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On surrogate methods for detecting lateral gene transfer.

M A Ragan1

  • 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia. m.ragan@imb.uq.edu.au

FEMS Microbiology Letters
|July 27, 2001
PubMed
Summary

This study used four surrogate methods to identify potential lateral gene transfer in Escherichia coli K12. Only two methods agreed on the same open reading frames (ORFs), suggesting distinct detection capabilities.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Lateral gene transfer (LGT) is a significant driver of microbial evolution.
  • Phylogenetic tree inference is a common but computationally intensive method for detecting LGT.
  • Surrogate methods offer alternative approaches to identify LGT without phylogenetic analysis.

Purpose of the Study:

  • To apply and compare four surrogate methods for detecting LGT-associated open reading frames (ORFs) in Escherichia coli K12.
  • To assess the concordance and unique contributions of different surrogate LGT detection methods.
  • To investigate potential differences in the age of LGT-derived ORFs detected by various methods.

Main Methods:

  • Application of four distinct surrogate methods for LGT detection.
  • Analysis of open reading frames (ORFs) within the Escherichia coli K12 genome.
  • Statistical comparison of ORF sets identified by each method against chance expectations.

Main Results:

  • Two of the four surrogate methods identified overlapping sets of ORFs more frequently than expected by chance.
  • Several intersections of methods yielded significantly fewer ORFs than expected, indicating method-specific biases.
  • Each of the four methods detected distinct, non-random sets of potential LGT-derived ORFs.

Conclusions:

  • Surrogate methods for LGT detection exhibit varying specificities and sensitivities.
  • The choice of surrogate method influences the identification of potential LGT events.
  • Further investigation, potentially involving phylogenetic inference, is needed to explore the relative ages of LGT-acquired ORFs.

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