Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

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

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

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

(2016) Jing Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

Germline replications and somatic mutation accumulation are independent of vegetative life span inArabidopsis

(2016) J. Matthew Watson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

(2015) Lindell Bromham et al.   AMERICAN NATURALIST

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

(2015) J. Wang et al.   GENETICS

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow

(2014) Amanda R. De La Torre et al.   MOLECULAR ECOLOGY

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

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

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

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

(2014) David B Neale et al.   GENOME BIOLOGY

Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

(2013) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

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

Somatic deleterious mutation rate in a woody plant: estimation from phenotypic data

(2013) K Bobiwash et al.   HEREDITY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

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

Taller plants have lower rates of molecular evolution

(2013) Robert Lanfear et al.   Nature Communications

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

(2012) Nathalie Pavy et al.   BMC BIOLOGY

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY 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

Weak Selection and Protein Evolution

(2012) H. Akashi et al.   GENETICS

Adaptive Evolution and Effective Population Size in Wild House Mice

(2012) M. Phifer-Rixey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Widespread Positive and Purifying Selection Across the European Rabbit (Oryctolagus cuniculus) Genome

(2012) M. Carneiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Hemisphere-scale differences in conifer evolutionary dynamics

(2012) A. B. Leslie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence variation patterns along a latitudinal cline in Scots pine (Pinus sylvestris): signs of clinal adaptation?

(2012) Sonja T. Kujala et al.   Tree Genetics & Genomes

The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates

(2011) Brandon Gaut et al.   Annual Review of Ecology Evolution and Systematics

Forest tree genomics: growing resources and applications

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

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

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

The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms

(2010) Juan P Jaramillo-Correa et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Effective Population Size Is Positively Correlated with Levels of Adaptive Divergence among Annual Sunflowers

(2010) J. L. Strasburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) T. I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size

(2010) T. Slotte et al.   MOLECULAR BIOLOGY AND EVOLUTION

Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests

(2010) J. A. HOLLIDAY et al.   MOLECULAR ECOLOGY

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)

(2010) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Aging in a Long-Lived Clonal Tree

(2010) Dilara Ally et al.   PLOS BIOLOGY

Mutation Accumulation in Real Branches: Fitness Assays for Genomic Deleterious Mutation Rate and Effect in Large‐Statured Plants

(2009) Stewart T. Schultz et al.   AMERICAN NATURALIST

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

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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

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

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

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

Selection on Nuclear Genes in a Pinus Phylogeny

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

Evidence for Variation in the Effective Population Size of Animal Mitochondrial DNA

(2009) Gwenael Piganeau et al.   PLoS One

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

(2008) Witold Wachowiak et al.   Tree Genetics & Genomes