Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

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

(2015) Baocheng Guo et al.   BMC BIOLOGY

Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks

(2015) N. A. Ellis et al.   DEVELOPMENT

A 190 base pair, TGF-β responsive tooth and fin enhancer is required for stickleback Bmp6 expression

(2015) Priscilla A. Erickson et al.   DEVELOPMENTAL BIOLOGY

Hybrid ‘superswarm’ leads to rapid divergence and establishment of populations during a biological invasion

(2015) Denis Roy et al.   MOLECULAR ECOLOGY

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Evolution of stickleback in 50 years on earthquake-uplifted islands

(2015) Emily A. Lescak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing

(2015) Andrew M. Glazer et al.   G3-Genes Genomes Genetics

Genetic Mapping of Natural Variation in Schooling Tendency in the Threespine Stickleback

(2015) Anna K. Greenwood et al.   G3-Genes Genomes Genetics

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

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

Dosage Changes of a Segment at 17p13.1 Lead to Intellectual Disability and Microcephaly as a Result of Complex Genetic Interaction of Multiple Genes

(2014) Claudia M.B. Carvalho et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GENETIC ARCHITECTURE OF SKELETAL EVOLUTION IN EUROPEAN LAKE AND STREAM STICKLEBACK

(2014) Daniel Berner et al.   EVOLUTION

DISENTANGLING THE ROLE OF PHENOTYPIC PLASTICITY AND GENETIC DIVERGENCE IN CONTEMPORARY ECOTYPE FORMATION DURING A BIOLOGICAL INVASION

(2014) Kay Lucek et al.   EVOLUTION

Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci

(2014) Craig T. Miller et al.   GENETICS

Quick divergence but slow convergence during ecotype formation in lake and stream stickleback pairs of variable age

(2014) K. Lucek et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

Recent novel approaches for population genomics data analysis

(2014) Kimberly R. Andrews 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

Genetics of ecological divergence during speciation

(2014) Matthew E. Arnegard et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6

(2014) P. A. Cleves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks

(2014) P. A. Erickson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Parallel developmental genetic features underlie stickleback gill raker evolution

(2014) Andrew M Glazer et al.   EvoDevo

Identification of Major and Minor QTL for Ecologically Important Morphological Traits in Three-Spined Sticklebacks ( Gasterosteus aculeatus )

(2014) Jun Liu et al.   G3-Genes Genomes Genetics

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

(2014) Nadezhda V. Terekhanova et al.   PLoS Genetics

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks

(2013) Jun Kitano et al.   BMC GENOMICS

PI4K2β/AP-1-Based TGN-Endosomal Sorting Regulates Wnt Signaling

(2013) Marnix Wieffer et al.   CURRENT BIOLOGY

Genetic and Neural Modularity Underlie the Evolution of Schooling Behavior in Threespine Sticklebacks

(2013) Anna K. Greenwood et al.   CURRENT BIOLOGY

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Repeated and predictable patterns of ecotypic differentiation during a biological invasion: lake-stream divergence in parapatric Swiss stickleback

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

Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping

(2013) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

Recombination in the threespine stickleback genome-patterns and consequences

(2013) Marius Roesti et al.   MOLECULAR ECOLOGY

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

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

Genetic Architecture of Variation in the Lateral Line Sensory System of Threespine Sticklebacks

(2013) Abigail R. Wark et al.   G3-Genes Genomes Genetics

Uninformative polymorphisms bias genome scans for signatures of selection

(2012) Marius Roesti et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary forces shaping genomic islands of population differentiation in humans

(2012) Tamara Hofer et al.   BMC GENOMICS

GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK

(2012) Sean M. Rogers et al.   EVOLUTION

Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks

(2012) Anna K. Greenwood et al.   EVOLUTION & DEVELOPMENT

Zebrafish hmx1 promotes retinogenesis

(2012) Gaëlle Boisset et al.   EXPERIMENTAL EYE RESEARCH

On the Roles and Regulation of Chondroitin Sulfate and Heparan Sulfate in Zebrafish Pharyngeal Cartilage Morphogenesis

(2012) Katarina Holmborn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Parallel and nonparallel ecological, morphological and genetic divergence in lake-stream stickleback from a single catchment

(2012) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

When Phenotypes Do Not Match Genotypes--Unexpected Phenotypic Diversity and Potential Environmental Constraints in Icelandic Stickleback

(2012) K. Lucek et al.   JOURNAL OF HEREDITY

Integrin α5/fibronectin1 and focal adhesion kinase are required for lens fiber morphogenesis in zebrafish

(2012) Julie M. Hayes et al.   MOLECULAR BIOLOGY OF THE CELL

Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback

(2012) TIFFANY B. MALEK et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey 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 genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Evidence of Adaptive Evolutionary Divergence during Biological Invasion

(2012) Kay Lucek et al.   PLoS One

Repeated Lake-Stream Divergence in Stickleback Life History within a Central European Lake Basin

