Genomic architecture and introgression shape a butterfly radiation

A critical comparison of technologies for a plant genome sequencing project

(2019) Pirita Paajanen et al.   GigaScience

Recombination rate variation shapes barriers to introgression across butterfly genomes

(2019) Simon H. Martin et al.   PLOS BIOLOGY

Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-based Genome Diversification and Multiple SINE Births and Deaths

(2019) David A Ray et al.   Genome Biology and Evolution

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

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Genomic evidence of gene flow during reinforcement in Texas Phlox

(2017) Federico Roda et al.   MOLECULAR ECOLOGY

Ancient hybridization fuels rapid cichlid fish adaptive radiations

(2017) Joana I. Meier et al.   Nature Communications

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

(2017) Reuben W. Nowell et al.   GigaScience

Complex modular architecture around a simple toolkit of wing pattern genes

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

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly

(2016) R. Rebecca Love et al.   BMC GENOMICS

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Admixture, Population Structure, and F-Statistics

(2016) B. M. Peter   GENETICS

Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

(2016) Hugo F. Gante et al.   MOLECULAR ECOLOGY

The gene cortex controls mimicry and crypsis in butterflies and moths

(2016) Nicola J. Nadeau et al.   NATURE

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

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

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Skipper genome sheds light on unique phenotypic traits and phylogeny

(2015) Qian Cong et al.   BMC GENOMICS

Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

(2015) Jeffrey M. Good et al.   EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

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

(2015) Hideki Nishikawa 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

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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 genetics of monarch butterfly migration and warning colouration

(2014) Shuai Zhan et al.   NATURE

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

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

(2014) Virpi Ahola et al.   Nature Communications

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

HAL: a hierarchical format for storing and analyzing multiple genome alignments

(2013) Glenn Hickey et al.   BIOINFORMATICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

A heterozygous moth genome provides insights into herbivory and detoxification

(2013) Minsheng You et al.   NATURE GENETICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

(2012) Andrew H. Chan et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A Metric on the Space of Reduced Phylogenetic Networks

(2009) Luay Nakhleh   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

The genome of a lepidopteran model insect, the silkworm Bombyx mori

(2008) The International Silkworm Genome   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY