Related Experiment Video
Updated: Feb 22, 2026
04:59
Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster
Published on: March 28, 2025
1.3K
Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism
Zi-Ming Zhao1, Michael C Campbell1,2, Ning Li3
1Department of Biostatistics, Yale University, New Haven, CT.
Molecular Biology and Evolution
|September 30, 2017
Summary
New method MASS-PRF detects varying natural selection within genes. It reveals regional differences in selection intensity, highlighting important gene domains in human evolution.
Area of Science:
- Evolutionary biology
- Genomics
- Population genetics
Background:
- Detecting uniform selection across genes is common.
- Regions within genes show varied selection pressures, particularly clusters of amino acid substitutions.
- Existing methods struggle to quantify this intragenic selection heterogeneity.
Purpose of the Study:
- To develop a method for quantifying selection heterogeneity within protein-coding genes.
- To identify specific gene regions under varying selection pressures.
Main Methods:
- Developed Model Averaged Site Selection via Poisson Random Field (MASS-PRF).
- MASS-PRF uses an ensemble of intragenic clustering models within a Poisson Random Field framework.
- Estimates selection intensity on a site-by-site basis.
Main Results:
- MASS-PRF effectively detects amino acid variant clusters in small genic regions.
- The method reliably estimates variant probabilities and is robust to demographic trends and recombination.
- Analysis of human and chimpanzee data revealed significant regional variation in selection intensity within genes.
Conclusions:
- Striking regional variation in selection intensity exists within human genes.
- These variations are linked to neurological, immune, and reproductive functions.
- Amino acid substitutions in these regions likely conferred selective advantages in human evolution, impacting protein function.
Related Concept Videos
02:05Gene Evolution - Fast or Slow?
8.3K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
8.3K
02:54Evolutionary Relationships through Genome Comparisons
7.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.1K
02:26Comparing Copy Number Variations and SNPs
18.8K
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%...
18.8K
01:05Single Nucleotide Polymorphisms-SNPs
18.7K
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,...
18.7K
01:29Modern Molecular Taxonomy
753
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
753
01:25Genetic Variation
1.5K
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,...
Genes exist in different versions called alleles,...
1.5K