DATA DECISIVENESS, DATA QUALITY, AND INCONGRUENCE IN PHYLOGENETIC ANALYSIS - AN EXAMPLE FROM THE MONOCOTYLEDONS USING MITOCHONDRIAL ATPA SEQUENCES

We examined three parallel data sets with respect to qualities relevan t to phylogenetic analysis of 20 exemplar monocotyledons and related d icotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotid e sequence variation in the chloroplast-encoded gene rbcL and in the m itochondrion-encoded gene atp A, the latter of which encodes the a-sub unit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide seq uence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analy ses, with a focus on patterns of congruence, homoplasy, and data decis iveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in ter ms of the degree to which those trees are shorter than the average len gth of all possible trees. Because indecisive data sets require relati vely fewer additional steps than decisive ones to be optimized on nonp arsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between dec isiveness and character incongruence is that if incongruence is used a s a criterion of noncombinability, decisive data sets, which provide r obust support for relationships, are more likely to be assessed as non combinable with other data sets than are indecisive data sets, which p rovide weak support for relationships. For the sampling of taxa in thi s study, the atpA data set has about half as many cladistically inform ative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least d ecisive of the three, exhibits the lowest levels of character incongru ence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homop lasy and the fact that it is performing especially poorly at nonsynony mous sites.