Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Preference for nearshore and estuarine habitats in anadromous Arctic char (Salvelinus alpinus) from the Canadian high Arctic (Victoria Island, Nunavut) revealed by acoustic telemetry

(2016) Jean-Sébastien Moore et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Vertebrate sex-determining genes play musical chairs

(2016) Qiaowei Pan et al.   COMPTES RENDUS BIOLOGIES

“Islands of Divergence” in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements

(2016) Marte Sodeland et al.   Genome Biology and Evolution

Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster ( Pinctada maxima )

(2016) Maria G. Nayfa et al.   Marine Genomics

Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

(2016) Monal M. Lal et al.   Marine Genomics

Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna ( Thunnus albacares )

(2016) Carlo Pecoraro et al.   Marine Genomics

Comprehensive transcriptomic analysis of the process of gonadal sex differentiation in the turbot ( Scophthalmus maximus )

(2016) L. Ribas et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis

(2016) Lani U. Gleason et al.   MOLECULAR ECOLOGY

Contrasting patterns of population connectivity between regions in a commercially important molluscHaliotis rubra: integrating population genetics, genomics and marine LiDAR data

(2016) A. D. Miller et al.   MOLECULAR ECOLOGY

Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

(2016) A. Le Moan et al.   MOLECULAR ECOLOGY

Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

(2016) Quentin Rougemont et al.   MOLECULAR ECOLOGY

Conservation genomics of natural and managed populations: building a conceptual and practical framework

(2016) Laura Marilyn Benestan et al.   MOLECULAR ECOLOGY

Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus )

(2016) Laura Benestan et al.   MOLECULAR ECOLOGY

Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

(2016) Naiara Rodríguez-Ezpeleta et al.   Molecular Ecology Resources

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

The life aquatic: advances in marine vertebrate genomics

(2016) Joanna L. Kelley et al.   NATURE REVIEWS GENETICS

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod

(2016) Paul R. Berg et al.   Scientific Reports

Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

(2016) Cristián Araneda et al.   Ecology and Evolution

Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrusspp, Serranidae)

(2016) Sophie Picq et al.   Ecology and Evolution

A SNP Based Linkage Map of the Arctic Charr ( Salvelinus alpinus ) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication

(2016) Cameron M. Nugent et al.   G3-Genes Genomes Genetics

When is dispersal for dispersal? Unifying marine and terrestrial perspectives

(2015) Scott C. Burgess et al.   BIOLOGICAL REVIEWS

Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks

(2015) Baocheng Guo et al.   BMC BIOLOGY

Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L.

(2015) Salih Kafkas et al.   BMC GENOMICS

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

RAD Sequencing Highlights Polygenic Discrimination of Habitat Ecotypes in the Panmictic American Eel

(2015) Scott A. Pavey et al.   CURRENT BIOLOGY

Nuclear pore proteins and the control of genome functions

(2015) Arkaitz Ibarra et al.   GENES & DEVELOPMENT

Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod ( Gadus morhua L.)

(2015) Paul R. Berg et al.   Genome Biology and Evolution

High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex

(2015) A Brelsford et al.   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

Genetic differentiation of brackish water populations of cod Gadus morhua in the southern Baltic, inferred from genotyping using SNP-arrays

(2015) A. Poćwierz-Kotus et al.   Marine Genomics

RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

(2015) M. Laporte et al.   MOLECULAR ECOLOGY

Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

(2015) Marine S. O. Brieuc et al.   MOLECULAR ECOLOGY

Transcriptome sequencing reveals both neutral and adaptive genome dynamics in a marine invader

(2015) C. K. Tepolt et al.   MOLECULAR ECOLOGY

Genomewide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

(2015) Kristina M. Cammen 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

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

(2015) Laura Benestan et al.   MOLECULAR ECOLOGY

Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)

(2015) Bai-Dong Zhang et al.   Molecular Ecology Resources

Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt

(2015) John R. Candy et al.   Molecular Ecology Resources

Subtle tissue and sex-dependent proteome variation in mussel (Mytilus galloprovincialis) populations of the Galician coast (NW Spain) raised in a common environment

(2015) Şebnem Atasaral-Şahin et al.   PROTEOMICS

Population Genomics Reveals Seahorses (Hippocampus erectus) of the Western Mid-Atlantic Coast to Be Residents Rather than Vagrants

(2015) J. T. Boehm et al.   PLoS One

Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing

(2015) Yniv Palti et al.   PLoS One

A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus)

(2014) Anne-Laure Ferchaud et al.   BMC GENOMICS

Multilocus Adaptation Associated with Heat Resistance in Reef-Building Corals

(2014) Rachael A. Bay et al.   CURRENT BIOLOGY

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

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

Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum

(2014) Andre E. Moura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar)

(2014) Susan E. Johnston et al.   MOLECULAR ECOLOGY

Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snailNucella lapillus

(2014) Nathaniel D. Chu et al.   MOLECULAR ECOLOGY

Genomic footprints of speciation in Atlantic eels (Anguilla anguillaandA. rostrata)

(2014) Magnus W. Jacobsen et al.   MOLECULAR ECOLOGY

Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

(2014) Jean-Sébastien Moore et al.   MOLECULAR ECOLOGY

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

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

Population Structure and Phylogeography in Nassau Grouper (Epinephelus striatus), a Mass-Aggregating Marine Fish

(2014) Alexis M. Jackson et al.   PLoS One

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

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

(2014) Camille Berthelot et al.   Nature Communications

Sex Determination: Why So Many Ways of Doing It?

(2014) Doris Bachtrog et al.   PLOS BIOLOGY

Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

(2014) Daniel C. Ilut et al.   Biomed Research International

High degree of cryptic population differentiation in the Baltic Sea herringClupea harengus

(2013) Jukka Corander et al.   MOLECULAR ECOLOGY

Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod

(2013) Nina O. Therkildsen et al.   MOLECULAR ECOLOGY

Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

(2013) R. Ogden et al.   MOLECULAR ECOLOGY

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel 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

Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley

(2013) Martin Mascher et al.   PLoS One

Identification of a Sex-Linked SNP Marker in the Salmon Louse (Lepeophtheirus salmonis) Using RAD Sequencing

(2013) Stephen N. Carmichael et al.   PLoS One

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

(2012) Lucy W. Barrett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids

(2012) Ayaka Yano et al.   Evolutionary Applications

Genotyping of two populations of Southern Baltic Sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array

(2012) Agata Drywa et al.   Marine Genomics

Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

(2012) Matthieu Bruneaux et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit 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

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

(2012) Jon E. Hess et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome evolution in the fish family salmonidae: generation of a brook charr genetic map and comparisons among charrs (Arctic charr and brook charr) with rainbow trout

(2011) Evan R Timusk et al.   BMC GENETICS

The Sockeye Salmon Neo-Y Chromosome Is a Fusion between Linkage Groups Orthologous to the Coho Y Chromosome and the Long Arm of Rainbow Trout Chromosome 2

(2011) J. Faber-Hammond et al.   CYTOGENETIC AND GENOME RESEARCH

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

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

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis

(2010) J. GALINDO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Steroid catabolism in marine and freshwater fish

(2010) Margaret O. James   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

(2010) I. R. Bradbury et al.   PROCEEDINGS 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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cep164 is a mediator protein required for the maintenance of genomic stability through modulation of MDC1, RPA, and CHK1

(2008) S. Sivasubramaniam et al.   GENES & DEVELOPMENT

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

(2008) M. Foll et al.   GENETICS