Extensive recent secondary contacts between four European white oak species

Using joint multivariate analyses of leaf morphology and molecular-genetic markers for taxon identification in three hybridizing European white oak species (Quercus spp.)

(2016) Christian Rellstab et al.   ANNALS OF FOREST SCIENCE

High-density linkage mapping and distribution of segregation distortion regions in the oak genome

(2016) Catherine Bodénès et al.   DNA RESEARCH

Signatures of local adaptation in candidate genes of oaks (Quercusspp.) with respect to present and future climatic conditions

(2016) Christian Rellstab et al.   MOLECULAR ECOLOGY

Unusually limited pollen dispersal and connectivity of Pedunculate oak (Quercus robur) refugial populations at the species' southern range margin

(2016) E. Moracho et al.   MOLECULAR ECOLOGY

Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

(2016) A. Le Moan et al.   MOLECULAR ECOLOGY

Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

(2016) Camille Christe et al.   MOLECULAR ECOLOGY

When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts inVenturia inaequalis

(2016) Thibault Leroy et al.   NEW PHYTOLOGIST

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

(2015) Isabelle Lesur et al.   BMC GENOMICS

Late Quaternary history of North Eurasian Norway spruce (Picea abies) and Siberian spruce (Picea obovata) inferred from macrofossils, pollen and cytoplasmic DNA variation

(2015) Mari Mette Tollefsrud et al.   JOURNAL OF BIOGEOGRAPHY

Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

(2015) C. Lepoittevin et al.   Molecular Ecology Resources

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

(2015) Christophe Plomion et al.   Molecular Ecology Resources

Emergence of new virulent populations of apple scab from nonagricultural disease reservoirs

(2015) Christophe Lemaire et al.   NEW PHYTOLOGIST

History of Larix decidua Mill. (European larch) since 130 ka

(2015) Stefanie Wagner et al.   QUATERNARY SCIENCE REVIEWS

Genetic variation of Central European oaks: shaped by evolutionary factors and human intervention?

(2015) Charalambos Neophytou et al.   Tree Genetics & Genomes

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Anil Raj et al.   GENETICS

When virulence originates from non-agricultural hosts: New insights into plant breeding

(2014) Thibault Leroy et al.   INFECTION GENETICS AND EVOLUTION

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in aMytilushybrid zone

(2014) C. Roux et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus

(2014) François Hubert et al.   SYSTEMATICS AND BIODIVERSITY

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing

(2013) Saneyoshi Ueno et al.   BMC GENOMICS

Speciation of two desert poplar species triggered by Pleistocene climatic oscillations

(2013) J Wang et al.   HEREDITY

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection

(2013) Yoan Fourcade et al.   MOLECULAR ECOLOGY

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes

(2013) Charalambos Neophytou   Tree Genetics & Genomes

Strength and variability of postmating reproductive isolating barriers between four European white oak species

(2013) O. Lepais et al.   Tree Genetics & Genomes

Comparative mapping in the Fagaceae and beyond with EST-SSRs

(2012) Catherine Bodénès et al.   BMC PLANT BIOLOGY

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.)

(2011) P. ABADIE et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation?

(2011) Camille Roux et al.   PLoS One

A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genomic libraries

(2011) Isabelle Lesur et al.   Tree Genetics & Genomes

Role of waterlogging-responsive genes in shaping interspecific differentiation between two sympatric oak species

(2011) G. Le Provost et al.   TREE PHYSIOLOGY

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

(2011) Vincent Castric et al.   PLoS Genetics

Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)

(2010) Jean-Marie Cornuet et al.   BMC BIOINFORMATICS

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

(2010) Saneyoshi Ueno et al.   BMC GENOMICS

REPRODUCTIVE PATTERNS SHAPE INTROGRESSION DYNAMICS AND SPECIES SUCCESSION WITHIN THE EUROPEAN WHITE OAK SPECIES COMPLEX

(2010) Olivier Lepais et al.   EVOLUTION

The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

(2010) S T Kalinowski   HEREDITY

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

Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus

(2010) Kenneth D. Whitney et al.   NEW PHYTOLOGIST

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Historical Divergence and Gene Flow in the Genus Zea

(2009) J. Ross-Ibarra et al.   GENETICS

Who believes in whole-genome scans for selection?

(2009) J Hermisson   HEREDITY

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Species relative abundance and direction of introgression in oaks

(2009) O. LEPAIS et al.   MOLECULAR ECOLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Leaf morphological analyses in four European oak species (Quercus) and their hybrids: A comparison of traditional and geometric morphometric methods

(2009) V. Viscosi et al.   PLANT BIOSYSTEMS

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

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

Why sampling scheme matters: the effect of sampling scheme on landscape genetic results

(2008) Michael K. Schwartz et al.   CONSERVATION GENETICS

Paleoecology meets genetics: deciphering past vegetational dynamics

(2008) Feng Sheng Hu et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

The genic view of plant speciation: recent progress and emerging questions

(2008) C. Lexer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

(2008) Jeffrey Ross-Ibarra et al.   PLoS One