MBE Advance Access published online on October 26, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl163
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1 Dept. of Computer Science, Rice University
* To whom correspondence should be addressed. 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 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. Further, 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 chimaeric genes whose evolutionary histories are a mix of vertical and horizontal evolution. Beside the performance analysis of MP, our findings offer new insights into the evolution of four biological data sets, and new possible explanations of HGT scenarios in their evolutionary history.
Accepted October 20, 2006
Research Article
Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study
Guohua Jin 1, Luay Nakhleh 1 *, Sagi Snir 2, and Tamir Tuller 3
2 Dept. of Mathematics, University of California
3 School of Computer Science, Tel Aviv University
Luay Nakhleh, E-mail: nakhleh{at}cs.rice.edu
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