The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression

Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

(2017) Asano Ishikawa et al.   EVOLUTION

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Frequency dependence limits divergent evolution by favouring rare immigrants over residents

(2017) Daniel I. Bolnick et al.   NATURE

Ancient hybridization fuels rapid cichlid fish adaptive radiations

(2017) Joana I. Meier et al.   Nature Communications

The genomic mosaicism of hybrid speciation

(2017) Tore O. Elgvin et al.   Science Advances

Transitions between phases of genomic differentiation during stick-insect speciation

(2017) Rüdiger Riesch et al.   Nature Ecology & Evolution

Tipping points in the dynamics of speciation

(2017) Patrik Nosil et al.   Nature Ecology & Evolution

Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species

(2016) Christina A. Muirhead et al.   AMERICAN NATURALIST

Powerful methods for detecting introgressed regions from population genomic data

(2016) Benjamin K. Rosenzweig et al.   MOLECULAR ECOLOGY

Demographic modelling with whole-genome data reveals parallel origin of similarPundamiliacichlid species after hybridization

(2016) Joana I. Meier et al.   MOLECULAR ECOLOGY

Reproductive isolation and introgression between sympatricMimulusspecies

(2016) Amanda M. Kenney et al.   MOLECULAR ECOLOGY

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

(2016) Christopher H. Martin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

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

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

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

A New Method to Scan Genomes for Introgression in a Secondary Contact Model

(2015) Anthony J. Geneva et al.   PLoS One

Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

(2014) Megan Phifer-Rixey et al.   GENETICS

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

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

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

ABC inference of multi-population divergence with admixture from unphased population genomic data

(2014) John D. Robinson 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

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Comparative Analysis of Japanese Three-Spined Stickleback Clades Reveals the Pacific Ocean Lineage Has Adapted to Freshwater Environments while the Japan Sea Has Not

(2014) Mark Ravinet et al.   PLoS One

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

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

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

(2014) Kohta Yoshida et al.   PLoS Genetics

Genomic divergence between nine- and three-spined sticklebacks

(2013) Baocheng Guo et al.   BMC GENOMICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen 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

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics

(2013) Christopher W. Wheat et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2013) S. Renaut et al.   Nature Communications

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

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

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

The genomics of speciation-with-gene-flow

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

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

(2012) Thomas Mailund et al.   PLoS Genetics

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 signature of balancing selection in the region upstream to the human UGT2B4 gene and implications for breast cancer risk

(2011) Chang Sun et al.   HUMAN GENETICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genomic divergence during speciation: causes and consequences

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

Genomic impacts of chromosomal inversions in parapatric Drosophila species

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

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled et al.   SYSTEMATIC BIOLOGY

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

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

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

(2011) Vincent Castric et al.   PLoS Genetics

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Genomic Admixture Analysis in European Populus spp. Reveals Unexpected Patterns of Reproductive Isolation and Mating

(2010) C. Lexer et al.   GENETICS

Ecological divergence and habitat isolation between two migratory forms of Japanese threespine stickleback (Gasterosteus aculeatus)

(2010) M. KUME et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

(2010) G. BERTORELLE et al.   MOLECULAR ECOLOGY

Genome scan of hybridizing sunflowers from Texas (Helianthus annuusandH. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation

(2010) M. SCASCITELLI et al.   MOLECULAR ECOLOGY

msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis

(2010) P. PAVLIDIS et al.   Molecular Ecology Resources

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Population Genomics of Secondary Contact

(2010) Anthony Geneva et al.   Genes

Statistical Phylogeography

(2009) L. Lacey Knowles   Annual Review of Ecology Evolution and Systematics

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The World's Oldest Fossil Threespine Stickleback Fish

(2009) Michael A. Bell et al.   COPEIA

THE EVOLUTION OF STRONG REPRODUCTIVE ISOLATION

(2009) Nicholas H. Barton 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

Along the speciation continuum in sticklebacks

(2009) A. P. Hendry et al.   JOURNAL OF FISH BIOLOGY

introgress: a software package for mapping components of isolation in hybrids

(2009) ZACHARIAH GOMPERT et al.   Molecular Ecology Resources

A role for a neo-sex chromosome in stickleback speciation

(2009) Jun Kitano et al.   NATURE

Non-linear regression models for Approximate Bayesian Computation

(2009) Michael G. B. Blum et al.   STATISTICS AND COMPUTING

Ecological explanations for (incomplete) speciation

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

A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE

(2008) Michael P. Cummings et al.   EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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