The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

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

(2023) Kalle Tunström et al.   Science Advances

Molecular mechanisms underlying metamorphosis in the most-ancestral winged insect

(2022) Genta Okude et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single locus regulates a female-limited color pattern polymorphism in a reptile

(2022) Nathalie Feiner et al.   Science Advances

Sex-specific morphs: the genetics and evolution of intra-sexual variation

(2022) Judith E. Mank   NATURE REVIEWS GENETICS

Functional genomic tools for emerging model species

(2022) Erik Gudmunds et al.   TRENDS IN ECOLOGY & EVOLUTION

Intersexual social dominance mimicry drives female hummingbird polymorphism

(2022) Jay J. Falk et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

The genomic architecture and evolutionary fates of supergenes

(2021) Juanita Gutiérrez-Valencia et al.   Genome Biology and Evolution

Inversion breakpoints and the evolution of supergenes

(2021) Romain Villoutreix et al.   MOLECULAR ECOLOGY

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish

(2021) Benjamin A. Sandkam et al.   Nature Ecology & Evolution

Evolution of sexual development and sexual dimorphism in insects

(2021) Ben R Hopkins et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Male-like ornamentation in female hummingbirds results from social harassment rather than sexual selection

(2021) Jay J. Falk et al.   CURRENT BIOLOGY

Massive genome inversion drives coexistence of divergent morphs in common quails

(2021) Ines Sanchez-Donoso et al.   CURRENT BIOLOGY

The important contribution of transposable elements to phenotypic variation and evolution

(2021) Nathan S. Catlin et al.   CURRENT OPINION IN PLANT BIOLOGY

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

(2021) Kishwar Shafin et al.   NATURE METHODS

A masculinizing supergene underlies an exaggerated male reproductive morph in a spider

(2021) Frederik Hendrickx et al.   Nature Ecology & Evolution

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

(2020) Vasavi Sundaram et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Interspecific crossing between blue‐tailed damselflies Ischnura elegans and I. senegalensis in the laboratory

(2020) Genta Okude et al.   ENTOMOLOGICAL SCIENCE

Changes in gene expression during female reproductive development in a color polymorphic insect

(2020) Beatriz Willink et al.   EVOLUTION

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Identifying genetic variants underlying phenotypic variation in plants without complete genomes

(2020) Yoav Voichek et al.   NATURE GENETICS

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes

(2020) Adam G. Diehl et al.   Nature Communications

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

(2019) Pedro Andrade et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pterin-pigmented nanospheres create the colours of the polymorphic damselfly Ischnura elegans

(2019) Miriam J. Henze et al.   Journal of the Royal Society Interface

Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird

(2019) Kang-Wook Kim et al.   Nature Communications

Macroevolutionary origin and adaptive function of a polymorphic female signal involved in sexual conflict

(2019) Beatriz Willink et al.   AMERICAN NATURALIST

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Temperature drives pre‐reproductive selection and shapes the biogeography of a female polymorphism

(2019) Erik I. Svensson et al.   ECOLOGY LETTERS

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

(2019) Mahul Chakraborty et al.   Nature Communications

The genomic footprint of sexual conflict

(2019) Ahmed Sayadi et al.   Nature Ecology & Evolution

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

(2019) Alyssa Woronik et al.   Nature Communications

The Genomics of Sexual Conflict

(2018) Locke Rowe et al.   AMERICAN NATURALIST

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Candidate genes associated with color morphs of female-limited polymorphisms of the damselfly Ischnura senegalensis

(2018) Michihiko Takahashi et al.   HEREDITY

The impact of transposable elements in adaptive evolution

(2018) Lukas Schrader et al.   MOLECULAR ECOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Molecular and ecological signatures of an expanding hybrid zone

(2018) Maren Wellenreuther et al.   Ecology and Evolution

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Coevolution between transposable elements and recombination

(2017) Tyler V. Kent et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Intra- and intersexual differences in parasite resistance and female fitness tolerance in a polymorphic insect

(2017) Beatriz Willink et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

(2017) Diwash Jangam et al.   TRENDS IN GENETICS

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

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

Evolutionary Time-Series Analysis Reveals the Signature of Frequency-Dependent Selection on a Female Mating Polymorphism

(2015) Arnaud Le Rouzic et al.   AMERICAN NATURALIST

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

(2015) Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

A single female-specific piRNA is the primary determiner of sex in the silkworm

(2014) Takashi Kiuchi et al.   NATURE

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Evolution of increased phenotypic diversity enhances population performance by reducing sexual harassment in damselflies

(2014) Yuma Takahashi et al.   Nature Communications

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

Polyandry and alternative mating tactics

(2013) B. D. Neff et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Transposable element small RNAs as regulators of gene expression

(2012) Andrea D. McCue et al.   TRENDS IN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Male mate choice based on ontogenetic colour changes of females in the damselfly Ischnura senegalensis

(2011) Yuma Takahashi et al.   JOURNAL OF ETHOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Density‐Dependent Male Mating Harassment, Female Resistance, and Male Mimicry

(2009) Thomas P. Gosden et al.   AMERICAN NATURALIST

Alternative mating strategies may favour the persistence of a genetically based colour polymorphism in a pentamorphic fish

(2009) Jorge L. Hurtado-Gonzales et al.   ANIMAL BEHAVIOUR

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Correlated morphological and colour differences among females of the damselflyIschnura elegans

(2009) JESSICA K. ABBOTT et al.   ECOLOGICAL ENTOMOLOGY

The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination

(2009) Alejandra Delprat et al.   PLoS One

Sex Chromosomes and the Evolution of Sexual Dimorphism: Lessons from the Genome

(2008) Judith E. Mank   AMERICAN NATURALIST

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY