Reliable phylogenetic resolution of morphological data can be better than that of molecular data

The use of nonparametric statistics and null hypotheses (Kendall & al., 1987) are powerful tools in science, and are essential in evaluating the question "What is the chance that these data are due to chance alone? " They have been widely used in systematics only recently with the rise of techniques in statistical phylogenetics that can deal with obscure and conflicting data (Avise, 1994: 314; Philippe & al., 1996; Sites & al., 1996; Seberg & al., 1997). A major problem of cladistic analysis in the past 30 years has been lack of a means to measure the degree of support for contrary arrangements of branches. By this I do not mean homoplasy, which is well recognized as an expected result of macro-evolution (Mickevich, 1982; Donoghue, 1990), but support for the immediate two alternative branch arrangements for any interode. These two arrangements are obtained through simply switching one of the branches terminating the interode (of the optimal branch) with the free (not rooted) lineage at its base, then doing the same with the other terminal lineage and the basal free lineage, and is called "nearest neighbor interchange". Three alternative arrangements-one optimal and two suboptimal-are obtained with any four lineages or taxa in unrooted trees, and the arrangement with the best supported interode represents a parsimonious choice between these three arrangements. If the optimal (shortest tree) branch arrangement is noted as ((AB)C), the support in numbers of steps for the two alternatives ((AC)B) and ((BC)A) may be determined by recalculation with constraint trees. Comparing the relative support (in steps of advanced character states) for ((AB)C, ((AC)B, and ((BC)A allows evaluation of how much greater is the support in numbers of steps for the optimal branch arrangement over that for the two immediate alternatives, and is the basis for the Conditional Probability of Reconstruction measure (Zander, 200 la). For instance, a dataset for 20 characters of 22 species of the moss genus Didymodon (Pottiaceae) with one species, Barbula unguiculata, as outgroup, was presented and cladistically analyzed by Zander (1998), and evaluated with constraint trees (Zander, 2001 a) to obtain support for the two alternative arrangements for each internode of the optimum tree. With the null hypothesis that the number of steps (unweighted) of the sum of the internodes of the entire optimal tree are 1/3 of the sum of the steps supporting all three alternative branch arrangements at each internode, and all resolution is random, o e might expect that any significant variation is due to shared ncestry. This null hypothesis may be applied to one internode, any lineage, or the whole cladogram. In f ct, the number of steps of the entire optimal tree, 34 (not including those of the basal internode), is significantly greater than the sum of the steps supporting the pairs of alternative branches, 16. An exact binomial calculation (Lowry, 2002) indicated that the possibility that this ratio (34:16) or better would occur by chance alone (at probability 1/3) is less than one out of a thousand. This yields a confidence level of 99.9+% that considerable phylogenetic signal is present in the optimal tree (as alternative hypothesis). This same assurance-that the Didymodon cladogram is solidly based on shared ancestry-is also obtained with a parametric bootstrap (Huelsenbeck & Hillis, 1996) using randomized datasets. Fifty datasets were generated with a random dataset generator (Zander, 2001b), but otherwise identical to the original dataset (i.e., identical numbers of taxa, of columns, and of states in each column). Parsimony analysis with PAUP* (Swofford, 1998) found that all random datasets produced fully resolved trees (demonstrating that resolution alone gives no support of reliability) that were much longer than the length of the optimal tree. The trees averaged 126 steps in a binomial distribution of the 50 trees between extremes of 118 and 134 steps. The original dataset produced a tree only 63 steps in length. Thus, parametric bootstrapping using random data also demonstrates considerable phylogenetic signal for the tree as a whole.