Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

Human adaptation and evolution by segmental duplication

(2016) Megan Y Dennis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genomic signatures amongOncorhynchus nerkaecotypes to inform conservation and management of endangered Sockeye Salmon

(2016) Krista M. Nichols et al.   Evolutionary Applications

Next-generation biology: Sequencing and data analysis approaches for non-model organisms

(2016) Rute R. da Fonseca et al.   Marine Genomics

Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toadBufo andrewsi

(2016) Baocheng Guo et al.   MOLECULAR ECOLOGY

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

(2016) Wesley A. Larson 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

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations

(2016) Garrett J. McKinney et al.   Molecular Ecology Resources

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

(2016) Jon E. Hess et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations

(2016) Florian Mattenberger et al.   G3-Genes Genomes Genetics

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers

(2016) John Gilbey et al.   PLoS One

Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains

(2015) Guangxi Wu et al.   BMC GENOMICS

Effects of Crossovers Between Homeologs on Inheritance and Population Genomics in Polyploid-Derived Salmonid Fishes

(2015) F. W. Allendorf et al.   JOURNAL OF HEREDITY

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

Don't throw the baby out with the bathwater: identifying and mapping paralogs in salmonids

(2015) France Dufresne   Molecular Ecology Resources

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

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

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

(2015) G. J. McKinney et al.   Molecular Ecology Resources

Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

(2015) Paul D. Blischak et al.   Molecular Ecology Resources

Polyploidy can drive rapid adaptation in yeast

(2015) Anna M. Selmecki et al.   NATURE

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

Drought-Responsive Hsp70 Gene Analysis in Populus at Genome-Wide Level

(2015) Esra Nurten Yer et al.   PLANT MOLECULAR BIOLOGY REPORTER

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

(2015) Shosei Kubota et al.   PLoS Genetics

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

(2015) Fernando Ayllon et al.   PLoS Genetics

SNP Discovery in Complex Allotetraploid Genomes (Gossypiumspp., Malvaceae) Using Genotyping by Sequencing

(2015) Carla Jo Logan-Young et al.   Applications in Plant Sciences

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

(2014) Imtiaz Ahmed Randhawa et al.   BMC GENETICS

Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub

(2014) Alicia Mastretta-Yanes et al.   Genome Biology and Evolution

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing

(2014) Jennifer J. Mosher et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Genome-wide single-generation signatures of local selection in the panmictic European eel

(2014) J. M. Pujolar et al.   MOLECULAR ECOLOGY

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

(2014) D. J. Macqueen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

(2014) D. E. Pearse et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

A Dense Linkage Map for Chinook salmon ( Oncorhynchus tshawytscha ) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event

(2014) Marine S. O. Brieuc et al.   G3-Genes Genomes Genetics

Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

(2014) M. Kodama et al.   G3-Genes Genomes Genetics

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

Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools

(2013) France Dufresne et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

(2012) Meredith V Everett et al.   BMC GENOMICS

The effects of inheritance in tetraploids on genetic diversity and population divergence

(2012) P G Meirmans et al.   HEREDITY

A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

(2011) Sigbjørn Lien et al.   BMC GENOMICS

Extent and scale of local adaptation in salmonid fishes: review and meta-analysis

(2011) D J Fraser et al.   HEREDITY

Polyploidy and ecological adaptation in wild yarrow

(2011) J. Ramsey   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Microsatellite Genome Screen Identifies Chromosomal Regions under Differential Selection in Steelhead and Rainbow Trout

(2011) Andrés Martínez et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Single-Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed-Stock Analyses of Sockeye Salmon from the Copper River, Alaska

(2011) Michael W. Ackerman 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

Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array

(2010) Lars Gidskehaug et al.   BIOINFORMATICS

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

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

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

EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION

(2009) SUSUMU OHNO et al.   HEREDITAS

Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation

(2009) JÜRGEN TOMIUK et al.   Molecular Ecology Resources

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

Segregation Models for Disomic, Tetrasomic and Intermediate Inheritance in Tetraploids: A General Procedure Applied to Rorippa (Yellow Cress) Microsatellite Data

(2008) M. Stift et al.   GENETICS

The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss

(2008) K. M. Nichols et al.   GENETICS

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

(2008) M. Foll et al.   GENETICS

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

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