Plant adaptation and speciation studied by population genomic approaches

Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population

(2018) Xufeng Wang et al.   Molecular Plant

Soil environment is a key driver of adaptation in Medicago truncatula : new insights from landscape genomics

(2018) Jimena Guerrero et al.   NEW PHYTOLOGIST

Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa

(2018) Athena D. McKown et al.   NEW PHYTOLOGIST

Combining population genomics and fitness QTLs to identify the genetics of local adaptation inArabidopsis thaliana

(2018) Nicholas Price et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of population history using coalescent HMMs: review and outlook

(2018) Jeffrey P Spence et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Patterns of Polymorphism at the Self-Incompatibility Locus in 1,083 Arabidopsis thaliana Genomes

(2017) Takashi Tsuchimatsu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation

(2017) Shaun J. Curtin et al.   PLANT PHYSIOLOGY

African genomes illuminate the early history and transition to selfing inArabidopsis thaliana

(2017) Arun Durvasula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

(2017) Claudia Bartoli et al.   Frontiers in Plant Science

Young inversion with multiple linked QTLs under selection in a hybrid zone

(2017) Cheng-Ruei Lee et al.   Nature Ecology & Evolution

Understanding the coevolutionary dynamics of mutualism with population genomics

(2016) Jeremy B. Yoder   AMERICAN JOURNAL OF BOTANY

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

(2016) Jun Wang et al.   NATURE GENETICS

The evolution of symbiont preference traits in the model legume Medicago truncatula

(2016) Rebecca T. Batstone et al.   NEW PHYTOLOGIST

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

(2016) Maggie R. Wagner et al.   Nature Communications

Evolution of Selfing: Recurrent Patterns in Molecular Adaptation

(2015) Kentaro K. Shimizu et al.   Annual Review of Ecology Evolution and Systematics

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Population Genomics for Understanding Adaptation in Wild Plant Species

(2015) Detlef Weigel et al.   Annual Review of Genetics

Genomic Signature of Selective Sweeps Illuminates Adaptation ofMedicago truncatulato Root-Associated Microorganisms

(2015) Maxime Bonhomme et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coselected genes determine adaptive variation in herbivore resistance throughout the native range ofArabidopsis thaliana

(2015) Benjamin Brachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in theMedicago truncatula dnf7mutant

(2015) Beatrix Horváth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella

(2015) Adrien Sicard et al.   Nature Communications

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

(2014) Eunyoung Chae et al.   CELL

Root microbiome relates to plant host evolution in maize and other Poaceae

(2014) Marie-Lara Bouffaud et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

(2014) Luke M Evans et al.   NATURE GENETICS

Partner selection in the mycorrhizal mutualism

(2014) Gijsbert D. A. Werner et al.   NEW PHYTOLOGIST

Running with the Red Queen: the role of biotic conflicts in evolution

(2014) M. A. Brockhurst et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide association study of Arabidopsis thaliana leaf microbial community

(2014) Matthew W. Horton et al.   Nature Communications

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

(2014) Natacha Bodenhausen et al.   PLoS Genetics

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

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

(2013) Timothy Paape et al.   MOLECULAR ECOLOGY

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Natural Variation in Maize Aphid Resistance Is Associated with 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxazin-3-One Glucoside Methyltransferase Activity

(2013) L. N. Meihls et al.   PLANT CELL

Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera)

(2013) Miklós Bálint et al.   PLoS One

Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula

(2013) John Stanton-Geddes et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana

(2013) J. Agren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system

(2013) S. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary consequences of self-fertilization in plants

(2013) S. I. Wright et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella

(2012) Gesseca Gos et al.   BMC EVOLUTIONARY BIOLOGY

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

(2012) Anja C. Hörger et al.   PLoS Genetics

Independent Domestication of Asian Rice Followed by Gene Flow from japonica to indica

(2011) C.-c. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Induction and detoxification of maize 1,4-benzoxazin-3-ones by insect herbivores

(2011) Gaétan Glauser et al.   PLANT JOURNAL

Benzoxazinoid Metabolites Regulate Innate Immunity against Aphids and Fungi in Maize

(2011) Shakoor Ahmad et al.   PLANT PHYSIOLOGY

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

The polymorphic prelude to Bateson–Dobzhansky–Muller incompatibilities

(2011) Asher D. Cutter   TRENDS IN ECOLOGY & EVOLUTION

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

(2010) Marco Todesco et al.   NATURE

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping

(2010) A. Nemri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging Concepts in Effector Biology of Plant-Associated Organisms

(2009) Saskia A. Hogenhout et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Benzoxazinoid biosynthesis, a model for evolution of secondary metabolic pathways in plants

(2009) Monika Frey et al.   PHYTOCHEMISTRY

Recent speciation associated with the evolution of selfing in Capsella

(2009) J. P. Foxe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?

(2009) Catherine Masson-Boivin et al.   TRENDS IN MICROBIOLOGY