Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis

Sebastien Roch, Sagi Snir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common tree-like signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the tree-like trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally we show that our results have implications for the discovery of highways of gene sharing.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings
Pages224-238
Number of pages15
DOIs
StatePublished - 2012
Event16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012 - Barcelona, Spain
Duration: 21 Apr 201224 Apr 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7262 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012
Country/TerritorySpain
CityBarcelona
Period21/04/1224/04/12

Keywords

  • Lateral Gene Transfer
  • Phylogenetic Reconstruction
  • Quartet Reconstruction

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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