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

Genomic Profiles of Diversification and Genotype–Phenotype Association in Island Nematode Lineages

(2016) Angela McGaughran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Speciation by selection: A framework for understanding ecology’s role in speciation

(2016) R. Brian Langerhans et al.   Current Zoology

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

(2015) Baocheng Guo et al.   BMC BIOLOGY

Genome-wide tests for introgression between cactophilicDrosophilaimplicate a role of inversions during speciation

(2015) Konrad Lohse et al.   EVOLUTION

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

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

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

A recombination suppressor contributes to ecological speciation in OSTRINIA moths

(2015) C B Wadsworth et al.   HEREDITY

Phylogeography of the prickly sculpin (Cottus asper) in north-western North America reveals parallel phenotypic evolution across multiple coastal-inland colonizations

(2015) Stefan Dennenmoser et al.   JOURNAL OF BIOGEOGRAPHY

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

(2015) Kira E. Delmore et al.   MOLECULAR ECOLOGY

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

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients inPopulus trichocarpa

(2015) Jason A. Holliday et al.   NEW PHYTOLOGIST

Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata

(2015) Marco Fracassetti et al.   PLoS One

Trait dimensionality explains widespread variation in local adaptation

(2015) A. MacPherson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus)

(2015) Jie Cheng et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

(2015) Philine G. D. Feulner et al.   PLoS Genetics

Genetic population structure in prickly sculpin (Cottus asper) reflects isolation-by-environment between two life-history ecotypes

(2014) Stefan Dennenmoser et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Effects of salinity on metabolic rate and branchial expression of genes involved in ion transport and metabolism in Mozambique tilapia (Oreochromis mossambicus)

(2014) Aris Zikos et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Evolutionary diversification in freshwater sculpins (Cottoidea): a review of two major adaptive radiations

(2014) Akira Goto et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Effect of salinity on oxygen consumption in fishes: a review

(2014) R. Ern et al.   JOURNAL OF FISH BIOLOGY

Genome-Wide Congealing and Rapid Transitions across the Speciation Continuum during Speciation with Gene Flow

(2014) Jeffrey L. Feder et al.   JOURNAL OF HEREDITY

Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multilocus analysis surpasses genome scan

(2014) Vincent Bourret et al.   MOLECULAR ECOLOGY

Divergent immunity and energetic programs in the gills of migratory and residentOncorhynchus mykiss

(2014) Ben J. G. Sutherland et al.   MOLECULAR ECOLOGY

A role for migration-linked genes and genomic islands in divergence of a songbird

(2014) Kristen Ruegg et al.   MOLECULAR ECOLOGY

Theoretical models of the influence of genomic architecture on the dynamics of speciation

(2014) Samuel M. Flaxman et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Relaxed selection causes microevolution of seawater osmoregulation and gene expression in landlocked Alewives

(2014) Jonathan P. Velotta et al.   OECOLOGIA

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology

(2013) Aaron B. A. Shafer et al.   ECOLOGY LETTERS

PARALLEL EVOLUTION OF LOCAL ADAPTATION AND REPRODUCTIVE ISOLATION IN THE FACE OF GENE FLOW

(2013) Roger K. Butlin et al.   EVOLUTION

GENOME EVOLUTION AND SPECIATION: TOWARD QUANTITATIVE DESCRIPTIONS OF PATTERN AND PROCESS

(2013) Patrik Nosil et al.   EVOLUTION

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

FUNCTIONAL AND POPULATION GENOMIC DIVERGENCE WITHIN AND BETWEEN TWO SPECIES OF KILLIFISH ADAPTED TO DIFFERENT OSMOTIC NICHES

(2013) Genevieve M. Kozak et al.   EVOLUTION

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

The genomics of incompatibility factors and sex determination in hybridizing species of Cottus (Pisces)

(2013) J Cheng et al.   HEREDITY

Local adaptation to salinity in the three-spined stickleback?

