Evaluating Results
This chapter explores the tools used to evaluate the quality and plausibility of results of phylogenetic analyses. The term “fit” has been widely used in the phylogenetic literature to indicate the degree to which data conform to (or are explained by) a cladogram. The most commonly used measure of fit applied to discrete character data is the consistency index, or ci. Meanwhile, measures of synapomorphy are less frequently reported than the consistency index. The chapter then considers the resolution of branches; multiple equally parsimonious cladograms; successive approximations weighing; and data decisiveness. It also differentiates between total evidence and consensus, before describing supertrees. Finally, the chapter looks at approaches for evaluating support or stability of phylogenetic results, including branch support, jackknifing, bootstrapping, randomization tests, and sensitivity analysis.