MBE Advance Access originally published online on October 26, 2006
Molecular Biology and Evolution 2007 24(1):324-337; doi:10.1093/molbev/msl163
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Research Articles |
Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study
* Department of Computer Science, Rice University, Houston, Texas
Department of Mathematics, University of California
School of Computer Science, Tel Aviv University, Tel Aviv, Israel
E-mail: nakhleh{at}cs.rice.edu.
Accepted for publication October 20, 2006.
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.
Key Words: reticulate evolution • phylogenetic networks • horizontal gene transfer • maximum parsimony • computational phylogenetics
Dan Graur, Associate Editor
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