Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary for calculating the probabilities that define Popper's corroboration, likelihood methods of phylogenetic inference--with their explicit probabilistic basis--are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as described by certain advocates of those methods, are less easily reconciled with Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corroboration. Conversely, if parsimony methods are to be considered compatible with corroboration, then they must be interpreted as carrying implicit probabilistic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Popper's concept of corroboration. In addition to being compatible with Popperian corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的分支系统学研究

本文概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本文同时以华东地区樟科山胡椒属Linderal2个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这12个种的分支系统学研究得出了一些不同于传统系统学方法所推测的山胡椒属内的系统发育关系,如分支系统学研究显示山胡椒组和球果组很近缘。在严格一致性分支图上,杯托组的黑壳楠和江浙山胡椒分别位于最原始和最进化的分支,表明这个组是复系类群。分支图也显示山胡椒组可能是复系类群。     

A Review of Current Theories and Methods in Cladistics and a Cladistic Study of Twelve Lindera Species in Eastern China

Cladistics has become a widely used method for phylogenetic reconstruction．Because of rapid improvement Of cladistic theories and methodologies,and application of new data,especially,molecular data,it is becoming realistic to reconstruct phylogenies of organisms,and to establish natural classifications based on these phylogenies．This paper reviews some current cladistic theories and methods in a practical way,such as choosing characters,defining character states,polarizing characters,analyzing data matrices, calculating consensus cladograms,choosing among multiple equally most parsimonious cladograms,estimating reliability of cladograms,and applying cladograms to classification, character evolution,and biogeography． Based on 36 morphological characters．a parsimony analysis of 12 species representing six sections in subgenus Lindera and an outgroup species from subgenus lteodaphne of the genus Lindera(Lauraceae)was conducted．The results suggest a close relationship between section Lindera and section Sphaerocarpae,which is different from the previous phylogenetic hypothesis within the genus．In the strict consensus cladogram,two species,L．megaphylla and L.chienii,from section Cupuliformes are in the most primitive and the most advanced clades respectively,indicating that the section is polyphyletic．The cladogram also suggests that section Lindera be a polyphyletic group．     

Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration

Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a single body of data; however, both classes of methods can be used to perform severe tests. The assumption of descent with modification is insufficient background knowledge to justify cladistic parsimony as a method for assessing degree of corroboration. Invoking equivalency between parsimony methods and likelihood models that assume no common mechanism emphasizes the necessity of additional assumptions, at least some of which are probabilistic in nature. Incongruent characters do not qualify as falsifiers of phylogenetic hypotheses except under extremely unrealistic evolutionary models; therefore, justifications of parsimony methods as falsificationist based on the idea that they minimize the ad hoc dismissal of falsifiers are questionable. Probabilistic concepts such as degree of corroboration and likelihood provide a more appropriate framework for understanding how phylogenetics conforms with Popper's philosophy of science. Likelihood ratio tests do not assume what is at issue but instead are methods for testing hypotheses according to an accepted standard of statistical significance and for incorporating considerations about test severity. These tests are fundamentally similar to Popper's degree of corroboration in being based on the relationship between the probability of the evidence e in the presence versus absence of the hypothesis h, i.e., between p(e|hb) and p(e|b), where b is the background knowledge. Both parsimony and likelihood methods are inductive in that their inferences (particular trees) contain more information than (and therefore do not follow necessarily from) the observations upon which they are based; however, both are deductive in that their conclusions (tree lengths and likelihoods) follow necessarily from their premises (particular trees, observed character state distributions, and evolutionary models). For these and other reasons, phylogenetic likelihood methods are highly compatible with Karl Popper's philosophy of science and offer several advantages over parsimony methods in this context.     

A Review on Cladistics

The theoretical bases and approaches of cladistics and some specific problems that, directly or indirectly, rely on cladistic analysis for their revolution, are outlined and discussed. Seven sections comprise this paper: a ) the philosophical foundation of cladistics; b) the theoretical tenets of cladistics; c) the operational procedure of cladisties; d) three schools of classification; e) cladistics and biogeography; f) cladistics and hybrid recognition; and g) is cladistic systematics a scientific theory ? Considerations of scientific methodology involve philosophical questions. From this point, Popper'falsificationism serves a good foundation. Popper emphasizes that all scientific knowledge is hypothetical-deductive, consisting of general statements (theories) that can never be confirmed or verified but only falsified. The theories, that can be tested most effectively, are preferable. Cladistics, aiming at generating accurately expressed and strictly testable systematic hypotheses, is well compatible with this requirement. The principles central to the cladistic theory and methodology are: the Principle of Synapomorphy; the Principle of Strict Monophyly; and the Principle of Strict Parsimony. The first requires forming nested groups by nesting statements about shared evolutionary novelties (synapomorphy) postulated from observed similarities and is the primary one. The second is mainly methodological, subject to modification and compromise. The principle of strict parsimony specifies the most preferable hypothesis (namely the one exhibiting the most congruence in the synapomorphy pattern). The operational procedure that might be followed in formulating and testing hypotheses of the synapomorphy pattern (the cladogram itself) consists of five steps. The erections of monophyletic groups, to a greater or lesser extent, rely on the hypothesis of the previous systematic studies and is the starting point for cladistic analysis. Character analysis, which focuses on character distribution and determination of the polarities, decides the reconstructed phylogeny. A detailed discussion on the methodological principles for identifying transformation sequence is presented. Many algorithms have been designated to infer the cladogram, and are basically of parsimony techniques and Compatibility techiques. The thus yielded cladograms, with their expected pattern of congruent synapomorphies, are tests of a particular hypothesis of synapomorphy and reciprocally synapomorphies are tests of cladistic hypothesis (cladogram). Such reciprocity is a strong stimulus to profound understanding on phylogenetic process and phyletic relationships. The cladogram and the Linnaean classification have the identical logic structure and the set-membership of the two can be made isomorphic. There are three principal approaches to biological classification : cladistics, phenetics and evolutionary classification. Cladistics is the determination of the branching pattern of evolution, and in the context of classification, the development of nested sets based on cladograms. Phenetics is the classification by overall similarities, without regard to evolutionary considerations. Evolutionary classification attempts to consider all meaningful aspects of phylogeny and to use these for making a classification. The last approach has been done intuitively, without explicit methods. An enumeration of their differences and a discussion on their relative merits are presented. Three theoretical approaches have been proposed for interpreting biogeographical history: the phylogenetic theory of biogeography, classical evolutionary biogeography and vicariance biogeography. The former two show some similarities in that they usually look upon biogeography in terms of centers of origin and dispersal from the centers. But the first puts a strong emphasis on the construction of hypotheses about the phylogenetic relationships of the organisms in question and the subsequent inference of their geographic relationships; the second advocates a theory which does not have a precise deductive link with phylogenetic construction and often results in wildly narratative-type hypotheses. The vicariance approach de-emphasizes the concepts of centers of origin and dispersal and attempts to analyse distribution patterns in terms of subdivision (vicariance) of ancestral biotas. The development of the theory of plate tectonics and its universal acceptance enormously stimulate biogeographers to look at the world's continents and oceans from a mobilist point, which, along with the establishment of the rigorous tool of the phylogenetic analysis (cladistics), profoundly reshapes the above three theories. Hybridization and polyploidy are outstanding features of many plant groups. But hybridization, or reticulate evolution, is inconsistent with the basic concepts of cladistics which is an ever-branching pattern. Cladists have suggested several approaches. One of them analyses all the taxa by a standard cladistic procedure and closely examines the cladograms for polytomies and character conflicts that may indicate possible hybrids. Such generated hypothesis of hybridization can be corroborated or falsified by other forms of data, such as distribution, polyploidy, karyotype and pollen fertility. There are three criteria to justify a theory to be scientific: a) whether it is a theory composed of hypotheses strictly falsifiable; b) whether it has predictive effect; and c) whether it has a explanatory value. Cladistic systematics aims at generating cladograms, which are hypotheses of the nested pattern of synapomorphy, phylogenetic process and phyletic relationships, susceptible to testing by postulated synapomorphies. The predictive effect of systematics relies on the acceptance of hypotheses of congruence about the correlation of characters, which has been well founded. For non-systematic biologists, phylogenetic classification can be used as axiom to form a preliminary and fundamental explanation.     

Early stages and the classification of the milkweed butterflies (Lepidoptera: Danainae)

The Danainae, or milkweed butterflies, are a moderate-sized group of around 150 species that are of considerable ecological, physiological and behavioural interest. There are two currently accepted classifications for the subfamily and the aim of this study was to try to resolve this conflict using characters derived from the eggs, larvae and pupae. The 130 new characters (of which 85 are illustrated) are analysed by both phenetic methods (average linkage cluster analysis and principal coordinate analysis) and by cladistic techniques (Wagner tree, character compatibility analysis and manually derived cladograms). Overall, the results corroborate the more recent classification of the Danainae. However, some points of difference are found and, after component analysis, an alternative classification is presented in accordance with the conventions for constructing annotated Linnaean hierarchies.     

