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

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

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

Genetic analysis of the reproductive axis in fish using genome-editing nucleases

(2017) Yun Liu et al.   Science Bulletin

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

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

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

Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape

(2016) Maeva Leitwein 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

Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments

(2016) Qian Zhang et al.   Genome Biology and Evolution

Gene of the month:HGF

(2016) Ana Belen Fajardo-Puerta et al.   JOURNAL OF CLINICAL PATHOLOGY

Differentially expressed genes associated with adaptation to different thermal environments in three sympatric CubanAnolislizards

(2016) Hiroshi D. Akashi et al.   MOLECULAR ECOLOGY

Genetic basis for variation in salinity tolerance between stickleback ecotypes

(2016) Makoto Kusakabe et al.   MOLECULAR ECOLOGY

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

(2016) Wesley A. Larson et al.   MOLECULAR ECOLOGY

Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

(2016) Anja M. Westram 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

Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

(2016) Stefan Dennenmoser et al.   MOLECULAR ECOLOGY

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

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

(2016) Jon E. Hess et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

(2016) Brittany A. Garner et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

(2016) David A. Marques et al.   PLoS Genetics

The geography of introgression in a patchy environment and the thorn in the side of ecological speciation

(2016) Nicolas Bierne et al.   Current Zoology

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

Regulation of bone metabolism by Wnt signals

(2015) Yasuhiro Kobayashi et al.   JOURNAL OF BIOCHEMISTRY

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 evidence for ecological divergence in kokanee salmon

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

Shared and nonshared genomic divergence in parallel ecotypes ofLittorina saxatilisat a local scale

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

(2015) G. J. McKinney et al.   Molecular Ecology Resources

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

Incubation success and habitat selection of shore-spawning kokaneeOncorhynchus nerka: effects of water-level regulation and habitat characteristics

(2014) Steven L. Whitlock et al.   ECOLOGY OF FRESHWATER FISH

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

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

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

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

A novel common variant in DCST2 is associated with length in early life and height in adulthood

(2014) Ralf J.P. van der Valk et al.   HUMAN MOLECULAR GENETICS

Standing and flowing: the complex origins of adaptive variation

(2014) John J. Welch et al.   MOLECULAR ECOLOGY

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

Targeted Mutagenesis in Atlantic Salmon (Salmo salar L.) Using the CRISPR/Cas9 System Induces Complete Knockout Individuals in the F0 Generation

(2014) Rolf B. Edvardsen et al.   PLoS One

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

(2013) Pierre-Alexandre Gagnaire et al.   EVOLUTION

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

A genomic island linked to ecotype divergence in Atlantic cod

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

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen 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

diveRsity: AnRpackage for the estimation and exploration of population genetics parameters and their associated errors

(2013) Kevin Keenan et al.   Methods in Ecology and Evolution

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Do highly divergent loci reside in genomic regions affecting reproductive isolation? A test using next-generation sequence data in Timema stick insects

(2012) Patrik Nosil et al.   BMC EVOLUTIONARY BIOLOGY

A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers

(2012) A. VILAS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Fsh and Lh have common and distinct effects on gene expression in rainbow trout testis

(2012) Elisabeth Sambroni et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Neutral Loci Reveal Population Structure by Geography, not Ecotype, in Kootenay Lake Kokanee

(2012) Matthew A. Lemay et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

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

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

Angiopoietin-like 4: a decade of research

(2011) Pengcheng Zhu et al.   BIOSCIENCE REPORTS

The genetic basis of salinity tolerance traits in Arctic charr (Salvelinus alpinus)

(2011) Joseph D Norman et al.   BMC GENETICS

Detection of outlier loci and their utility for fisheries management

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

Extent and scale of local adaptation in salmonid fishes: review and meta-analysis

(2011) D J Fraser et al.   HEREDITY

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

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

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

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

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

Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

(2011) S. Via   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress

(2011) Nicole L. Quinn et al.   PHYSIOLOGICAL GENOMICS

The genes underlying the process of speciation

(2011) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

Identification of a candidate adaptive polymorphism forDrosophilalife history by parallel independent clines on two continents

(2010) ANNALISE B. PAABY et al.   MOLECULAR ECOLOGY

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

Population diversity and the portfolio effect in an exploited species

(2010) Daniel E. Schindler et al.   NATURE

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

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

THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION

(2009) Jeffrey L. Feder et al.   EVOLUTION

Mutation of the bone morphogenetic protein GDF3 causes ocular and skeletal anomalies

(2009) M. Ye et al.   HUMAN MOLECULAR GENETICS

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

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

ORIGINAL ARTICLE: Recurrent evolution of life history ecotypes in sockeye salmon: implications for conservation and future evolution

(2008) Chris C. Wood 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

The Genetic Basis of Phenotypic Convergence in Beach Mice: Similar Pigment Patterns but Different Genes

(2008) C. C. Steiner et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genetic mosaic suggests a new role for hitchhiking in ecological speciation

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?

(2007) J ARENDT et al.   TRENDS IN ECOLOGY & EVOLUTION

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION