On MaHo

摘要

In their paper describing what is claimed to be a new method for evaluating multiple equally parsimonious trees, Cao et al. (2008) suggest that parsimony, on its own, does not suffice as an optimality criterion. Instead they ‘‘propose a method to identify the tree or trees that has (have) the highest number(s) of secondary homologies amongMPTs’’. Their Perl script MaHo parses text output from PAUP* (Swofford, 2002) for those tree(s) among a suite of optimal trees that have the highest ‘‘quantity of homologous characters’’, that is the number of characters with an RI of 1.00, or their interpretation of de Pinnas (1991) ‘‘secondary homologies’’. Most seasoned readers will immediately recognize this strategy as the largest clique of perfectly congruent (compatible) characters. Unlike the a priori use only of cliques of compatible characters, in favor of which and against which, there is a considerable body of literature (e.g., Estabrook et al., 1977; Farris and Kluge, 1979; Meacham, 1980; Farris, 1986), none cited by Cao et al. (2008), their method differs in that the suite of equally parsimonious trees is arrived at with all available data, and the resulting trees are then filtered on the largest clique.