ArticleGenome biology and evolution2018
Effect of Collapsed Duplications on Diversity Estimates: What to Expect.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The highly heterozygous European amphioxus (Branchiostoma lanceolatum) at the edge of panmixia.PLoS genetics · 2026Article
- De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference.Molecular ecology resources · 2026Article
- Assessing the Evolutionary Potential of Endangered Populations Using Genomic Analyses of Selection in Ecologically Important Gene Regions.Molecular ecology · 2026Article
- The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity.Genome biology and evolution · 2025Review
- ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data.Genome biology · 2025Article
- Article
- Human-specific gene expansions contribute to brain evolution.bioRxiv : the preprint server for biology · 2025Article
- Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies.Genome biology and evolution · 2024Article
- Genomic structural variation: A complex but important driver of human evolution.American journal of biological anthropology · 2023Review
- Parallel evolution of amphioxus and vertebrate small-scale gene duplications.Genome biology · 2022Article
- Host genotype controls ecological change in the leaf fungal microbiome.PLoS biology · 2022Article
- A complete reference genome improves analysis of human genetic variation.Science (New York, N.Y.) · 2022Article
- Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes.Molecular biology and evolution · 2021Article
- Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations.Nature communications · 2020Article
- Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta).PLoS genetics · 2020Article
- Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes.Genome biology and evolution · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The study of segmental duplications (SDs) and copy-number variants (CNVs) is of great importance in the fields of genomics and evolution. However, SDs and CNVs are usually excluded from genome-wide scans for natural selection. Because of high identity between copies, SDs and CNVs that are not included in reference genomes are prone to be collapsed-that is, mistakenly aligned to the same region-when aligning sequence data from single individuals to the reference. Such collapsed duplications are additionally challenging because concerted evolution between duplications alters their site frequency spectrum and linkage disequilibrium patterns. To investigate the potential effect of collapsed duplications upon natural selection scans we obtained expectations for four summary statistics from simulations of duplications evolving under a range of interlocus gene conversion and crossover rates. We confirm that summary statistics traditionally used to detect the action of natural selection on DNA sequences cannot be applied to SDs and CNVs since in some cases values for known duplications mimic selective signatures. As a proof of concept of the pervasiveness of collapsed duplications, we analyzed data from the 1,000 Genomes Project. We find that, within regions identified as variable in copy number, diversity between individuals with the duplication is consistently higher than between individuals without the duplication. Furthermore, the frequency of single nucleotide variants (SNVs) deviating from Hardy-Weinberg Equilibrium is higher in individuals with the duplication, which strongly suggests that higher diversity is a consequence of collapsed duplications and incorrect evaluation of SNVs within these CNV regions.
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