ArticleGenome research2016
High mutational rates of large-scale duplication and deletion in Daphnia pulex.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- Discovery and Evaluation of Cadmium-Adapted Daphnia pulex Genotypes in a Region of Historical Mining Reveals Adaptation Protects the Germline From Cadmium-Induced Mutations.Molecular ecology · 2026Article
- Copy number and sequence variation in ribosomal DNA and the transposon, Pokey, in mutation accumulation lines of Daphnia obtusa.G3 (Bethesda, Md.) · 2026Article
- The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability.Molecular biology and evolution · 2026Article
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- Genomic evidence of divergence-with-gene-flow in the pink shrimp Farfantepenaeus brasiliensis.Heredity · 2025Article
- A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes.BMC biology · 2025Article
- The effect of spontaneous mutations onbioRxiv : the preprint server for biology · 2025Article
- The mutation landscape ofbioRxiv : the preprint server for biology · 2025Article
- The mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system.Heredity · 2025Article
- What can we infer about mutation calling by using time-series mutation accumulation data and a Bayesian Mutation Finder?Ecology and evolution · 2024Article
- The genome-wide signature of short-term temporal selection.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Balancing selection and the functional effects of shared polymorphism in crypticbioRxiv : the preprint server for biology · 2024Article
- Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects ofbioRxiv : the preprint server for biology · 2024Article
- Germline mutation rate is elevated in young and old parents inEvolution letters · 2023Article
- Evolutionary Insights from a Large-Scale Survey of Population-Genomic Variation.Molecular biology and evolution · 2023Article
- Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates.Genome biology and evolution · 2023Article
- The effects of mutations on gene expression and alternative splicing.Proceedings. Biological sciences · 2023Article
- Evolutionary Insights from a Large-scale Survey of Population-genomic Variation.bioRxiv : the preprint server for biology · 2023Article
- CDMAP/CDVIS: context-dependent mutation analysis package and visualization software.G3 (Bethesda, Md.) · 2023Article
- Chromatin structure influences rate and spectrum of spontaneous mutations inGenome research · 2023Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.
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