Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact

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

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

Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicussapsuckers)

(2016) Sampath S. Seneviratne et al.   JOURNAL OF AVIAN BIOLOGY

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

(2016) Richard G. Harrison et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

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

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

(2015) Philip Lavretsky et al.   MOLECULAR ECOLOGY

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

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

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

Spatiotemporally consistent genomic signatures of reproductive isolation in a moving hybrid zone

(2014) Scott A. Taylor et al.   EVOLUTION

A role for migration-linked genes and genomic islands in divergence of a songbird

(2014) Kristen Ruegg 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

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Interspecific introgressive origin of genomic diversity in the house mouse

(2014) Kevin J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

(2014) Christine Grossen et al.   PLoS Genetics

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

(2014) Cassandra N. Trier et al.   PLoS Genetics

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

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

Gene flow and the maintenance of species boundaries

(2013) Erica L. Larson et al.   MOLECULAR ECOLOGY

hzar: hybrid zone analysis using an R software package

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

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

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

WHERE ARE THE WORMY MICE? A REEXAMINATION OF HYBRID PARASITISM IN THE EUROPEAN HOUSE MOUSE HYBRID ZONE

(2012) Stuart J. E. Baird et al.   EVOLUTION

GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES

(2012) Zachariah Gompert et al.   EVOLUTION

Concordance of genetic and phenotypic characters across a sapsucker hybrid zone

(2012) Sampath S. Seneviratne et al.   JOURNAL OF AVIAN BIOLOGY

New(t)s and views from hybridizing MHC genes: introgression rather than trans-species polymorphism may shape allelic repertoires

(2012) K. MATHIAS WEGNER et al.   MOLECULAR ECOLOGY

bgc: Software for Bayesian estimation of genomic clines

(2012) Z. Gompert et al.   Molecular Ecology Resources

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The genomics of speciation-with-gene-flow

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints

(2011) B M Skinner et al.   HEREDITY

Genetic structure in a dynamic baboon hybrid zone corroborates behavioural observations in a hybrid population

(2011) M. J. E. CHARPENTIER et al.   MOLECULAR ECOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE 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

Genomics of isolation in hybrids

(2011) Z. Gompert 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 Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comparative analyses of the Conserved Oligomeric Golgi (COG) complex in vertebrates

(2010) Rita Quental et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Estimating linkage disequilibria

(2010) N H Barton   HEREDITY

Mixed linear model approach adapted for genome-wide association studies

(2010) Zhiwu Zhang et al.   NATURE GENETICS

Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences

(2010) M. K. N. Lawniczak et al.   SCIENCE

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

(2009) Jeffrey L. Feder et al.   EVOLUTION

THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE

(2009) Katherine C. Teeter et al.   EVOLUTION

Linkage Disequilibrium Between Loci With Unknown Phase

(2009) A. R. Rogers et al.   GENETICS

Extensive hybridization in a contact zone between MacGillivray's warblersOporornistolmieiand mourning warblersO. philadelphiadetected using molecular and morphological analyses

(2009) Darren E. Irwin et al.   JOURNAL OF AVIAN BIOLOGY

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

(2009) ZACHARIAH GOMPERT et al.   MOLECULAR ECOLOGY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Divergent Evolution of Duplicate Genes Leads to Genetic Incompatibilities Within A. thaliana

(2009) D. Bikard et al.   SCIENCE

A comparison of synteny and gene order on the homologue of chicken chromosome 7 between two passerine species and between passerines and chicken

(2008) M.C. Hale et al.   CYTOGENETIC AND GENOME RESEARCH

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

(2008) Laurène Gay et al.   EVOLUTION

A Linkage Map of the Zebra Finch Taeniopygia guttata Provides New Insights Into Avian Genome Evolution

(2008) J. Stapley et al.   GENETICS

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

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Genomic evidence for a large-Z effect

(2008) H. Ellegren   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES