Systematics and Science: A Comment

Science is communicated through statements about things, sets of things, and processes. The scientific method includes testing statements or hypotheses. An examination of the procedures used in science and the assumptions on which the procedures are based is necessary in order to verify the veracity of the statement made. Commenting on errors is necessary to prevent future workers in the field from adopting a technique or interpretation that lacks support (Blackwelder, 1967). Inferring evolutionary relationships of organisms are categorized into three school of thought: evolutionary taxonomy (e.g., Simpson, 1953,1961; Mayr, 1963,1969), numerical taxonomy (e.g., Sneath and Sokal, 1973) and phylogenetic systematics (e.g., Hennig, 1966; Farris, 1979, 1982, 1983; Wiley, 1981). Only one of these, phylogenetic systematics, provides a means for examining results by reassessing data under adherence to the principles of homology and parsimony (Hennig, 1966). Phylogenetic systematics requires that characters comprising the data sets be understood by the investigator. Ideally, differences in the ontogeny of characters among taxa are known (de Queiroz, 1985) but generally this is not possible and may be unknowable (Kluge, 1985). Characters for which ontogenetic information is not available can be placed within the data sets. This enables the investigator to observe the distribution of the character states in question within the topology of the resultant cladogram and can lead to additional hypotheses concerning the evolution of the characters. Two methods are used to produce cladograms. The hand-generated method is a useful technique for small, clear-cut data sets in which homoplasies are few or absent. As the size of the data set or the possible number of homoplasies increases or both, calculating all possible hypotheses (i.e., trees) and determining which hypothesis best explains the data becomes increasingly difficult (Felsenstein, 1978; Nelson and Platnick, 1981). The second method utilizes high speed computers (Felsenstein, 1982). This requires some procedural step-by-step direction, an algorithm. Although a particular series of steps within the algorithm may reflect a particular philosophy (e.g., in PAUP using the optimizing options ACCTRAN vs. DELTRAN), the computer follows the rules of procedure contained in the algorithm and is not subject to a priori modification at any step during the analysis. Only the investigator can make mistakes in coding or by not including all the data due to some a priori assumptions (Hecht and Edwards, 1977). The workings of phylogenetic systematics determines the results, not the computer (Wiley, 1981; Churchill et al., 1984, 1985). I re-analyzed three recently published data sets that illustrate problems that can result from misapplied algorithms and character transformations. The examples are taken from the herpetological literature, but similar examples exist in other groups (see discussions in Smith and Hood, 1984; Cracraft, 1987). The first example deals with problems encountered when data sets exceed the ability of the hand-generated method of analysis. Figure 1A is a cladogram taken from a recently published paper on the African/Malagasy frogs in the Old World family Hyperoliidae (Drewes, 1984). In the "Materials and Methods" section Drewes stated that he followed the principles of Hennig (1966). The Hennigian principles