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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.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
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.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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...
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).

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Related Experiment Video

Updated: May 10, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Published on: December 7, 2021

Inferring selection intensity and allele age from multilocus haplotype structure.

Hua Chen1, Montgomery Slatkin

  • 1Department of Integrative Biology, University of California, Berkeley, California 94720, USA. hchen007@gmail.com

G3 (Bethesda, Md.)
|June 26, 2013
PubMed
Summary

Estimating selection intensity and allele age from population genetic data is challenging. This study introduces an efficient method using multilocus haplotype structure to infer these parameters, improving accuracy for positive selection studies.

Keywords:
allele agehaplotype structureimportance samplingselection coefficientstructured coalescenttime-varying population size

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Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Inferring selection intensity and allele age from population genetic data presents significant challenges.
  • Existing methods often struggle with the complexity of multilocus haplotype structures and linked neutral markers.

Purpose of the Study:

  • To develop an efficient computational method for estimating selection intensity and allele age.
  • To utilize multilocus haplotype patterns near positively selected mutations for accurate parameter inference.

Main Methods:

  • Employed a structured-coalescent approach to model directional selection's impact on linked neutral marker genealogies.
  • Developed a simplified multilocus haplotype model to efficiently capture ancestral haplotype dynamics under selection and recombination.
  • Utilized importance sampling algorithms to evaluate sample probabilities across allele frequency trajectories and genealogies.

Main Results:

  • The method accurately estimates selection intensity for moderate to strong positive selection, validated by simulations.
  • Applied to G6PD gene data in an African population, yielding a selection intensity estimate of 0.0456 (95% CI 0.0144-0.0769).
  • The model successfully handles large DNA regions (hundreds of kilobases) by reducing state space complexity.

Conclusions:

  • The novel method jointly models multilocus haplotype patterns influenced by recombination and mutation in recombining regions.
  • It offers accurate estimation of selection intensity and allele age, applicable to diverse demographic histories including exponential growth.
  • This approach enhances the analysis of population genetic data for understanding evolutionary processes.