ArticleGenetics2012
The coalescent with selection on copy number variants.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- Article
- Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection.Scientific reports · 2021Article
- Population Genetics of the Highly PolymorphicGenes · 2019Article
- Effect of Collapsed Duplications on Diversity Estimates: What to Expect.Genome biology and evolution · 2018Article
- Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest.BMC genomics · 2016Article
- Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Estimating copy numbers of alleles from population-scale high-throughput sequencing data.BMC bioinformatics · 2015Article
- Human gene copy number variation and infectious disease.Human genetics · 2014Review
- Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario.G3 (Bethesda, Md.) · 2014Article
- Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene.Genome biology and evolution · 2013Article
- Both positive and negative selection pressures contribute to the polymorphism pattern of the duplicated human CYP21A2 gene.PloS one · 2013Article
- Hard selective sweep and ectopic gene conversion in a gene cluster affording environmental adaptation.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop a coalescent-based simulation tool to generate patterns of single nucleotide polymorphisms (SNPs) in a wide region encompassing both the original and duplicated genes. Selection on the new duplicated copy and interlocus gene conversion between the two copies are incorporated. This simulation enables us to explore how selection on duplicated copies affects the pattern of SNPs. The fixation of an advantageous duplicated copy causes a strong reduction in polymorphism not only in the duplicated copy but also in its flanking regions, which is a typical signature of a selective sweep by positive selection. After fixation, polymorphism gradually increases by accumulating neutral mutations and eventually reaches the equilibrium value if there is no gene conversion. When gene conversion is active, the number of SNPs in the duplicated copy quickly increases by transferring SNPs from the original copy; therefore, the time when we can recognize the signature of selection is decreased. Because this effect of gene conversion is restricted only to the duplicated region, more power to detect selection is expected if a flanking region to the duplicated copy is used.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.