Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

16.9K
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%...
16.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

13.8K
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,...
13.8K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
12.3K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
Pleiotropy01:33

Pleiotropy

38.9K
Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
38.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The Exact Hypergeometric Posterior Method for Accurate Inference of Population Size from Mark-Recapture Data.

Bulletin of mathematical biology·2026
Same author

Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.

bioRxiv : the preprint server for biology·2026
Same author

Movi Color: fast and accurate taxonomic classification with the move structure.

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine·2026
Same author

Boolean logic links chromatin accessibility states to gene expression variability across cell types.

Nucleic acids research·2026
Same author

Minimizing reference bias with an imputed personalized reference.

Genome research·2026
Same author

Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.

Journal of molecular evolution·2025
Same journal

Evidence for cryptic sex in Escovopsis, a mycoparasite in the fungus-growing ant symbiosis.

Genome biology and evolution·2026
Same journal

Experimental evolution under biased sex ratios: phenotypic and genomic responses in the bulb mite, Rhizoglyphus robini.

Genome biology and evolution·2026
Same journal

Optimal organelle inheritance strategies under different changing environments and mutational pressures.

Genome biology and evolution·2026
Same journal

A reassessment of positive growth effects of expressed random sequence clones in E. coli suggests direct adaptive functions.

Genome biology and evolution·2026
Same journal

Genome Scanning Reveals the Genetic Basis of a Color Pattern Morphotype in an Island Population of the European Adder (Vipera berus).

Genome biology and evolution·2026
Same journal

Exploring the determinants of polydnavirus chromosomal integration across host-parasitoid wasp systems.

Genome biology and evolution·2026
See all related articles

Related Experiment Video

Updated: May 21, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

11.6K

Inferring the Selective History of CNVs Using a Maximum Likelihood Model.

Seyed Amir Malekpour1, Ata Kalirad2, Sina Majidian3,4

  • 1School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran.

Genome Biology and Evolution
|March 18, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces PoMoCNV, a new method to analyze copy number variations (CNVs) using population genetics data. It helps understand how CNVs impact evolution and genetic disorders.

Keywords:
C. eleganscopy number variationslikelihood-based inferencepolymorphism-aware phylogenetic model

More Related Videos

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

903
Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

19.5K

Related Experiment Videos

Last Updated: May 21, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

11.6K
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

903
Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

19.5K

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Population Genetics

Background:

  • Copy number variations (CNVs) are structural genomic alterations with significant phenotypic effects, implicated in both disease and adaptation.
  • Inferring the selective advantage of CNVs is challenging due to their large and variable phenotypic impacts, unlike single-nucleotide variations.
  • Understanding CNV evolution requires robust analytical tools to estimate evolutionary parameters.

Purpose of the Study:

  • To develop a likelihood-based computational approach, PoMoCNV, for estimating evolutionary parameters of CNVs from population genetics data.
  • To investigate the relationship between chromatin accessibility and CNV mutation rates and fitness.
  • To validate the PoMoCNV model using experimental data from Caenorhabditis elegans.

Main Methods:

  • Developed PoMoCNV, a phylogenetic model incorporating polymorphism data to estimate CNV mutation rates and fitness costs.
  • Applied PoMoCNV to analyze genomics data from 40 Caenorhabditis elegans strains across four populations.
  • Integrated chromatin accessibility data to interpret inferred CNV evolutionary parameters in open and closed chromatin regions.

Main Results:

  • PoMoCNV successfully estimated evolutionary parameters, including mutation rates and fitness effects, for CNVs at genomic loci.
  • Analysis revealed distinct mutation rate and fitness landscapes for CNVs in open versus closed chromatin regions.
  • The model's reliability was confirmed through its application to mutation-accumulation experiments in C. elegans.

Conclusions:

  • PoMoCNV provides a powerful framework for dissecting the evolutionary dynamics of copy number variations.
  • Chromatin accessibility is a key factor influencing the evolutionary trajectory of CNVs.
  • This approach advances our ability to study the role of CNVs in adaptation and disease.