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Related Concept Videos

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...
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...
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...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Viral Recombination00:57

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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...

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Related Experiment Video

Updated: Jul 9, 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 and phylogeny: effects and detection.

Derek Ruths, Luay Nakhleh

    International Journal of Bioinformatics Research and Applications
    |December 1, 2007
    PubMed
    Summary
    This summary is machine-generated.

    Recombination events can inaccurately affect phylogenetic tree reconstruction. This study introduces a new method to detect recombination by analyzing incongruence among phylogenetic trees in sequence alignments, showing good results on synthetic and biological data.

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    Last Updated: Jul 9, 2026

    Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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    Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
    08:57

    Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

    Published on: August 14, 2018

    Area of Science:

    • Evolutionary biology
    • Bioinformatics
    • Computational phylogenetics

    Background:

    • Phylogenetic analyses are crucial for comparative studies in the post-genomic era.
    • Traditional phylogeny reconstruction methods often assume a single evolutionary tree for sequence alignments.
    • Recombination events can lead to different evolutionary histories across different regions of a sequence alignment.

    Purpose of the Study:

    • To investigate the impact of recombination on the accuracy of phylogeny reconstruction methods.
    • To develop an efficient and accurate method for detecting recombination in sequence datasets.

    Main Methods:

    • Simulations were used to demonstrate the effect of recombination on phylogeny reconstruction accuracy.
    • A novel method was developed to detect recombination based on incongruence among phylogenetic trees derived from different alignment regions.
    • The method's performance was evaluated using both synthetic and biological datasets.

    Main Results:

    • Recombination significantly affects the accuracy of standard phylogeny reconstruction methods.
    • The proposed method effectively detects recombination by identifying incongruence in phylogenetic trees across sequence alignment regions.
    • The method demonstrated good performance on both simulated and real biological sequence data.

    Conclusions:

    • The prevalence of recombination necessitates the development of robust methods for its detection in phylogenetic studies.
    • The introduced method offers a simple yet effective approach for identifying recombination events in sequence alignments.
    • Accurate recombination detection is vital for reliable phylogenetic inference and comparative evolutionary analyses.