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Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

https://doi.org/10.1534/genetics.113.151670

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What this work says

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

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Mutation accumulation and the effect of copia insertions in Drosophila melanogaster

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DNA loss and evolution of genome size in Drosophila

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High intrinsic rate of DNA loss in Drosophila

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High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome

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Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila

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Systematic assessment of copy number variant detection via genome-wide SNP genotyping

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Variation in genome-wide mutation rates within and between human families

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Fine-scale structural variation of the human genome

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Diet and the evolution of human amylase gene copy number variation

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A genome-wide view of the spectrum of spontaneous mutations in yeast

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A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

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Rate, molecular spectrum, and consequences of human mutation

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Evidence for elevated mutation rates in low-quality genotypes

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Drift-barrier hypothesis and mutation-rate evolution

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Spontaneous mutation rates at enzyme loci in Drosophila melanogaster.

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Rapid decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection

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Variation in Base-Substitution Mutation in Experimental and Natural Lineages of Caenorhabditis Nematodes

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Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection

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Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution.

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Pseudogene Evolution in Drosophila Suggests a High Rate of DNA Loss

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Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

inferredcites →https://doi.org/10.1101/gr.107680.110openalex-snapshot

De novo rates and selection of large copy number variation

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Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

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Dindel: Accurate indel calls from short-read data

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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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Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

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New Genes in Drosophila Quickly Become Essential

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Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

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The Genome Sequence of Drosophila melanogaster

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Structural Variation in the Human Genome and its Role in Disease

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Selection in the evolution of gene duplications

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Different evolutionary patterns between young duplicate genes in the human genome

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The Diploid Genome Sequence of an Individual Human

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Gene Family Evolution across 12 Drosophila Genomes

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

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inferred← citeshttps://doi.org/10.1098/rspb.2015.3065openalex-snapshot

Factors influencing the effect size distribution of adaptive substitutions

inferred← citeshttps://doi.org/10.1098/rspb.2016.1016openalex-snapshot

Mutation rate analysis via parent–progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids

inferred← citeshttps://doi.org/10.1098/rspb.2018.1864openalex-snapshot

An experimental test of the mutation-selection balance model for the maintenance of genetic variance in fitness components

inferred← citeshttps://doi.org/10.1101/009837openalex-snapshot

Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex

inferred← citeshttps://doi.org/10.1101/015693openalex-snapshot

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii

inferred← citeshttps://doi.org/10.1101/065003openalex-snapshot

Exact calculation of the joint allele frequency spectrum for isolation with migration models

inferred← citeshttps://doi.org/10.1101/096289openalex-snapshot

Natural diversity of the malaria vector Anopheles gambiae

inferred← citeshttps://doi.org/10.1101/103796openalex-snapshot

Spontaneous mutations and transmission distortions of genic copy number variants shape the standing genetic variation in Picea glauca

inferred← citeshttps://doi.org/10.1101/122234openalex-snapshot

Mitochondrial genome variation affects the mutation rate of the nuclear genome in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1101/2020.02.05.935197openalex-snapshot

Short-term heritable variation overwhelms two hundred generations of mutational variance for metabolic traits in Caenorhabditis elegans

inferred← citeshttps://doi.org/10.1101/2020.02.12.946392openalex-snapshot

Widespread selection against deleterious mutations in the Drosophila genome

inferred← citeshttps://doi.org/10.1101/2021.03.18.435925openalex-snapshot

A two-type branching process model of gene family evolution

inferred← citeshttps://doi.org/10.1101/2021.04.12.439444openalex-snapshot

Selection in a growing bacterial/yeast colony biases results of mutation accumulation experiments

inferred← citeshttps://doi.org/10.1101/2021.06.28.450192openalex-snapshot

Analysis of the leaf metabolome in Arabidopsis thaliana mutation accumulation lines reveals association of pleiotropy and fitness consequences

inferred← citeshttps://doi.org/10.1101/2023.05.08.539910openalex-snapshot

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

inferred← citeshttps://doi.org/10.1101/2023.05.10.539957openalex-snapshot

Striking allelic diversity despite structural homogeneity of ace-1 duplications in Anopheles mosquitoes

inferred← citeshttps://doi.org/10.1101/2023.07.20.549788openalex-snapshot

Robust inference of historical human generation times

inferred← citeshttps://doi.org/10.1101/2024.02.12.579890openalex-snapshot

De novo ORFs are more likely to shrink than to elongate during neutral evolution

inferred← citeshttps://doi.org/10.1101/2025.09.12.675866openalex-snapshot

Gene copy number variation (gCNV) contributes to adaptation along environmental gradient

inferred← citeshttps://doi.org/10.1101/2025.10.16.682755openalex-snapshot

Transposable elements drive much of naturally occurring genetic lethality in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1101/349563openalex-snapshot

