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    Carpenter 1994 Successive Weighting

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    Lisandro Negrete

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    FORUM Cladistics (1994) 10:215-220 SUCCESSIVE WEIGHTING, RELIABILITY AND EVIDENCE James M. Carpenter! "Department of Entomology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 110024, U.S.A. Received for publication 18 September 1993; accepted 12 January 1995 Barrett et al. (1991) argue against consensus techniques in systematics, charac- terizing their argument as “far more compelling than previous criticisms” (p. 491). Readers may well disagree that their example is any more compelling than the repeated observation that most-parsimonious cladograms explain evidence better than consensus trees (Mickevich and Farris, 1981; Miyamoto, 1985; Carpenter, 1988; Kluge, 1989), of course—or whether it is compelling at all (Nelson, 1993). Be that as it may, I wish to correct a misconception Barrett et al. have about my 1988 paper. Barrett et al. (1991: 491) conclude: “If the consensus tree disagrees with the best tree inferred from the pooled data, the consensus tree cannot be considered to be the best inference. In this respect, we agree with Kluge (1989) and not with Carpenter (1988), who suggested that consensus is appropriate for different data sets but not for trees from a single data set”. Nothing in my 1988 paper remotely resembles such a suggestion. The only mention of consensus trees in that paper is the initial paragraph, where I pointed out that consensus trees were originally developed to produce compromise classifications for cladograms from different data sets, that consensus might be applied to the problem of multiple cladograms for a given data set, but that to do so would be a misapplication. Barrett et al. (1991: 486) even cite my 1988 paper for the original purpose of consensus trees, but do not then conclude that they themselves are advocating that usage! There have been other misconceptions about Carpenter (1988), misconceptions other than superficial scholarship, and I wish to treat those now. In the 1988 paper, T pointed out that successive weighting (Farris, 1969) could be used to choose among equally parsimonious cladograms. This recommendation has occasioned criticism. The criticism comes in two forms. First, successive weighting itself has been criticized, by Swofford and Olsen (1990), who characterize it as circular. As has been pointed out elsewhere (Carpenter et al., 1993), that “criticism” is a simple confusion of circularity with recursion. Initial and final cladograms can indeed differ. This was clear in Farris (1969: table 2), who showed decreasing differences between the “correct” and estimated trees with successive weighting, under a variety of simulations. Change in both topology and length (increased for the “unweighted” data) with successive weighting have been demonstrated by Platnick et al. (1991) and Brothers and Carpenter (1993). The only “argument” offered by Swofford and Olsen (1990) is citation of Neff (1986), who mentioned successive weighting in passing, stating only that “a stronger evaluation of characters in such situations would require information relevant to 0748:3007/94/020215+06808.00/0 © 1994 The Willi Hennig Society 216 J.-M. CARPENTER testing individual characters” (p. 112) because “Only a priori methods clearly have the capability of affecting the estimate of phylogeny” (p. 114). This claim is plainly false. The application of successive weighting to choose among cladograms has also been criticized. Swofford and Olsen (1990: 500) and Maddison and Maddison (1992: 67) assume that choice among equally parsimonious cladograms (for “unweighted” data) must be arbitrary. Does this mean, say, that if the watches of these authors indicated differing times they would conclude that all were correct? If there is one true phylogeny, but character data admit of multiple equally parsi- monious solutions, that is usually taken to indicate that the data are ambiguous, not as support for spontaneous generation. If there is a defensible basis for choice among cladograms, then choice is scarcely arbitrary. It is significant that none of these critics has dealt with the rationale for successive weighting. I staied (Carpen- ter, 1988: 299) that “This character weighting method is developed directly from the concept of ‘cladistic reliability’ (Farris, 1969), and thus is related to evidential support” and characterized the technique as “an extension of parsimony”. Succes- sive weighting allows the characters of a given data set to judge themselves in terms of their reliability; that is, best fit to the solution supported by all the characters. Homoplastic characters, being less reliable, are downweighted, hence successive weighting employs evidence that would otherwise be discarded, namely that the characters themselves indicate that some are less reliable than others (Farris et al., in prep.). The basis of this choice among cladograms is thus cladistic parsimony; that is, character evidence (Farris, 1983), Swofford and Olsen (1990) and Maddison and Maddison (1992) do not miss only this point, they miss the point of cladistic parsi- mony as well. These authors in fact advocate @ prion’ assumptions as the basis of choice among methods of phylogenetic inference. Cladistic parsimony is just one of many “parsimony variants” subsumed under their “generalized parsimony” (e. g- by Swofford and Maddison, 1992: 193). By this