Recycled

Both three-taxon analysis (3ta) and conventional parsimony analysis (CPA) fall within the cladistic framework. Attempts to exclude 3ta from the general cladistic framework so far seem to amount to declaring CPA as the only permissible analytic technique within cladistics. Critics of 3ta have failed to fully implement it in examples; as a result this criticism is faulty and does not support the claims made. Ultimately, the relative merit of 3ta will be resolved empirically, by comparison of classifications produced from it with classifications using other methods.     

PHYLOGENY OF THE NEMERTEAN SUBCLASS PALAEONEMERTEA (ANOPLA, NEMERTEA)

Abstract— A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty-five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum . An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo- and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy-two equally most parsimonious cladograms were found; the consistency index was low but tree-length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella ), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.     

CLADISTIC AND BIOGEOGRAPHIC ANALYSIS OF THE "BLUE ASH' EUCALYPTS

Abstract— A cladistic analysis of the "blue ash" eucalypts ( Eucalyptus , Myrtaceae) is presented. Five equally parsimonious trees were found, and a strict consensus tree constructed. A revised informal classification, recognizing five series ( Planchonianinae, Sphaerocarpinae, Piperitinae, Fraxininae and Haemastominae , informal subgenus Monocalyptus ) is based on the consensus cladogram. A biogeographic analysis applies a new implementation of Assumptions 0 and 1, coding data in the form of three-area statements and using parsimony analysis. These results are used to evaluate hand resolution of Assumption 2. In comparison, Brooks parsimony analysis did not produce area cladograms that best fit the data. Series and subseries were analysed separately for area relationships, which showed a repeated pattern across the blue ash clade; combining all the data in one analysis was seen as equivalent to confounding paralogy and orthology in molecular studies. A resolved area cladogram is presented for southeastern Australia.     

A falsificationist perspective on the usage of process frequencies in phylogenetics

By referring to Popperian falsificationism, proponents of cladistic parsimony claim the superiority of parsimony over likelihood. They conclude that likelihood as a statistical approach is inconsistent with falsificationism, and base their argumentation on four claims: (1) congruence tests cladograms against observational evidence and represents the most important test in phylogenetics, in which minimum‐step trees represent most corroborated trees; (2) frequency probabilities cannot be used for evaluating degree of corroboration; (3) phylogeny represents a unique process and thus frequencies cannot be applied as they require statistical reference classes that are necessarily general; (4) likelihood is a verificationist approach. After discussing the deficiencies of the cladistic phylogeneticists’ conceptualisation of the congruence test and the presentation of an alternative conceptualisation, it is shown that these four claims cannot be sustained within a falsificationist framework, and that the weighting of characters is a necessity. A differentiation between the theoretical concept of apomorphy and the epistemological concept of character weight is proposed. While apomorphies have to be independent from each other, the weighting of characters is interdependent due to human inability to distinguish organismic traits that are structurally identical though they do not share a common evolutionary origin. The possibility of this epistemological interdependence can best be dealt with by the application of process frequencies. The importance of process frequencies of specific transformation classes is exemplified in reference to Popper's formula for the measure of degree of corroboration and its consistency is shown. Therefore, the application of statistical methods is reasonable. As a consequence, the question whether likelihood or parsimony methods represent the best approaches in phylogenetics remains a genuinely empirical question that cannot be decided only in reference to Popper's falsificationism.     

A preliminary cladistic study of the families of the superorder Lamiiflorae

LU AN-MING, 1990. A preliminary cladistic study of the families of the superorder Lamiiflorae. A preliminary cladistic analysis was undertaken to evaluate the relationships between families of the superorder Lamiiflorae sensu Dahlgren. Several character complexes were surveyed, and ultimately 29 informative characters were used for the study. Three families, Clethraceae, Oleaceae and Solanaceae were selected for outgroup comparison and polarization of the characters. A data matrix was constructed for the 23 ingroup families. The data matrix was analysed with the cladistic parsimony program Hennig86. Three equally parsimonious cladograms were found. Many family interrelationships could not be resolved, although several groups were common to all three cladograms, as shown by a strict consensus tree. The Retziaceae emerged as the sister group to the remaining families. About half of those appeared in a large polytomy in the consensus tree. There was also one possibly monophyletic complex of families involving the Lamiales with the families Verbenaceae, Lamiaceae, Phrymaceae and Callitrichaceae as well as the three isolated families Trapellaceae, Hippuridaceae, and Hydrostachyaceae. Within this complex, Verbenaceae and Lamiaceae came out as sister groups, as did Callitrichaceae and Hydrostachyaceae, with Hippuridaceae as sister group to them. However, the results must be regarded as tentative.     

