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

Lengths of coding and noncoding regions of a gene correlate with gene essentiality and rates of evolution

(2015) Seung-Ho Shin et al.   Genes & Genomics

Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level inA. thaliana

(2015) Stephen J. Bush et al.   MOLECULAR ECOLOGY

Conservation and divergence of gene expression plasticity followingc. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

(2014) Sam Yeaman et al.   NEW PHYTOLOGIST

Insights into Conifer Giga-Genomes

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

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

(2014) Robert J. Williamson et al.   PLoS Genetics

Patterns of Selection in Plant Genomes

(2013) Josh Hough et al.   Annual Review of Ecology Evolution and Systematics

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

(2013) A. J. Eckert et al.   GENETICS

Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals

(2013) Maria Warnefors et al.   Genome Biology and Evolution

Potential for evolutionary responses to climate change - evidence from tree populations

(2013) Florian J. Alberto et al.   GLOBAL CHANGE BIOLOGY

Divergence in Gene Expression Is Uncoupled from Divergence in Coding Sequence in a Secondarily Woody Sunflower

(2013) Brook T. Moyers et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (PinussubgenusStrobus)

(2013) Andrew J. Eckert et al.   MOLECULAR ECOLOGY

Selection, genome-wide fitness effects and evolutionary rates in the model legumeMedicago truncatula

(2013) Timothy Paape et al.   MOLECULAR ECOLOGY

A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences

(2013) Jared D. Lockwood et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta , Pinaceae)

(2012) Andrew J. Eckert et al.   AMERICAN JOURNAL OF BOTANY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution

(2012) David Alvarez-Ponce   BMC EVOLUTIONARY BIOLOGY

Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

(2012) Michael J McLeish et al.   BMC EVOLUTIONARY BIOLOGY

Characterization and evolution of 5′ and 3′ untranslated regions in eukaryotes

(2012) Honglei Liu et al.   GENE

Genome-wide association genetics of an adaptive trait in lodgepole pine

(2012) THOMAS L. PARCHMAN et al.   MOLECULAR ECOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis

(2011) Tanja Slotte et al.   Genome Biology and Evolution

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

(2011) Kirk E. Lohmueller et al.   PLoS Genetics

Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

(2010) T. I. Gossmann 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

Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity

(2009) Emilie C. Snell-Rood et al.   BIOESSAYS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Natural Selection on Synonymous and Nonsynonymous Mutations Shapes Patterns of Polymorphism in Populus tremula

(2009) P. K. Ingvarsson   MOLECULAR BIOLOGY AND EVOLUTION

The Correlation of Evolutionary Rate with Pathway Position in Plant Terpenoid Biosynthesis

(2009) Heather Ramsay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation, migration or extirpation: climate change outcomes for tree populations

(2008) Sally N. Aitken et al.   Evolutionary Applications

Positive and Negative Selection on Noncoding DNA in Drosophila simulans

(2008) P. R. Haddrill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Evolution of gene sequence and gene expression are not correlated in yeast

(2008) Itay Tirosh et al.   TRENDS IN GENETICS

Evolution of protein-coding genes in Drosophila

(2008) Amanda M. Larracuente et al.   TRENDS IN GENETICS