Synapomorphies

The adult pentaradial symmetry shown by sea urchin seems to contradict the general head-associated Otx expression rule. It is generally held that the radial symmetry in echinoderms is a shared derived character (synapomorphy) because of their embryonic and larval bilateral symmetry (Lowe and Wray, 1997). Thus the highly divergent and non-head specific Otx expression in sea urchin can be justified as a consequence of the highly modified body plan of this phylum. 

What happens in parsimony analysis, in principle, is that all conjectures of synapomorphies (homologies) represent observable states of affairs or data points, which are then... 

Fiypotheses that characters are apomorphies are used to support hypotheses of mono-phyly putative synapomorphies support sister-group relationships. 

FIGURE 5.4 In Hennigian terminology, homology and synapomorphy are not the same. In this example, characters I to 3 are homologies of the species A and B. However, only character 3 is a synapomorphy of the monophylum (A, B). 

Characters are used that may contain more noise than phylogenetic signal (characters of low probability of homology) and are not weighted to express their value. For example, reduction of epidermal microvilli, reductions of motile cilia and reductions of endodermal cilia are considered to be synapomorphies of the Ecdysozoa (Zrzavy et al., 1998). Simple reductions of this type are not very specific characters and occur frequently in unrelated organisms. 

The discussion between cladists and their critics is not new. Panchen reviewed the issues in 1982 (Panchen, 1982). He attacked the restriction to just parsimony, by the optimization of synapomorphies of cladograms, and pointed out that in the real world parallel evolution is common. What he did not offer was a theory that allows the classification of characters into those that are predisposed to parallelism or chance similarity and those that are not, and therefore he thought that cladists may have to admit the persistent intuitive element in classification. Today, intuition (in the sense of unfounded ad hoc assumptions) can be avoided in phylogenetic cladistics using objective criteria of character weighting. 

Lyons-Weiler, J., Hoelzer, G.A., and Tausch, R.J., Relative apparent synapomorphy analysis (RASA). I. The statistical measurement of phylogenetic signal, Mol. Biol. Evol., 13,749-757, 1996. 

Paleontology of the past is revived in molecular systematics of the present, in its search for ancestors and centers of origin. The revival ignores, or retreats from, the cladistic reform of paleontology of the 1970s, with historical roots in the work of Louis Dollo (1857-1931) and fossil Inngfishes. The subsequent development of cladistics has been arrested, too, by compnter implementations of character optimization and the ideology of total evidence, which reflects a phenetic rather than cladistic objective the overall similarity of synapomorphy. 

Among English speakers, neither of the two borrowed terms ever caught on (cf.. Hill and Crane, 1982 297 for an explanation of the term [heterobathmy. Hill, 1986 124] and for comment on related ideas of Arber and Parkin [1907 35] and of Davis and Heywood [1963 34] Schoch, 1986 25, 335 for heterobathmy of characters [a concept fundamental to cladistic analysis ] Schuh, 2000 69 for heterobathmy of synapomorphy ). 

The mix — the heterobathmy, unproblematic in itself — requires sorting and arranging the parts in proper order up and down the steps, according to their origins. Afterwards, the parts, as evidence of relationship, may then be properly understood as the marks of synapomorphy, in contrast to symplesiomorphy and convergence each synapomorphy at the proper taxonomic level, each upon the proper step of, and thereby associated with, a more or less inclusive taxon. One lesson often overlooked is that taxon and synapomorphy are different names for the same thing the same step of the same stair — the same relationship. 

In other words, the Is represent not just the feature, but its significance, the relationship. Similarly, character 2 shows B and D related. Character 3 shows C and D related. The characters conflict, but agree in excluding taxon A from whatever group is evidenced. Programs see matrices of this type as uninformative. The programs find no synapomorphy for the group BCD. 

Expanded matrices (Figure 6.5) give the same result. So do many other matrices in this series (Nelson, 1996). For Matrix 3 (Figure 6.6), the programs find no synapomorphy for the group BCDE. 

Among these characters, some are constant, others vary each character, taken separately, is found in one or many other families but their combination is found only in the family of the buttercups for that family, it is this combination that constitutes the synapomorphy [the essential and invariable character]. 

With total evidence, need no such asymptote be expected If it were we might witness the reemergence, even the vindication, of phenetics as the overall similarity of synapomorphy. 

This marries perfectly with Mayr s (1969) definition of relationship — genes in common. It is also the justification for the grouping organisms on the basis of parallelisms in cladistic analysis as advocated by Saether (1979 underlying synapomorphy ) or Mayr (1974 concealed genotype ). 

Saether, O.A., Underlying synapomorphies and anagenetic analysis, Zool. Scr., 8, 305-312,1979. 

Current usage of the term homoplasy appears to suggest, like Osborn, that homoplasy does involve some homology ( Homoplasy is derived similarity that is not synapomorphy [homology], [Wake, 1996 xvii see also Mayr and Ashlock, 1991 418]). That seems to suggest that homoplasy is equivalent to homologue. A more accurate viewpoint, underlined by Osborn s semantic puzzle, is that homoplasy is simply a term used today to explain away character conflict (Nelson and Platnick, 1981 342), a problem that has yet to find any real solution (cf. Nelson, 1996 Nelson et al., 2003) and looks increasingly likely to become redundant. 

The issue was that although synapomorphies (shared derived characters) might be successfully identified, proposed or hypothesised, not all would ultimately indicate monophyletic groups a certain number will mislead. Once identified, true synapomorphy might readily be called homology ... 

I emphasise the concept of synapomorphy instead of homology, the former being viewed as an estimator, the latter the parameter. I do so because synapomorphy... 

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