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

Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers

(2016) Jasmin Zohren 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

Harnessing the power of RADseq for ecological and evolutionary genomics

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

The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines

(2015) Brian L. Stockwell et al.   CONSERVATION GENETICS

Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis

(2015) Soraya Leal-Bertioli et al.   GENETICS

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

Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis

(2015) Soraya Leal-Bertioli et al.   GENETICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

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

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

Using Mendelian Inheritance To Improve High-Throughput SNP Discovery

(2014) N. Chen et al.   GENETICS

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

Trade-offs and utility of alternative RADseq methods: Reply to Puritzet al.

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

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

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

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

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

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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions

(2012) Jinzhuang Dou et al.   Biology Direct

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

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

(2012) P G Meirmans et al.   HEREDITY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey 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

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

(2011) Angel Amores et al.   GENETICS

Whole genome duplication: challenges and considerations associated with sequence orthology assignment in Salmoninae

(2011) H. K. Moghadam et al.   JOURNAL OF FISH BIOLOGY

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

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

(2011) PAUL A. HOHENLOHE et al.   Molecular Ecology Resources

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

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

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

(2009) Cecilia Sánchez et al.   BMC GENOMICS

EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION

(2009) SUSUMU OHNO et al.   HEREDITAS

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