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Related Concept Videos

Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Gene Conversion02:08

Gene Conversion

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...
Gene Conversion02:08

Gene Conversion

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...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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...
Crossing Over01:30

Crossing Over

Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I, duplicated...
Crossing Over01:34

Crossing Over

Unlike mitosis, meiosis aims for genetic diversity in its creation of haploid gametes. Dividing germ cells first begin this process in prophase I, where each chromosome—replicated in S phase—is now composed of two sister chromatids (identical copies) joined centrally.
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...

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Related Experiment Video

Updated: May 26, 2026

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Recombination detection under evolutionary scenarios relevant to functional divergence.

Rachael A Bay1, Joseph P Bielawski

  • 1Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada. rbay@stanford.edu

Journal of Molecular Evolution
|January 3, 2012
PubMed
Summary

Recombination detection methods show increased false positives with sequence divergence when no recombination is present. Researchers recommend pre-testing for recombination in functional divergence studies.

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Last Updated: May 26, 2026

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Published on: September 11, 2022

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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

Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Recombination can interfere with gene function divergence studies relying on gene trees.
  • Limited understanding exists on recombination detection method performance under relevant evolutionary scenarios.

Purpose of the Study:

  • Evaluate false positive rates of six recombination detection methods (GENECONV, MaxChi, Chimera, RDP, GARD-SBP, GARD-MBP).
  • Assess method performance under evolutionary scenarios potentially increasing false positives, including asymmetric tree topology, sequence divergence, non-stationary codon bias, selection pressure shifts, and positive selection.
  • Evaluate the power of these methods to detect true recombination events.

Main Methods:

  • Simulated evolutionary histories to test six recombination detection methods.
  • Scenarios included varying tree topologies, sequence divergence levels, codon bias, selection pressures, and positive selection.
  • Evaluated false positive rates in non-recombinant histories and detection power in recombinant histories.

Main Results:

  • Detection power increases with sequence divergence, but accuracy in identifying breakpoint numbers is low.
  • Increased sequence divergence leads to higher false positives when recombination is absent.
  • GARD-SBP showed sensitivity to asymmetric tree topologies, increasing false positive rates.
  • All tested methods demonstrated robustness against codon bias heterogeneity, selection pressure shifts, and positive selection.

Conclusions:

  • Studies investigating functional divergence in systems prone to recombination should incorporate pre-testing for recombination.
  • Application to Prochlorococcus core genome revealed significant discordance among method results.
  • Guidelines are provided for investigating recombination in genes undergoing functional divergence, based on simulated and real data analysis.