Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

摘要

This paper will attempt to resolve some controversies about the effects of missing data on phylogenetic analysis. Whether missing data are generally problematic is a critical issue in modern phylogenetics, especially as wildly different amounts of molecular data become available for different taxa, ranging from entire genomes, to single genes, to none (e.g., fossils). Our perception of the impact of missing data (or lack thereof) may strongly influence which taxa and characters we include in a phylogenetic analysis (Wiens 2006) and may lead to a diversity of serious errors. For example, if we think that missing data are problematic when they are not, then we may exclude taxa and characters that would otherwise benefit our analyses, given the abundant evidence that increasing numbers of both taxa and characters can potentially improve the accuracy of phylogenetic analyses (e.g., Huelsenbeck 1995; Rannala et al. 1998; Poe 2003), where accuracy is generally defined as the similarity between the estimated tree and the correct, known phylogeny. In contrast, if missing data cells are themselves intrinsically problematic (e.g., Huelsenbeck 1991), including taxa or characters with many missing data cells may lead to inaccurate phylogenetic estimates.