© 2005 Society of Systematic Biologists
Evaluating Intraspecific "Network" Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach?
Laboratory of Evolutionary Genetics, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles rue Jeener et Brachet 12, 6041 Gosselies Belgium E-mail: pmarduly{at}ulb.ac.be P.M.
Edited by Mike Steel: Associate Editor
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Abstract |
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In intraspecific studies, reticulated graphs are valuable tools for visualization, within a single figure, of alternative genealogical pathways among haplotypes. As available software packages implementing the global maximum parsimony (MP) approach only give the possibility to merge resulting topologies into less-resolved consensus trees, MP has often been neglected as an alternative approach to purely algorithmic (i.e., methods defined solely on the basis of an algorithm) "network" construction methods. Here, we propose to search tree space using the MP criterion and present a new algorithm for uniting all equally most parsimonious trees into a single (possibly reticulated) graph. Using simulated sequence data, we compare our method with three purely algorithmic and widely used graph construction approaches (minimum-spanning network, statistical parsimony, and median-joining network). We demonstrate that the combination of MP trees into a single graph provides a good estimate of the true genealogy. Moreover, our analyses indicate that, when internal node haplotypes are not sampled, the median-joining and MP methods provide the best estimate of the true genealogy whereas the minimum-spanning algorithm shows very poor performances.
Keywords: Intraspecific genealogy; maximum parsimony; median-joining; minimum spanning; network; reticulated graph; statistical parsimony; simulated sequence data
Received March 3, 2004; Revised May 6, 2004; Accepted December 14, 2004
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