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PHYLOGENIES OF PLANT FAMILIES: A DEMONSTRATION OF PHYLOGENETIC RANDOMNESS IN DNA SEQUENCE DATA DERIVED FROM PROTEINS

Considerable effort is being expended in the collection of molecular sequence data for phylogenetic analysis with the hope of providing new sources of information on the relationships between organisms, both plant and animal, at a variety of different taxonomic levels (e.g., Baroin et al., 1988; Field et al., 1988; Hasegawa et al., 1985; Hillis and Davis, 1986, 1987; Guoy and Li, 1989; Larson and Wilson, 1989; Martin et al., 1985; Zimmer et al., 1989). Recently there has been general concern over whether sets of molecular data can provide sufficient evidence, in a statistical sense, to support particular groupings of taxa over other groupings in an estimated tree (Felsenstein, 1985a. 1985b. 1988). Similar concerns have been expressed about the significance ofentire trees over other possible trees (Templeton, 1983). Among the methods available for phylogenetic inference from molecular data, the most commonly used is Wagner parsimony. (Felsenstein [1988] fully summarizes the available methods for sequence data and questions whether the method of parsimony is the best available.) Under the principle of parsimony, the preferred tree is the one that requires the fewest characterstate changes to explain the distribution of character states among the taxa. The question that arises is whether such a minimum-length tree is "significantly" shorter than other possible trees. In some cases (with some computer programs), it has become possible to examine tree topologies that are very similar in length to the minimum-length tree. For example, the program PAUP (Swofford, 1985) permits the examination ofall trees that are within a specified length ofthe minimumlength tree when the number of taxa is less than about 15. Trees that differ from the minimum-length tree by less than a few additional steps are generally considered to be not significantly different from the minimumlength tree. When trees are found that do not differ substantially in length from the minimum-length tree or when two or more tree topologies have minimumlength, a consensus tree (Rohlf, 1982) between trees may be calculated. Such trees are often presented as representations of the information on shared relationships provided by the data from all trees used to calculate the consensus. Bremer (1988) presented a phylogenetic analysis of nine plant families for a set of DNA sequence that had been derived from a series of protein sequences using the methods of Penny et al. (1980) and Fitch and Farris