The roles of hybridization and habitat fragmentation in the evolution of Brazil’s enigmatic longwing butterflies, Heliconius nattereri and H. hermathena

Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

(2019) Rei Kajitani et al.   Nature Communications

Comparative transcriptomics provides insights into reticulate and adaptive evolution of a butterfly radiation

(2019) Wei Zhang 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

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion

(2018) Paul Jay et al.   CURRENT BIOLOGY

Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography

(2018) Steven M. Van Belleghem et al.   MOLECULAR ECOLOGY

Facultative pupal mating in Heliconius erato : Implications for mate choice, female preference, and speciation

(2018) Timothy J. Thurman et al.   Ecology and Evolution

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

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

A New Subspecies of Heliconius hermathena (Nymphalidae: Heliconiinae) from Southern Amazonia

(2018) A V L Freitas et al.   NEOTROPICAL ENTOMOLOGY

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

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

Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies

(2017) Juan Enciso-Romero et al.   MOLECULAR ECOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Complex modular architecture around a simple toolkit of wing pattern genes

(2017) Steven M. Van Belleghem et al.   Nature Ecology & Evolution

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives

(2016) Yuval B Simons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

(2016) Justin B. Lack et al.   MOLECULAR BIOLOGY AND EVOLUTION

The gene cortex controls mimicry and crypsis in butterflies and moths

(2016) Nicola J. Nadeau et al.   NATURE

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Redundans: an assembly pipeline for highly heterozygous genomes

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

The BIG Data Center: from deposition to integration to translation

(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

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

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

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

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

The diversification ofHeliconiusbutterflies: what have we learned in 150 years?

(2015) R. M. Merrill et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Visualizing spatial population structure with estimated effective migration surfaces

(2015) Desislava Petkova et al.   NATURE GENETICS

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

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

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Habitat fragmentation and its lasting impact on Earth's ecosystems

(2015) N. M. Haddad et al.   Science Advances

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Environmental change and the carbon balance of Amazonian forests

(2014) Luiz E. O. C. Aragão et al.   BIOLOGICAL REVIEWS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Estimation of the Spontaneous Mutation Rate in Heliconius melpomene

(2014) Peter D. Keightley et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The deleterious mutation load is insensitive to recent population history

(2014) Yuval B Simons et al.   NATURE GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Hybridization Reveals the Evolving Genomic Architecture of Speciation

(2013) Marcus R. Kronforst et al.   Cell Reports

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

(2013) Peter J.A. Cock et al.   PeerJ

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

(2012) Pablo Cingolani et al.   FLY

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

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

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Pollen Processing Behavior ofHeliconiusButterflies: A Derived Grooming Behavior

(2011) Anna-Laetitia Hikl et al.   JOURNAL OF INSECT SCIENCE

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

The fate of Amazonian forest fragments: A 32-year investigation

(2010) William F. Laurance et al.   BIOLOGICAL CONSERVATION

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

(2010) A. McKenna et al.   GENOME RESEARCH

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

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

Fast model-based estimation of ancestry in unrelated individuals

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

Homoploid hybrid speciation in animals

(2008) JESÚS MAVÁREZ et al.   MOLECULAR ECOLOGY

Hybrid trait speciation and Heliconius butterflies

(2008) C. D Jiggins et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES