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Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans

https://doi.org/10.1093/molbev/msu124
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster
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Partial gene duplication as a cause of human disease
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Sex chromosomes and speciation in Drosophila
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Basic Local Alignment Search Tool
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High intrinsic rate of DNA loss in Drosophila
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Mapping copy number variation by population-scale genome sequencing
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The Drosophila melanogaster Genetic Reference Panel
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Personalized copy number and segmental duplication maps using next-generation sequencing
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Fine-scale structural variation of the human genome
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Turning a hobby into a job: How duplicated genes find new functions
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Evolving protein functional diversity in new genes of Drosophila
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Parallel evolution of chimeric fusion genes
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A portrait of copy-number polymorphism in Drosophila melanogaster
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Extensive genomic copy number variation in embryonic stem cells
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Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
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The Relative Rates of Evolution of Sex Chromosomes and Autosomes
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Rapidly Evolving Genes and Genetic Systems
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Evolution of Drosophila seminal proteins and their networks
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Rapid evolution of innate immune response genes
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A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
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Fast and accurate short read alignment with Burrows–Wheeler transform
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The Sequence Alignment/Map format and SAMtools
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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
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Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster
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Effective Population Size and the Efficacy of Selection on the X Chromosomes of Two Closely Related Drosophila Species
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Widespread Polymorphism in the Positions of Stop Codons in Drosophila melanogaster
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Population genetics of polymorphism and divergence.
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Meiotic Recombination Involving Heterozygous Large Insertions in Saccharomyces cerevisiae: Formation and Repair of Large, Unpaired DNA Loops
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EVOLUTION IN MENDELIAN POPULATIONS
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EVOLUTION IN MENDELIAN POPULATIONS
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Positive and Negative Selection on Noncoding DNA in Drosophila simulans
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Inference for the Initial Stage of Domain Shuffling: Tracing the Evolutionary Fate of the PIPSL Retrogene in Hominoids
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Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster
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Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources
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Contrasting Patterns of X-Linked and Autosomal Nucleotide Variation in Drosophila melanogaster and Drosophila simulans
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Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution
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On the origin of new genes in Drosophila
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A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
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Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
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Reconstructing complex regions of genomes using long-read sequencing technology
inferredcites →https://doi.org/10.1101/gr.8.3.175openalex-snapshot
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
inferredcites →https://doi.org/10.1101/gr.8.3.186openalex-snapshot
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
inferredcites →https://doi.org/10.1109/tit.1967.1054010openalex-snapshot
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
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EXTENSIVE INTROGRESSION OF MITOCHONDRIAL DNA RELATIVE TO NUCLEAR GENES IN THE DROSOPHILA YAKUBA SPECIES GROUP
inferredcites →https://doi.org/10.1126/science.1085881openalex-snapshot
Sex-Dependent Gene Expression and Evolution of the Drosophila Transcriptome
inferredcites →https://doi.org/10.1126/science.1149504openalex-snapshot
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome
inferredcites →https://doi.org/10.1126/science.1158078openalex-snapshot
Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster
inferredcites →https://doi.org/10.1126/science.1197005openalex-snapshot
Diversity of Human Copy Number Variation and Multicopy Genes
inferredcites →https://doi.org/10.1126/science.287.5461.2185openalex-snapshot
The Genome Sequence of Drosophila melanogaster
inferredcites →https://doi.org/10.1126/science.7682012openalex-snapshot
Natural Selection and the Origin of jingwei , a Chimeric Processed Functional Gene in Drosophila
inferredcites →https://doi.org/10.1186/1471-2105-10-80openalex-snapshot
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
inferredcites →https://doi.org/10.1186/1471-2105-13-238openalex-snapshot
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
inferredcites →https://doi.org/10.1186/1471-2148-9-252openalex-snapshot
Positive selection for the male functionality of a co-retroposed gene in the hominoids
inferredcites →https://doi.org/10.1186/gb-2012-13-12-r119openalex-snapshot
Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing
inferredcites →https://doi.org/10.1371/journal.pgen.0030197openalex-snapshot
Gene Family Evolution across 12 Drosophila Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1002340openalex-snapshot
Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome
inferredcites →https://doi.org/10.1534/genetics.104.037283openalex-snapshot
Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guancheSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY874360, AY874361, AY874362, AY874363, AY874364, AY874365, AY874366, AY874367,…
inferredcites →https://doi.org/10.1534/genetics.108.091538openalex-snapshot
Formation and Longevity of Chimeric and Duplicate Genes inDrosophila melanogaster
inferredcites →https://doi.org/10.1534/genetics.111.138073openalex-snapshot
The Role of Background Selection in Shaping Patterns of Molecular Evolution and Variation: Evidence from Variability on the Drosophila X Chromosome
inferredcites →https://doi.org/10.1534/genetics.112.141622openalex-snapshot
Sequence-Based Detection and Breakpoint Assembly of Polymorphic Inversions
inferredcites →https://doi.org/10.1534/genetics.113.151670openalex-snapshot
Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster
inferredcites →https://doi.org/10.17615/2dgf-x182openalex-snapshot
Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guanche
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Meiotic recombination involving heterozygous large insertions in Saccharomyces cerevisiae: formation and repair of large, unpaired DNA loops.

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Evidence that Environmental Heterogeneity Maintains a Detoxifying Enzyme Polymorphism in Drosophila melanogaster
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Demography and its effects on genomic variation in crop domestication
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Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions
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Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans
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Young duplicate genic DNA
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Hidden genetic variation shapes the structure of functional elements in Drosophila
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High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens
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Recurrent specialization on a toxic fruit in an island Drosophila population
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Dinucleotide preferences underlie apparent codon preference reversals in the Drosophila melanogaster lineage
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Copy number variation of the USP16 gene and its association with milk traits in Chinese Holstein cattle
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Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster
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Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster
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Chromosomal Rearrangements and Transposable Elements in Locally Adapted Island Drosophila
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Genome Diversity and Divergence in Drosophila mauritiana : Multiple Signatures of Faster X Evolution
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Molecular Evolution ofDrosophilaGermline Stem Cell and Neural Stem Cell Regulating Genes
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Variation in the intensity of selection on codon bias over time causes contrasting patterns of base composition evolution in Drosophila
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Small Segmental Duplications inDrosophila—High Rate of Emergence and Elimination
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Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century
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Parallel Evolution of Copy-Number Variation across Continents inDrosophila melanogaster
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Rapidly Evolving Toll-3/4 Genes Encode Male-Specific Toll-Like Receptors in Drosophila
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Functional Consequences of the Evolution of Matrimony, a Meiosis-Specific Inhibitor of Polo Kinase
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Gap genes are involved in inviability in hybrids between Drosophila melanogaster and D. santomea
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Genomic islands of divergence between Drosophila yakuba subspecies predominantly overlap with chromosomal inversions
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Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species
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Genetic Novelty and Short-Term Evolutionary Dynamics in Drosophila yakuba mayottensis
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Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
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Genome‐wide identification and comparative analysis of lipocalin families in Lepidoptera with an emphasis on Bombyx mori
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P ‐elements strengthen reproductive isolation within the Drosophila simulans species complex
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Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract
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Contemporary evolution of resistance at the major insecticide target site gene Ace‐1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae
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Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa
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Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape
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Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
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Excess of genomic defects in a woolly mammoth on Wrangel island
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Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba
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Fine scale mapping of genomic introgressions within the Drosophila yakuba clade
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Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia
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Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba
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Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development
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IntroUNET: Identifying introgressed alleles via semantic segmentation
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Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species
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Tandem Duplications and the Limits of Natural Selection in Drosophila yakuba and Drosophila simulans
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Population genetic analysis of autophagy and phagocytosis genes in Drosophila melanogaster and D. simulans
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Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis
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A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data
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Molecular Population Genetics
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Support for the Dominance Theory in Drosophila Transcriptomes
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Detection of copy number variants in African goats using whole genome sequence data
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Detection of copy number variants in African goats using whole genome sequence data
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Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak
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Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population
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Hydrocarbon Patterns and Mating Behaviour in Populations of Drosophila yakuba
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Faculty Opinions recommendation of Recurrent specialization on a toxic fruit in an island Drosophila population.
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Additional file 1 of Detection of copy number variants in African goats using whole genome sequence data
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Additional file 2 of Detection of copy number variants in African goats using whole genome sequence data
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Adaptive evolution of Topoisomerase II triggers reproductive isolation in Drosophila
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Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci.
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Gene flow mediates the role of sex chromosome meiotic drive during complex speciation
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Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons
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Species-specific chromatin landscape determines how transposable elements shape genome evolution
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