Highly accelerated rates of heritable large-scale mutations under prolonged exposure to a metal mixture of copper and nickel

inferred← citeshttps://doi.org/10.1101/498378openalex-snapshot

Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting

inferred← citeshttps://doi.org/10.1101/573576openalex-snapshot

Universal trends of post-duplication evolution revealed by the genomes of 13 Paramecium species sharing an ancestral whole-genome duplication

inferred← citeshttps://doi.org/10.1101/gr.170696.113openalex-snapshot

Error-prone polymerase activity causes multinucleotide mutations in humans

inferred← citeshttps://doi.org/10.1101/gr.191338.115openalex-snapshot

High mutational rates of large-scale duplication and deletion in Daphnia pulex

inferred← citeshttps://doi.org/10.1101/gr.191494.115openalex-snapshot

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii

inferred← citeshttps://doi.org/10.1101/gr.204669.116openalex-snapshot

Direct estimate of the rate of germline mutation in a bird

inferred← citeshttps://doi.org/10.1101/gr.219956.116openalex-snapshot

Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

inferred← citeshttps://doi.org/10.1101/gr.234724.118openalex-snapshot

Accelerated rates of large-scale mutations in the presence of copper and nickel

inferred← citeshttps://doi.org/10.1101/gr.275168.120openalex-snapshot

Temperature dependence of spontaneous mutation rates

inferred← citeshttps://doi.org/10.1101/gr.275372.121openalex-snapshot

Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans

inferred← citeshttps://doi.org/10.1101/gr.277383.122openalex-snapshot

Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans

inferred← citeshttps://doi.org/10.1101/gr.278062.123openalex-snapshot

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

inferred← citeshttps://doi.org/10.1111/1755-0998.13930openalex-snapshot

Population genetic simulation: Benchmarking frameworks for non‐standard models of natural selection

inferred← citeshttps://doi.org/10.1111/eea.12807openalex-snapshot

The implications of rapid eco‐evolutionary processes for biological control ‐ a review

inferred← citeshttps://doi.org/10.1111/eva.12619openalex-snapshot

Adaptive deletion in resistance gene duplications in the malaria vector Anopheles gambiae

inferred← citeshttps://doi.org/10.1111/evo.12448openalex-snapshot

SPONTANEOUS MUTATION ACCUMULATION IN MULTIPLE STRAINS OF THE GREEN ALGA, CHLAMYDOMONAS REINHARDTII

inferred← citeshttps://doi.org/10.1111/evo.13955openalex-snapshot

Relative importance of isolation‐by‐environment and other determinants of gene flow in an alpine amphibian

inferred← citeshttps://doi.org/10.1111/evo.14104openalex-snapshot

Short‐term heritable variation overwhelms 200 generations of mutational variance for metabolic traits in Caenorhabditis elegans

inferred← citeshttps://doi.org/10.1111/febs.15299openalex-snapshot

Evolution of new enzymes by gene duplication and divergence

inferred← citeshttps://doi.org/10.1111/mec.13610openalex-snapshot

Powerful methods for detecting introgressed regions from population genomic data

inferred← citeshttps://doi.org/10.1111/mec.13671openalex-snapshot

A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation

inferred← citeshttps://doi.org/10.1111/mec.14463openalex-snapshot

The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation

inferred← citeshttps://doi.org/10.1111/mec.14534openalex-snapshot

Faster‐X evolution: Theory and evidence from Drosophila

inferred← citeshttps://doi.org/10.1111/mec.15701openalex-snapshot

Adaptation, ancestral variation and gene flow in a ‘Sky Island’ Drosophila species

inferred← citeshttps://doi.org/10.1111/mec.15936openalex-snapshot

Unboxing mutations: Connecting mutation types with evolutionary consequences

inferred← citeshttps://doi.org/10.1111/mec.17234openalex-snapshot

Forward‐in‐time simulation of chromosomal rearrangements: The invisible backbone that sustains long‐term adaptation

