Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations

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

(2019) Suzanne V. Saenko et al.   EvoDevo

Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion

(2018) Paul Jay et al.   CURRENT BIOLOGY

Parallel evolution of Batesian mimicry supergene in twoPapiliobutterflies,P. polytesandP. memnon

(2018) Takuro Iijima et al.   Science Advances

Aristaless Controls Butterfly Wing Color Variation Used in Mimicry and Mate Choice

(2018) Erica L. Westerman et al.   CURRENT BIOLOGY

Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

(2018) Steven M. Van Belleghem et al.   PLoS Genetics

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Macroevolutionary shifts ofWntAfunction potentiate butterfly wing-pattern diversity

(2017) Anyi Mazo-Vargas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence

(2017) Linlin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracing the origin and evolution of supergene mimicry in butterflies

(2017) Wei Zhang et al.   Nature Communications

Mimicry in butterflies: co-option and a bag of magnificent developmental genetic tricks

(2017) Riddhi Deshmukh et al.   Wiley Interdisciplinary Reviews-Developmental Biology

The gene cortex controls mimicry and crypsis in butterflies and moths

(2016) Nicola J. Nadeau et al.   NATURE

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis -Regulatory Evolution in Lepidoptera

(2016) James J. Lewis et al.   Cell Reports

The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry

(2015) M. R. Kronforst et al.   GENETICS

Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in the silkworm Bombyx mori

(2015) K Ito et al.   HEREDITY

A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly

(2015) Hideki Nishikawa et al.   NATURE GENETICS

Phylogeny and Historical Biogeography of Asian Pterourus Butterflies (Lepidoptera: Papilionidae): A Case of Intercontinental Dispersal from North America to East Asia

(2015) Li-Wei Wu et al.   PLoS One

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

(2015) Krzysztof M. Kozak et al.   SYSTEMATIC BIOLOGY

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

(2015) Xueyan Li et al.   Nature Communications

Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense

(2015) Qian Cong et al.   Cell Reports

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems

(2014) Arnaud Martin et al.   DEVELOPMENTAL BIOLOGY

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns

(2014) Emily V. Daniels et al.   MOLECULAR ECOLOGY

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Comparative genomics of the mimicry switch in Papilio dardanus

(2014) M. J. T. N. Timmermans et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient homology underlies adaptive mimetic diversity across butterflies

(2014) Jason R. Gallant et al.   Nature Communications

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

(2014) Virpi Ahola et al.   Nature Communications

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

snow white, a Zebrafish Model of Hermansky-Pudlak Syndrome Type 5

(2013) C. M. S. Daly et al.   GENETICS

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths)

(2013) Niklas Wahlberg et al.   PLoS One

A homolog of the human Hermansky–Pudluck syndrome-5 (HPS5) gene is responsible for the oa larval translucent mutants in the silkworm, Bombyx mori

(2012) T. Fujii et al.   GENETICA

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

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Unraveling the thread of nature’s tapestry: the genetics of diversity and convergence in animal pigmentation

(2012) Marcus R. Kronforst et al.   Pigment Cell & Melanoma Research

Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand

(2012) A. Martin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The probability of genetic parallelism and convergence in natural populations

(2012) G. L. Conte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

(2012) Carolina Pardo-Diaz et al.   PLoS Genetics

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

(2012) Russell B. Corbett-Detig et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

(2011) Shuai Zhan et al.   CELL

New genome size estimates of 134 species of arthropods

(2011) Shawn Jason Hanrahan et al.   CHROMOSOME RESEARCH

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

(2011) Ying Song et al.   CURRENT BIOLOGY

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

(2011) K T J Davies et al.   HEREDITY

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

Coalescent patterns for chromosomal inversions in divergent populations

(2011) R. F. Guerrero et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

Linkage disequilibrium and natural selection for mimicry in the Batesian mimic Hypolimnas misippus (L.) (Lepidoptera: Nymphalidae) in the Afrotropics

(2010) IAN J. GORDON et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2010) G. Lunter et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at theHmYb/Sblocus

(2010) LAURA FERGUSON et al.   MOLECULAR ECOLOGY

Convergence in pigmentation at multiple levels: mutations, genes and function

(2010) M. Manceau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sox proteins in melanocyte development and melanoma

(2010) Melissa L. Harris et al.   Pigment Cell & Melanoma Research

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato

(2010) Brian A. Counterman et al.   PLoS Genetics

Female-limited mimetic polymorphism: a review of theories and a critique of sexual selection as balancing selection

(2009) Krushnamegh Kunte   ANIMAL BEHAVIOUR

The causes of repeated genetic evolution

(2009) Nicolas Gompel et al.   DEVELOPMENTAL BIOLOGY

THE DIVERSITY AND EVOLUTION OF BATESIAN MIMICRY INPAPILIOSWALLOWTAIL BUTTERFLIES

(2009) Krushnamegh Kunte   EVOLUTION

The SoxD transcription factors – Sox5, Sox6, and Sox13 – are key cell fate modulators

(2009) Véronique Lefebvre   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A Gene-Based Linkage Map for Bicyclus anynana Butterflies Allows for a Comprehensive Analysis of Synteny with the Lepidopteran Reference Genome

(2009) Patrícia Beldade et al.   PLoS Genetics

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Gene flow persists millions of years after speciation in Heliconius butterflies

(2008) Marcus R Kronforst   BMC EVOLUTIONARY BIOLOGY

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH