RANDLE, CHRISTOPHER P.1*, MARK P. SIMMONS2, JOHN V. FREUDENSTEIN2, and JOHN W. WENZEL3. 1The Ohio State University, Department of Evolution, Ecology and Organismal Biology, 1735 Neil Ave., Columbus, OH 43210; 2Herbarium, 1315 Kinnear Rd., Columbus, OH 43212; 3Department of Entomology, 1315 Kinnear Rd., Columbus, OH 43212. - Limitations of Relative Apparent Synapomorphy Analysis (RASA) for measuring phylogenetic signal.
We 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 best outgroup. In no case was one of the two
outgroup terminals 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)
process to identify and remove terminals subject to long branch
attraction. We conclude that RASA should not be used for any of these
purposes.
Key words: long branch attraction, outgroup selection, phylogenetic signal, RASA, Relative Apparent Synapomorphy Analysis