Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal

We have developed a new approach to the measurement of phylogenetic signalin character state matrices called relative apparent synapomorphy analysis(RASA). RASA provides a deterministic, statistical measure of naturalcladistic hierarchy (phylogenetic signal) in character state matrices. Themethod works by determining whether a measure of the rate of increase ofcladistic similarity among pairs of taxa as a function of pheneticsimilarity is greater than a null equiprobable rate of increase. Ourinvestigation of the utility and limitations of RASA using simulated andbacteriophage T7 data sets indicates that the method has numerousadvantages over existing measures of signal. A first advantage iscomputational efficiency. A second advantage is that RASA employs knownmethods of statistical inference, providing measurable sensitivity andpower. The performance of RASA is examined under various conditions ofbranching evolution as the number of characters, character states percharacter, and mutations per branch length are varied. RASA appears toprovide an unbiased and reliable measure of phylogenetic signal, and thegeneral approach promises to be useful in the development of new techniquesthat should increase the rigor and reliability of phylogenetic estimates.