Mapping Evolution: A Primer on Cladistic Methodology
The German entomologist Willi Hennig, who in 1965 and 1966 introduced a procedure for systematic treatment of animal taxa, which was meant to more accurately reflect genealogy, than previous methods, first elaborated cladistic methodology for phylogenetic reconstruction. Cladistics is considered one of the more useful tools for deciphering phylogenetic history, and its practice has immeasurably advanced our knowledge of the evolutionary history of life. The greatest triumph of cladistics has been the revision of inaccurate systematic treatments of taxa based on the classification system employed by Carl von Linne—and its concomitant typological suppositions. Principle examples include the recognition of paraphyly of Reptilia and Aves in the Linnean sense, and holophyly of Dinosauria (Bakker & Galton 1974, Gauthier 1986, Bakker 1986, Carroll 1988, Dodson et al 1990, Paul 2002).
Despite these achievements, and the usefulness of cladistics notwithstanding, the theory and practice thereof often strike even well educated individuals as esoteric, and uninteresting. One might suppose that this sort of blase attitude owes much to the disrespect systematics has earned from its scientific confreres—being just pigeonholing and abstruse cataloguing (Mayr 1942). This is most unfortunate, however. Cladistics is one of the most robust tools for bringing the profoundly powerful concept of common descent into concrete, graphical terms. To approach evolutionary biology without an understanding and appreciation of the genealogy of life that is entailed by common descent is of course, foolhardy, and thus one must be versed in phylogenetic reconstruction and the business of cladistics. And that is the purpose of thus primer: to engender in the reader a sense of the sublimity of systematics—the study of evolution in action—and how it in turn, demonstrates the elegance of evolutionary biology.
Fundamental Concepts of Cladistics
At its heart, cladistics addresses the dichotomy between typological classification and classification which reflects common ancestry. The Linnaean classification system employed with little modification for nearly two centuries is incapable of reflecting genealogy, in that it predated the elaboration of Darwinian evolution by nearly a hundred years. The Linnaean system, which we can refer to as the system whereby organisms were classified on the basis of general similarity or similar criteria, as opposed to their phylogenetic affinities, is an artifact of Platonic essentialism (Hull 1965, Wiley 1981, Mayr 1982, 2001, Carroll 1988, de Queiroz 1988, de Queiroz & Gauthier 1990, 1992, 1994). However, since the work of Alfred Wallace and Charles Darwin and the publication of a comprehensive theory of evolution in 1859, it has become increasingly clear that taxa are not typological units or duplicates of the fundamental “essence” of the parental lineage (Dingus & Rowe 1998, Mayr 2001). Rather, taxa display phenotypic dynamism—morphological plasticity—and most crucially, are descended from common ancestors in a nested hierarchy.
However, if one has a system of classification which is founded upon the notion that just the opposite is true, it becomes evident that said system cannot adequately reflect genealogy. While the terminological infrastructure which Linne devised, and the concomitant system of binomial nomenclature will no doubt always remain a fundamental part of our taxonomic science, only by using other methods than those used by Linne himself, mapped onto that infrastructure, can we begin to reflect phylogeny in our classifications, and not trivial similarities.
Today the principal goal of phylogenetic reconstruction is delimiting taxa, which reflect genealogy. Thus, systematists seek to define taxa on grounds such that all members included within a taxon are derived from the same ancestor, and all descendants of that common ancestry are included within the taxon. Hennig used the term monophyletic to distinguish such “natural” taxa from the polyphyletic or “artificial” taxa that consist of a hodgepodge of unrelated forms (with which the classification of plants and animals remains strewn). As some systematists have used the term monophyly to denote taxa which while displaying common ancestry still exclude all forms derived from that ancestry (paraphyly), an alternative and preferable term has been coined for monophyly in the Hennigian sense, “holophyly” (Ashlock 1971, Carroll 1988). Holophyletic taxa have been termed clades. Paraphyletic taxa are referred to as grades.
