Cladistics 17, 79±103 (2001) doi:10.1006/clad.2000.0161, available online at http://www.idealibrary.com on CORE Metadata, citation and similar papers at core.ac.uk Provided by LiriasTaxic Revisions James S. Farris,* Arnold G. Kluge,² and Jan E. De Laet*,³ *MolekylaÈrsystematiska laboratoriet, Naturhistoriska riksmuseet, Box 50007 SE-104 05 Stockholm, Sweden; ²Division of Reptiles and Amphibians, Museum of Zoology, The University of Michigan, Ann Arbor, Michigan 48109-1079; and ³Laboratorium voor Systematiek, Instituut voor Plantkunde en Microbiologie, K.U. Leuven, Kard. Mercierlaan 92, B-3001 Leuven, Belgium Accepted December 19, 2000 Parsimony analysis provides a straightforward way of employed for classification, but instead means that sys- assessing homology on a tree: a state shared by two tematic methods must be logically capable of phyloge- terminals comprises homologous similarity if optimiza- netic interpretation. Neither m3ta nor rm3ta satisfies tion attributes that state to all the stem species lying that requirement because of their contradictory assess- between those terminals. Three-taxon statements (3ts), ments of homology. ᭧ 2001 The Willi Hennig Society although seemingly ªexactº in that each either fits a tree or does not, do not provide a satisfactory assessment of homology, because that assessment can be internally contradictory and because 3ts systematically exclude homologous resemblance in reversed states. Modified 3ts OVERVIEW analysis (m3ta), a method in which both plesiomorphic and apomorphic states of ªpaired homologueº (PH) characters (those other than presence/absence data) are Carine and Scotland (1999) followed Patterson's regarded as ªinformativeº (able to distinguish groups), (1982) taxic approach to homology, and on that basis can (obviously) group by symplesiomorphy and so form they proposed a new method, modi®ed three-taxon paraphyletic groups unless data are clocklike enough. statement analysis (m3ta). The modi®cation did not Patterson's pattern analysis (ppa) has the same short- affect the treatment of presence/absence data, called coming, to which it adds the drawback that only charac- ªcomplement relationº (CR), but only that of other ters fitting the tree perfectly are used, a restriction that characters, called ªpaired homologueº (PH).1 Whereas can easily lead to discarding most of the structure in Nelson and Platnick's (1991) original 3ta (N/P 3ta) the data. Revised m3ta (rm3ta), a method in which treated only putatively apomorphic similarities as plesiomorphic states are not taken as informative, can grounds for grouping, m3ta treated both apomorphic also form paraphyletic groups, because it cannot apply reversals as apomorphies. The idea that knowledge of 1ªPairedº because it originally referred to two-state characters. phylogeny has been derived from classifications does Scotland (2000a) now calls multistate characters ªshared homo- not imply that nonevolutionary methods should be logues,º apparently in order to rhyme. 0748-3007/01 $35.00 79 Copyright ᭧ 2001 by The Willi Hennig Society All rights of reproduction in any form reserved 80 Farris, Kluge, and De Laet and plesiomorphic states of PH characters as informa- calling attention to relevant aspects of Carine and Scot- tive,2 that is, able to support groups. But Kluge and land's (1999) earlier treatment. Farris (1999) pointed out that this treatment of PH characters makes m3taÐlike phenetic clusteringÐ sensitive to autapomorphy, so that unless data are clocklike enough, m3ta can group by symplesiomor- ROOTS phy and so form paraphyletic groups. Scotland and Carine (2000) now object to that obser- vation. At ®rst they claim to refute itÐby arguing The crucial premise of Carine and Scotland's (1999, that autapomorphy does not affect their method for p. 121) position was what may be called their taxic analyzing CR characters! Later they stress that m3ta assumption. Note that the bracketed insertion ª[to the gets the right tree for a real PH (nucleotide) matrix for study of homology]º is theirs; Patterson's original com- apes. But then those data happen to be clocklike, and ment had ª(the one I am advocating)º in that place other real cases show the autapomorphy effect quite Patterson (1982: 34) distinguished two approaches to the study dramatically. Scotland and Carine seem to realize this, of homology which he called taxic and transformational homol- for while they never acknowledge such cases, they do ogy, terms derived from the taxic and transformational ap- ®nally try to address the problem, by discarding the proaches to evolutionary theory described by Eldredge (1979). taxic idea that plesiomorphic PH states must be treated According to Patterson (1982: 34), ªThe taxic approach [to the as informative. When they change their clustering study of homology] is concerned with monophyly of groups. The transformational approach is concerned with change, method accordingly, the revised version (rm3ta) is like which need not imply grouping.