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Related Experiment Videos

A likelihood framework to measure horizontal gene transfer.

Simone Linz1, Achim Radtke, Arndt von Haeseler

  • 1Department of Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany. linz@cs.uni-duesseldorf.de

Molecular Biology and Evolution
|March 22, 2007
PubMed
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This study introduces a new method to estimate horizontal gene transfer (HGT) rates using a Poisson process model. The findings reveal an average of 11 HGT events across 44 taxa, providing crucial insights into microbial evolution.

Area of Science:

  • Evolutionary Biology
  • Genomics
  • Computational Biology

Background:

  • Horizontal gene transfer (HGT) is a significant evolutionary mechanism.
  • Estimating the rate of HGT is crucial for understanding genome evolution.
  • Previous methods for HGT rate estimation have limitations.

Purpose of the Study:

  • To develop a likelihood-based approach for estimating the overall rate of horizontal gene transfer (HGT).
  • To simulate phylogenetic tree topologies under different HGT scenarios.
  • To provide a corrected HGT rate accounting for gene tree reconstruction inaccuracies.

Main Methods:

  • Modeled HGT events using a Poisson process.
  • Simulated tree topologies on a clocklike species tree for varying HGT event counts.

Related Experiment Videos

  • Estimated HGT rates using simulated distributions and gene trees from the Clusters of Orthologous Groups (COGs) dataset.
  • Applied a correction for gene tree reconstruction errors.

    • Main Results:

    • Estimated a corrected HGT rate of approximately 0.36 per gene per unit time.
    • Inferred an average of 11 HGT events across the 44 taxa in the COG species tree.
    • Developed and validated a computational method for HGT rate estimation.

    Conclusions:

    • The proposed likelihood-based method provides a robust estimation of HGT rates.
    • The study quantifies the extent of HGT in a specific dataset, offering insights into evolutionary dynamics.
    • A software package is available to facilitate HGT rate estimation for researchers.