Complex modular architecture around a simple toolkit of wing pattern genes

[1]  Simon H. Martin,et al.  Exploring Evolutionary Relationships Across the Genome Using Topology Weighting , 2016, Genetics.

[2]  James J. Lewis,et al.  ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera. , 2016, Cell reports.

[3]  M. Quail,et al.  The industrial melanism mutation in British peppered moths is a transposable element , 2016, Nature.

[4]  David B. Jaffe,et al.  Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly , 2016, BMC Genomics.

[5]  M. Arias,et al.  Warning signals are under positive frequency-dependent selection in nature , 2016, Proceedings of the National Academy of Sciences.

[6]  Simon H. Martin,et al.  Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling , 2016, PLoS biology.

[7]  J. Mallet,et al.  Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution , 2015, G3: Genes, Genomes, Genetics.

[8]  Pasi Rastas,et al.  Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example , 2015, Genome biology and evolution.

[9]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[10]  H. Hines,et al.  Divergence with gene flow across a speciation continuum of Heliconius butterflies , 2015, BMC Evolutionary Biology.

[11]  M. Kronforst,et al.  The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry , 2015, Genetics.

[12]  A. Whibley,et al.  Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies , 2015, Heredity.

[13]  M. Grabherr,et al.  Evolution of Darwin’s finches and their beaks revealed by genome sequencing , 2015, Nature.

[14]  J. Mallet,et al.  Stable Heliconius butterfly hybrid zones are correlated with a local rainfall peak at the edge of the Amazon basin , 2014, Evolution; international journal of organic evolution.

[15]  Arnaud Martin,et al.  Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems. , 2014, Developmental biology.

[16]  C. Nusbaum,et al.  Comprehensive variation discovery in single human genomes , 2014, Nature Genetics.

[17]  M. Kronforst,et al.  Ancient homology underlies adaptive mimetic diversity across butterflies , 2014, Nature Communications.

[18]  Eric S. Lander,et al.  The genomic substrate for adaptive radiation in African cichlid fish , 2014, Nature.

[19]  Leena Salmela,et al.  LoRDEC: accurate and efficient long read error correction , 2014, Bioinform..

[20]  M. Borodovsky,et al.  Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm , 2014, Nucleic acids research.

[21]  Paul Greenfield,et al.  Blue: correcting sequencing errors using consensus and context , 2014, Bioinform..

[22]  M. O’Connor,et al.  Transcriptional Control of Steroid Biosynthesis Genes in the Drosophila Prothoracic Gland by Ventral Veins Lacking and Knirps , 2014, PLoS genetics.

[23]  David P. Kreil,et al.  Corrigendum: A doublecortin containing microtubule-associated protein is implicated in mechanotransduction in Drosophila sensory cilia , 2014, Nature Communications.

[24]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[25]  A. Sourakov ASSOCIATION FOR TROPICAL LEPIDOPTERA , 2014 .

[26]  N. Patel,et al.  Multiple recent co-options of Optix associated with novel traits in adaptive butterfly wing radiations , 2014, EvoDevo.

[27]  Petri Auvinen,et al.  Lep-MAP: fast and accurate linkage map construction for large SNP datasets , 2013, Bioinform..

[28]  Patricio A. Salazar,et al.  Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato , 2013, bioRxiv.

[29]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[30]  Camilo Salazar,et al.  Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies , 2013, Genome research.

[31]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[32]  Durrell D. Kapan,et al.  Multi-Allelic Major Effect Genes Interact with Minor Effect QTLs to Control Adaptive Color Pattern Variation in Heliconius erato , 2013, PloS one.

[33]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[34]  R. Gibbs,et al.  Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.

[35]  C. Jiggins,et al.  Partial Complementarity of the Mimetic Yellow Bar Phenotype in Heliconius Butterflies , 2012, PloS one.

[36]  R. I. Hill,et al.  Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand , 2012, Proceedings of the National Academy of Sciences.

[37]  Simon H. Martin,et al.  Butterfly genome reveals promiscuous exchange of mimicry adaptations among species , 2012, Nature.