ON CONSENSUS, COLLAPSIBILITY, AND CLADE CONCORDANCE

Abstract — Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter-cladogram character conflict for all characters among a set of cladograms.     

The jazz of cladistics*

In this metaphorical ‘composition’, I comment on nine ‘dissonant chords’ related to the drowning out of cladistic performance: (1) DNA-based phylogenetic hypotheses supported only by bootstrap values and without molecular synapomorphies; (2) the use of molecular data to the exclusion of morphological data, with the classification of clades diagnosed by morphological plesiomorphies plus bootstrap values; (3) neglect of the results of the congruence test and how they are interpreted; (4) the combination of character optimization using both model-based and parsimony methods, and its consequences; (5) the need to effectively integrate ontogeny and phylogeny; (6) the estimation of the ages of clades based on molecular-clock analyses; (7) the belief that new methods, theories, and hypotheses are more reliable than old ones, with the idea that model-based analyses achieve better results than parsimony analyses; (8) the false assumption of the irrelevance of classification; and (9) clashes amongst cladists themselves, who endorse distinct methods, philosophies, and theories. Finally, I present 10 ‘refrains’ in order to intensify the cladistic performance.     

Outline of an Explanatory Account of Cladistic Practice

A naturalistic account of the strengths and limitations of cladistic practice is offered. The success of cladistics is claimed to be largely rooted in the parsimony-implementing congruence test. Cladists may use the congruence test to iteratively refine assessments of homology, and thereby increase the odds of reliable phylogenetic inference under parsimony. This explanation challenges alternative views which tend to ignore the effects of parsimony on the process of character individuation in systematics. In a related theme, the concept of homeostatic property cluster natural kinds is used to explain why cladistics is well suited to provide a traditional, verbal reference system for the evolutionary properties of species and clades. The advantages of more explicitly probabilistic approaches to phylogenetic inference appear to manifest themselves in situations where evolutionary homeostasis has for the most part broken down, and predictive classifications are no longer possible.     

Comparative biology and the importance of cladistic classification: a case study from the sensory biology of squamate reptiles

Evolutionary taxonomy has all but succumbed to cladistic methodology, but it continues to exert considerable influence in the realm of higher classification. Some systematists accept cladistic methods in phylogeny inference, but allow paraphyly in formal classifications. Most important, however, many traditional classifications based on paraphyletic groups (e.g. 'Reptilia') remain in force, deeply entrenched in the literature. Cladists have argued that such paraphyletic classifications can mislead comparative biologists into false evolutionary generalizations, but this assertion has rarely, if ever, been supported by example. This paper provides a case study, illustrating in detail the influence of a traditional paraphyletic classification of squamate reptiles on the historical development of ideas regarding the evolution of sensory modes (chemoreception vs. vision) in the group. The paraphyletic classification is shown to have led to false generalizations and incorrect conclusions stemming directly from the fact that the classification did not reflect accurately the phylogeny of Squamata, particularly the cladistic relationships of Gekkota. This study provides direct evidence that evolutionary generalization must be rooted in the branching pattern of phylogeny and not the potentially arbitrary categorical ranks of traditional taxonomies. It further supports recent calls for a truly phylogenctic taxonomy that has as its philosophical core the concept of descent.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

IN SEARCH OF A METHOD FOR CLADISTIC BIOGEOGRAPHY: AN EMPIRICAL COMPARISON OF COMPONENT ANALYSIS, BROOKS PARSIMONY ANALYSIS, AND THREE-AREA STATEMENTS

Abstract— Three quantitative cladistic biogeographic methods, namely, component analysis, Brooks parsimony analysis (BPA), and three-area statements (TAS) have been proposed for obtaining general area cladograms from taxon-area cladograms. Available programs implementing these methods include COMPONENT versions 1.5 and 2.0 for component analysis, TAS for three-area statements, and Hennig86 for analysing matrices for both three-area statements and BPA. Ten different data sets were analysed with these programs and items of error were used to evaluate the general area cladograms obtained. None of the computer implementations of the methods compared proved to be more effective than the others.
"…all methodologies, even the most obvious ones, have their limits…"
Feyerabend (1993:231)     

