Genomic islands of divergence linked to ecotypic variation in sockeye salmon

Identification and Characterization of Sex-Associated Loci in Sockeye Salmon Using Genotyping-by-Sequencing and Comparison with a Sex-Determining Assay Based on thesdYGene

(2016) Wesley A. Larson et al.   JOURNAL OF HEREDITY

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

(2016) Sam Yeaman et al.   MOLECULAR ECOLOGY

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod

(2016) Tina Graceline Kirubakaran et al.   MOLECULAR ECOLOGY

Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing

(2016) Morten T. Limborg et al.   MOLECULAR ECOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

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

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

Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map

(2015) Wesley A. Larson et al.   JOURNAL OF HEREDITY

Genetic evidence for ecological divergence in kokanee salmon

(2015) Matthew A. Lemay et al.   MOLECULAR ECOLOGY

Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and residentOncorhynchus mykiss

(2015) Garrett J. McKinney et al.   MOLECULAR ECOLOGY

The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments

(2015) Anne-Laure Ferchaud et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

(2015) R. K. Waples et al.   Molecular Ecology Resources

Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data

(2015) Morten T. Limborg et al.   G3-Genes Genomes Genetics

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

(2014) Wesley A. Larson et al.   Evolutionary Applications

Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

(2014) Wesley A. Larson 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

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

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

Local adaptation limits lifetime reproductive success of dispersers in a wild salmon metapopulation

(2014) Daniel A. Peterson et al.   Nature Communications

Copy number variants in patients with short stature

(2013) Hermine A van Duyvenvoorde et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES

(2013) Rose L. Andrew 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

A genomic island linked to ecotype divergence in Atlantic cod

(2013) Jakob Hemmer-Hansen 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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

(2013) C. Do et al.   Molecular Ecology Resources

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

Evaluating Adaptive Divergence Between Migratory and Nonmigratory Ecotypes of a Salmonid Fish, Oncorhynchus mykiss

(2013) Matthew C. Hale et al.   G3-Genes Genomes Genetics

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

(2012) Meredith V Everett et al.   BMC GENOMICS

Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka)

(2012) Daniel Gomez-Uchida et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

(2012) Michael W. Ackerman et al.   CONSERVATION GENETICS

The differentiation and movement of presomitic mesoderm progenitor cells are controlled by Mesogenin 1

(2012) R. Fior et al.   DEVELOPMENT

Role of estrogen receptor-α (ESR1) and the type 1 insulin-like growth factor receptor (IGFR1) in estradiol-stimulated proliferation of cultured bovine satellite cells

(2012) E. Kamanga-Sollo et al.   DOMESTIC ANIMAL ENDOCRINOLOGY

Association between geomorphic attributes of watersheds, water temperature, and salmon spawn timing in Alaskan streams

(2012) Peter J. Lisi et al.   GEOMORPHOLOGY

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

SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

(2012) Vincent Bourret et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Closed-form density-based framework for automatic detection of cellular morphology changes

(2012) T. Duong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

(2011) Daniel Gomez-Uchida et al.   BMC EVOLUTIONARY BIOLOGY

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome

(2011) M. V. EVERETT et al.   Molecular Ecology Resources

Comparison ofFSToutlier tests for SNP loci under selection

(2011) SHAWN R. NARUM et al.   Molecular Ecology Resources

Genomic divergence during speciation: causes and consequences

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

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

(2011) P. A. Hohenlohe 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

Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

(2011) S. Via   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter et al.   PLoS One

Spawning Habitat and Geography Influence Population Structure and Juvenile Migration Timing of Sockeye Salmon in the Wood River Lakes, Alaska

(2011) Molly T. McGlauflin et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

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

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

The tubby family proteins

(2011) Saikat Mukhopadhyay et al.   GENOME BIOLOGY

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

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

Population diversity and the portfolio effect in an exploited species

(2010) Daniel E. Schindler et al.   NATURE

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

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

RECENT ECOLOGICAL DIVERGENCE DESPITE MIGRATION IN SOCKEYE SALMON (ONCORHYNCHUS NERKA)

(2009) Scott A. Pavey et al.   EVOLUTION

POPTREE2: Software for Constructing Population Trees from Allele Frequency Data and Computing Other Population Statistics with Windows Interface

(2009) N. Takezaki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

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

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Fine-scale differentiation between sockeye salmon ecotypes and the effect of phenotype on straying

(2008) J Lin et al.   HEREDITY

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

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources