Inferring phylogenetic networks by the maximum parsimony criterion: A case study

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller

Research output: Contribution to journalArticlepeer-review

Abstract

Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.

Original languageEnglish
Pages (from-to)324-337
Number of pages14
JournalMolecular Biology and Evolution
Volume24
Issue number1
DOIs
StatePublished - Jan 2007
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported in part by the National Science Foundation under grant DDM-9102370 and by the Material Handling Research Center at the Georgia Institute of Technology. We thank Bob Leavitt at IBM T.J. Watson Research Center for his encouragement and support of our work. We also appreciate the comments of the reviewers of an earher draft of thls art~cle; thelr comments have strengthened the content of the paper.

Keywords

  • Computational phylogenetics
  • Horizontal gene transfer
  • Maximum parsimony
  • Phylogenetic networks
  • Reticulate evolution

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology

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