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Genetic Variation01:25

Genetic Variation

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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,...
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Gene Conversion02:08

Gene Conversion

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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

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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.
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Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

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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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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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Related Experiment Video

Updated: May 27, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

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Multiple-testing corrections in selection scans using identity-by-descent segments.

Seth D Temple1,2,3, Sharon R Browning4

  • 1Department of Statistics, University of Washington, Seattle, Washington, USA.

Biorxiv : the Preprint Server for Biology
|February 20, 2025
PubMed
Summary
This summary is machine-generated.

Accurate detection of genetic adaptation requires correcting for multiple testing. We developed an efficient method using identity-by-descent (IBD) rates to control false discoveries in selection scans, successfully identifying recent human adaptations.

Keywords:
identity-by-descentmean-reverting processesmultiple testingnatural selection

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Area of Science:

  • Population Genetics
  • Genomics
  • Evolutionary Biology

Background:

  • Selection scans aim to identify recent genetic adaptations.
  • Multiple testing correction is crucial to avoid false discoveries.
  • Current methods struggle with complex statistics for genome-wide significance.

Purpose of the Study:

  • To propose a computationally efficient method for determining genome-wide significance levels in identity-by-descent (IBD) based selection scans.
  • To control the family-wise error rate (FWER) in detecting recent positive selection.
  • To identify statistically significant signals of recent selection in human populations.

Main Methods:

  • Modeling the autocorrelation of identity-by-descent (IBD) rates.
  • Developing a computationally efficient method for significance level determination.
  • Utilizing whole genome simulations to validate the method's performance.
  • Analyzing large-scale human genetic data from TOPMed and UK Biobank.

Main Results:

  • The proposed method demonstrates approximate control of the family-wise error rate (FWER).
  • The method adapts to varying test spacing across the genome.
  • High power (>50%) was observed for detecting hard sweeps with specific selection coefficients and allele frequencies.
  • Statistically significant excesses of IBD segments were found in human genes across African, European, and South Asian ancestry groups.
  • Many identified selection signals were shared across different ancestry groups.
  • A particularly strong signal of recent selection was detected in a skeletal cell development gene in African ancestry samples.

Conclusions:

  • The developed IBD-based method provides a computationally efficient and reliable approach for detecting recent positive selection.
  • The findings highlight shared and ancestry-specific signals of recent human adaptation.
  • The study identifies specific genes and gene complexes under recent selection, with notable signals in African populations.