Nakhleh Luay, Jin Guohua, Zhao Fengmei, Mellor-Crummey John
Department of Computer Science, Rice University, Houston, TX 77005, USA.
Proc IEEE Comput Syst Bioinform Conf. 2005:93-102. doi: 10.1109/csb.2005.47.
Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.
系统发育树——生物群体的进化历史——是整个生命科学中使用最广泛的工具之一，也是系统学、进化生物学、流行病学等领域的研究对象。迄今为止，几乎所有用于重建系统发育树的工具都会生成树状图；然而，人们普遍理解并接受的是，树状图过度简化了许多生物群体的进化历史，最显著的是细菌（由于水平基因转移）和植物（由于杂交物种形成）。已经引入了各种方法和标准来重建系统发育树。简约性是使用最广泛且研究最多的标准之一，并且已经设计出了各种基于简约性来重建树的准确而有效的启发式方法。约通·海因提出了将简约性标准直接扩展到系统发育网络的方法。在本文中，我们将这一概念形式化，并首次对简约性作为构建和评估系统发育网络的标准的质量进行了实验研究。我们的结果表明，当扩展到系统发育网络时，简约性标准产生了令人满意的结果。在我们实验中的绝大多数情况下，简约性标准准确地预测了非树状事件的数量和位置。
