Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms

Balancing selection via life-history trade-offs maintains an inversion polymorphism in a seaweed fly

(2020) Claire Mérot et al.   Nature Communications

A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

(2020) Claire Mérot et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolution and genetic architecture of disassortative mating at a locus under heterozygote advantage

(2020) Ludovic Maisonneuve et al.   EVOLUTION

Evolving Inversions

(2019) Rui Faria et al.   TRENDS IN ECOLOGY & EVOLUTION

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

(2019) Tony Kess et al.   Science Advances

Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata

(2019) Suzanne V. Saenko et al.   EvoDevo

Evolutionary and functional impact of common polymorphic inversions in the human genome

(2019) Carla Giner-Delgado et al.   Nature Communications

Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion

(2018) Paul Jay et al.   CURRENT BIOLOGY

Life history variation is maintained by fitness trade-offs and negative frequency-dependent selection

(2018) Mark R. Christie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data

(2018) Fabricio Almeida Araujo et al.   Scientific Reports

Chromosome assembly of large and complex genomes using multiple references

(2018) Mikhail Kolmogorov et al.   GENOME RESEARCH

Degenerative expansion of a young supergene

(2018) Eckart Stolle et al.   MOLECULAR BIOLOGY AND EVOLUTION

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

(2017) Dorothea Lindtke et al.   MOLECULAR ECOLOGY

Genetic architecture and balancing selection: the life and death of differentiated variants

(2017) Violaine Llaurens et al.   MOLECULAR ECOLOGY

A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success

(2017) Ulrich Knief et al.   Nature Ecology & Evolution

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

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

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

The gene cortex controls mimicry and crypsis in butterflies and moths

(2016) Nicola J. Nadeau et al.   NATURE

Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive

(2016) Quentin Helleu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Warning signals are under positive frequency-dependent selection in nature

(2016) Mathieu Chouteau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

(2016) John W. Davey et al.   G3-Genes Genomes Genetics

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

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

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Evolution of dominance mechanisms at a butterfly mimicry supergene

(2014) Yann Le Poul et al.   Nature Communications

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

(2013) Christine A Lavoie et al.   Mobile DNA

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

(2012) X. Zheng et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution

(2012) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(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