latter, they mean a framework based on Sankoff-style cost matrices. Such a matrix can be used to assign different costs to steps between character states, and the costs may be asymmetrical; that is, trans- formations between the same states in different directions may have different costs. Cladistic parsimony is then a “Variant” in which cost matrices are symmetrical, The chief effect of asymmetrical cost matrices in character analysis is to permit non- metric transformation series, hence logically inconsistent homology statements (Wheeler, 1998). Consider an additive multistate character, with states 012, where the cost of change of state 0 to 1 and 1 to 2 are each specified as 1, but 2 to 0 is also 1. Change from 0 to 2 is then 2 steps, but “loss” of state 2 is 1 step. The implication is that the primitive and derived state 0’s are the same, but even if indistinguishable, they are not homologous. The evolutionary distance from 2 “back” to 0 is really 8 steps, which is not £2, the reverse distance. This cost matrix entails distances that are not interpretable as evolutionary change (Wheeler, 1993)!, ' The commentary on Wheeler's paper by Fitch (1993) completely misses the point on non-homology of character states. Treating non-homologous states as the “same” considers states as classes. This is an obvious error, but applies for example to a prion differential transition transversion costs. The ratios of transitions /tcansversions vary with data sct, but the criticism of states a8 classes also applies to empirical attempts to estimate a priori step matrices, such as that of Wheeler (1990). FORUM: WEIGHTING, RELIABILITY, EVIDENCE 27 Why bury cladistic parsimony under such a framework? Swofford and Olsen (1990), Maddison and Maddison (1992) and Swofford and Maddison (1992) are proponents of the notion that just about anything is “parsimony”, a notion that can be traced to Felsenstein, whom they cite liberally. Cladistic parsimony is seen as dependent on particular assumptions; that is, a model, Choice among the plethora of “variants” is then choice among models, and they can recommend no grounds for that choice. Maddison and Maddison (1992; 72), for example, state of cladistic parsimony: “no argument for or against it is overly compelling”. Maddison et al. (1984: 99) even cite Farris (1983) to the effect that “even when parsimony, sup- ports a particular ancestral state assessment, that support may not be convincing”; Farris’ (1983) position was if anything the opposite! Maddison et al. (1984) conflate under their term “global parsimony” cladistic parsimony, character state optimization and a priori assumptions that relax parsimony (Nixon and Carpenter, 1993). Swofford and Olsen (1990) and Maddison and Maddison (1992) fail to grasp the logical asymmetry between cladistic parsimony and other methods, even though they cite Farris’ (1983) demonstration that cladistic parsimony is minimization of ad hoc hypotheses of homoplasy in phylogenetic inference, They apparently do not understand the basis for this conclusion. It follows for a general scientific reason. Cladistic parsimony treats characters as evidence of phylogenetic relationship. This is not true of the other “parsimony variants”, which entail that a priori assumptions be treated as evidence in conclusions as well. There are compelling reasons not to do that. Such assumptions comprise claims about evolutionary process, which should instead be tested by cladistic parsimony. If, say, irreversibility is thought likely, phylogenetic inference should not be undertaken with a method that presumes it. By contrast, inference with cladistic parsimony could provide empirical support for irreversibility, for if the result shows irreversibility, that is not an artifact of method, it is what evidence supports. Maddison and Maddison (1992: 38) come to a different conclusion about that last observation. They state: “if our theories of genetic process are to explain successfully biological evolution and diversity, they must yield predictions con- sistent with our observed phylogenetic patterns. We might note, however, that Lynch (1989) legitimately makes the converse statement”. That is, phylogenetic patterns must be consistent with some particular assumption. One or another such assumption might conceivably even have some empirical support, but it does not then follow that phylogenetic evidence must be “consistent” with that assumption. The supposed support comprises just one line of evidence, As was pointed out by Hennig (1966: 22): “Making the phylogenetic system the general reference system for special systematics has the inestimable advantage that the relations to all other conceivable biological systems can be most easily represented through it. This is because the historical development of organisms must necessarily be reflected in some way in all relationships between organisms. Consequently, direct relations extend from the phylogenetic system to all other possible systems, whereas there are often no such direct relations between these other systems”. Cladistic parsi- mony, by treating characters as evidence, is potentially able to marshal all conceiv- able sources of evidence, and relate them to one another. That is not true of any other approach to phylogenetic inference, and indeed it is difficult to conceive 218 JM. CARPENTER how progress in phylogenetic reconstruction would ever proceed under approaches that do not give primacy to characters as evidence. Advocates of model

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