recognition and Targeting of Substrates in Different Cellular Environments

(2011) Victor Aguilar-Hernández et al.   PLoS One

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

(2011) Yupeng Wang et al.   PLoS One

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

GreenPhylDB v2.0: comparative and functional genomics in plants

(2010) Mathieu Rouard et al.   NUCLEIC ACIDS RESEARCH

Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats

(2010) N. Schumann et al.   PLANT PHYSIOLOGY

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

Population genetic models of duplicated genes

(2009) Hideki Innan   GENETICA

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

(2009) Eduard Kejnovsky et al.   TRENDS IN ECOLOGY & EVOLUTION

The flowering world: a tale of duplications

(2009) Yves Van de Peer et al.   TRENDS IN PLANT SCIENCE

Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana

(2009) Cheng Zou et al.   PLoS Genetics

The Evolutionary Rate of Duplicated Genes Under Concerted Evolution

(2008) S. Mano et al.   GENETICS

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY

The F-Box Gene Family Is Expanded in Herbaceous Annual Plants Relative to Woody Perennial Plants

(2008) X. Yang et al.   PLANT PHYSIOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics