Missing data and the accuracy of Bayesian phylogenetics

作     者：John J. WIENS Daniel S. MOEN 

作者机构：Department of Ecology and Evolution Stony Brook University Stony Brook NY 11794-5245 USA 

出 版 物：《植物分类学报》 (Acta Phytotaxonomica Sinica)

年 卷 期：2008年第46卷第3期

页      面：307-314页

核心收录：

学科分类：0710[理学-生物学] 0830[工学-环境科学与工程（可授工学、理学、农学学位）] 07[理学] 0901[农学-作物学] 0902[农学-园艺学] 071002[理学-动物学] 0713[理学-生态学] 

基　　金：国家自然科学基金 

主　　题：贝叶斯定理 系统发生学 数据缺失 准确度 

摘      要：The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that in-complete taxa can be accurately placed as long as the overall number of characters in the analysis is large. How-ever, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.