Towards an inclusive philosophy for phylogenetic inference

We defend and expand on our earlier proposal for an inclusive philosophical framework for phylogenetics, based on an interpretation of Popperian corroboration that is decoupled from the popular falsificationist interpretation of Popperian philosophy. Any phylogenetic inference method can provide Popperian "evidence" or "test statements" based on the method's goodness-of-fit values for different tree hypotheses. Corroboration, or the severity of that test, requires that the evidence is improbable without the hypothesis, given only background knowledge that includes elements of chance. This framework contrasts with attempted Popperian justifications for cladistic parsimony--in which evidence is the data, background knowledge is restricted to descent with modification, and "corroboration," as a by-product of nonfalsification, is to be measured by cladistic parsimony. Recognition that cladistic "corroboration" reflects only goodness-of-fit, not corroboration/severity, makes it clear that standard cladistic prohibitions, such as restrictions on the evolutionary models to be included in "background knowledge," have no philosophical status. The capacity to assess Popperian corroboration neither justifies nor excludes any phylogenetic method, but it does provide a framework in phylogenetics for learning from errors--cases where apparent good evidence is probable even without the hypothesis. We explore these issues in the context of corroboration assessments applied to likelihood methods and to a new form of parsimony. These different forms of evidence and corroboration assessment point also to a new way to combine evidence--not at the level of overall fit, but at the level of overall corroboration/severity. We conclude that progress in an inclusive phylogenetics will be well served by the rejection of cladistic philosophy.     

A botanical critique of cladism

Clade versus grade is an old question in taxonomy, going back as far as Darwin himself. Taxonomists have long believed that both must be taken into account in the formation of a general-purpose system. Recently clade has been elevated to a position of total dominance by a group of taxonomists who take their inspiration from Willi Hennig. Mayr has dubbed this approach cladism, and its exponents cladists. Cladistic theory is being vigorously developed and propounded by Hennig’s disputatious disciples, and much of the present-day theory would scarcely be recognized by the founder. I here address myself to what I consider the core features of present-day cladism. The essential distinctive feature of cladism, and its fatal flaw, is that a group is considered to be monophyletic, and thus taxonomically acceptable, only if it includesall the descendants from the most recent common ancestor. The traditional taxonomic view has been that a group can still be considered monophyletic (and thus taxonomically acceptable) after some of its more divergent branches have been trimmed off. This simple and seemingly innocuous difference has profound consequences to the taxonomic system. In Hennigian classification, organisms are ranked entirely on the basis of recency of common descent, that is, on the basis of the sequence of dichotomies in the inferred phylogeny. Theamount of divergence scarcely enters into the picture. This procedure represents an effort to capture taxonomy for a narrowly limited special purpose, at the expense of the important and necessary function of providing a general-purpose system that can be used by all who are concerned with similarities and differences among organisms. The first corollary of the Hennigian concept of phylogenetic taxonomy is that no existing taxon can be ancestral to any other existing taxon. The descendant must be included in the same taxon as its ancestor. At the level of species this is palpably false. The ancestral species often continues to exist for an indefinite time after giving rise to one or more descendants. At the higher taxonomic levels adherence to the principle often requires excessive lumping or excessive splitting to avoid paraphyletic groups (i.e., groups that do not include all of their own descendants), and it forbids the taxonomic recognition of many conceptually useful groups. Neither the prokaryotes nor the dicotyledons form a cladistically acceptable taxon, since both are paraphyletic. The prokaryotes are putatively ancestral to the eukaryotes, and the dicotyledons are putatively ancestral to the monocotyledons. Many other traditional and readily recognizable taxa would have to be abandoned, without being replaced by conceptually useful groups. Fossils present a special problem, because the whole concept of cladistic classification depends on the absence of taxa at the branch points of the cladogram. Presumably all of these branch points were at some time in the past represented by actual taxa, which under cladistic theory can neither be assigned to one of their descendants nor treated as paraphyletic taxa. The difficulty is mitigated somewhat by the gaps in the known fossil record. Once it is admitted that paraphyletic as well as holophyletic groups are taxonomically acceptable, there is much value in cladistic methodology. Formal outgroup comparison for the establisment of polarity, and the emphasis on synapomorphies in the construction of a cladogram can both be usefully incorporated into taxonomic theory and practice. These require no revolution in taxonomic thought. There are unresolved problems, however, in how to gather and manipulate the data, and how to interpret the cladogram produced by computers. In any complex group, the computer may produce several or many cladograms of equal or nearly equal parsimony. This is particularly true in angiosperms, among which the extensive evolutionary parallelism casts doubt on the importance of parsimony and may lead to the production of hundreds of such cladograms for a single group. Despite the claims of objectivity and repeatability in cladistic taxonomy, the necessity for some subjective decisions remains. The Wagner groundplan-divergence method has most of the advantages of formal cladism without the most important disadvantages. Wagner accepts paraphyletic taxa in principle, and he casts a wider net for data bearing on the polarity of characters. In complex groups consisting of many taxa, however, both methods retain a strong subjective component in the computer manipulation and in the degree of reliance on absolute parsimony.