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Horizontal Gene Transfer Phylogenetics: A Random Walk Approach.

Gur Sevillya1, Daniel Doerr2, Yael Lerner1

  • 1Department of Evolutionary Biology, University of Haifa, Haifa, Israel.

Molecular Biology and Evolution
|December 18, 2019
PubMed
Summary

We developed a statistical model for the synteny index (SI) to quantify genome evolution in prokaryotes. This model uses gene neighborhood dynamics to estimate horizontal gene transfer (HGT) rates and evolutionary time, revealing significant genome dynamics within genera.

Keywords:
Markovian processesgene orderhorizontal gene transferphylogenetics

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Decreasing costs of genetic sequencing enable high-resolution evolutionary studies.
  • Standard phylogenetic markers are insufficient for closely related strains.
  • Genome dynamics, including horizontal gene transfer (HGT) and gene loss, offer richer phylogenetic signals in prokaryotes.

Purpose of the Study:

  • To develop a rigorous statistical model for the synteny index (SI) to quantify genome evolution.
  • To establish additivity for the SI measure, enabling estimation of evolutionary time periods.
  • To analyze genome dynamics and HGT rates in prokaryotes.

Main Methods:

  • Modeled gene neighborhood as a birth-death-immigration process influenced by HGT.
  • Developed an analytical model relating HGT rate and time to expected SI.
  • Created a heuristic exponential decay model for biologically realistic genome sizes.
  • Applied models to 1,133 prokaryotes across 39 genera.

Main Results:

  • Provided the first statistical model and additivity proof for the SI measure under HGT.
  • The asymptotic model offers accurate results for infinite genomes; the heuristic model performs well for realistic genomes.
  • Analysis of 1,133 prokaryotes revealed an average of 0.5 genome dynamics events per gene within the genus phylogenetic depth.

Conclusions:

  • The developed statistical models provide a robust framework for analyzing genome evolution using the SI.
  • Significant variability in genome dynamics exists between prokaryotic genera.
  • The findings confirm and extend previous observations on genome dynamics within specific genera.