Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists

Abstract:  As phylogenetic analyses become larger, one of the greatest methodological difficulties is representing speciose supraspecific clades in higher-level analyses (e.g. trilobites within studies of arthropod phylogeny). Several strategies have been proposed, including using representative single composite terminals or species-level exemplars, and various methods are currently used in the palaeontological literature. However, this is problematic, as simulation studies and empirical arguments in the systematics literature have clearly identified multiple exemplars as the optimal method. The continuing usage of suboptimal strategies in palaeontology may lessen the accuracy of phylogenies and hampers comparison between alternative studies. Here, I outline problems with suboptimal strategies, review arguments in support of multiple exemplars and provide guidelines for palaeontologists undertaking higher-level phylogenetic analyses.