Massive genome inversion drives coexistence of divergent morphs in common quails

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

(2020) Salvatore Mastrangelo et al.   Animals

A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird

(2020) Jennifer R. Merritt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body

(2020) Yang Xi et al.   Frontiers in Cell and Developmental Biology

Correction to: Hair follicles transcriptome profiles in Bashang long-tailed chickens with different plumage colors

(2019) Xiaohui Liu et al.   Genes & Genomics

Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion

(2018) Paul Jay et al.   CURRENT BIOLOGY

Interglacial refugia on tropical mountains: Novel insights from the summit rat (Rattus baluensis ), a Borneo mountain endemic

(2018) Miguel Camacho-Sanchez et al.   DIVERSITY AND DISTRIBUTIONS

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

ATR is required to complete meiotic recombination in mice

(2018) Sarai Pacheco et al.   Nature Communications

Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis )

(2018) Mikus Abolins-Abols et al.   MOLECULAR ECOLOGY

Chromosomal inversions associated with environmental adaptation in honeybees

(2018) Matthew J. Christmas et al.   MOLECULAR ECOLOGY

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

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

Direct estimate of the rate of germline mutation in a bird

(2016) Linnéa Smeds et al.   GENOME RESEARCH

Candidate Gene Analysis Suggests Untapped Genetic Complexity in Melanin-Based Pigmentation in Birds

(2016) Yann X. C. Bourgeois et al.   JOURNAL OF HEREDITY

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

(2016) Tina Graceline Kirubakaran et al.   MOLECULAR ECOLOGY

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

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

The ATM Signaling Cascade Promotes Recombination-Dependent Pachytene Arrest in Mouse Spermatocytes

(2015) Sarai Pacheco et al.   PLoS Genetics

Interactions between a Candidate Gene for Migration (ADCYAP1), Morphology and Sex Predict Spring Arrival in Blackcap Populations

(2015) Raeann Mettler et al.   PLoS One

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

(2012) Anna Zlotina et al.   CHROMOSOME RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Effects of Inversions on Within- and Between-Species Recombination and Divergence

(2011) Laurie S. Stevison et al.   Genome Biology and Evolution

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

Chromosomal speciation revisited: rearranging theory with pieces of evidence

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

Mouse TRIP13/PCH2 Is Required for Recombination and Normal Higher-Order Chromosome Structure during Meiosis

(2010) Ignasi Roig et al.   PLoS Genetics

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

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

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The effects of mowing and agricultural landscape management on population movements of the common quail

(2009) José Domingo Rodríguez-Teijeiro et al.   JOURNAL OF BIOGEOGRAPHY

Evolution of Coloration Patterns

(2008) Meredith E. Protas et al.   Annual Review of Cell and Developmental Biology

Search for informative polymorphisms in candidate genes: clock genes and circadian behaviour in blue tits

(2008) C. Steinmeyer et al.   GENETICA

Plumage development and moult in the European Quail Coturnix c. coturnix: criteria for age determination

(2008) M. SAINT JALME et al.   IBIS