Patrocladistic classification

For nearly a century from the time of Darwin’s Origin of Species (1859) to the first phenetic paper by Michener & Sokal (1957), the theory of biological classification remained reasonably stable. Classifications were based on combinations of characters selected for presumptive evolutionary import. These phylogenetic ( = phyletic or evolutionary) classifications took into consideration not only the branching pattern of phylogeny, but also divergence within lineages, all done without explicit methods (i.e., intuitively). Biological classification has now changed dramatically within the past 50 years, the most notable changes being efforts to classify through explicit methods. The phenetic revolution (1957–1975; e.g., Sokal & Sneath, 1963) stressed concepts of characters and states, importance of the basic data matrix coded numerically, use of specific algorithms to determine affinity, and use of quantitative data to construct a branching diagram (phenogram). The cladistic revolution (1965–1990; e.g., Hennig 1966) emphasized using characters and states of high phylogenetic content, determination of polarity ( = directionality) of these states, use of shared derived character states (synapomorphies) for determining relationships, and employment of new algorithms for building trees (cladograms). Throughout its history, phenetics has remained eclectic, i.e., there have been numerous opinions and studies on how many characters to use, to weight or not to weight, and use of different algorithms for assessing relationships as well as for constructing diagrams, not only in dendrogram form (phenogram) but also through coordinate plots (ordinations) in twoor three-dimensional space. No rigid rules for classification directly from these diagrams were ever adopted seriously. Cladistics, in contrast, has gone through considerable theoretical and methodological change during its period of growth from 1965–1990. In the 1970s and 1980s occurred healthy efforts to seek different methods for tree construction, e.g., parsimony and character compatibility (e.g., Farris, 1970; Estabrook & al., 1976), but these began to narrow during the late 1980s nearly exclusively on parsimony. Due to the explosion of DNA studies and need for fast algorithms to deal with the mountains of new data, however, earlier phenetic algorithms have been recycled and are now being used routinely for tree construction (e.g., neighbor-joining). The utility of networks is also being examined carefully (Huson & Bryant 2006). Furthermore, interest has returned to reexamine the utility of compatibility methods (e.g., Pisani 2004). Algorithms based on models of evolution, such as maximum likelihood and Bayesian analysis, are now also routine for phylogeny reconstruction, especially with molecular data (Felsenstein, 2004). Despite this new conceptual flexibility (or practicality) in cladistic analysis, the concepts of how to classify directly from a cladogram have not matured correspondingly. This has led to an acceptance by many workers of a series of rules, most important of which being that all groups must be holophyletic (i.e., those containing all descendents from a common ancestor; Ashlock, 1971; called Patrocladistic classification