Mosaic genome evolution in a recent and rapid avian radiation

Repeated divergent selection on pigmentation genes in a rapid finch radiation

(2017) Leonardo Campagna et al.   Science Advances

Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers

(2016) David P.L. Toews et al.   CURRENT BIOLOGY

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

(2016) Darren E. Irwin 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

A beak size locus in Darwins finches facilitated character displacement during a drought

(2016) S. Lamichhaney et al.   SCIENCE

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

(2016) Nagarjun Vijay et al.   Nature Communications

Mapping centromeres of microchromosomes in the zebra finch (Taeniopygia guttata) using half-tetrad analysis

(2015) Ulrich Knief et al.   CHROMOSOMA

New Zealand Passerines Help Clarify the Diversification of Major Songbird Lineages during the Oligocene

(2015) Gillian C. Gibb et al.   Genome Biology and 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

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

(2015) Sangeet Lamichhaney et al.   NATURE

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution

(2015) Thomas J. Givnish   NEW PHYTOLOGIST

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

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

(2015) M. Malinsky et al.   SCIENCE

The genomics of organismal diversification illuminated by adaptive radiations

(2015) Daniel Berner et al.   TRENDS IN GENETICS

A new time tree reveals Earth historys imprint on the evolution of modern birds

(2015) S. Claramunt et al.   Science Advances

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Epistatic and Combinatorial Effects of Pigmentary Gene Mutations in the Domestic Pigeon

(2014) Eric T. Domyan et al.   CURRENT BIOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

A molecular basis for classic blond hair color in Europeans

(2014) Catherine A Guenther et al.   NATURE GENETICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

(2014) Jeffrey M. DaCosta et al.   PLoS One

Selection Signatures in Worldwide Sheep Populations

(2014) Maria-Ines Fariello et al.   PLoS One

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

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

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

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

The Genetic Basis of White Tigers

(2013) Xiao Xu et al.   CURRENT BIOLOGY

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

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

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

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Conserved distal promoter of the agouti signaling protein (ASIP) gene controls sexual dichromatism in chickens

(2012) Eri Oribe et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

(2012) Eva-Maria Willing et al.   PLoS One

Specifying and Sustaining Pigmentation Patterns in Domestic and Wild Cats

(2012) C. B. Kaelin et al.   SCIENCE

Limits to Speciation Inferred from Times to Secondary Sympatry and Ages of Hybridizing Species along a Latitudinal Gradient

(2011) Jason T. Weir et al.   AMERICAN NATURALIST

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Gene Duplication of endothelin 3 Is Closely Correlated with the Hyperpigmentation of the Internal Organs ( Fibromelanosis ) in Silky Chickens

(2011) Ai Shinomiya et al.   GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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 Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10

(2011) Ulrika Gunnarsson et al.   Pigment Cell & Melanoma Research

Rapid phenotypic evolution during incipient speciation in a continental avian radiation

(2011) L. Campagna et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau 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

A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken

(2011) Ben Dorshorst et al.   PLoS Genetics

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

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Vertebrate pigmentation: from underlying genes to adaptive function

(2010) Joanna K. Hubbard et al.   TRENDS IN GENETICS

Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin‐1 Receptor

(2009) J. Albert C. Uy et al.   AMERICAN NATURALIST

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Balancing Selection of a Frame-Shift Mutation in the MRC2 Gene Accounts for the Outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle

(2009) Corinne Fasquelle et al.   PLoS Genetics

Recessive black Is Allelic to the yellow Plumage Locus in Japanese Quail and Associated With a Frameshift Deletion in the ASIP Gene

(2008) T. Hiragaki et al.   GENETICS

Characterization of Japanese Quail yellow as a Genomic Deletion Upstream of the Avian Homolog of the Mammalian ASIP (agouti) Gene

(2008) N. J. Nadeau et al.   GENETICS

Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors

(2008) R. C. Pratt et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Interpreting principal component analyses of spatial population genetic variation

(2008) John Novembre et al.   NATURE GENETICS