Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Reconstructing reticulate evolution in species: theory and practice
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconstructing Phylogenetic Networks Using Maximum Parsimony
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Maximum likelihood of phylogenetic networks
Bioinformatics
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Reconstruction of reticulate networks from gene trees
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Identifiability issues in phylogeny-based detection of horizontal gene transfer
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
| Hi-index | 0.00 |
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 the approaches for augmenting species trees into phylogenetic networks.We conducted data analysis and performance study of our methods on a data set of 20 genes from the Amborellamitochondrial genome, in which Jeffrey Palmer and his co-workers postulated a massive amount of horizontal gene transfer. As expected, we found that including poorly supported gene tree branches in the analysis results in a high rate of false positive gene transfer events. Further, the bootstrap-based support measure assessed, with high accuracy, the support of the inferred gene transfer events. Further, we obtained very promising results, in terms of both speed and accuracy, when applying our integrative method on these data sets (we are currently studying the performance in extensive simulations). All methods have been implemented in the PhyloNet and NEPAL tools, which are available in the form of executable code from http://bioinfo.cs.rice.edu.