User:Berton/Cladistics

Cladistics as method not compatible with Linnaean Taxonomy

Cladistics is a method that suggests hypotheses of phylogenetic relationship based on the statistical analysis of similar elements, detecting traits (characters) derived (apomorphics) or primitive (plesiomorphics) in a certain taxonomic group, generating cladograms, that are graphic representations of the several clades (hypotheses of relationships according to the homology criterion). The main function of Cladistics would be support to the classifications such as Linnaean Taxonomy (Darwinian); excluding the elements that represent evolutionary convergence which are not similars (not affined). Then Cladistics is only a method, but this by itself doesn't mean anything! The problem is in cladism and cladonomy!

With regard to cladonomy: Brummitt, R. K. (1997). Taxonomy versus cladonomy, a fundamental controversy in biological systematics. Taxon 46(4):723-734: "Those who argue for eliminating paraphyletic taxa from classification, and recognizing only monophyletic (in the modern cladistic sense) taxa, are in fact arguing for a classification based on clades, not on taxa, which is quite different concept. Referring organisms to clades is perfectly possible, but it is not Linnaean classification. In an illumining recent paper Mayr (1995) has stressed the distinction between classifying organisms into a taxon and referring them to a clade, which he has designated a 'cladon'. "

With regard to cladism: Brummitt, R. K. (2006), Am I a bony fish? Letter to the editor. Taxon 55(2)268-269): "The question of paraphyly is, I feel, the most important issue debate in Taxonomy today. ...The theory of cladistic classification is so wrong that distinctive groups which are sunk into another family or genus can usually no longer be recognized even at subfamily or subgeneric rank because they would just make another subfamily or subgenus paraphyletic.... The statement of Nordal & Stedje noted that cladistic classification is causing chaos in taxonomy, but this has been denied in the responses. It depends on how you perceive chaos. The recent disintegration of the Scrophulariaceae may seem like chaos to some. If we have to sink Hydrostachyaceae into Hydrangeaceae, Podostemaceae into Clusiaceae, Hippuridaceae (flowers consisting of an inferior ovary and a single stamen) into Scrophulariaceae, the whole of the Juncaceae into Juncus, many distinctive genera into Lobelia, and many other cases, we are moving towards a generally chaotic situation in my opinion.... But I feel very confident that future generations will thank Inger Nordal and Brita Stedje for raising the profile of the discussion and showing that many taxonomists have serious objections to the theory and practice of cladistic classification."

As method of relationship analysis (actually hypothetical) among similar beings, it can be made a cladistic analysis of the elements (even objects) but not to establish your "relationship degree" or kinship; it is only applied by Systematics (that is, general science of classification, including among others: Taxonomy), as approach, when using of the phylogenetic criterion. To establish the relationship degree implicates in using a ordering system of hierarchical and formal type like taxonomic categories, which are mutually exclusive and that assign living beings (taxa) at the ranks (several classes) that form a taxonomic system.

To classify phylogeneticly, we should to apply the darwinian concepts of the descent (cladogenesis) with modification (anagenesis). Cladism only applies cladogenesis criterion, thus it makes a "cladification" (after Mayr & Bock, 2002). The basic error of Cladism is to ignore that to classify means to analyze similarities and differences, and not only similarities, like they do. And to classify doesn't mean merely to create genealogies of species. Its terminology is "funny" (sister groups, etc).

By the way phylogenetic criterion is not exclusive of Cladistics. It must not be called "Phylogenetic Systematics" because it is not the unique to use this criterion (that is an arrogance!).

The Truthful Taxonomy is based (solidly) in rules established by Linnaeus, initially, and defined later by International Code of Botanical Nomenclature or ICBN and International Code of Zoological Nomenclature or ICZN. Thus Cladistics is not Taxonomy!

Clades do not fit the taxonomic categories (taxa), like Genus, Family, Order, etc, they are just informal hierarchical levels (and therefore must not be named, it is preferable to use numbers to not to augment the confusion, that already is great). Another common error is the "taxonomization" of clades, that is, the creation of several useless "pseudotaxa" to fit to clades.

Clades do not exist in Nature! They do not have exact correspondence to natural beings. They are just hypotheses of relationships among taxa according to their homologous similarities. Taxonomic categories are abstractions (with the important exception of the category species, see below), but they correspond to natural and concrete elements (= taxa), specimens of plants or animals registered at the several herbaria and Natural History museums from world-wide as holotypes, isotypes, syntypes, neotypes, epitypes or lectotypes (nomenclatural types). The nomenclatural type is permanently associated with name of taxon. Clades are distinguished for its informality and instability (see Critic of Method), and therefore they represent a risk for Biology. Cladism doesn't do more than to gather everything in a deformed mass of clades, useless entities that only generate more confusion and that goes back to the polinomials of the pre-Linnaean age.

The Phylocode (system of rules for Cladonomy) will never substitute the Linnaean Taxonomy and ICBN.

Homogeneity versus Homology

Both are criteria to classify, but Homogeneity represents a something plus with relationship to Homology.

Homogeneity besides including the Homology (descent, cladogenesis), it still reveals the subsequent evolutionary modifications (modification, anagenesis) of Darwin's formula for the natural classification.

Homology unites similar beings of origin seemingly common (structural analogy of ancestral shared) but it is not useful to distinguish individuals classes.

Homogeneity on the contrary, allows to define a class of individuals different from other, but that has an "inherent nexus", vital for the scientific knowledge.

Homology can be seen (metaphorically) as a step in a ladder that carries to a perfect classification, but Homogeneity allows to focus where the ladder will be placed to reach this aim. Example: Cactaceae although similar homologically, are homogeneously different from Portulacaceae and for that reason should be considered distinct taxon from Portulacaceae.

The perfect Taxonomy is which takes into account not only Homology (like Cladistics), but above all, the beings homogeneity and it allows to differentiate them of their homologous.

Phylogenetic Concepts

Phylogeny's corollary: "The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical." Charles Darwin: On the Origin of Species.1859:391 [cited by Judd et al. 2002] This is the criterion that distinguishes a natural classification of an artificial one. August W. Eichler is the first person to recognize this criterion in Botany and therefore his system was also the first one to be considered phylogenetic (that is, natural).(after Aaron Goldberg (1986). Classification, Evolution and Phylogeny of the Families of Dicotyledons. Smithsonian Contributions to Botany 58:1–314.)

Note: To qualify a classification as artificial, not at all, reduces your practical importance, as in the identification of specimens. And this is vital for the taxonomic practice.

"One of these original five theories of Darwin, and indeed the most important one to biologists in the latter part of the 19th century was that of common descent.

In 1866, Haeckel introduced the term ‘phylogeny’, which corresponded quite strictly to this theory of common descent of Darwin’s bundle of five theories. That is, Haeckelian phylogeny is equivalent to Darwinian common descent (genealogy: theory 2 of Darwin, Mayr 1985. [Darwin's five theories of evolution. In D. Kohn, ed., The Darwinian Heritage, Princeton NJ: Princeton University Press], p. 758) and not to the entire bundle of Darwin’s five theories of evolution as often assumed by biologists and philosophers. Haeckelian phylogeny clearly does not include Darwin’s mechanism for evolutionary change (= Darwinian natural selection). But Haeckelian phylogeny clearly does include both the amount of evolutionary change (anagenesis [= modification sensu Darwin]) and branching (cladogenesis)." (from Mayr & Bock 2002)

The origin of this confusion is in Haeckel's Generelle Morphologie (1866: p. 50): "Both ontogeny and phylogeny deal with the knowledge of the sequence of changes that organism (in the first case, the individual, in the second case the stem or type) passes through during its developmental motions." ... (1866: p. 60): "Phylogeny is the developmental history [Entwicklungsgeschichte] of the abstract, genealogical individual; ontogeny, on the other hand, is the developmental history of the concrete, morphological individual." Thus Haeckel's phylogeny is purely a derivative abstract concept of the concrete morphological (typological) individual, by the way Entwicklungsgeschichte, German word that translated into English means as Phylogeny as Ontogeny.

Haeckel influenced by Darwin (he was Darwin's Apostle in Germany), had a dream, to complete the "genealogical" tree of all species. How? Through the embryological analysis (see Biogenetic law). Well this terminated by transforming in nightmare ("Holy Grail" for the optimists and taxonomic "Black Hole" for the pessimists).

