Epistatic selection on a selfish Segregation Distorter supergene – drive, recombination, and genetic load

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

An Ancient and Eroded Social Supergene Is Widespread across Formica Ants

(2020) Alan Brelsford et al.   CURRENT BIOLOGY

Different structural variants of roo retrotransposon are active in Drosophila melanogaster

(2020) J. Díaz-González et al.   GENE

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura

(2020) Zachary L. Fuller et al.   GENETICS

FlyBase: updates to the Drosophila melanogaster knowledge base

(2020) Aoife Larkin et al.   NUCLEIC ACIDS RESEARCH

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Asexual reproduction reduces transposable element load in experimental yeast populations

(2019) Jens Bast et al.   eLife

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Multiple convergent supergene evolution events in mating-type chromosomes

(2018) Sara Branco et al.   Nature Communications

The Molecular and Genetic Characterization of Second Chromosome Balancers in Drosophila melanogaster

(2018) Danny E. Miller et al.   G3-Genes Genomes Genetics

Local Inversion Heterozygosity Alters Recombination throughout the Genome

(2018) K. Nicole Crown et al.   CURRENT BIOLOGY

The Demographic History of African Drosophila melanogaster

(2018) Adamandia Kapopoulou et al.   Genome Biology and Evolution

Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome

(2018) Ching-Ho Chang et al.   GENETICS

Degenerative expansion of a young supergene

(2018) Eckart Stolle et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements

(2018) Jesper Svedberg et al.   Nature Communications

Complex History and Differentiation Patterns of thet-Haplotype, a Mouse Meiotic Driver

(2017) Reka K. Kelemen et al.   GENETICS

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci inDrosophila melanogaster

(2017) Daniel E. Khost et al.   GENOME RESEARCH

Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura

(2017) Zachary L. Fuller et al.   MOLECULAR ECOLOGY

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Complex History and Differentiation Patterns of thet-Haplotype, a Mouse Meiotic Driver

(2017) Reka K. Kelemen et al.   GENETICS

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

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

Occasional recombination of a selfish X-chromosome may permit its persistence at high frequencies in the wild

(2016) K. E. Pieper et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

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

Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage

(2016) Mahul Chakraborty et al.   NUCLEIC ACIDS RESEARCH

The Ecology and Evolutionary Dynamics of Meiotic Drive

(2016) Anna K. Lindholm et al.   TRENDS IN ECOLOGY & EVOLUTION

Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events in Drosophila melanogaster

(2016) Danny E. Miller et al.   G3-Genes Genomes Genetics

Origin, evolution, and population genetics of the selfishSegregation Distortergene duplication in European and African populations ofDrosophila melanogaster

(2015) Cara L. Brand et al.   EVOLUTION

The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations

(2015) Deborah Charlesworth   Evolutionary Applications

Tempo and Mode of Transposable Element Activity in Drosophila

(2015) Robert Kofler et al.   PLoS Genetics

The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive

(2014) Amanda M Larracuente   BMC EVOLUTIONARY BIOLOGY

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

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

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

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

The Selfish Segregation Distorter Gene Complex of Drosophila melanogaster

(2012) A. M. Larracuente et al.   GENETICS

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

(2012) Raquel S. Linheiro et al.   PLoS One

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

(2012) John E. Pool et al.   PLoS Genetics

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo

(2011) Charles H. Langley et al.   GENETICS

Effects of Inversions on Within- and Between-Species Recombination and Divergence

(2011) Laurie S. Stevison et al.   Genome Biology and Evolution

Approximate Bayesian Analysis of Drosophila melanogaster Polymorphism Data Reveals a Recent Colonization of Southeast Asia

(2011) Stefan J.Y. Laurent et al.   MOLECULAR BIOLOGY AND EVOLUTION

Drosophila melanogaster recombination rate calculator

(2010) Anna-Sophie Fiston-Lavier et al.   GENE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster

(2009) Daven C. Presgraves et al.   PLoS Genetics

Recombination within mouse t haplotypes has replaced significant segments of t-specific DNA

(2008) Lyle T. Wallace et al.   MAMMALIAN GENOME