º Thus, for four taxa (ABCD) the old N/P 3ta. in which taxa A and B share character state X and taxa C Yet despite abandoning their old taxic principles, and D share character state XЈ, two groups (AB) and (CD) are Scotland and Carine (2000) still wish to connect their hypothesized from a taxic perspective (Fig. 1). views to Patterson's (1982) taxic homology, and for The taxic tree would then be ((A B) (C D)), as they that purpose they maintain that their method can test showed in their Fig. 1D. This effectively assumed that homology, whereas parsimony cannot. But their criti- neither state could have arisen from the other. If state cism of parsimony consists only of not mentioning X' were a modi®ed (or substituted) form of X, for exam- how parsimony is actually used in evaluating homol- ple, the tree could obviously be (A B (C D)) instead. ogy, while their own approach gives internally contra- Readers accustomed to Eldredge's (1979) usage of dictory assessments and systematically excludes ho- ªtaxicº should keep in mind that Patterson (1982) mologous similarities in reversed states. The latter changed the meaning of the term substantially (cf. dif®culty arises because their revised clustering Farris, 2000a). Eldredge (1979, p. 17) used taxic for method suffers from the reappearance of a weakness evolutionary theories that include transformational found in N/P 3ta, that reversals are not applied as theories: synapomorphies. Their attempt to relate their ap- proach to Patterson's views, moreover, rests only on A complete evolutionary theory requires the presence of two ignoring the differences between their method and Pat- distinct componentsÐ(a) a theory of mechanics to explain ge- terson's own. netic, morphologic, and behavioral change, and (b) a theory pertaining to the origin of species. Many of the classic areas These issues are straightforward in themselves, but of investigation, especially in paleontology and genetics, em- exposing them turns out to be another matter. While phasize the aspect of evolutionary mechanics (the ªtransforma- Scotland and Carine (2000) have revised both their tionalº approach) to the point of near exclusion of consideration method and their taxic principles they go to some of the origin of taxa (the ªtaxicº approach). Integration of lengths to avoid stating that fact directly. Because of the two approaches is best effected by considering the issues of the transformational approach as a subset of those of the that complication, we will begin our discussion by taxic approach. 2This is not the usual meaning of ªinformativeº; we have employed In his taxic approach to homology, in contrast, Pat- it here only to facilitate discussion of Scotland and Carine's com- terson (1982, p. 67) admitted no connection with evolu- ments. tionary changeÐor with evolution: Copyright ᭧ 2001 by The Willi Hennig Society All rights of reproduction in any form reserved Taxic Revisions 81 The role of homology in phylogenetic reconstruction is limited to the production of cladograms, or classi®cations. These activi- ties need have no evolutionary connotations. If phylogeny has to be about evolution, homology has nothing to contribute to it. Unfortunately for the curious, Patterson never ex- plained what phylogeny would be about, if not evolu- tion. Whatever that might be, however, the taxic as- sumption ®ts a nonevolutionary view very well, for as Kluge and Farris (1999, p. 207) pointed out: The taxic choice of ((A B) (C D)) thus rests on a ruling out a priori the possibility that either state has replaced (changed into, been substituted for) the other. If applied to nucleotide data, then, the taxic assumption would have the paradoxical implica- tion that substitution could not have occurred at all! Carine and Scotland (1999, p. 122f) applied the taxic assumption only to PH characters. For CR characters they retained N/P 3ta,3 explaining Scotland (1999b) [sic] has shown that for three-taxon statement analysis the two relations [i.e., complement relation and paired homologue] need to be dealt with differently. This is because in t.t.s. analysis it is only the ones (1's) in a matrix that can provide evidence of group membership. For complement rela- tion characters this is unproblematic because presence coded one (1) is the only part of the relation which provides evidence of grouping. However, for paired homologue data both homo- logues [states] constitute hypotheses of groups. By designating one of the homologues zero (0), that homologue is rendered uninformative because an all zero ªfunctional outgroupº is an essential part of implementing t.t.s. To overcome this problem Scotland (1999b) [sic] proposed a modi®cation of t.t.s. analysis (hereinafter called modi®ed t.t.s.) which treats all homologues [states] as being potentially informative. 3Except that, unlike Nelson and Platnick (1991), Carine and Scot- land (1999) used Nelson and Ladiges' (1992) fractional weighting, discussed further below, but this has no connection with their views on outgroups. FIG. 1. Matrix from Kluge (1994, his Table 2), presented ®rst as 0/1 characters (the original version) and then as nucleotide codes for selected sites.