Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

The geography of introgression in a patchy environment and the thorn in the side of ecological speciation

(2016) Nicolas Bierne et al.   Current Zoology

Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

(2014) C. Fraisse et al.   GENETICS

The genetics of speciation: are complex incompatibilities easier to evolve?

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

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

Standing and flowing: the complex origins of adaptive variation

(2014) John J. Welch et al.   MOLECULAR ECOLOGY

Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the musselMytilus edulis

(2014) Célia C. Gosset et al.   MOLECULAR ECOLOGY

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

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

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

(2013) Pierre-Alexandre Gagnaire et al.   EVOLUTION

GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

(2013) Samuel M. Flaxman et al.   EVOLUTION

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Neandertal Origin of Genetic Variation at the Cluster of OAS Immunity Genes

(2013) F. L. Mendez 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

Pervasive selection or is it…? why areFSToutliers sometimes so frequent?

(2013) Nicolas Bierne et al.   MOLECULAR ECOLOGY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Genomic rearrangements and the evolution of clusters of locally adaptive loci

(2013) S. Yeaman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea

(2012) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

EVIDENCE OF ADAPTATION FROM ANCESTRAL VARIATION IN YOUNG POPULATIONS OF BEACH MICE

(2012) Vera S. Domingues et al.   EVOLUTION

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

(2012) V. Nolte et al.   GENOME RESEARCH

Differential introgression from a sister species explains highFSToutlier loci within a mussel species

(2012) C. C. Gosset et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

(2012) Ronald S. Burton et al.   MOLECULAR ECOLOGY

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Massively Parallel RNA Sequencing Identifies a Complex Immune Gene Repertoire in the lophotrochozoan Mytilus edulis

(2012) Eva E. R. Philipp et al.   PLoS One

Annual Variation in the Levels of Transcripts of Sex-Specific Genes in the Mantle of the Common Mussel, Mytilus edulis

(2012) Sandhya Anantharaman et al.   PLoS One

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) H. Li   BIOINFORMATICS

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

(2011) Ying Song et al.   CURRENT BIOLOGY

Change and stasis in marine hybrid zones in response to climate warming

(2011) Thomas J. Hilbish et al.   JOURNAL OF BIOGEOGRAPHY

Mytilus trossulus in Northern Europe

(2011) Risto Väinölä et al.   MARINE BIOLOGY

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

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Establishment of new mutations under divergence and genome hitchhiking

(2011) J. L. Feder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

smatr 3- an R package for estimation and inference about allometric lines

(2011) David I. Warton et al.   Methods in Ecology and Evolution

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection

(2010) E. M. Kenny et al.   DNA RESEARCH

THE DISTINCTIVE FOOTPRINTS OF LOCAL HITCHHIKING IN A VARIED ENVIRONMENT AND GLOBAL HITCHHIKING IN A SUBDIVIDED POPULATION

(2010) Nicolas Bierne   EVOLUTION

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

Adaptation – not by sweeps alone

(2010) Jonathan K. Pritchard et al.   NATURE REVIEWS GENETICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

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

MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences

(2009) Paola Venier et al.   BMC GENOMICS

THE EVOLUTION OF STRONG REPRODUCTIVE ISOLATION

(2009) Nicholas H. Barton et al.   EVOLUTION

THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION

(2009) Jeffrey L. Feder et al.   EVOLUTION

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Quantifying Adaptive Evolution in the Drosophila Immune System

(2009) Darren J. Obbard et al.   PLoS Genetics

A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE

(2008) Michael P. Cummings et al.   EVOLUTION

The genetic mosaic suggests a new role for hitchhiking in ecological speciation

(2008) SARA VIA et al.   MOLECULAR ECOLOGY