Data from: Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

We examined three parallel data sets with respect to qualities relevant to
phylogenetic analysis of 20 exemplar monocotyledons and related
dicotyledons. The three data sets represent restriction site variation in
the inverted repeat region of the chloroplast genome, and nucleotide
sequence variation in the chloroplast-encoded gene rbcL and in the
mitochondrion-encoded gene atpA, the latter of which encodes the *-subunit
of mitochondrial ATP synthase. The plant mitochondrial genome has been
little-used in plant systematics, in part because nucleotide sequence
evolution in enzyme-encoding genes of this genome evolve relatively
slowly. The three data sets were examined in separate and combined
analyses, with a focus on patterns of congruence, homoplasy, and data
decisiveness. Data decisiveness (described by P. Goloboff) is a measure of
robustness of support for most-parsimonious trees by a data set in terms
of the degree to which those trees are shorter than the average length of
all possible trees. Because indecisive data sets require relatively fewer
additional steps than decisive ones to be optimized on nonparsimonious
trees, they will have a lesser tendency to be incongruent with other data
sets. One consequence of this relationship between decisiveness and
character incongruence is that if incongruence is used as a criterion of
noncombinability, decisive data sets, which provide robust support for
relationships, are more likely to be assessed as noncombinable with other
data sets than are indecisive data sets, which provide weak support for
relationships. For the sampling of taxa in this study, the atpA data set
has about half as many cladistically informative nucleotides as the rbcL
data set per site examined, and is less homoplastic and more decisive. The
rbcL data set, which is the least decisive of the three, exhibits the
lowest levels of character incongruence. 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 homoplasy and the fact that it is
performing especially poorly at nonsynonymous sites.