inferred← citeshttps://doi.org/10.1111/mec.70357openalex-snapshot

Discovery and Evaluation of Cadmium‐Adapted Daphnia pulex Genotypes in a Region of Historical Mining Reveals Adaptation Protects the Germline From Cadmium‐Induced Mutations

inferred← citeshttps://doi.org/10.1126/science.adw1931openalex-snapshot

Multispecies pangenomes reveal a pervasive influence of population size on structural variation

inferred← citeshttps://doi.org/10.1128/jb.00593-21openalex-snapshot

Genetic Signatures from Adaptation of Bacteria to Lytic Phage Identify Potential Agents To Aid Phage Killing of Multidrug-Resistant Acinetobacter baumannii

inferred← citeshttps://doi.org/10.1146/annurev-animal-050422-092520openalex-snapshot

Interrogating the Roles of Mutation–Selection Balance, Heterozygote Advantage, and Linked Selection in Maintaining Recessive Lethal Variation in Natural Populations

inferred← citeshttps://doi.org/10.1146/annurev-genet-120213-092525openalex-snapshot

The Relations Between Recombination Rate and Patterns of Molecular Variation and Evolution inDrosophila

inferred← citeshttps://doi.org/10.1186/s12864-015-2253-2openalex-snapshot

Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans

inferred← citeshttps://doi.org/10.1186/s12864-018-4753-3openalex-snapshot

Muver, a computational framework for accurately calling accumulated mutations

inferred← citeshttps://doi.org/10.1186/s12915-025-02449-8openalex-snapshot

A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes

inferred← citeshttps://doi.org/10.1186/s13104-017-2741-3openalex-snapshot

Evolutionary impact of copy number variation rates

inferred← citeshttps://doi.org/10.1371/journal.pbio.1002419openalex-snapshot

Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum

inferred← citeshttps://doi.org/10.1371/journal.pbio.2000618openalex-snapshot

The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications

inferred← citeshttps://doi.org/10.1371/journal.pbio.3003467openalex-snapshot

Transposable elements contribute substantially to naturally occurring genetic lethality in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1371/journal.pgen.1004434openalex-snapshot

Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

inferred← citeshttps://doi.org/10.1371/journal.pgen.1004830openalex-snapshot

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

inferred← citeshttps://doi.org/10.1371/journal.pgen.1005331openalex-snapshot

Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila

inferred← citeshttps://doi.org/10.1371/journal.pgen.1006240openalex-snapshot

On the Trail of Linked Selection

inferred← citeshttps://doi.org/10.1371/journal.pgen.1006455openalex-snapshot

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum

inferred← citeshttps://doi.org/10.1371/journal.pgen.1007341openalex-snapshot

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

inferred← citeshttps://doi.org/10.15252/embr.202357561openalex-snapshot

The divergence of mutation rates and spectra across the Tree of Life

inferred← citeshttps://doi.org/10.1534/g3.114.014860openalex-snapshot

Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements ofDrosophila pseudoobscura

inferred← citeshttps://doi.org/10.1534/g3.116.029769openalex-snapshot

Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae

inferred← citeshttps://doi.org/10.1534/g3.116.030890openalex-snapshot

Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life

inferred← citeshttps://doi.org/10.1534/g3.117.1135openalex-snapshot

Genome Dynamics of HybridSaccharomyces cerevisiaeDuring Vegetative and Meiotic Divisions

inferred← citeshttps://doi.org/10.1534/g3.119.400596openalex-snapshot

A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data

inferred← citeshttps://doi.org/10.1534/g3.120.401704openalex-snapshot

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

inferred← citeshttps://doi.org/10.1534/genetics.113.158758openalex-snapshot

Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family

inferred← citeshttps://doi.org/10.1534/genetics.115.176834openalex-snapshot

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia

inferred← citeshttps://doi.org/10.1534/genetics.115.177329openalex-snapshot

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

inferred← citeshttps://doi.org/10.1534/genetics.115.185736openalex-snapshot

Mutation Is a Sufficient and Robust Predictor of Genetic Variation for Mitotic Spindle Traits in Caenorhabditis elegans

inferred← citeshttps://doi.org/10.1534/genetics.115.186171openalex-snapshot

Hermann Muller on Measuring Mutation Rates

inferred← citeshttps://doi.org/10.1534/genetics.116.190611openalex-snapshot

Population Genomics of Daphnia pulex

inferred← citeshttps://doi.org/10.1534/genetics.116.192492openalex-snapshot

A Variable Genetic Architecture of Melanic Evolution in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1534/genetics.116.194019openalex-snapshot

Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models

inferred← citeshttps://doi.org/10.1534/genetics.116.197285openalex-snapshot

Evolution of Resistance Against CRISPR/Cas9 Gene Drive

inferred← citeshttps://doi.org/10.1534/genetics.117.201251openalex-snapshot

Inferring Demographic History Using Two-Locus Statistics

inferred← citeshttps://doi.org/10.1534/genetics.118.300848openalex-snapshot

Discovery of Lineage-Specific Genome Change in Rice Through Analysis of Resequencing Data

inferred← citeshttps://doi.org/10.1534/genetics.119.300160openalex-snapshot

Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster

inferred← citeshttps://doi.org/10.1534/genetics.119.301951openalex-snapshot

The Effects on Neutral Variability of Recurrent Selective Sweeps and Background Selection

inferred← citeshttps://doi.org/10.1534/genetics.119.302054openalex-snapshot

Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size

inferred← citeshttps://doi.org/10.1534/genetics.119.303002openalex-snapshot

Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection

inferred← citeshttps://doi.org/10.1534/genetics.120.303469openalex-snapshot

Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps

inferred← citeshttps://doi.org/10.20944/preprints202009.0279.v1openalex-snapshot

The Population Genetics of Ploidy Change in Fungi

inferred← citeshttps://doi.org/10.21203/rs.3.rs-1056862/v1openalex-snapshot

Analysis of the leaf metabolome in Arabidopsis thaliana mutation accumulation lines reveals association of pleiotropy and fitness consequences

inferred← citeshttps://doi.org/10.22541/au.159242077.72607009openalex-snapshot

Selection and demography shape genomic variation in a ‘Sky Island’ species

inferred← citeshttps://doi.org/10.24072/pcjournal.497openalex-snapshot

A genomic duplication spanning multiple P450s contributes to insecticide resistance in the dengue mosquito Aedes aegypti

inferred← citeshttps://doi.org/10.3389/fcell.2021.796249openalex-snapshot

KNNCNV: A K-Nearest Neighbor Based Method for Detection of Copy Number Variations Using NGS Data

inferred← citeshttps://doi.org/10.3389/fgene.2013.00273openalex-snapshot

Copy-number changes in evolution: rates, fitness effects and adaptive significance

inferred← citeshttps://doi.org/10.3389/finsc.2022.1063789openalex-snapshot

Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive Drosophila suzukii

inferred← citeshttps://doi.org/10.3390/cells10051224openalex-snapshot

Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair

inferred← citeshttps://doi.org/10.3390/genes10110894openalex-snapshot

Evolution of Codon Usage Bias in Diatoms

inferred← citeshttps://doi.org/10.3390/genes12091381openalex-snapshot

No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals

inferred← citeshttps://doi.org/10.3390/genes13122263openalex-snapshot

Genomic Analyses Implicate the Amazon–Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab

inferred← citeshttps://doi.org/10.4995/thesis/10251/191452openalex-snapshot

Mutation Rate and Gene Expression in Genetic Admixtures of Domesticated Citrus

inferred← citeshttps://doi.org/10.64898/2026.01.27.702068openalex-snapshot

The tortured past of young polymorphic sex chromosomes revealed through multiple de novo genome assemblies of the mountain pine beetle

inferred← citeshttps://doi.org/10.64898/2026.05.28.728420openalex-snapshot

Structure can emerge from disorder under neutral evolution

inferred← citeshttps://doi.org/10.70675/2967bc12zaa3ez4d05zbf40z16688b339e1dopenalex-snapshot

Étude de l’impact mutationnel d’une perte de méthylation de l’ADN chez Arabidopsis thaliana

inferred← citeshttps://doi.org/10.70675/738358caz5e8az4c8cza0c5z8eb894d1277eopenalex-snapshot

Influence de l’architecture génétique et des variations environnementales sur l’adaptation : la résistance aux insecticides chez les moustiques

inferred← citeshttps://doi.org/10.70675/ad443f1azbcddz4496zb5bbze4348b3ff51eopenalex-snapshot

Evolution beyond substitutions : Computational modeling of the impact of chromosomal rearrangements on evolutionary dynamics

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