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Related Concept Videos

Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Frequency-dependent Selection01:21

Frequency-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.Positive Frequency-Dependent SelectionIn positive...
Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).Mechanisms of Genetic VariationThe original sources of genetic variation are mutations,...
What is Population Genetics?01:25

What is Population Genetics?

A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.While some alleles of a given gene might be observed commonly, other variants...

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Related Experiment Video

Updated: Jun 21, 2026

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing
11:36

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

Estimating selection intensity on synonymous codon usage in a nonequilibrium population.

Kai Zeng1, Brian Charlesworth

  • 1Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. kai.zeng.cn@gmail.com

Genetics
|July 22, 2009
PubMed
Summary
This summary is machine-generated.

Population size changes can distort codon usage bias, impacting genetic parameter estimates. A new method accurately estimates demographic and codon usage parameters, revealing selection favors preferred codons in Drosophila melanogaster.

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Related Experiment Videos

Last Updated: Jun 21, 2026

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing
11:36

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Published on: July 3, 2016

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04:52

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Published on: February 3, 2023

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
10:41

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Area of Science:

  • Population Genetics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Codon usage bias is the nonrandom selection of synonymous codons.
  • Population genetic models often assume mutation-selection-drift equilibrium.
  • Natural populations may deviate from equilibrium due to demographic changes.

Purpose of the Study:

  • To develop a model accounting for demographic changes on codon usage bias.
  • To create a new method for estimating demographic and codon usage parameters accurately.
  • To investigate the influence of gene length and expression on selection intensity.

Main Methods:

  • Constructed a matrix model incorporating population size changes.
  • Applied a novel method to estimate demographic and codon usage parameters.
  • Analyzed Drosophila melanogaster polymorphism data for twofold degenerate codons.

Main Results:

  • Synonymous polymorphisms can show erratic patterns after demographic shifts.
  • Statistical methods ignoring demographic effects can yield inaccurate parameter estimates.
  • Selection favors preferred codons, counteracted by a mutation bias towards unpreferred codons.

Conclusions:

  • Shorter genes and highly expressed genes experience stronger selection on codon usage.
  • The Zimbabwe population of Drosophila melanogaster shows little evidence of recent population size change.
  • The proposed method accurately estimates parameters and tests for covariate effects on selection intensity.