Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer

Abstract. One phylogeny-based approach to horizontal gene transfer (HGT) detection entails comparing the topology of a gene tree to that of the species tree, and using their differences to locate HGT events. Another approach is based on augmenting a species tree into a phylogenetic network to improve the fitness of the evolution of the gene sequence data under an optimization criterion, such as maximum parsimony (MP). One major problem with the first approach is that gene tree estimates may have wrong branches, which result in false positive estimates of HGT events, and the second approach is accurate, yet suffers from the computational complexity of searching through the space of possible phylogenetic networks. The contributions of this paper are two-fold. First, we present a measure that computes the support of HGT events inferred from pairs of species and gene trees. The measure uses the bootstrap values of the gene tree branches. Second, we present an integrative method to speed up...

• Type: Conference
• Year: 2008
• Where: RECOMB
• Authors: Cuong Than, Guohua Jin, Luay Nakhleh
• Keywords: Computational Biology, Gene Transfer Events, Gene Tree Branches, Horizontal Gene Transfer, RECOMB 2008