Making sense of genomic islands of differentiation in light of speciation

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila

(2016) Jim A. Mossman et al.   GENETICS

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod

(2016) Tina Graceline Kirubakaran et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

(2016) Andrew D. Foote et al.   Nature Communications

Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis

(2016) Matthew J. Markert et al.   G3-Genes Genomes Genetics

Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing

(2016) Aaron B. A. Shafer et al.   PLOS BIOLOGY

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

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

Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila

(2016) Jim A. Mossman et al.   GENETICS

GC-biased gene conversion links the recombination landscape and demography to genomic base composition

(2015) Carina F. Mugal et al.   BIOESSAYS

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

(2015) Konrad Lohse et al.   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

Transcriptomics of colour patterning and coloration shifts in crows

(2015) J. W. Poelstra et al.   MOLECULAR ECOLOGY

Connecting genotypes, phenotypes and fitness: harnessing the power of CRISPR/Cas9 genome editing

(2015) Jeremy M. Bono 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

Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

(2015) Petri Kemppainen et al.   Molecular Ecology Resources

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

(2015) Sangeet Lamichhaney et al.   NATURE

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

A male-determining factor in the mosquito Aedes aegypti

(2015) A. B. Hall et al.   SCIENCE

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

(2015) M. Malinsky et al.   SCIENCE

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

The genomics of organismal diversification illuminated by adaptive radiations

(2015) Daniel Berner et al.   TRENDS IN GENETICS

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

Evolutionary analysis of the female-specific avian W chromosome

(2015) Linnéa Smeds et al.   Nature Communications

Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene

(2015) Suzanne V. Saenko et al.   Scientific Reports

RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs

(2015) Martin Laporte et al.   G3-Genes Genomes Genetics

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

(2015) Russell B. Corbett-Detig et al.   PLOS BIOLOGY

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

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

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Models of Speciation: Where Are We Now?

(2014) Sergey Gavrilets   JOURNAL OF HEREDITY

Speciation Continuum

(2014) K. L. Shaw et al.   JOURNAL OF HEREDITY

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti 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

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

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

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

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

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

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Disputed islands

(2014) E. Pennisi   SCIENCE

Comparative population genomics: power and principles for the inference of functionality

(2014) David S. Lawrie et al.   TRENDS IN GENETICS

Thinking too positive? Revisiting current methods of population genetic selection inference

(2014) Claudia Bank et al.   TRENDS IN GENETICS

Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes

(2014) Yuheng Huang et al.   PLoS Genetics

Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast

(2014) Sarah E Zanders et al.   eLife

Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations

(2014) Jeffrey L. Feder et al.   Frontiers in Genetics

Geographic Mode of Speciation and Genomic Divergence

(2013) Jeffrey L. Feder et al.   Annual Review of Ecology Evolution and Systematics

Unsupervised genome-wide recognition of local relationship patterns

(2013) Neda Zamani et al.   BMC GENOMICS

Experimental evidence for ecological selection on genome variation in the wild

(2013) Zachariah Gompert et al.   ECOLOGY LETTERS

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

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

DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES

(2013) Rose L. Andrew et al.   EVOLUTION

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

(2013) Patrik Nosil et al.   EVOLUTION

GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

(2013) Samuel M. Flaxman et al.   EVOLUTION

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Inferring population size changes with sequence and SNP data: lessons from human bottlenecks

(2013) L M Gattepaille et al.   HEREDITY

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Background Selection 20 Years on

(2013) Brian Charlesworth   JOURNAL OF HEREDITY

Recombination in the threespine stickleback genome-patterns and consequences

(2013) Marius Roesti et al.   MOLECULAR ECOLOGY

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Ecological genomics of local adaptation

(2013) Outi Savolainen 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

Hybridization Reveals the Evolving Genomic Architecture of Speciation

(2013) Marcus R. Kronforst et al.   Cell Reports

The lavender plumage colour in Japanese quail is associated with a complex mutation in the region of MLPH that is related to differences in growth, feed consumption and body temperature

(2012) Bertrand Bed’hom et al.   BMC GENOMICS

The Relationship Between FST and the Frequency of the Most Frequent Allele

(2012) M. Jakobsson et al.   GENETICS

A coalescent model of background selection with recombination, demography and variation in selection coefficients

(2012) K Zeng   HEREDITY

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau 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 Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

The genomics of speciation-with-gene-flow

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

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

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

(2011) Matthew V. Rockman   EVOLUTION

Quantifying the Variation in the Effective Population Size Within a Genome

(2011) Toni I. Gossmann et al.   GENETICS

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

A framework for comparing processes of speciation in the presence of gene flow

(2011) CAROLE M. SMADJA et al.   MOLECULAR ECOLOGY

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

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

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

Coalescent patterns for chromosomal inversions in divergent populations

(2011) R. F. Guerrero 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

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

Speciation with gene flow on Lord Howe Island

(2011) Alexander S. T. Papadopulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

(2011) Thomas Mailund et al.   PLoS Genetics

Admixture Mapping Comes of Age

(2010) Cheryl A. Winkler et al.   Annual Review of Genomics and Human Genetics

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

The role of meiotic drive in hybrid male sterility

(2010) S. R. McDermott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Speciation genetics: current status and evolving approaches

(2010) J. B. W. Wolf et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Chromosomal speciation revisited: rearranging theory with pieces of evidence

(2010) Rui Faria et al.   TRENDS IN ECOLOGY & 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

A powerful regression-based method for admixture mapping of isolation across the genome of hybrids

(2009) ZACHARIAH GOMPERT et al.   MOLECULAR ECOLOGY

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Natural selection in action during speciation

(2009) S. Via   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Origin of Species by Natural and Sexual Selection

(2009) G. S. van Doorn et al.   SCIENCE

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

(2009) Y. F. Chan et al.   SCIENCE

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

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

Mayr's view of Darwin: was Darwin wrong about speciation?

(2008) JAMES MALLET   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2008) M. Foll et al.   GENETICS

Speciation through evolution of sex-linked genes

(2008) A Qvarnström et al.   HEREDITY

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

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

GSTand its relatives do not measure differentiation

(2008) LOU JOST   MOLECULAR ECOLOGY

Sex chromosomes and speciation in Drosophila

(2008) Daven C. Presgraves   TRENDS IN GENETICS