The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression

Significant Synteny and Co-localization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes

(2017) Arne Jacobs et al.   GENETICS

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

(2017) Clément Rougeux et al.   Genome Biology and Evolution

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

(2017) Fan Han et al.   GENOME RESEARCH

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The effect of foraging and ontogeny on the prevalence and intensity of the invasive parasite Anguillicola crassus in the European eel Anguilla anguilla

(2017) J Barry et al.   JOURNAL OF FISH DISEASES

Demography and genome divergence of lake and stream populations of an East African cichlid fish

(2017) Bernd Egger et al.   MOLECULAR ECOLOGY

Speciation as a sieve for ancestral polymorphism

(2017) Rafael F. Guerrero et al.   MOLECULAR ECOLOGY

Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate

(2017) Daniel Berner et al.   MOLECULAR ECOLOGY

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

(2017) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Recent evolution of extreme cestode growth suppression by a vertebrate host

(2017) Jesse N. Weber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

(2017) Tao Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of divergence or opportunities for introgression?

(2017) Rachael A. Bay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Dense Brown Trout ( Salmo trutta ) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

(2017) Maeva Leitwein et al.   G3-Genes Genomes Genetics

Significant Synteny and Co-localization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes

(2017) Arne Jacobs et al.   GENETICS

Transitions between phases of genomic differentiation during stick-insect speciation

(2017) Rüdiger Riesch et al.   Nature Ecology & Evolution

Parentally acquired differences in resource acquisition ability between brown trout from alternative life history parentage

(2016) Martin R. Hughes et al.   ECOLOGY OF FRESHWATER FISH

EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations

(2016) G-B Chen et al.   HEREDITY

Morphological, ecological and behavioural differentiation of sympatric profundal and pelagic Arctic charr (Salvelinus alpinus) in Loch Dughaill Scotland

(2016) O. E. Hooker et al.   HYDROBIOLOGIA

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

(2016) Kathryn R. Elmer   HYDROBIOLOGIA

Lake bathymetry and species occurrence predict the distribution of a lacustrine apex predator

(2016) M. R. Hughes et al.   JOURNAL OF FISH BIOLOGY

Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown troutSalmo truttacompared to wild Mediterranean populations

(2016) M. Leitwein et al.   JOURNAL OF FISH BIOLOGY

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

(2016) Jing Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Sam Yeaman et al.   MOLECULAR ECOLOGY

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

(2016) Wesley A. Larson 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

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

(2016) Nagarjun Vijay et al.   Nature Communications

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

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

(2016) David A. Marques et al.   PLoS Genetics

The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland

(2016) Alastair Thorne et al.   PeerJ

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

(2016) Nicolas Bierne et al.   Current Zoology

Parallel evolutionary divergence in Arctic char Salvelinus alpinus complex from Transbaikalia: variation in differentiation degree and segregation of genetic diversity among sympatric forms

(2015) Natalia V. Gordeeva et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

If Arctic charrSalvelinus alpinusis ‘the most diverse vertebrate’, what is the lake charrSalvelinus namaycush?

(2015) Andrew Michael Muir et al.   FISH AND FISHERIES

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

Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms

(2015) Hans Recknagel et al.   Molecular Ecology Resources

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella

(2015) Adrien Sicard et al.   Nature Communications

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Speciation in Freshwater Fishes

(2014) Ole Seehausen et al.   Annual Review of Ecology Evolution and Systematics

Fine-scale phylogeographic contact zone in Austrian brown trout Salmo trutta reveals multiple waves of post-glacial colonization and a pre-dominance of natural versus anthropogenic admixture

(2014) T. Schenekar et al.   CONSERVATION GENETICS

Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model

(2014) Nicolas Duforet-Frebourg et al.   MOLECULAR BIOLOGY AND EVOLUTION

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 genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand 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

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

(2014) Mbaye Tine et al.   Nature Communications

Geographic Mode of Speciation and Genomic Divergence

(2013) Jeffrey L. Feder et al.   Annual Review of Ecology Evolution and Systematics

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

Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations

(2013) M. I. Fariello et al.   GENETICS

Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers

(2013) Sebastien Renaut et al.   MOLECULAR ECOLOGY

Ecological speciation in postglacial European whitefish: rapid adaptive radiations into the littoral, pelagic, and profundal lake habitats

(2013) Kim Praebel et al.   Ecology and Evolution

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts

(2012) René Guyomard et al.   BMC GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

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

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Phylogeographic structure of brown troutSalmo truttain Britain and Ireland: glacial refugia, postglacial colonization and origins of sympatric populations

(2010) N. J. McKeown et al.   JOURNAL OF FISH BIOLOGY

Extent and timing of the Last Glacial Maximum (LGM) in Britain and Ireland: a review

(2010) Richard C. Chiverrell et al.   JOURNAL OF QUATERNARY SCIENCE

Genomic islandsofspeciation or genomic islandsandspeciation?

(2010) THOMAS L. TURNER et al.   MOLECULAR ECOLOGY

Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population

(2010) DIMITAR SERBEZOV et al.   MOLECULAR ECOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   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

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

(2010) A. G. Hudson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss)

(2009) Ruth B Phillips et al.   BMC GENETICS

Ontogenetic niche shifts and resource partitioning of lake trout morphotypes

(2009) Mara S. Zimmerman et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander 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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

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

ORIGINAL ARTICLE: Recurrent evolution of life history ecotypes in sockeye salmon: implications for conservation and future evolution

(2008) Chris C. Wood et al.   Evolutionary Applications

Genetic variability within and among sympatric brown trout {Salmo trutta) populations: multi-locus DNA fingerprint analysis

(2008) PAULO A. PRODÖHL et al.   HEREDITAS