A genomic map of clinal variation across the European rabbit hybrid zone

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

(2017) Fan Han et al.   GENOME RESEARCH

Come on feel the noise - from metaphors to null models

(2017) K. Lohse   JOURNAL OF EVOLUTIONARY BIOLOGY

Speciation, species persistence and the goals of studying genomic barriers to gene flow

(2017) C. E. Wagner et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Identifying the loci of speciation: the challenge beyond genome scans

(2017) D. Lindtke et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Inconvenient truths in population and speciation genetics point towards a future beyond allele frequencies

(2017) C. A. Buerkle   JOURNAL OF EVOLUTIONARY BIOLOGY

Glittering gold and the quest for Isla de Muerta

(2017) C. D. Jiggins et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The impact of high-throughput sequencing technology on speciation research: maintaining perspective

(2017) S. J. E. Baird   JOURNAL OF EVOLUTIONARY BIOLOGY

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

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

Gene Regulation and Speciation

(2017) Katya L. Mack et al.   TRENDS IN GENETICS

Gene regulation and speciation in house mice

(2016) Katya L. Mack et al.   GENOME RESEARCH

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

(2016) Jing Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

(2016) Sean Stankowski et al.   MOLECULAR ECOLOGY

Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones

(2016) Richard G. Harrison 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

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

(2016) Camille Roux et al.   PLOS BIOLOGY

Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering

(2016) Santosh Anand et al.   Scientific Reports

Biometrical analysis reveals major differences between the two subspecies of the European rabbit

(2015) Catarina Campos Ferreira et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models

(2015) Brian W. Davis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional Organization of the Genome May Shape the Species Boundary in the House Mouse

(2015) Václav Janoušek et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations

(2015) Matthew D. McGee et al.   MOLECULAR ECOLOGY

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

(2014) Megan Phifer-Rixey et al.   GENETICS

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

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

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

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

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

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

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

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

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

Genomic Networks of Hybrid Sterility

(2014) Leslie M. Turner et al.   PLoS Genetics

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

(2014) Miguel Carneiro et al.   PLoS Genetics

Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

(2014) Leslie M Turner et al.   eLife

Identification of large selective sweeps associated with major genes in cattle

(2013) T. Druet et al.   ANIMAL GENETICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

(2013) Vitor C. Sousa et al.   GENETICS

Meiotic Sex Chromosome Inactivation Is Disrupted in Sterile Hybrid Male House Mice

(2013) P. Campbell et al.   GENETICS

The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

(2013) T. L. Parchman et al.   MOLECULAR ECOLOGY

Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

(2013) Miguel Carneiro et al.   MOLECULAR ECOLOGY

hzar: hybrid zone analysis using an R software package

(2013) Elizabeth P. Derryberry et al.   Molecular Ecology Resources

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

(2013) S. Renaut et al.   Nature Communications

Uninformative polymorphisms bias genome scans for signatures of selection

(2012) Marius Roesti et al.   BMC EVOLUTIONARY BIOLOGY

THE LANGUAGE OF SPECIATION

(2012) Richard G. Harrison   EVOLUTION

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

(2012) J. A. Andres et al.   GENETICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (Fundulus heteroclitus)

(2012) Allan E. Strand et al.   PLoS One

Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width

(2011) Jitka Polechová et al.   GENETICS

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

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

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

The genes underlying the process of speciation

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

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

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

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

THE CONTRIBUTION OF GENE MOVEMENT TO THE “TWO RULES OF SPECIATION”

(2010) Leonie C. Moyle et al.   EVOLUTION

SPECIATION IN THE EUROPEAN RABBIT (ORYCTOLAGUS CUNICULUS): ISLANDS OF DIFFERENTIATION ON THE X CHROMOSOME AND AUTOSOMES

(2010) Miguel Carneiro et al.   EVOLUTION

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

(2010) A. McKenna et al.   GENOME RESEARCH

Extensive Gene Conversion Drives the Concerted Evolution of Paralogous Copies of the SRY Gene in European Rabbits

(2010) A. Geraldes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using differential introgression in hybrid zones to identify genomic regions involved in speciation

(2010) BRET A. PAYSEUR   Molecular Ecology Resources

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Speciation genetics: current status and evolving approaches

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

Chromosomal speciation revisited: rearranging theory with pieces of evidence

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

Widespread Over-Expression of the X Chromosome in Sterile F1 Hybrid Mice

(2010) Jeffrey M. Good et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Detecting Selective Sweeps: A New Approach Based on Hidden Markov Models

(2009) S. Boitard et al.   GENETICS

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

Gene Expression Divergence and Hybrid Misexpression between Lake Whitefish Species Pairs (Coregonus spp. Salmonidae)

(2009) S. Renaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Altered Heterochromatin Binding by a Hybrid Sterility Protein in Drosophila Sibling Species

(2009) J. J. Bayes et al.   SCIENCE

Characterization of Two Cytoplasmic Poly(A)-Binding Proteins, PABPC1 and PABPC2, in Mouse Spermatogenic Cells1

(2008) Masanori Kimura et al.   BIOLOGY OF REPRODUCTION

Ecological Speciation in Mimetic Butterflies

(2008) Chris D. Jiggins   BIOSCIENCE

Genetic conflict outweighs heterogametic incompatibility in the mouse hybrid zone?

(2008) Miloš Macholán et al.   BMC EVOLUTIONARY BIOLOGY

COMPARING CLINES ON MOLECULAR AND PHENOTYPIC TRAITS IN HYBRID ZONES: A WINDOW ON TENSION ZONE MODELS

(2008) Laurène Gay et al.   EVOLUTION

A Complex Genetic Basis to X-Linked Hybrid Male Sterility Between Two Species of House Mice

(2008) J. M. Good et al.   GENETICS

Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

(2008) M. Carneiro et al.   GENETICS

Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula

(2008) A. GERALDES et al.   MOLECULAR ECOLOGY

The UCSC Genome Browser Database: update 2009

(2008) R. M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids

(2008) N. Phadnis et al.   SCIENCE

A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase

(2008) O. Mihola et al.   SCIENCE