(2013) J. DeFaveri et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2013) Charles Perrier et al.   MOLECULAR ECOLOGY

A genomic island linked to ecotype divergence in Atlantic cod

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

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Population genomics from pool sequencing

(2013) Luca Ferretti et al.   MOLECULAR ECOLOGY

Common functional targets of adaptive micro- and macro-evolutionary divergence in killifish

(2013) Andrew Whitehead et al.   MOLECULAR ECOLOGY

Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

(2013) Eric C. Anderson et al.   MOLECULAR ECOLOGY

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

Genomic rearrangements and the evolution of clusters of locally adaptive loci

(2013) S. Yeaman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

Close Association of Carbonic Anhydrase (CA2a and CA15a), Na+/H+ Exchanger (Nhe3b), and Ammonia Transporter Rhcg1 in Zebrafish Ionocytes Responsible for Na+ Uptake

(2013) Yusuke Ito et al.   Frontiers in Physiology

LARGE-SCALE CANDIDATE GENE SCAN REVEALS THE ROLE OF CHEMORECEPTOR GENES IN HOST PLANT SPECIALIZATION AND SPECIATION IN THE PEA APHID

(2012) Carole M. Smadja et al.   EVOLUTION

Differential expression of Na+, K+-ATPase α-1 isoforms during seawater acclimation in the amphidromous galaxiid fish Galaxias maculatus

(2012) Mauricio A. Urbina et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Mechanism of osmoregulatory adaptation in tilapia

(2012) Biao Yan et al.   MOLECULAR BIOLOGY REPORTS

Parallel and lineage-specific molecular adaptation to climate in boreal black spruce

(2012) JULIEN PRUNIER et al.   MOLECULAR ECOLOGY

A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus)

(2012) SPIROS PAPAKOSTAS et al.   MOLECULAR ECOLOGY

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE 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

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Ion regulation in fish gills: recent progress in the cellular and molecular mechanisms

(2011) Pung-Pung Hwang et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler 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

PARALLEL AND NONPARALLEL ASPECTS OF ECOLOGICAL, PHENOTYPIC, AND GENETIC DIVERGENCE ACROSS REPLICATE POPULATION PAIRS OF LAKE AND STREAM STICKLEBACK

(2011) Renaud Kaeuffer et al.   EVOLUTION

GLOBAL ANALYSIS OF GENES INVOLVED IN FRESHWATER ADAPTATION IN THREESPINE STICKLEBACKS (GASTEROSTEUS ACULEATUS)

(2011) Jacquelin DeFaveri et al.   EVOLUTION

PUMPING IONS: RAPID PARALLEL EVOLUTION OF IONIC REGULATION FOLLOWING HABITAT INVASIONS

(2011) Carol Eunmi Lee et al.   EVOLUTION

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.)

(2011) KATHRYN C. STEMSHORN et al.   MOLECULAR ECOLOGY

Genomic divergence during speciation: causes and consequences

(2011) P. Nosil et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Genomic mechanisms of evolved physiological plasticity in killifish distributed along an environmental salinity gradient

(2011) A. Whitehead et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of osmoregulatory function by modification of gene transcription in steelhead trout

(2010) Tutku Aykanat et al.   GENETICA

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Female-Biased Expression on the X Chromosome as a Key Step in Sex Chromosome Evolution in Threespine Sticklebacks

(2010) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

A High Incidence of Selection on Physiologically Important Genes in the Three-Spined Stickleback, Gasterosteus aculeatus

(2010) Y. Shimada et al.   MOLECULAR BIOLOGY AND EVOLUTION

History vs. habitat type: explaining the genetic structure of European nine-spined stickleback (Pungitius pungitius) populations

(2010) TAKAHITO SHIKANO et al.   MOLECULAR ECOLOGY

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

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

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

Role of SLC12A10.2, a Na-Cl cotransporter-like protein, in a Cl uptake mechanism in zebrafish (Danio rerio)

(2009) Yi-Fang Wang et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ADAPTIVE DIVERGENCE BETWEEN FRESHWATER AND MARINE STICKLEBACKS: INSIGHTS INTO THE ROLE OF PHENOTYPIC PLASTICITY FROM AN INTEGRATED ANALYSIS OF CANDIDATE GENE EXPRESSION

(2009) R. J. Scott McCairns et al.   EVOLUTION

Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology

(2009) ANNE C. DALZIEL et al.   MOLECULAR ECOLOGY

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

Teleost fish osmoregulation: what have we learned since August Krogh, Homer Smith, and Ancel Keys

(2008) David H. Evans   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

(2008) Ary A. Hoffmann et al.   Annual Review of Ecology Evolution and Systematics

Interpopulation differences in expression of candidate genes for salinity tolerance in winter migrating anadromous brown trout (Salmo trutta L.)

(2008) Peter F Larsen et al.   BMC GENETICS

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

(2008) M. Foll et al.   GENETICS

Landscape genetic analyses reveal cryptic population structure and putative selection gradients in a large-scale estuarine environment

(2008) R. J. SCOTT McCAIRNS et al.   MOLECULAR ECOLOGY