[38]  James Mallet,et al.  Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[39]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[40]  M. Siol,et al.  EggLib: processing, analysis and simulation tools for population genetics and genomics , 2012, BMC Genetics.

[41]  Robert D Reed,et al.  Wing patterning gene redefines the mimetic history of Heliconius butterflies , 2011, Proceedings of the National Academy of Sciences.

[42]  Camilo Salazar,et al.  Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry , 2011, Nature.

[43]  H. Nijhout,et al.  optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry , 2011, Science.

[44]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[45]  Ashwini Patil,et al.  Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins , 2010, BMC Bioinformatics.

[46]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[47]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[48]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[49]  M. Cobb,et al.  Radial Spoke Protein 3 Is a Mammalian Protein Kinase A-anchoring Protein That Binds ERK1/2* , 2009, Journal of Biological Chemistry.

[50]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[51]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[52]  C. Jiggins,et al.  Butterfly speciation and the distribution of gene effect sizes fixed during adaptation , 2009, Heredity.

[53]  V. Hartenstein,et al.  Drosophila melanogaster , 2005 .

[54]  S. Carroll Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution , 2008, Cell.

[55]  Alejandro A. Schäffer,et al.  Database indexing for production MegaBLAST searches , 2008, Bioinform..

[56]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[57]  James Mallet,et al.  A Conserved Supergene Locus Controls Colour Pattern Diversity in Heliconius Butterflies , 2006, PLoS biology.

[58]  Durrell D. Kapan,et al.  Parallel Genetic Architecture of Parallel Adaptive Radiations in Mimetic Heliconius Butterflies , 2006, Genetics.

[59]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[60]  Durrell D. Kapan,et al.  Localization of Müllerian Mimicry Genes on a Dense Linkage Map of Heliconius erato , 2006, Genetics.

[61]  H. Reichert,et al.  ventral veins lacking is required for specification of the tritocerebrum in embryonic brain development of Drosophila , 2006, Mechanisms of Development.

[62]  Burkhard Morgenstern,et al.  Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.

[63]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[64]  Pavel A. Pevzner,et al.  De novo identification of repeat families in large genomes , 2005, ISMB.

[65]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[66]  T. Wetter,et al.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. , 2004, Genome research.

[67]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[68]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[69]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[70]  Jon D. McAuliffe,et al.  Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.

[71]  J. Mallet,et al.  Disruptive sexual selection against hybrids contributes to speciation between Heliconius cydno and Heliconius melpomene , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[72]  Durrell D. Kapan,et al.  Three-butterfly system provides a field test of müllerian mimicry , 2001, Nature.

[73]  C. Tanford,et al.  The man with faith in the unseeable , 2001, Nature.

[74]  D. Heckel,et al.  Genetic mapping of resistance to Bacillus thuringiensis toxins in diamondback moth using biphasic linkage analysis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[75]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[76]  C. Jiggins,et al.  The genetic basis of an adaptive radiation: warning colour in two Heliconius species , 1997, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[77]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[78]  M. Llimargas,et al.  Ventral veinless, the gene encoding the Cf1a transcription factor, links positional information and cell differentiation during embryonic and imaginal development in Drosophila melanogaster. , 1995, Development.

[79]  M. Slatkin,et al.  Estimation of levels of gene flow from DNA sequence data. , 1992, Genetics.

[80]  H. Nijhout,et al.  The development and evolution of butterfly wing patterns , 1991 .

[81]  L. Jin,et al.  Variances of the average numbers of nucleotide substitutions within and between populations. , 1989, Molecular biology and evolution.

[82]  J. Mallet The genetics of warning colour in Peruvian hybrid zones of Heliconius erato and H. melpomene , 1989, Proceedings of the Royal Society of London. B. Biological Sciences.

[83]  N. Barton,et al.  STRONG NATURAL SELECTION IN A WARNING‐COLOR HYBRID ZONE , 1989, Evolution; international journal of organic evolution.

[84]  K. S. Brown,et al.  Genetics and the Evolution of Muellerian Mimicry in Heliconius Butterflies , 1985 .

[85]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.