Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

The Genetics of Seasonal Migration and Plumage Color

(2016) Kira E. Delmore et al.   CURRENT BIOLOGY

History repeats itself: genomic divergence in copepods

(2016) Sébastien Renaut et al.   MOLECULAR ECOLOGY

Transcriptome-wide patterns of divergence during allopatric evolution

(2016) Ricardo J. Pereira et al.   MOLECULAR ECOLOGY

A Spatial Framework for Understanding Population Structure and Admixture

(2016) Gideon S. Bradburd et al.   PLoS Genetics

The Effects of Background and Interference Selection on Patterns of Genetic Variation in Subdivided Populations

(2015) K. Zeng et al.   GENETICS

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

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

(2015) S J Oyler-McCance et al.   HEREDITY

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

Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets

(2015) Laura C. Norris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeatability of evolution on epistatic landscapes

(2015) Benedikt Bauer et al.   Scientific Reports

Evolution of leaf warbler songs (Aves: Phylloscopidae)

(2015) Dieter Thomas Tietze et al.   Ecology and Evolution

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami 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

Genomic divergence in a ring species complex

(2014) Miguel Alcaide et al.   NATURE

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

(2014) Miguel Carneiro et al.   PLoS Genetics

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

The Evolutionary Genomics of Birds

(2013) Hans Ellegren   Annual Review of Ecology Evolution and Systematics

Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers

(2013) Sebastien Renaut et al.   MOLECULAR ECOLOGY

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

(2013) S. Renaut et al.   Nature Communications

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu 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

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

(2012) J. R. Meyer et al.   SCIENCE

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

(2012) Fabian Staubach et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Replaying the Tape of Life: Quantification of the Predictability of Evolution

(2012) Alexander E. Lobkovsky et al.   Frontiers in Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The Joint Effects of Background Selection and Genetic Recombination on Local Gene Genealogies

(2011) Kai Zeng 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

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

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genomic islandsofspeciation or genomic islandsandspeciation?

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

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

The roles of time and ecology in the continental radiation of the Old World leaf warblers (Phylloscopus and Seicercus)

(2010) T. D. Price   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION

(2009) Jeffrey L. Feder 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

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Speciation through evolution of sex-linked genes

(2008) A Qvarnström et al.   HEREDITY

Cryptic species in the genus Phylloscopus (Old World leaf warblers)

(2008) DARREN E. IRWIN et al.   IBIS

Call divergence is correlated with geographic and genetic distance in greenish warblers (Phylloscopus trochiloides): a strong role for stochasticity in signal evolution?

(2008) D. E. IRWIN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY