Bootstrap-based Support of HGT Inferred by Maximum Parsimony

BMC Evolutionary Biology

Methodology Article

Hyun Jung Park¹  Guohua Jin¹  Luay Nakhleh¹ 

[1] Department of Computer Science, Rice University, 6100 Main Street, MS 132, 77005, Houston, Texas, USA;

关键词: Maximum Parsimony;    Horizontal Gene Transfer;    Maximum Parsimony Analysis;    Phylogenetic Network;    Horizontal Gene Transfer Event;   

DOI  :  10.1186/1471-2148-10-131

 received in 2009-12-14, accepted in 2010-05-05,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundMaximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold.ResultsIn 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.ConclusionsWe have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), 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.

【 授权许可】

Unknown   
© Park et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.