Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

(2016) Sara Branco et al.   MOLECULAR ECOLOGY

Strong phylogeographic co-structure between the anther-smut fungus and its white campion host

(2016) Alice Feurtey et al.   NEW PHYTOLOGIST

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

(2015) George P. Tiley et al.   BMC EVOLUTIONARY BIOLOGY

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

(2015) Michael H Perlin et al.   BMC GENOMICS

The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen

(2015) D. Croll et al.   GENETICS

Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae

(2015) Hélène Badouin et al.   GENETICS

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

(2015) J D Manthey et al.   HEREDITY

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

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

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

APhytophthora sojaeGlycoside Hydrolase 12 Protein Is a Major Virulence Factor during Soybean Infection and Is Recognized as a PAMP

(2015) Zhenchuan Ma et al.   PLANT CELL

Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae

(2015) Hélène Badouin et al.   GENETICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Characterization of Genetic Diversity in the NematodePristionchus pacificusfrom Population-Scale Resequencing Data

(2014) Christian Rödelsperger et al.   GENETICS

Performance of a Hybrid Fungal Pathogen on Pure-Species and Hybrid Host Plants

(2014) Amanda K. Gibson et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana

(2014) Christian D. Huber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

(2014) Eric Fontanillas et al.   MOLECULAR BIOLOGY AND EVOLUTION

GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis

(2014) Sylvain Glémin et al.   TRENDS IN GENETICS

Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes

(2014) Nitin Udpa et al.   GENOME BIOLOGY

The evolving fungal genome

(2014) Eva H. Stukenbrock et al.   Fungal Biology Reviews

Diversity of Lactase Persistence Alleles in Ethiopia: Signature of a Soft Selective Sweep

(2013) Bryony L. Jones et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

(2013) Yann Lesecque et al.   MOLECULAR BIOLOGY AND EVOLUTION

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

SIBLING COMPETITION ARENA: SELFING AND A COMPETITION ARENA CAN COMBINE TO CONSTITUTE A BARRIER TO GENE FLOW IN SYMPATRY

(2012) A. K. Gibson et al.   EVOLUTION

Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus

(2012) M. E. Hood et al.   GENETICS

Limited Evidence for Classic Selective Sweeps in African Populations

(2012) J. M. Granka et al.   GENETICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

(2012) Erik C Andersen et al.   NATURE GENETICS

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Copper at the Front Line of the Host-Pathogen Battle

(2012) Richard A. Festa et al.   PLoS Pathogens

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans

(2011) Shmuel Sattath et al.   PLoS Genetics

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

(2010) D. E. Neafsey et al.   GENOME RESEARCH

No Evidence of Reproductive Character Displacement between Two Sister Fungal Species Causing Anther Smut Disease in Silene

(2010) Guislaine Refrégier et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Maintenance of Fungal Pathogen Species That Are Specialized to Different Hosts: Allopatric Divergence and Introgression through Secondary Contact

(2010) P. Gladieux 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

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Distribution of the anther-smut pathogen Microbotryum on species of the Caryophyllaceae

(2010) Michael E. Hood et al.   NEW PHYTOLOGIST

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evidence for widespread adaptive evolution of gene expression in budding yeast

(2010) H. B. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking the emergence of fungal plant diseases with ecological speciation

(2010) Tatiana Giraud et al.   TRENDS IN ECOLOGY & EVOLUTION

Glacial Refugia in Pathogens: European Genetic Structure of Anther Smut Pathogens on Silene latifolia and Silene dioica

(2010) Elodie Vercken et al.   PLoS Pathogens

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

The Fungi

(2009) Jason E. Stajich et al.   CURRENT BIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Silene as a model system in ecology and evolution

(2009) G Bernasconi et al.   HEREDITY

Hybrid sterility and inviability in the parasitic fungal species complexMicrobotryum

(2009) D. M. DE VIENNE et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Recent Strong Positive Selection on Drosophila melanogaster HDAC6, a Gene Encoding a Stress Surveillance Factor, as Revealed by Population Genomic Analysis

(2009) N. Svetec et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population Genetics of Fungal and Oomycete Effectors Involved in Gene-for-Gene Interactions

(2009) Eva H. Stukenbrock et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10

(2009) F. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice

(2009) Asis Khan et al.   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Mating System of the Anther Smut FungusMicrobotryum violaceum: Selfing under Heterothallism

(2008) Tatiana Giraud et al.   EUKARYOTIC CELL

PERMANENT GENETIC RESOURCES: Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum

(2007) T. GIRAUD et al.   Molecular Ecology Resources