(2012) Dario Moser et al.   PLoS One

The probability of genetic parallelism and convergence in natural populations

(2012) G. L. Conte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The genomics of speciation-with-gene-flow

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

Nrdp1 governs differentiation of the melanocyte lineage via Erbb3b signaling in the zebrafish embryogenesis

(2011) Sateesh Maddirevula et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart 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

Ecology, sexual selection and speciation

(2011) Martine E. Maan et al.   ECOLOGY LETTERS

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

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks

(2011) A K Greenwood et al.   HEREDITY

Growth plate regulation and osteochondroma formation: insights from tracing proteoglycans in zebrafish models and human cartilage

(2011) Carlos E de Andrea et al.   JOURNAL OF PATHOLOGY

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

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

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

Genome-wide patterns of divergence during speciation: the lake whitefish case study

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

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

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

Establishment of new mutations under divergence and genome hitchhiking

(2011) J. L. Feder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions

(2011) B. E. Deagle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Magic traits in speciation: ‘magic’ but not rare?

(2011) Maria R. Servedio et al.   TRENDS IN ECOLOGY & EVOLUTION

Adaptive Divergence in the Thyroid Hormone Signaling Pathway in the Stickleback Radiation

(2010) Jun Kitano et al.   CURRENT BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Alternative developmental pathways and the propensity to migrate: a case study in the Atlantic salmon

(2010) D. J. PÁEZ et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Cartilage ultrastructure in proteoglycan-deficient zebrafish mutants brings to light new candidate genes for human skeletal disorders

(2010) Malgorzata I Wiweger et al.   JOURNAL OF PATHOLOGY

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

Genomic islandsofspeciation or genomic islandsandspeciation?

(2010) THOMAS L. TURNER et al.   MOLECULAR ECOLOGY

Constraints on speciation suggested by comparing lake-stream stickleback divergence across two continents

(2010) DANIEL BERNER et al.   MOLECULAR ECOLOGY

Hybridization between distant lineages increases adaptive variation during a biological invasion: stickleback in Switzerland

(2010) KAY LUCEK 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

ZFIN: enhancements and updates to the zebrafish model organism database

(2010) Y. Bradford et al.   NUCLEIC ACIDS RESEARCH

Widespread genomic divergence during sympatric speciation

(2010) A. P. Michel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Analysis of Fin Development in Zebrafish Identifies Furin and Hemicentin1 as Potential Novel Fraser Syndrome Disease Genes

(2010) Thomas J. Carney et al.   PLoS Genetics

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

Parallels, nonparallels, and plasticity in population differentiation of threespine stickleback within a lake

(2009) GUÐBJÖRG Á. ÓLAFSDÓTTIR et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Control of extracellular matrix assembly along tissue boundaries via Integrin and Eph/Ephrin signaling

(2009) D. Julich et al.   DEVELOPMENT

PHENOTYPE-DEPENDENT NATIVE HABITAT PREFERENCE FACILITATES DIVERGENCE BETWEEN PARAPATRIC LAKE AND STREAM STICKLEBACK

(2009) Daniel I. Bolnick et al.   EVOLUTION

VARIABLE PROGRESS TOWARD ECOLOGICAL SPECIATION IN PARAPATRY: STICKLEBACK ACROSS EIGHT LAKE-STREAM TRANSITIONS

(2009) Daniel Berner et al.   EVOLUTION

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

S14-03 From trait to base pairs: Parallel evolution of pelvic reduction in three-spined sticklebacks occurs by repeated deletion of a tissue-specific pelvic enhancer at Pitx1

(2009) Yingguang Frank Chan et al.   MECHANISMS OF DEVELOPMENT

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

Ecological explanations for (incomplete) speciation

(2009) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

Mutation in the Human Homeobox Gene NKX5-3 Causes an Oculo-Auricular Syndrome

(2008) Daniel F. Schorderet et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Ecological predictions lead to the discovery of a benthic–limnetic sympatric species pair of threespine stickleback in Little Quarry Lake, British Columbia

(2008) J. L. Gow et al.   CANADIAN JOURNAL OF ZOOLOGY

Hitchhiking Mapping Reveals a Candidate Genomic Region for Natural Selection in Three-Spined Stickleback Chromosome VIII

(2008) Hannu S. Mäkinen et al.   GENETICS

Identifying footprints of directional and balancing selection in marine and freshwater three-spined stickleback (Gasterosteus aculeatus) populations

(2008) H. S. MÄKINEN et al.   MOLECULAR ECOLOGY

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

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Hitching a lift on the road to speciation

(2008) CAROLE SMADJA et al.   MOLECULAR ECOLOGY

Speciation with gene flow could be common

(2008) PATRIK NOSIL   MOLECULAR ECOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe—Evidence for multiple glacial refugia

(2007) H.S. Mäkinen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION