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; o Cl < >- to chloroplast st ruct ure phragmoplast gametangia with s t e r i l e t i s s ue ( mul t i l aye r ed st ruct ure ( g l y c o l a t e oxidasesingle microbody attached to basal bodies
open spindle phycoplast
collapsing telophase spindle
starch within chloroplast
Fig. 2.16 Cladogram (rooted tree) of the major groups of green plants, taken from Bremer and Wanntorp50, showing the character-state transformations (synapomorphies).
totally novel classifications has led to the suggested substitution of convexity for monophyly as a criterion of taxon recognition.103,119,281 All monophyletic groups are convex, but paraphyletic groups (often defined by symplesiomor- phies) are also convex. Convex groups may be defined as those groups in a cladogram that are wholly connected by lines that are not needed to connect taxa in a different group in the same cladogram. In Fig. 2.6B, groups YQZ and XPQY are both convex, but, in Fig. 2.6C, XY is not. In addition, not all cladists maintain that sister-groups must always be recognized at the same rank, and the extent to which the nodes of the cladogram are given taxonomic ranks also varies. Some maintain that all should be given a rank, since all are considered natural taxa. However, this introduces a practical problem in that
there are often too few ranks to accommodate all the levels of nodes. This is a major problem in cladistics that has been addressed in several ways, none wholly satisfactorily. Nevertheless, all the solutions are quite different from the method of higher taxon delimitation (i.e. by drawing phenon lines) used in taxometrics.
Notwithstanding deviations that some cladists advocate and practise, the ideal is still to recognize as taxa monophyletic groups that are defined by synapomorphies. Such groups are monothetic, in strong contrast to taxa defined in taxometrics, which are polythetic. This is seen by many as a disadvantage, for it tends to accentuate single unique features at the expense of several nearly unique ones. Insistence upon all members of a taxon possessing any particular apomorphous character can cause problems. It is quite likely, for example, that if the angiosperms were examined sufficiently thoroughly no characters would be found to be both unique and universal. For such reasons this rule is now relaxed by some cladists.
The cladograms shown in Figs 2.16 and 2.17 are termed rooted trees or dendrograms, i.e. their evolutionary polarity is decided and hence an ancestral taxon (usually the hypothetical one included among the EUs) is pinpointed. However, as mentioned above, some workers now advocate not specifying the polarity of characters, so that the dendrogram obtained is not directional; this is known as an unrooted tree or network (Fig. 2.18). Networks can, if desired, become rooted by deciding a posteriori which end is the most primitive. Such decisions are based upon the overall nature of the taxa possessing their particular combinations of character-states (as in the method of Sporne described earlier), rather than upon a priori consideration of individual characters.
58 The development o f plant taxonomy
M J S T R A L / 4
L e ve l o f D ivergence
Fig. 2.17 Ciadogram (Wagner tree) of 30 species of Gossypium (Malvaceae), modified from Frywell142.
Phase 8. M odem phylogenetic methods (cladistics) 59
Aurea Alsinoides :
Fig. 2.18 Cladogram (unrooted tree or network) of seven taxa of Pentachaeta (Asterac- cae), modified from Nelson and Van Horn.303 Character-state transformations are represented by the numbers.
Cladistic methods basically view evolution as an ordered, divergent, step-wise transformation of characters from plesiomorphous to apomorphous states. It is known, however, that in evolution characters may sometimes evolve in a parallel or convergent fashion (Figs 2.6C and D), or may reverse direction so that an apomorphous character-state reverts to its plesiomor phous one (e.g. loss of stomata in some aquatic or chlorophyll-less angio- sperms). Although convergence may cause the greatest distortion in clado- grams, it is the most easily detected of these three phenomena. Character- states that arise by convergence are generally not logically correlated with other characters, and if a substantial number of characters is analysed those showing convergence are usually obvious. Parallelism and reversion, together termed homoplasy, are less easily recognized. The presence of homoplasy means that the correct cladogram might notbe the one that appears to be the most parsimonious, and therefore methods based on parsimony are less than perfect in these cases. Reversals are allowed for in some parsimony methods, and there are ways of detecting parallelisms,144,214,456 but the known frequency of homoplasy remains an important problem in parsimony methods.
Realization that one can rarely fo r certain deduce the phylogeny of a group solely from examination of extant organisms and known fossils has led some cladists to use cladistics {pattern or transformed cladistics) merely to unravel the pattern of variation rather than detect the true genealogy.321,326 They believe that the pattern is nearly always close to the genealogy, and sometimes coincident with it, but there is no certainty that it is the same. This philosophy of transformation is strongly resisted by more traditional cladists.
Apart from the above parsimony methods, there are methods that utilize the concept of character compatibility and are known as compatibility analysis or clique analysis.120,278 These have the advantage that they can detect and
therefore omit homoplasy. As with parsimony methods, they can be carried out manually or via a computer program, and the characters used can be evolutionarily polarized or not to produce a rooted tree or network respec tively. Groups of mutually compatible characters are termed cliques, and are considered to represent a group of characters in which homoplasy is absent. If we consider two characters (A and B) each with two states (A1 and A2, B1 and B2), four character-state combinations are possible—A1B1, A1B2, A2B1 and A2B2. Taking the direction of evolution to be A1 to A2 and B1 to B2, then if all four character-state combinations are found in nature there must have been at least one reversal (e.g. A2 to 'A l) or parallelism (e.g. A1 to A2 occurring twice). If so, A and B are incompatible, but if only two or three of the four combinations occur then A and B are compatible. Cliques are formed by comparing all pairs of characters and finding mutually compatible sets. From the data the largest clique is selected in order to produce the cladogram. The method is described in detail by Meacham,278 but in essence it involves using one character (A) to separate the EUs into two groups (those with A1 and A2 respectively), and then further resolving each of the two groups by successively using further suitable characters. Finally, a rooted tree or a network (Fig. 2.19) is obtained according to whether or not a hypothet ical ancestor was included among the EUs. There is argument as to whether the polarity of character transformations should be carried out a priori or a
posteriori'^ 2'219,280 in the writer’s view the latter is preferable as it is less prone
to error.
Some authors consider that character compatibility is not a true cladistic method at all, whereas others believe it falls closer to the original methods of Hennig than do the parsimony methods of Wagner. In the writer’s opinion there is little profit in such arguments. Any methods that give new insights into routes of evolution or new methods of classification are worthy of consideration, whatever their categorization and whatever they are called; they should all be tried and the one that best helps solve a given problem be utilized.
Cladistics has been adopted as a methodology far more readily and widely by zoologists than by botanists. There may be several reasons for this, but the botanists’ caution is in fact to some extent justified by what seems to be a genuine difference in emphasis in the modes of evolution of at least higher plants and most animals. Hybridization is known to be common among higher plants and a major route in the evolution of new species (see Chapter 6). If the genealogy of a hybrid species is drawn out in the form of a cladogram it will, of course, show reticulations. Since cladistic methodology is based upon detecting phylogenetic branching by charting character transformations, it is normally unable to reveal reticulations. Actual points of reticulation are normally misinterpreted, or ‘they obscure the underlying hierarchy’.145 In fact the existence of hybrid EUs often causes the appearance of trichotomies or polychotomies in the cladogram; this is not a correct depiction of the actual situation. This major problem has been addressed on many occasions in recent years,145,457,464 with very varied remedies similar only in that they are all unsatisfactory. For example, it has been suggested that hybrids should first be removed from the group of EUs under study, and then later be added to the completed cladogram of non-hybrid EUs. However, apart from obvious cases
W a n g e n h e i m i a C a s t e l l i a
Fig. 2.19 Network constructed from compatibility analysis carried out according to
Meacham's manual method by D. Shinn. The EUs are the genera listed in Figs. 2.11 and 2.14, plus two others and with Vulpia divided into its five sections. Character-state transformations are indicated by the numbers. The tree can be unequivocally rooted at
Vulpia sect. Loretta by a posteriori reasoning. The tree agrees closely with the current
classification; obvious suggestions are that Psilurus is relatively isolated, and that
of neopolyploids, there is no certain way of detecting hybridogenous taxa, especially where the parents are now extinct. Because of this, others believe that hybrids should be retained in the primary analysis, despite the fact that interpreting them correctly is largely beyond current methodology. Hybri dization remains a widespread and fundamental obstacle to the application of cladistics in many plant groups.
Cladists are all agreed that a prerequisite for cladistic analysis is a thorough knowledge of the group concerned. It is essential that the group and its constituent EUs be properly circumscribed, and that the characteristics to be used be understood sufficiently for homologies to be demonstrated and character transformation to be correctly assigned. Exactly the same prere quisite holds for taxometric analysis. The gaining of this knowledge and application is subjective. However objective the computational methods applied to the basic data might be, the results of analysis are not fully objective, since the use of different data will produce a different end result. Moreover, the interpretation of the cladograms in terms of a classification are also subjective; for example cladists argue whether convexity or monophyly should be the hallmark of a taxon. ‘Objectivity is a m yth/369
The fact that successful cladistic and taxometric analyses are feasible only with well-studied groups indicates that the basic data used for these approaches, and indeed for ‘narrative’ methods, are the same. (Narrative methods are those which do not utilize an explicit, testable analytical approach, but rely heavily on taxonomic expertise and intuition; most of the work described under Phase 6 comes in this category). This offers the possibility that unless one or more of these approaches is seriously faulty, very similar or even identical dendrograms might result from whatever methodology is used. There is much evidence that this is often so. One example from several published is shown by a study of the monoraphid diatom family Achnanthaceae, from which cladograms and phenograms showed the same branching pattern.251 The network shown in Fig. 2.19, and. its rooted derivative, agree very closely with the current classification based on narrative methods, and phenograms of the same group are also extremely similar (Stace ined.). To many taxonomists it is not surprising that knowledge and ideas accumulated over many years of study can often produce results at least on a par with the most rigorous analytical methods.
If evolution proceeds at a constant rate and in a strictly divergent fashion, a correct phenogram will indeed appear exactly the same as a correct clado- gram, and a highly competent taxonomist might subjectively produce the same pattern as well. However, if the above conditions do not hold, a phenogram and a cladogram will not look the same. In such cases the most important practical question to be posed is ‘which is the best solution to adopt?’ This has already been answered in Chapter 1 (p. 10). The firm stance taken by the writer is that predictivity is the criterion to be adopted, and the most predictive classifications should be considered the most natural one. It is not realistic or profitable to dictate a priori that cladistic or phenetic (or, indeed, narrative) methods might best achieve this. Such a view is today most often taken by cladists, but it is clear that cladistic classifications are not
always the most predictive. If we consider a species (A) with several
geographically separate subspecies (Aa, Ab . . . An), it could be that one of
these subspecies (say Ab) gives rise, under extreme selective conditions imposed upon one or more of its subpopulations, to species B. Species B might well differ from species A by several apomorphous character-states, more than differentiate any of the constituent subspecies of species A. Hence phenetically species A and B are the most distinct entities, but cladistically species B and subspecies Ab are very close. In fact species A has become paraphyletic, but in this case the most predictive classification is obtained by recognizing it as a taxon. Exactly that conclusion was reached, for example, by Rahn336 in his study of Plantago.
As was concluded at the end of the discussion of Phase 7 (taxometrics), cladistics is, in the writer’s view, not likely to replace other disciplines, but to supplement them. Often its use will increase our understanding of a group and improve our classification. Paying heed to its methodology will always improve our approaches to data collection and manipulation and to the use of the results of taxonomic research in classification. But dogmatic insistence that the cladistic approach is always the best one, or the only valid one, will greatly hinder progress.