Genome-Wide Investigation of the Multiple Origins Hypothesis for Deep-Spawning Kokanee Salmon (Oncorhynchus nerka) across its Pan-Pacific Distribution

Genome‐wide analysis reveals demographic and life‐history patterns associated with habitat modification in landlocked, deep‐spawning sockeye salmon ( Oncorhynchus nerka )

(2021) Farida Samad‐zada et al.   Ecology and Evolution

Rapid repeatable phenotypic and genomic adaptation following multiple introductions

(2020) Lotte A. Boheemen et al.   MOLECULAR ECOLOGY

Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish ( Salvelinus alpinus )

(2020) Sarah J. Salisbury et al.   MOLECULAR ECOLOGY

What can be learned by scanning the genome for molecular convergence in wild populations?

(2019) Bonnie A. Fraser et al.   Annals of the New York Academy of Sciences

A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia

(2019) Alessandro Alves‐Pereira et al.   Evolutionary Applications

Detection and morphological characteristics of “Kunimasu” (Oncorhynchus kawamurae)/”Himemasu” (O. nerka) hybrids in Lake Motosu, Yamanashi Prefecture, Japan

(2018) Kouji Nakayama et al.   ICHTHYOLOGICAL RESEARCH

SNP panels for differentiating advanced-generation hybrid classes in recently diverged stocks: A sensitivity analysis to inform monitoring of sockeye salmon re-stocking programs

(2018) Lucas Elliott et al.   FISHERIES RESEARCH

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka)

(2017) Andrew J. Veale et al.   Genome Biology and Evolution

RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata)

(2017) Charles Babin et al.   Genome Biology and Evolution

Evidence of genomic adaptation to climate in Eucalyptus microcarpa : Implications for adaptive potential to projected climate change

(2017) Rebecca Jordan et al.   MOLECULAR ECOLOGY

An ancient selective sweep linked to reproductive life history evolution in sockeye salmon

(2017) Andrew J. Veale et al.   Scientific Reports

Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

(2017) Terry D. Beacham et al.   PLoS One

Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks

(2016) Priscilla A. Erickson et al.   EVOLUTION

Sockeye salmon repatriation leads to population re-establishment and rapid introgression with native kokanee

(2016) Andrew J. Veale et al.   Evolutionary Applications

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

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

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

(2016) Wesley A. Larson 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

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

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

The origin and genetic divergence of “black” kokanee, a novel reproductive ecotype of Oncorhynchus nerka

(2015) Amanda L. Moreira et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genetic evidence for ecological divergence in kokanee salmon

(2015) Matthew A. Lemay et al.   MOLECULAR ECOLOGY

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

Growth-related morphology of “Kunimasu” (Oncorhynchus kawamurae: family Salmonidae) from Lake Saiko, Yamanashi Prefecture, Japan

(2014) Tetsuji Nakabo et al.   ICHTHYOLOGICAL RESEARCH

Do the same genes underlie parallel phenotypic divergence in differentLittorina saxatilispopulations?

(2014) A. M. Westram et al.   MOLECULAR ECOLOGY

Genome scan methods against more complex models: when and how much should we trust them?

(2014) Pierre de Villemereuil et al.   MOLECULAR ECOLOGY

Lack of parallel genetic patterns underlying the repeated ecological divergence of beach and stream-spawning kokanee salmon

(2013) K. K. Frazer et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Identification of Nonvisual Photomotor Response Cells in the Vertebrate Hindbrain

(2013) D. Kokel et al.   JOURNAL OF NEUROSCIENCE

Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

(2013) Charles Perrier et al.   MOLECULAR ECOLOGY

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

(2013) C. Do et al.   Molecular Ecology Resources

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Distinct genetic isolation between “Kunimasu” (Oncorhynchus kawamurae) and “Himemasu” (O. nerka) in Lake Saiko, Yamanashi Prefecture, Japan, inferred from microsatellite analysis

(2012) Nozomu Muto et al.   ICHTHYOLOGICAL RESEARCH

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

The genetic population structure of lacustrine sockeye salmon, Oncorhynchus nerka, in Japan as the endangered species

(2011) Yuichiro Kogura et al.   ENVIRONMENTAL BIOLOGY OF FISHES

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

Detection of outlier loci and their utility for fisheries management

(2011) Michael A. Russello et al.   Evolutionary Applications

Oncorhynchus kawamurae “Kunimasu,” a deepwater trout, discovered in Lake Saiko, 70 years after extinction in the original habitat, Lake Tazawa, Japan

(2011) Tetsuji Nakabo et al.   ICHTHYOLOGICAL RESEARCH

Genetic structure and diversity of Japanese kokanee Oncorhynchus nerka stocks as revealed by microsatellite and mitochondrial DNA markers

(2011) S. Yamamoto et al.   JOURNAL OF FISH BIOLOGY

The parallel evolution of dwarfism in Arctic charr is accompanied by adaptive divergence in mTOR-pathway gene expression

(2011) DANIEL J. MACQUEEN et al.   MOLECULAR ECOLOGY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan 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

The Cost Effectiveness of Duplicate Genotyping for Testing Genetic Association

(2009) Nathan Tintle et al.   ANNALS OF HUMAN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus

(2009) Joshua B. Gross et al.   PLoS Genetics

SYNTHESIS: Evolutionary history of Pacific salmon in dynamic environments

(2008) Robin S. Waples et al.   Evolutionary Applications

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

(2008) M. Foll et al.   GENETICS

ldne: a program for estimating effective population size from data on linkage disequilibrium

(2008) ROBIN S. WAPLES et al.   Molecular Ecology Resources

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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