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

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

(2016) Nicolas Bierne et al.   Current Zoology

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

(2015) Pierre-Alexandre Gagnaire et al.   Evolutionary Applications

Evidence for population complexity of the European anchovy (Engraulis encrasicolus) along its distributional range

(2015) Sharif Jemaa et al.   FISHERIES RESEARCH

Shared and nonshared genomic divergence in parallel ecotypes ofLittorina saxatilisat a local scale

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

Geometric morphometrics, Fourier analysis of otolith shape, and nuclear-DNA markers distinguish two anchovy species (Engraulis spp.) in the Eastern Mediterranean Sea

(2014) Arzu Karahan et al.   FISHERIES RESEARCH

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

Hybridization, Introgression, and the Nature of Species Boundaries

(2014) Richard G. Harrison et al.   JOURNAL OF HEREDITY

Existence of two widespread semi-isolated genetic entities within Mediterranean anchovies

(2014) S. Oueslati et al.   MARINE BIOLOGY

Standing and flowing: the complex origins of adaptive variation

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

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

Do the same genes underlie parallel phenotypic divergence in differentLittorina saxatilispopulations?

(2014) A. M. Westram et al.   MOLECULAR ECOLOGY

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

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

Genome scan methods against more complex models: when and how much should we trust them?

(2014) Pierre de Villemereuil 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

Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

(2014) G. Silva et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2014) Mbaye Tine et al.   Nature Communications

PARALLEL EVOLUTION OF LOCAL ADAPTATION AND REPRODUCTIVE ISOLATION IN THE FACE OF GENE FLOW

(2013) Roger K. Butlin et al.   EVOLUTION

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

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

(2013) Vitor C. Sousa et al.   GENETICS

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

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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Mitochondrial DNA and microsatellite genetic differentiation in the European anchovy Engraulis encrasicolus L.

(2012) Y. J. Borrell et al.   ICES JOURNAL OF MARINE SCIENCE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

(2012) Iratxe Zarraonaindia et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

A framework for comparing processes of speciation in the presence of gene flow

(2011) CAROLE M. SMADJA et al.   MOLECULAR ECOLOGY

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

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Isolation and gene flow: inferring the speciation history of European house mice

(2011) LUDOVIC DUVAUX et al.   MOLECULAR ECOLOGY

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions

(2011) B. E. Deagle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2010) Gregory Ewing et al.   BIOINFORMATICS

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

On the origin of species: insights from the ecological genomics of lake whitefish

(2010) L. Bernatchez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Repeated evolution of reproductive isolation in a marine snail: unveiling mechanisms of speciation

(2010) K. Johannesson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Coastal lagoons: “transitional ecosystems” between transitional and coastal waters

(2010) Angel Pérez-Ruzafa et al.   JOURNAL OF COASTAL CONSERVATION

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

(2009) Jeffrey L. Feder et al.   EVOLUTION

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

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

Geographic structure of European anchovy: A nuclear-DNA study

(2008) Yanis Bouchenak-Khelladi et al.   JOURNAL OF SEA RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One