Then it is deduced that in 1859 the term phylogeny was not applied and therefore Darwin used the ambiguous term genealogical. By the way, Darwin didn't also use the terms evolution (previously used by the preformationists), nor speciation.

Distinction between phylogeny and genealogy

Yet, phylogeny is totally different from genealogy.

Definitions of genealogy:

• 1. A record or table of the descent of a person, family, or group from an ancestor or ancestors; a family tree.
• 2. Direct descent from an ancestor; lineage or pedigree.
• 3. The study or investigation of ancestry and family histories.

[Middle English genealogie, from Old French, from Late Latin geneâlogia, from Greek : genea, family + -logia, -logy.] (from The American Heritage Dictionary of the English Language, Third Edition)

It is totally evident that this is a notion applicable to humans or domesticated animals (pedigree).

This is the first (of many, see below) errors: the humanization of the phylogenetic criterion.

Definitions of phylogeny:

• 1. The evolutionary development and history of a species or higher taxonomic grouping of organisms. Also called phylogenesis.
• 2. The evolutionary development of an organ or other part of an organism: the phylogeny of the amphibian intestinal tract.
• 3. The historical development of a tribe or racial group.

[Greek phulon, race, class + -GENY.](from the same source cited above)

Then the first meaning is the one used in Systematics.

Evolution must not to be analysed genealogically, like a family tree, point-to-point, but collectively (at level of populations, populational criterion, with several elements = plural, "poly", not singular, mono = one).

If there was not Anagenesis, Evolution would not exist and the one that would be inferred would not be phylogeny but simply genealogy.

The cladistic analysis is of the genealogical (cladogenetic) type and not evolutionary, because it doesn't incorporate the anagenesis and therefore it is rigorously not totally phylogenetic, but just partially.

In other words: cladogenesis (= pure genealogy) + anagenesis = phylogenesis.

Monophyly

Monophyly is a concept totally erroneous and obscure.

Distinction between Haeckelian and Hennigian concept of Monophyly, Hennig's concept is called Holophyly by others

There is a great confusion on this concept (monophyly):

"If all the species of a tentatively delimited taxon are the descendants of the nearest common ancestor, the taxon following Haeckel (1866) is called monophyletic (Mayr 1969, Mayr and Ashlock, 1991 pp. 253–255). Hennig (1950) introduced an entirely different concept. The study of phylogeny was for him a forward (to the future) looking process; its starting point was a stem (mother) species. The Hennigian distinguishes a phyletic branch containing the stem species and all its descendants as a taxonomic unit, as a clade, no matter how different the beginning and the ending of a clade may be. Hennig transferred the traditional term monophyly to his new concept of phylogeny, causing great confusion. To terminate it, Ashlock (1971) introduced the term holophyly for Hennig’s new concept. The traditional monophyly concept and the Hennigian holophyly concept have drastically different consequences in taxonomy. A holophyletic clade encompasses a stem species and all of its descendants. A monophyletic taxon consists only of the descendants of the nearest ancestral taxon." from Mayr & Bock 2002.

Takhtajan also draws the attention to the difference of the Hennig's concept of monophyly and the one of Haeckel. Takhtajan, A.:Diversity and classification of flowering plants, pp. 2-3, 1997: "The Hennigian concept of monophyly and paraphyly is misleading and, as Cronquist (1988:40) pointed out, 'is destructive to the taxonomic system'. The acceptance of this Hennigian concept would mean the destruction of many of the best-known taxa. It is quite clear that the traditional evolutionary concept of monophyly [in the Haeckelian sense] is entirely unambiguous and creates no difficulties in its application to taxa..."

From page Evolution: "In biology, evolution is the change in the heritable traits of a population over successive generations, as determined by shifts in the allele frequencies of genes. Over time, this process can result in speciation, the development of new species from existing ones."

It is important to point out that the subject of the speciation and consequently of the evolution is the population (populational criterion, collectively, that is, plural) and not a species or isolated individual (singular).

Then, which evolves are several (prefix poly) lineages (phyle) that are in this case, divergent and that eventually form new species, which is called speciation. Contrarily to the many people think it is not a species that originates (directly) the other ones, that is a vestige of the typologic concept of species.