Cladistics is principally concerned with the mapping of cladogenetic evolution—the branching or divergent component of evolution, whereby two lineages arising from shared ancestry, pursue different evolutionary trajectories over time. A perfect example would be Deinonychosauria and Avialae, or humans, and chimps. Anagenesis is a comparatively simple process whereby one taxon is the phyletic progenitor of another: a linear progression from one form to another without divergence between lineages. Due to this bias of cladistics, the term grade, introduced above, has also been applied to taxa, which display anagenetic change over time, and lack a branching component in their phylogeny.
Semantics aside, cladistic systematists are primarily occupied with delimiting clades, and this is done on the basis of derived traits, or apomorphies, which are uniquely shared by the members of the putatively holophyletic assemblage, thus becoming synapomorphies. Concomitantly systematists seek to avoid erecting taxa based on “primitive” characters, or plesiomorphies, as such characters bear no relevance to phylogenetic reconstruction. As one moves “up” or “down” the Linnean hierarchy, any given character takes on a different status relative to the inclusiveness of the taxon being considered. For example, while a notochord is a synapomorphy of Chordata, within higher chordates a notochord it is a shared basal trait, or symplesiomorphy, and thus irrelevant to sorting out the interrelationships of chordates themselves.
Isolating any given character in a given lineage as either an apomorphy or plesiomorphy, requires comparison with others, and this is generally accomplished through a process called outgroup analysis. Contrasting character states found in taxon A (the ingroup) to those of its nearest relations, say taxa B and C, permits the determination of character polarity and thus differentiates basal from derived traits. Characters shared between the ingroup and outgroups, are considered plesiomorphic, while those uniquely excluded from outgroups are seen as apomorphic. In other words, traits common to taxa A, B, and C are of no phylogenetic relevance in upholding or rejecting the holophyly of any of these taxa, while oppositely, characters unique to taxon A and excluded from B and C are autapomorphic of taxon A and support holophyly thereof (Hennig 1966, Kluge 1977, Patterson 1981, Wiley 1981, Carroll 1988). The choice of outgroup is, in turn, determined by previous cladistic analyses.
In practice, the simple conceptual basis of outgroup analysis is muddled by ontogeny which does not often conform to our view of how it should appear. Such difficulties are most apparent in paleontology where the vagaries of the fossil record compound the matter, and for this reason paleontological systematists have classically used stratigraphy as a “yardstick” by which to quantify character polarity in the face of ontogenetic ambiguities (Carroll 1988). A sterling example of the usefulness of this method can be found in E. D. Cope’s work on establishing the character polarity of molar cusps in Cenozoic mammals (summarized in Butler 1982 and Carroll 1988).
And yet using stratigraphic data in this fashion to help tease out polarity of characters is fraught with problems. Foremost among the difficulties includes the inability to accurately isolate a character as plesiomorphic for a taxon simply because it appears at an earlier geologic horizon, as evidenced by the longevity of many genera and species and the fact that contrary to Hennig’s initial assertion in 1966, ancestral taxa need not suffer extinction following cladogenesis (Wiley 1981). Thus, one cannot solely rely on the geological occurrence of taxa for calculating polarity (Schaeffer, Hecht & Eldredge 1972, Carroll 1988), which in turn has led some practitioners of cladistic analysis to argue for reducing the role of the fossil record in establishing polarity (Hennig 1981, Wiley 1981, Patterson 1981).
In addition to a hodgepodge of other methods for establishing character polarity (summarized in Carroll 1988), one of the most useful criteria employed by systematists are structural morphoclines, characters, which vary quantitatively throughout a taxon. It is a general pattern of evolution that such morphoclines are directed more or less one way, for example, once lost, digits are rarely recapitulated. However, even this method for helping to elucidate polarity is prey to the vagaries of evolution, and like any other method, cannot be exclusively relied upon.
Once clades have been delimited, the inferred phylogeny can be presented in graphical form. Cladistics has employed a concise graphic to represent hypothetical phylogenies, a cladogram. Cladograms are constructed on the supposition that cladogenesis follows a bifurcating pattern, allying sister clades -- clades sharing most recent common ancestry -- in the context of holophyletic containing clades. While some researchers have argued that such a bifurcating pattern is not in fact reflective of the majority of cladogenetic events, there remains no convincing data to suggest otherwise.
A cladogram is constructed through statistical analysis of a data set (characters), which seeks to optimize the number of synapomorphies underwriting the holophyly of each node of the cladogram. Due to the size and complexity of the data set to be analyzed, computer programs such as PAUP (Phylogenetic Analysis Using Parsimony) are employed to more efficiently collate (Swafford 1991, Paul 2002). The resultant cladograms are then compared on the basis of parsimony—the postulate that the simplest cladogram requiring the least number of reversals and convergences will be most accurate (more or less Occam’s Razor applied to phylogeny).
Thus formulated, a cladogram represents a quantified hypothesis as to the evolutionary history of any given group, which can be tested against the data provided by multiple sources, including the paleontological record of whatever group was being analyzed. This ability to put together a coherent phylogenetic hypothesis, express it simply, and then subsequently test it against further data is perhaps the single greatest advantage offered by cladograms over other methods of phylogenetic mapping.
It is important to bear in mind, however, that cladograms are not absolute and immutable representations of phylogeny. Several researchers have rightly criticized the tendency of some to interpret cladograms too literally, in the process failing to realize that the utility of cladograms is their ability to present phylogenetic hypotheses (Halstead 1982, Carroll 1988). As happens all to often in science, certain researchers have in turn further distorted the situation by conversely claiming that cladograms are nothing more than mere speculation, produced through fairly meaningless “number crunching” and that they are adhered to dogmatically (see especially Feduccia 1996, 1999). This is as inaccurate as the opposing fallacy that cladograms are unassailably correct. The actual fact of the matter is that cladograms subsequently shown to be incorrect in their phylogenetic hypotheses have been abandoned, while those, which remain well substantiated by the data at hand, continue to be used. Like other scientific hypotheses, those generated cladistically are both open to further corroboration, or falsification in light of new data.
This general review of cladistic methodology already hints at the tremendous acrimony amongst systematists as to the utility of cladistics, and the extent to which it can be accurately used in phylogenetic reconstruction. Moreover, misrepresentations of cladistics abound. For instance, cladistics is not synonymous with phylogenetic reconstruction; rather it is a means towards that end. Cladistics is furthermore not synonymous with systematics or taxonomy, and indeed its goals are far more restricted than either of those broad disciplines (e.g., cladistics does not set out to define or redefine the species concept). Cladistics was explicitly outlined as a procedure for mapping the patterns of evolution in higher operational taxonomic units, and that is where its greatest strength will always lie.
In the final analysis, almost all researchers agree that taxa must be delimited on the basis of synapomorphies and not symplesiomorphies (Sereno 1990). The consensus ends there, however. Some of the more contentious issues pertaining to the utility of cladistics are summarized below.
While few would contest the need for classification to reflect genealogy via use of monophyletic groupings, it is when cladistic methods are carried to their logical end result and a system of complete hierarchy is established that bitter debate erupts. A taxon which is united by common descent and yet which excludes all the groups derived from that shared ancestry, is not at all reflective of evolutionary reality—it is instead a relict of a pre-evolutionary system of typological classification (Patterson 1981, 1982). In other words it is a taxonomic artifact, which cuts evolution off in midstream by implying disparity where there is none. Thus, proponents of cladistic methodology have long argued for the need to discourage the use of paraphyletic taxa and delimit in their stead, holophyletic clades.
The implications of this reasoning are profound—and to some systematists, unsettling. If paraphyletic grades are not indicative of evolution, then pre-evolutionary taxa established using Linnean methods are by default artificial constructs. No better example can be found than that of Reptilia sensu Linne. Linne defined Reptilia such that it excluded birds, and later systematists employed his definition with little modification for the next two hundred years. And yet, it has been evident since 1861 that birds are derived from ancestral stock somewhere within Archosauromorpha, and are therefore nested within Reptilia. Under a typological system such as Linne used, however, a form like Archaeopteryx cannot be both reptile and bird; it can only be one or the other. Yet it is both. And this is the fundamental dilemma: to extricate birds from Reptilia denudes Reptilia of any phylogenetic reality—it makes the taxon paraphyletic.
Including birds and defining the avian lineage such that it is nested within Archosauromorpha and Reptilia as a whole can resurrect Reptilia as a valid taxonomic category. Thus emended, Reptilia can be defined as: “the common ancestor of extant turtles and saurians, and all its descendants” (Gauthier et al 1988). Some authors have protested that this sort of phylogenetic “semantics” is confusing both in its counter-intuitiveness and its rejection of taxonomic convention (Paul 2002). Yet neither of these reasons are satisfactory reasons to distort the phylogeny of reptiles
The principal arguments, which have been advanced against a strict application of holophyly to phylogenetic reconstruction, do not dispute that holophyletic clades are preferable to paraphyletic groupings—in that the former is superior in modeling phylogeny than the latter. Rather, arguments from convention and clarity (at the expense of accuracy) have been made, but moreover, some systematists insist that there are practical difficulties in redefining taxa (particularly extinct taxa) such that they meet the requirements of holophyly (Carroll 1988). Carroll, for example, uses a cascade analogy whereby the problem of delimiting a clade is continuously offset to the next earliest representative of the lineage, and so on. Carroll uses the phylogenetic affinities of birds and dinosaurs as his primary example of this cascade in action, arguing that if one makes theropods birds, it renders Saurischia paraphyletic, and so on.
However, in this case, it is by including both the sister clade of birds—Deinonychosauria—and Avialae proper (Aves sensu Linne, emended by Chiappe) within a holophyletic containing node, Eumaniraptora, that the paraphyly of more inclusive nodes is avoided. Similarly, delimiting containing clades, or nodes on a cladogram, to prevent paraphyly can be effected in systematic review of any given lineages. The concomitant drawback is the need to name each node on a cladogram, which necessarily results in an explosive proliferation of taxa—cluttering and obfuscating the phylogenetic map and rendering it largely esoteric. This undesirable result is avoided through assigning names only to major nodes. Critics of cladistics have derided this process as arbitrary, and in so doing forget that all phylogenetic reconstruction is to a degree arbitrary. Latent arbitrariness notwithstanding, it is a general convention to consider major nodes as those robustly underwritten by synapomorphies (Paul 2002).
A remedy to this nomenclatural problem which has been suggested in some circles, namely amongst vertebrate paleontologists, is the use of apomorphy + clade names for taxa. Gauthier (1999) and Paul (2002) have outlined the methodology and protocol for employing apomorphy + clade names in phylogenetic reconstruction. Paul (2002) has extensively employed such a system in his review of the systematics of Dinosauria. Despite claims to the contrary, apomorphy + clade names are in no particular way more convenient than erecting new node-based names for containing clades, in that they do the same thing.
Ultimately, critiques such as those offered by Carroll (1988) and Carroll & Dong (1991) have asserted that paraphyly is largely inevitable in our systematic analyses, not the least of the reasons being the limit of our taxonomic nomenclature to articulate the dynamic processes of evolution. This objection is correct to an extent, but it is paramount to bear in mind that paraphyletic taxa do not accurately reflect phylogeny. Thus, it should remain a goal of systematists to avoid as much as possible, describing and naming such taxa.
Convergence vs. Cladistics
Critics of cladistic methodology present few arguments as vociferously as they do the argument that cladistics is unable to distinguish pseudo-homologies generated by homoplasy and parallelism from homologies derived through common ancestry (Mayr 1981, Olson 1985, Carroll 1988, Carroll & Dong 1991, Feduccia 1996). While some practitioners of cladistics have minimized the role of these processes in vertebrate evolution, it is well documented that both homoplasy and parallelism are powerful forces in that process (Simpson 1961, Mayr 1981, Cain 1982, Carroll 1982, Mayr 2001). The real question is whether or not homoplasy and parallelism occur at such a massive degree that they effectively overwhelm the statistical analysis of a data set—the process which cladistics rests upon—and thus preclude this methodology.
The proponents of this argument have advanced multiple cases of cladistic analyses, which upheld as synapomorphic, characters that in fact were not homologous (see mainly Mayr 1981, Olson 1985, Carroll 1988, Sibley & Ahlquist 1990 and Feduccia 1996, on Cracraft’s infamous 1982 attempt to reconstruct the phylogeny of Aves using cladistics). The examples most rigorously advanced are the convergence between Podicipediformes, Gaviiformes, and Hesperornithiformes, and the case of Hupehsuchus. Opponents of cladistics have cited these as cases of massive convergence, with which cladistic analysis is unable to cope.
Yet what do the facts of the matter indicate? To prevent this very problem cladistic analysis uses both the principle of parsimony, and attempts to collect as many characters as possible for analysis, to yield the largest data-set, following the logical conclusion that the number of homologous apomorphies will be greater than that of non-homologous apomorphies. The utility of both of these principles are tacitly or explicitly rejected in the critiques listed above, and the concomitant conclusion is drawn that even when using these methods, cladistics fails to tease out convergence.
Critical review of the sorry case of Cracraft’s “Gaviomorphae”—the putative clade allying Hesperornithiformes, Gaviiformes, and Podicipediformes—illustrates how this same taxon, seen as so emblematic of the shortcomings of cladistics by its opponents, is in fact a sterling example of poor cladistics. Cracraft asserted holophyly of Gaviomorphae on the basis of a handful of alleged synapomorphies, among which a sharply pointed and prominent cnemial crest was the principal character used to underwrite the validity of the “gaviomorph” assemblage. Yet the cnemial crest in the three constituent taxa of Cracraft’s “Gaviomorphae” is derived from entirely different elements, and thus is non-homologous, in each taxon (Storer 1971, Olson 1985, Feduccia 1996). It was upon this flaw, that Cracraft’s phylogeny collapsed. The question must be, is this indicative of an underlying flaw in cladistic methodology?
In their landmark review of avian phylogeny, Charles Sibley and Jon Ahlquist (1990), commented that: “the errors in Cracraft’s reconstruction of the phylogeny of the diving birds are due to the difficulties of interpreting morphological characters, not to the principles he used as the basis for his analysis.” Opponents of cladistics would do well to bear this in mind. It was Cracraft’s research, overlooking plain pseudo-homologies in the structure of the cnemial crest amongst the “gaviomorphs” which accounts for the rejection of that particular phylogenetic hypothesis. All this example illustrates is that cladistic practitioners, like all systematists, are human—and just as capable of errors and subjectivity as any other, which in and of itself is the more important point (i.e., it helps show that cladistics is not a panacea for systematics).
Yet some, (e.g., Feduccia 1996) have advanced this very same case as an example of “massive convergence.” It is nothing of the sort. It is in fact stereotypical convergence of elements associated with a particular biophysical function, in this case diving, and is no more a case of massive convergence than the independent derivation of a patella in varying tetrapod lineages. To maintain otherwise is at best mistaken, and at worst, specious.
The dubious "Gaviomorphae" aside, we can ask the question: are there any cases of bona fide “massive osteological convergence” which might be so thorough as to preclude accurate cladistic analysis? The answer may lie in the remains of a peculiar aquatic diapsid from the Triassic, Hupehsuchus nanchangensis, which Carroll & Dong (1991) have explicitly advanced as an example of extraordinary convergence, capable of both precluding the parsimony principle and fooling cladistic analysis.
Statistical evaluation of a character data set tabulated by PAUP produced a parsimonious cladogram inferring monophyly of Hupehsuchus, ichthyosaurs, and nothosaurs (Carroll & Dong 1991). However, the work of Rieppel (1989) and subsequent evaluation of this hypothetical phylogeny by Carroll & Dong has made it clear that the large number of synapomorphies used to support the monophyly of this aquatic diapsid assemblage, are in fact non-homologous and a function of significant convergence.
This much is not in dispute, what is in dispute is the contentious assertion that the case of Hupehsuchus is indicative of the evolutionary norm. Of Carroll & Dong’s three basic suppositions in their paper on Hupehsuchus, only one, that any given character is subject to homoplastic or parallel evolution, is correct. Their concomitant conclusions on the utility of parsimony, is entirely invalid and reflective of the convergence fallacy: that because homoplasy can foil cladistic analysis, it must. Hupehsuchus is a discrete case; an exception, which proves the rule: only in cases of large-scale convergence is the generally accurate principle of parsimony rendered suspect. The long-dead diapsid from China further emphasizes the far more meaningful conclusion which Carroll & Dong (and others who have parroted this example ceaselessly, such as Alan Feduccia) could draw were they not so concerned with discrediting cladistics: that this very discipline is by no means the infallible answer to all phylogenetic dilemmas.
The conclusion that parsimony combined with statistical analysis of characters is unreliable is a distortion; they can be unreliable. The greater the data set of characters, the more likely it is that convergent pseudo-homologies can be differentiated from synapomorphies, and this remains the single most effective procedure for distinguishing convergence or parallelism from common-descent. The convergence fallacy notwithstanding, cladistics remains a formidable tool for phylogenetic reconstruction.
Geological Time vs. Anatomy
Few debates in all of systematic biology are as acrimonious as the argument over which takes precedence in phylogenetic reconstruction: geological time, or anatomy? And while some disputes are esoteric quibbles between specialists, this particular dispute is a bona fide intellectual schism between systematists.
The former is the classical argument. The legendary Dean of vertebrate paleontology, Alfred Sherwood Romer, summarized the stratigraphic argument thusly, “In discussing fossils, some notion of the geological time scale in necessary” (1970). In general, time-dependent phylogenetic reconstruction asserts that a character, which appears earlier than another, especially in groups, which are well documented in the fossil record over long periods of time, is likely to be a basal character.
Robert Carroll, in his revision of Romer’s tome, Vertebrate Paleontology and Evolution (1988), further stresses that in establishing phylogeny, one must “emphasize the earliest known members” of a lineage, in that “they have had the shortest amount of time to evolve new characters since their initial divergence.” Carroll concludes with: “Hence, they should provide us with the best opportunity to identify the derived features that they share with their closest sister group.”
While these arguments are certainly coherent and intuitively appealing, it is an unfortunate fact that reality rarely conforms to our limited view of how it ought to behave. The cut and dry world of time-dependent phylogenetic reconstruction is just not the way of it—things are not that simple. As discussed earlier, relying on stratigraphic data exclusively to document polarity and ontogenetic change is fraught with problems, and these problems are only magnified as one considers a group whose fossil record is both spotty and of limited temporal distribution. Time-dependent arguments are prey to the vagaries of the fossil record and geology, among other factors, not the least of which being the inconsistent way in which lineages diverge, subsequent to cladogenesis (e.g., parental taxa outliving their descendants, see section 2).
This stratophenetic methodology is further weakened by the reliance on general similarity between taxa over time as a measure of phylogeny. Thus time-dependent phylogenies often chart the evolution of grades only, and do not reflect phylogeny accurately.
Recognizing these limitations, an opposing camp has stressed anatomy as the fundamental basis for phylogenetic reconstruction, arguing that generally speaking, character distribution is more indicative of phylogeny than mere stratigraphic occurrence, especially if one is dealing with a group whose fossil record is poor and distributed over a brief period of geological time. Considering that changes in ontogeny are the most concrete example of evolutionary progression in a lineage, the anatomy-dependent argument is entirely logical. Moreover, mere stratigraphic occurrence does not impute to fossils phylogenetic context or relevance. For this, one must refer to characters--anatomy. There is simply no rational way to make phylogenetic reconstruction dependendent upon stratigraphic context (Clark et al in Chiappe & Witmer 2002).
Logic notwithstanding, the assertion that anatomy generally takes precedence over stratigraphy, has been so distorted by opponents of this methodology, that flippant statements such as those of Alan Feduccia, to the effect that cladistics has “discarded geological time as a tool in deciphering evolution” (1996), are common. Such arguments are entirely specious—geological time has not been categorically dismissed, rather it’s utility has been minimized. Accurate phylogenetic reconstruction demands a critical view of stratigraphy as a criterion for establishing phylogenies, not dogmatic adherence.
Ultimately, one must advance a case where two phylogenies generated using each method can be compared side by side, their likelihood weighed against the data and our knowledge of evolutionary processes. There is no single example, which can more effectively fulfill that role, than the phylogeny of the acanthodian fishes.
Assuming that most readers are not familiar with so obscure a group as Acanthodia, an introduction of sorts is in order. Reader, meet Acanthodia—a curious group of extinct fishes, whose osteology and evolution was reviwed byMiles (1965, 1968, 1973) and Maisey (1996). Acanthodia represents a successful, but ultimately failed experiment in the gnathostome adaptive radiation, which culminated in the Lower Devonian—when the clade was at its zenith (Denison 1979, Carroll 1988).
The relationship of Acanthodia to other gnathostome clades has long been contentious in and of itself, and there remain arguments for a close affinity of Acanthodia and Chondrichthyes (Orvig 1973, Jarvik 1977). Without exhaustively cataloguing the data to support an alternative phylogenetic status for Acanthodia, I instead refer the reader to the work of Roger Miles, and summaries presented in Denison (1979), Carroll (1988) and Maisey (1996). These ongoing arguments aside, we can turn to the far more vitriolic debate over the intra-relationships of Acanthodia, a subject, which pits time-dependent phylogenetic reconstruction, against the anatomy-dependent school.
Stratophenetics isolates Climatiida, the earliest occurring acanthodian lineage, dating from the Middle Silurian, as basal to the entire taxon. Counter-intuitively, climatiid acanthodians display the most apomorphic morphology comparative to other members of the lineage, including the presence of two dorsal fins, and numerous paired intermediate spines on the ventral surface of the body—a condition autapomorphic of Acanthodia itself. The time-dependent phylogenies go on to isolate the Acanthodida, as the most derived acanthodian fishes, and yet they display the most plesiomorphic of all acanthodian morphologies, retaining a single dorsal fin, and with but one pair of intermediate spines. The two groups are separated by a mere 12 million years—which, to geology, is a blink of the eye.
The time-dependent phylogeny, therefore, has two significant flaws: it ignores the fact that the most basal members of a lineage, as Carroll himself would point out, are those which will display the most plesiomorphic anatomy comparative to other members of the ingroup, and will have more synapomorphies comparative to the outgroups, than will the most derived members of the lineage. Yet here we have the most derived members of the acanthodian lineage, from a morphological point of view, being advanced as the most basal. Furthermore, the time-dependent phylogeny must invoke massive reversal with no apparent causal factor, to explain why such a plesiomorphic form should have been recapitulated by the acanthodiids. All in all, this phylogeny is something of a mess.
An anatomy dependent phylogeny turns the matter upside down: the clearly plesiomorphic acanthodiids are labeled as the most basal Acanthodia, while the clearly apomorphic morphology of the climatiids is considered the most derived. This phylogenetic hypothesis, in addition to being far more congruent with what we know of evolution, has no need to invoke massive reversals to arrive at its conclusions, and is more parsimonious.
The acanthodian case, is exemplar of the difficulties in relying on stratigraphy alone, and stands as a warning to the prospective systematist who would naively adhere to idea that geological time must outrank all other considerations in phylogenetic reconstruction.
Acrimony, the Quest for Objectivity, and Cladistics
Cladistics being the immensely useful tool that it is, one must question naturally why it should be so contentious a subject. And contrary to the popular impression, there remains much debate on cladistics. While everyone agrees as noted that synapomorphic characters are the only traits which have phylogenetic relevance, nearly every other aspect of cladistic methodology and its implications are debated. Cladistics, quite simply, has been its own worst enemy, as there are practitioners thereof who fail to see cladistics as a tool only, however powerful and useful it is, and instead adhere to it with dogmatic tenacity, as great as that of any religious fundamentalist. For these systematists, cladistics has been elevated to the level of inerrant and purely objective, when in fact this is not the case. In their eyes cladistics has become the only objective and legitimate way of going about phylogenetic reconstruction, and all other methods are pseudoscientific, philosophical, or simply prejudiced on some personal grounds. This viewpoint is not only lacking in realistic corroboration, but it is immensely injurious to the science of phylogenetic reconstruction and will result in great damage to this very field. The ardent cladists have as warped a view of cladistic methodology as do those who categorically reject cladistics. This sort of religious deification of cladistic analysis is not science: those who advance cladistics as the "One True Way" are attempting to define nature, not describe it, and in so doing have taken up philosophy, and let science fall by the wayside.
Cladistics is a robust method for deciphering phylogeny, and like any such method, it has its strengths, and weaknesses. Opponents of cladistics, who categorically dismiss this procedure, are as wrong as those who elevate cladistics to the level of phylogenetic panacea—reality lies somewhere in the middle.
In an imperfect science, attempting to piece together a riddle wrapped inside an enigma, cladistics will continue to serve us well.
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