Separate versus combined analysis of phylogenetic evidence

TitleSeparate versus combined analysis of phylogenetic evidence
Publication TypeJournal Article
Year of Publication1995
Authorsde Queiroz A, Donoghue MJ, Kim J
JournalAnnual Review of Ecology and Systematics
KeywordsBiological Sciences, Ecology & Evolutionary Biology

There has been much discussion in the recent systematic literature over whether different data sets bearing on phylogenetic relationships should be analyzed separately or combined and analyzed simultaneously. We review arguments in favor of each of these views. Assuming that the goal is to uncover the true phylogeny of the entities in question, arguments for combining data based on the notions that one should use the ’total evidence’ available, or that the combined analysis gives the tree with the greatest descriptive and explanatory power, are not compelling. However, combining data sets can enhance detection of real phylogenetic groups. On the other hand, if there is heterogeneity among data sets with respect to some property that affects phylogeny estimation, then combining the data can give misleading results. Thus, there are reasonable arguments on both sides of the debate. We present a conceptual framework based on the reasons that different data sets may give conflicting estima