Primary error of Monophyly: a species don't create directly the other, they have to surpass (to leap) the barriers of the reproductive isolation (pre-zygotic and post-zygotic mechanisms) and ecological (occupation of habitats - different and isolated niches) and only divergent lineages can make this, and it is therefore that there is an evolutionary leap. The reproductive isolation initially inhibits the formation of species and later it protects them of the mutual assimilation.

Judd et al. 2002. Plant Systematics, 2nd. Ed. p. 4: "An important exception to the rule of monophyly in the recognition of taxa occurs at level of species. The problem with monophyly at the species level has to do with nature of relationships above and below the level of species...This is so because blackberries and cherries, for example, do not cross or hybridize with one another. Within species, in contrast, branches join through mating between members of a species. Thus, during the separation of one species into two, matings may occur between members of the nascent lineages such that one cannot identify a common ancestor that is unique to either or both species.

Brummitt (2003) citing J. Cullen & S. M. Walters: "...the value of monophyly as a principle in classification has been shown to be zero."

Only in the issue of November 2009 of the Taxon journal there is, at least, three articles that confirm the non-monophyly of the analyzed species:

• Ramdhani, Syd; Barker, Nigel P.; Baijnath, Himansu (2009). "Rampant non-monophyly of species in Kniphofia Moench (Asphodelaceae) suggests a recent Afromontane radiation." Taxon 58(4): 1141-1152.
• Hörandl, Elvira; Greilhuber, Johann; Klímová, Katarina; Paun, Ovidiu; Temsch, Eva; Emadzade, Khatere; Hodálová, Iva (2009). "Reticulate evolution and taxonomic concepts in the Ranunculus auricomus complex (Ranunculaceae): insights from analysis of morphological, karyological and molecular data." Taxon 58(4): 1194-1215.
• Hung, Kuo-Hsiang; Schaal, Barbara A.; Hsu, Tsai-Wen; Chiang, Yu-Chung; Peng, Ching-I; Chiang, Tzen-Yuh (2009). "Phylogenetic relationships of diploid and polyploid species in Ludwigia sect. Isnardia (Onagraceae) based on chloroplast and nuclear DNAs." Taxon 58(4): 1216-1225.

Thus Monophyly does not exist, it is an erroneous phylogenetic concept.

Paraphyly

On the other hand "Paraphyly does not exist in a Darwinian classification" [= Linnaean Taxonomy]. (!) from E. Mayr & W. J. Bock 2002, J. Zool. Syst. Evol. Research 40:181.

Polyphyly

Then only it remains the polyphyly of ALL taxa.

Evolution Concepts

Evolution is by leaps (that is, not continuous) (similar to the Thomas Henry Huxley's saltationism and punctuated equilibrium, but contrary to the phyletic gradualism). In honor to Hugo de Vries and others, this theory could be called neo-saltationism.

Even Darwin already knew about his erroneous ideas on gradualism in evolution in his letter to Joseph Hooker in July of 1879: "On the contrary, Darwin's abominable mystery is about his abhorrence that evolution could be both rapid and potentially even saltational. Throughout the last years of his life, it just so happens that flowering plants, among all groups of organisms, presented Darwin with the most extreme exception to his strongly held notion natura non facit saltum, nature does not make a leap."

As it is clear on Fig. 2 of the article , the evolutionary lineages ("lines") are parallel and they create the several ramifications of Angiosperms, everything very complex and dynamic, anything in a singular and static way as cladists want (with APG I, II and III, ahead).

After Stuessy: "By this time, many different evolutionary lineages have reached this stage, which helps explain the great diversity of the basal angiosperms. Seeking the one ancestor of angiosperms, therefore, would be futile." "In a more restrictive sense, they [basal angiosperms] are polyphyletic, as they may have had four or more different evolutionary origins from different seed fern ancestors."

By the way, Stuessy's classificatory scheme for Angiosperms in the end of the article should be, without a doubt, adopted, because it conciliates the tradition with the newest available knowledge on the subject. "In my view, the best way to deal with classification of this situation is to divide the angiosperms into three classes: monocots, dicots (eudicots), and Archaeangiospermae (basal angiosperms)."

This theory excludes single step mutations ("megaleaps", macromutations, Goldschmidt's "Hopeful monsters" hypothesis) and miraculous interventions (according to Darwin). It excludes such things, simply because it is not an analysis of macroevolution.

