title: Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal.
abstract: In this paper we use hypothetical and empirical data matrices to evaluate the ability of relative apparent synapomorphy analysis (RASA) to measure phylogenetic signal, select outgroups, and identify terminals subject to long-branch attraction. In all cases, except for equal character-state frequencies, RASA indicated extraordinarily high levels of phylogenetic information for hypothetical data matrices that are uninformative regarding relationships among the terminals. Yet, regardless of the number of characters or character-state frequencies, RASA failed to detect phylogenetic signal for hypothetical matrices with strong phylogenetic signal. In our empirical example, RASA indicated increasing phylogenetic signal for matrices for which the strict consensus of the most parsimonious trees is increasingly poorly resolved, clades are increasingly poorly supported, and for which many relationships are in conflict with more widely sampled analyses. RASA is an ineffective approach to identify outgroup terminal(s) with the most plesiomorphic character states for the ingroup. Our hypothetical example demonstrated that RASA preferred outgroup terminals with increasing numbers of convergent character states with ingroup terminals, and rejected the outgroup terminal with all plesiomorphic character states. Our empirical example demonstrated that RASA, in all three cases examined, selected an ingroup terminal, rather than an outgroup terminal, as the best outgroup. In no case was one of the two outgroup terminals even close to being considered the optimal outgroup by RASA. RASA is an ineffective means of identifying problematic long-branch terminals. In our hypothetical example, RASA indicated a terminal as being a problematic long-branch terminal in spite of the terminal being on a zero-length branch and having no possibility of undergoing long-branch attraction with another terminal. RASA also failed to identify actual problematic long-branch terminals that did undergo long-branch attraction, but only after following Lyons-Weiler and Hoelzer's (1997) three-step process to identify and remove terminals subject to long-branch attraction. We conclude that RASA should not be used for any of these purposes.
authors.affiliation: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA. psimmons@lamar.colostate.ued
authors.forename: Mark P
authors.initials: MP
authors.lastname: Simmons
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Randle
authors.forename: John V
authors.initials: JV
authors.lastname: Freudenstein
authors.forename: John W
authors.initials: JW
authors.lastname: Wenzel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics
chemical_list: D003062:Codon; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase