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

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

(2015) Lei Huang et al.   Annual Review of Genomics and Human Genetics

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

Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits

(2015) Yun Fan et al.   BMC GENOMICS

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Genotype and environment effects on tocopherol and plastochromanol-8 contents of winter oilseed rape doubled haploid lines derived from F1 plants of the cross between yellow and black seeds

(2015) Aleksander Siger et al.   INDUSTRIAL CROPS AND PRODUCTS

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

(2015) F. W. Allendorf 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

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

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

SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops

(2015) Josh P. Clevenger et al.   G3-Genes Genomes Genetics

Conservation Genetics and Genomics of Amphibians and Reptiles

(2015) H. Bradley Shaffer et al.   Annual Review of Animal Biosciences

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

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

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

Advances in plant chromosome genomics

(2014) Jaroslav Doležel et al.   BIOTECHNOLOGY ADVANCES

Parental genome contribution in maize DH lines derived from six backcross populations using genotyping by sequencing

(2014) Veronica Ogugo et al.   EUPHYTICA

Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

(2014) Meredith V. Everett et al.   Evolutionary Applications

Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes

(2014) Anna E. Savage et al.   GENE

Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon

(2014) Ian A. Warren et al.   Genome Biology and Evolution

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

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

Genome-Wide Patterns of Genetic Polymorphism and Signatures of Selection in Plasmodium vivax

(2014) Omar E. Cornejo et al.   Genome Biology and Evolution

Temporally Isolated Lineages of Pink Salmon Reveal Unique Signatures of Selection on Distinct Pools of Standing Genetic Variation

(2014) Morten T. Limborg et al.   JOURNAL OF HEREDITY

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

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

First Haploid Genetic Map Based on Microsatellite Markers in Senegalese Sole (Solea senegalensis, Kaup 1858)

(2014) Ma. Jesús Molina-Luzón et al.   MARINE BIOTECHNOLOGY

Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata)

(2014) Jackie Lighten et al.   Molecular Ecology Resources

The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout

(2014) Y. Palti et al.   Molecular Ecology Resources

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

(2014) Eric B. Rondeau et al.   PLoS One

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

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

Molecular adaptation of telomere associated genes in mammals

(2013) Claire C Morgan et al.   BMC EVOLUTIONARY BIOLOGY

Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar)

(2013) Susan E Johnston et al.   BMC GENOMICS

Exploiting genetic diversity to balance conservation and harvest of migratory salmon

(2013) Tyler H. Dann et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genetic and Genomic Interactions of Animals with Different Ploidy Levels

(2013) J.P. Bogart et al.   CYTOGENETIC AND GENOME RESEARCH

Understanding salmonid biology from the Atlantic salmon genome

(2013) William S. Davidson   GENOME

Entering the second century of maize quantitative genetics

(2013) J G Wallace et al.   HEREDITY

Molecular Markers for Variation in Spawning Date in a Hatchery Population of Rainbow Trout (Oncorhynchus mykiss)

(2013) M. S. Allen et al.   MARINE BIOTECHNOLOGY

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population

(2013) Anna W. Santure et al.   MOLECULAR ECOLOGY

A genomic island linked to ecotype divergence in Atlantic cod

(2013) Jakob Hemmer-Hansen et al.   MOLECULAR ECOLOGY

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

Transcriptome resources for the frogsLithobates clamitansandPseudacris regilla, emphasizing antimicrobial peptides and conserved loci for phylogenetics

(2013) Laura S. Robertson et al.   Molecular Ecology Resources

Parentage and sibship inference from markers in polyploids

(2013) Jinliang Wang et al.   Molecular Ecology Resources

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

(2013) V. L. Sork et al.   Tree Genetics & Genomes

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

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

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

(2012) Ross D Houston et al.   BMC GENOMICS

The Hitchhiker's guide toXenopusgenetics

(2012) Anita Abu-Daya et al.   GENESIS

Molecular Tools for Exploring Polyploid Genomes in Plants

(2012) Riccardo Aversano et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Defining the landscape of adaptive genetic diversity

(2012) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

(2012) Kai N. Stölting et al.   MOLECULAR ECOLOGY

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

Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout

(2012) Benjamin C. Hecht et al.   MOLECULAR ECOLOGY

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation

(2012) Lorenzo Barchi et al.   PLoS One

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Methods for generating triploid green sea urchin embryos: An initial step in producing triploid adults for land-based and near-shore aquaculture

(2011) S. Anne Böttger et al.   AQUACULTURE

Genotype calling in tetraploid species from bi-allelic marker data using mixture models

(2011) Roeland E Voorrips et al.   BMC BIOINFORMATICS

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

(2011) Yada Chutimanitsakun et al.   BMC GENOMICS

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

Genome duplication in amphibians and fish: an extended synthesis

(2011) B. K. Mable et al.   JOURNAL OF ZOOLOGY

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

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

(2010) Lars Gidskehaug et al.   BIOINFORMATICS

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)

(2010) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids

(2010) J. E. SEEB et al.   Molecular Ecology Resources

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

Rapid spread of invasive genes into a threatened native species

(2010) Benjamin M. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Light-Dependent Transcriptional Regulation of Genes of Biogeochemical Interest in the Diploid and Haploid Life Cycle Stages of Emiliania huxleyi

(2009) S. Richier et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hybridization rapidly reduces fitness of a native trout in the wild

(2009) C. C. Muhlfeld et al.   Biology Letters

A review of the need and possible uses for genetically standardized Atlantic salmon (Salmo salar) in research

(2009) U Grimholt et al.   LABORATORY ANIMALS

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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Introgression of fitness genes across a ploidy barrier

(2009) Mark A. Chapman et al.   NEW PHYTOLOGIST

Homoeologous recombination in allopolyploids: the polyploid ratchet

(2009) Robert T. Gaeta et al.   NEW PHYTOLOGIST

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