Related Experiment Video
Updated: May 26, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
The coalescent with selection on copy number variants.
Kosuke M Teshima1, Hideki Innan
1The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan.
Genetics
|December 17, 2011
Summary
We developed a simulation tool to study gene duplication. Positive selection on duplicated genes creates a sweep signature, but gene conversion can obscure this signal, impacting evolutionary studies.
Area of Science:
- Population Genetics
- Evolutionary Biology
- Bioinformatics
Background:
- Gene duplication is a major evolutionary force.
- Understanding the impact of selection and gene conversion on duplicated genes is crucial.
Purpose of the Study:
- To develop a coalescent-based simulation tool to study single nucleotide polymorphism (SNP) patterns around gene duplications.
- To investigate how selection on duplicated gene copies and interlocus gene conversion affect SNP patterns and the detectability of selection.
Main Methods:
- Coalescent-based simulation framework.
- Incorporation of selection on duplicated copies.
- Modeling of interlocus gene conversion between gene copies.
Main Results:
- Positive selection on a duplicated gene copy leads to a reduction in polymorphism (selective sweep signature) in both the copy and flanking regions.
- Gene conversion can obscure the selective sweep signature by increasing polymorphism in the duplicated copy.
- Using flanking regions enhances the power to detect selection due to gene conversion's localized effect.
Conclusions:
- The simulation tool effectively models SNP patterns under selection and gene conversion in duplicated regions.
- Gene conversion complicates the detection of positive selection following gene duplication.
- Flanking regions provide a more robust signal for detecting selection in the context of gene duplication and conversion.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
02:46Genome Copying Errors
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
01:25Genetic Variation
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Genes exist in different versions called alleles, which...
01:21Frequency-dependent Selection
When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.