Key Laboratory of Ecology and Environment Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China; Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario NIG 2W1, Canada.
Mol Phylogenet Evol. 2014 Feb;71:142-8. doi: 10.1016/j.ympev.2013.11.013. Epub 2013 Dec 6.
In order to assess how dataset-selection for multi-gene analyses affects the accuracy of inferred phylogenetic trees in ciliates, we chose five genes and the genus Paramecium, one of the most widely used model protist genera, and compared tree topologies of the single- and multi-gene analyses. Our empirical study shows that: (1) Using multiple genes improves phylogenetic accuracy, even when their one-gene topologies are in conflict with each other. (2) The impact of missing data on phylogenetic accuracy is ambiguous: resolution power and topological similarity, but not number of represented taxa, are the most important criteria of a dataset for inclusion in concatenated analyses. (3) As an example, we tested the three classification models of the genus Paramecium with a multi-gene based approach, and only the monophyly of the subgenus Paramecium is supported.
为了评估多基因分析中数据集选择如何影响纤毛虫推断系统发育树的准确性，我们选择了五个基因和 Paramecium 属，这是最广泛使用的模式原生动物属之一，并比较了单基因和多基因分析的树拓扑结构。我们的实证研究表明：(1) 使用多个基因可以提高系统发育准确性，即使它们的单基因拓扑结构相互冲突。(2) 缺失数据对系统发育准确性的影响是不确定的：分辨率和拓扑相似性，而不是代表类群的数量，是串联分析中纳入数据集的最重要标准。(3) 作为一个例子，我们使用基于多基因的方法测试了 Paramecium 属的三个分类模型，只有 Paramecium 亚属的单系性得到支持。
