Evidence for a single, ancient origin of a genus-wide alternative life history strategy

A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies

(2022) Vincent Ficarrotta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pixy : Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

(2021) Katharine L Korunes et al.   Molecular Ecology Resources

A molecular phylogeny of forktail damselflies (genus Ischnura) reveals a dynamic macroevolutionary history of female colour polymorphisms

(2021) Rachel Blow et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Stage- and sex-specific transcriptome analyses reveal distinctive sensory gene expression patterns in a butterfly

(2021) David A. Ernst et al.   BMC GENOMICS

Novel Doublesex Duplication Associated with Sexually Dimorphic Development of Dogface Butterfly Wings

(2021) Fernando Rodriguez-Caro et al.   MOLECULAR BIOLOGY AND EVOLUTION

BarH1 regulates odorant-binding proteins expression and olfactory perception of Monochamus alternatus Hope

(2021) Dong-Zhen Li et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data

(2020) Katherine M Siewert et al.   Genome Biology and Evolution

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A shared genetic basis of mimicry across swallowtail butterflies points to ancestral co-option of doublesex

(2020) Daniela H. Palmer et al.   Nature Communications

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

(2020) Claire Mérot et al.   Nature Communications

The Persistence of Polymorphisms across Species Radiations

(2020) Gabriel A. Jamie et al.   TRENDS IN ECOLOGY & EVOLUTION

Mechanisms of Change: A Population-Based Perspective on the Roles of Modularity and Pleiotropy in Diversification

(2020) James J. Lewis et al.   Frontiers in Ecology and Evolution

Deep Convergence, Shared Ancestry and Evolutionary Novelty in the Genetic Architecture of Heliconius Mimicry

(2020) Jake Morris et al.   GENETICS

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Tissue-specific developmental regulation and isoform usage underlie the role of doublesex in sex differentiation and mimicry in Papilio swallowtails

(2020) Riddhi Deshmukh et al.   Royal Society Open Science

Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone

(2020) James J. Lewis et al.   Science Advances

Priors and Posteriors in Bayesian Timing of Divergence Analyses: The Age of Butterflies Revisited

(2019) Nicolas Chazot et al.   SYSTEMATIC BIOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Estimates of introgression as a function of pairwise distances

(2019) Bastian Pfeifer et al.   BMC BIOINFORMATICS

Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

(2019) Jason Hill et al.   Science Advances

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Genome assembly of the dogface butterfly Zerene cesonia

(2019) L Rodriguez-Caro et al.   Genome Biology and Evolution

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

(2019) James J. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A transposable element insertion is associated with an alternative life history strategy

(2019) Alyssa Woronik et al.   Nature Communications

Does male preference play a role in maintaining female limited polymorphism in a Batesian mimetic butterfly?

(2018) E.L. Westerman et al.   BEHAVIOURAL PROCESSES

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Physiological differences between female limited, alternative life history strategies: The Alba phenotype in the butterfly Colias croceus

(2018) Alyssa Woronik et al.   JOURNAL OF INSECT PHYSIOLOGY

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus

(2018) Madlen Stange et al.   SYSTEMATIC BIOLOGY

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

The molecular genetic basis of herbivory between butterflies and their host plants

(2018) Sumitha Nallu et al.   Nature Ecology & Evolution

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

(2018) Milan Malinsky et al.   Nature Ecology & Evolution

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

(2017) Violaine Llaurens et al.   MOLECULAR ECOLOGY

Indexcov: fast coverage quality control for whole-genome sequencing

(2017) Brent S Pedersen et al.   GigaScience

The pdm3 Locus Is a Hotspot for Recurrent Evolution of Female-Limited Color Dimorphism in Drosophila

(2016) Amir Yassin et al.   CURRENT BIOLOGY

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

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

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

(2016) Richard W. R. Wallbank et al.   PLOS BIOLOGY

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The evolutionary history of the ‘alba’ polymorphism in the butterfly subfamily Coliadinae (Lepidoptera: Pieridae)

(2015) Lisa B. Limeri et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Detecting balancing selection in genomes: limits and prospects

(2015) Anna Fijarczyk et al.   MOLECULAR ECOLOGY

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

(2015) Christopher C Chang et al.   GigaScience

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

(2014) Virpi Ahola et al.   Nature Communications

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

(2014) Christine Grossen et al.   PLoS Genetics

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

2b-RAD: a simple and flexible method for genome-wide genotyping

(2012) Shi Wang et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

A model of developmental evolution: selection, pleiotropy and compensation

(2012) Mihaela Pavlicev et al.   TRENDS IN ECOLOGY & EVOLUTION

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera, Pieridae)

(2008) Christopher W. Wheat et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION