A Phylogenetic Analysis of the Caminalcules. II. Estimating the True Cladogram

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Abstract
The ability of numerical methods to estimate the true cladogram is examined, using the Caminalcules as an example. This group of ''''organisms'''' was generated artificially according to principles believed to resemble those operating in real organisms. Estimated cladograms obtained by numerical methods are only moderately good estimates of the true cladogeny. Of the various models applied in numerical cladistics, the closeness of approximation to the true cladogeny is in the following order: best-Wagner parsimony and Camin-Sokal parsimony; second-polymorphism parsimony; third-character compatibility and Fitch''s nonsequential method; fourth-UPGMA [unpaired groups using arithmetic averages] phenograms; worst-Dollo parsimony. Since the data matrix contains NC (no comparison) states, numerical cladistic algorithms that take account of these states give better results than those that do not. For distance Wagner algorithms, there is little difference in the outcome between midpoint rooting and rooting with a zero vector or with the true ancestor. By separate permutations of the order of the OTU [operational taxonomic units] that are input to the numerical algorithm, trees of varying length were obtained from which the shortest could be chosen. Shortest trees, computed globally over all OTU or separately for each Caminalcule genus, are not necessarily those that best estimate the true cladogeny. Numerical cladistic estimates separately computed for genera are poorer than those based on the entire taxon. The effects of homoplasy and divergence on the results of phenetic and cladistic algorithms are investigated in general and employed to explain in detail the differences among the true cladogram, the phenogram and the estimated cladogram. The agreements observed are all in cases where given taxa divergence greatly from ancestral stems. Discrepancies are due to parallelisms in the cladogeny affecting phenetic similarities and divergence of cladistically close relatives increasing the relative phenetic similiarity of cladistically more distant relatives. These 2 cases are about equally frequent.