Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)

The evolution of genomic islands by increased establishment probability of linked alleles

(2016) Sam Yeaman et al.   MOLECULAR ECOLOGY

Demographic modelling with whole-genome data reveals parallel origin of similarPundamiliacichlid species after hybridization

(2016) Joana I. Meier 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

Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

(2016) Quentin Rougemont et al.   MOLECULAR ECOLOGY

Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones

(2016) Richard G. Harrison et al.   MOLECULAR ECOLOGY

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

(2016) Camille Roux et al.   PLOS BIOLOGY

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids

(2016) Andreas F. Kautt et al.   PLoS Genetics

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

(2016) Nicolas Bierne et al.   Current Zoology

Genetic structure and within-generation genome scan analysis of fisheries-induced evolution in a Lake Whitefish (Coregonus clupeaformis) population

(2015) Jobran Chebib et al.   CONSERVATION GENETICS

RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs

(2015) Martin Laporte et al.   G3-Genes Genomes Genetics

The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV

(2015) Nicolas Alcala et al.   G3-Genes Genomes Genetics

RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species

(2014) Anne-Marie Dion-Côté et al.   MOLECULAR BIOLOGY AND EVOLUTION

Standing and flowing: the complex origins of adaptive variation

(2014) John J. Welch 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

The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits

(2014) Kirk E. Lohmueller   PLoS Genetics

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

On the accumulation of deleterious mutations during range expansions

(2013) S. Peischl et al.   MOLECULAR ECOLOGY

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

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish(Coregonus clupeaformis)

(2012) Pierre-Alexandre Gagnaire et al.   MOLECULAR ECOLOGY

Glacial cycles as an allopatric speciation pump in north-eastern American freshwater fishes

(2012) Julien April et al.   MOLECULAR ECOLOGY

Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonusspp.)

(2012) MAGNUS W. JACOBSEN et al.   MOLECULAR ECOLOGY

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Asymmetric and differential gene introgression at a contact zone between two highly divergent lineages of field voles (Microtus agrestis)

(2011) M. BEYSARD et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Genome-wide patterns of divergence during speciation: the lake whitefish case study

(2011) S. Renaut et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Role of epibenthic resource opportunities in the parallel evolution of lake whitefish species pairs (Coregonus sp.)

(2010) L. LANDRY et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Using differential introgression in hybrid zones to identify genomic regions involved in speciation

(2010) BRET A. PAYSEUR   Molecular Ecology Resources

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

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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

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

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

Glacial bottleneck and postglacial recolonization of a seed parasitic weevil,Curculio hilgendorfi, inferred from mitochondrial DNA variation

(2008) K. AOKI et al.   MOLECULAR ECOLOGY