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Bootstrap-based Support of HGT Inferred by Maximum Parsimony

DOI: 10.1186/1471-2148-10-131

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In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples.We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/ webcite), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.The massive evidence of horizontal gene transfer in prokaryotes and higher organisms and the significant role hybridization plays in speciation of various groups of species in the plant kingdom and beyond, have highlighted the need for developing models and methodologies that augment trees to enable modeling of reticulate evolutionary relationships. Indeed, the computational biology and bioinformatics communities have developed a host of such models and methodologies for reconstructing and evaluating phylogenetic networks. Several extensive surveys have been written recently about phylogenetic networks; we refer the reader to [1-7].One of the most commonly used criteria for reconstructing phylogenetic trees is maximum parsimony (MP). Under this criterion, the phylogenetic tree that best fits a sequence data set is one that minimizes the total number of mutations over all possible tree topologies and sequence assignments to internal nodes of the tree topologies. There is a polynomial time algorithm for computing the parsimony length of a fixed phylogenetic tree leaf-labeled by a set of sequences, due to [8], while solving the MP

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