Ghost taxa, ancestors, assumptions, and expectations: a reply to Norell

Estimates of phylogenetic relationships currently are very important to many evolutionary research programs and they likely will become even more important in the future. It therefore is vital to discuss any potential problems in methods used in these research programs. Two issues arise regarding Norell's comment. The first concerns the assumptions, explicit and implicit, of a method of deciphering evolutionary patterns within phylogenetic estimates. The second concerns methods of recognizing errors in parsimony estimates and understanding the implications of those errors. For methodological reasons, some aspects of both concerns are intertwined. This reply will focus on the difference between null assumptions and probabilistic expectations and how they pertain to phylogenetic research programs, including (but not limited to) ghost taxon studies and stratigraphic tests of parsimony estimates. Norell correctly points out a key error in Wagner (1995a), as that paper does imply that ghost taxon studies (see, e.g., Norell 1992, 1993) necessarily assume that speciation proceeded via bifurcation and that no ancestors were sampled. The section that Norell cites actually is not in error, as it refers to a specific example outlined in the figures on page 155. The real error is on page 156, which states that "The method presented here makes fewer assumptions than do ghost taxon studies. " Instead, it should state that the method presented makes fewer assumptions than do ghost taxon studies conducted as in the example on page 155. Norell (1992, 1993; see also Fisher 1991) explicitly describes how paraphyletic taxa affect ghost taxon studies, and both Smith (1988) and Wagner (1995b) present phylogenetic diversity studies that allowed for the presence of ancestors and for nonbifurcating models of speciation. However, the extreme example presented in Wagner (1995a) is not a strawman, as other ghost taxon studies (see comments in Smith 1994: pp. 144-147) proceed on the assumptions listed in Wagner (1995a), as has at least one comparative biological study using fossil species (Sanderson and Bharathan 1993). These studies are typical of the cladistic research, not because of literal readings of cladograms (as suggested by Norell), but rather because of the many statements that sister taxa stem from common branching events (see, e.g., Hennig 1966; Doyle and Donoghue 1993). The possibility of ancestral morphologies surviving speciation events and later producing additional daughter species (and thus producing two monophyletic groups with different origination times) is dismissed as improbable and rare in many important papers on phylogenetic systematic and comparative biological methods (see, e.g., Maddison 1989; Slowinski and Guyer 1989; Purvis and Garland 1993; Mooers et al. 1995). Thus, bifurcation is a general assumption of an entire research program. Although Norell is correct that ghost taxon studies need not assume models of speciation or anything about sampling of ancestors, I strongly disagree with Norell's assertion that the accuracy of the tree is irrelevant to ghost taxon interpolations. Norell cites pattern cladistics (Frost and Kluge 1994; see also Nelson 1979; Nelson and Platnick 1984) to contend that accuracy is "not particularly relevant to modern schools of phylogenetic inference. " However, in an effort to remove assumptions, pattern cladistics does not assume that a phylogeny necessarily links the species in question. As ghost taxa depend on phylogenetic links, pattern cladist logic thus cannot infer ghost lineages. This dependence on phylogenetic estimates also means that ghost taxon interpolations are