Resolving allele dosage in duplicated loci using genotyping-by-sequencing data: A path forward for population genetic analysis

Single-nucleotide polymorphism data describe contemporary population structure and diversity in allochronic lineages of pink salmon (Oncorhynchus gorbuscha)

(2018) Carolyn M. Tarpey et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

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

(2017) Morten T. Limborg et al.   MOLECULAR ECOLOGY

Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta )

(2017) R. K. Waples et al.   MOLECULAR ECOLOGY

Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

(2017) Zachariah Gompert et al.   Molecular Ecology Resources

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage

(2017) Stuart C. Willis et al.   Molecular Ecology Resources

The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

(2017) Daniel J. Prince et al.   Science Advances

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

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird

(2016) Aleksandra Biedrzycka et al.   Molecular Ecology Resources

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation inRobinia pseudoacaciaL.

(2016) Cindy F. Verdu et al.   Ecology and Evolution

The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land

(2016) Maria Assunta Biscotti et al.   Scientific Reports

Polyploidy in Amphibia

(2015) Michael Schmid et al.   CYTOGENETIC AND GENOME RESEARCH

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Large-scale genotyping of highly polymorphic loci by next-generation sequencing: how to overcome the challenges to reliably genotype individuals?

(2015) M Ferrandiz-Rovira et al.   HEREDITY

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

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

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

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

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

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

Massive expansion and functional divergence of innate immune genes in a protostome

(2015) Linlin Zhang et al.   Scientific Reports

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

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell et al.   Molecular Ecology Resources

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

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

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

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

Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification

(2012) E. W. L. Chow et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang 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

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Genome duplication in amphibians and fish: an extended synthesis

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

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

(2011) MICHAEL R. MILLER et al.   MOLECULAR ECOLOGY

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

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

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

Analysis of recent segmental duplications in the bovine genome

(2009) George E Liu et al.   BMC GENOMICS

EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION

(2009) SUSUMU OHNO et al.   HEREDITAS

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

(2009) J. A. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Evolution of Duplicate Genes Leads to Genetic Incompatibilities Within A. thaliana

(2009) D. Bikard et al.   SCIENCE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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