This is an extremely easy concept: the divergent lineages have to give an evolutionary leap to surpass (to leap) the barriers of the reproductive isolation (pre-zygotic and post-zygotic mechanisms) and ecological (occupation of habitats - different and isolated niches) to form new species.

Definitely, taxonomic groups do not have sisters, fathers or mothers and they are not "evolving", that is simply ridiculous, the subject of evolution, are actually, divergent lineages.

It is therefore that transitional fossils are not found.

The evolutionary lines are always discontinuous, suffering a true genic conflict, complex interaction of factors (mechanisms of speciation): genotypic (mutations, alleles, polyploidy, etc) and phenotypic (natural selection, allogenomic processes as endosymbiosis, plasmid and other horizontal gene transfers, infections for retrovirus:important mutation vectors, transposons and retrotransposons, etc) besides interferences of environment (hybridization, etc). See also Horizontal gene transfer in evolution.

Everything is discontinuous, divergent lineages differ and evolutionarily leap for other species, nothing in that process is in a direct way.

The appearance of a new species does not implicate (necessarily) in the "progenitor species" extinction.

About the Species Concept

Although several species concepts exist, the only really consistent and fully applicable is the linnaean species concept. Providing the stable base of the whole taxonomic system.

Three Metaphors

• Tree-of-life
• Web-of-life
• Dynamic jigsaw puzzle

The real metaphor for the Evolution is not the Tree-of-life, full of ramifications (cladogenesis) of "mythical" common ancestor but a great dynamic jigsaw puzzle, where each placed piece conditions the fitting of the following piece (that is: adaptation to the ecological niches, for instance). "A divergent phylogenetic tree is a useful tool for communicating information about evolutionary history and for quantitative analyses of evolutionary patterns. However, relationships are not always strictly tree-like, which raises the question of whether the tree metaphor can be adapted to cases where there is considerable reticulation. In the face of reticulate evolution, must we abandon tree conventions (e.g., Rivera & Lake, 2004; Bapteste & al., 2005 ), or can we find effective means to use tree concepts to analyze genealogical histories that are not fully divergent?"

Arnold introduces the web-of-life metaphor that allows much more interactions among the several elements based on "genetic exchange" concept: "In the past decade, numerous research groups—studying a wide array of species complexes—have reported findings that indicate an evolutionary pattern best described as web rather than as a bifurcating tree."

Hybridization, introgression, allopolyploid speciation, horizontal gene transfer

Hybridization as a process of speciation was known as early as 1760 by Linnaeus: "Linnaeus...surprisingly, he also held that species could arise through hybridization (i.e. hybrid speciation) between previously created forms. In this regard, he wrote in his Disquisitio de Sexu Plantarum (1760; as cited by Grant 1981, p. 245), 'It is impossible to doubt that there are new species produced by hybrid generation'.

"The occurrence of reticulations in the evolutionary history of species poses serious challenges for all modern practitioners of phylogenetic analysis. Such events, including hybridization, introgression, and lateral gene transfer, lead to evolutionary histories that cannot be adequately represented in the form of phylogenetic trees."

The hybridization (major mechanism of speciation, mainly in plants) is the principal evidence of polyphyly of taxa. Allopolyploidy also is a main factor of speciation, in plants (example: Spartina anglica, see Salmon et al. 2005 ).

The example of Spartina anglica breaks two "dogmas":

• 1. a monophyly of taxa.
• 2. hybrids are always sterile.

E. Hörandl 2006: "For higher plants, several authors (e.g., Grant, 1981; Arnold, 1997) have estimated that the majority of taxa are indeed of hybrid origin."

Judd et al. 2002. Plant Systematics, 2nd. Ed. p.122: "Interspecific gene flow (hybridization, sometimes referred to as reticulation) plays a dual role in speciation. On the one hand it may reduce diversity by merging species. On the other hand, it can be a powerful force leading to speciation, especially when coupled with polyploidy, an important source of genetic variation within plant species".

Soltis et al 2008: "McDade (1992) concluded that “cladistics may not be specially useful in distinguishing hybrids from normal taxa” and that “hybridization is one of many sources of error in cladistic analyses” (pg. 1329; see also Hull 1979 ). Our molecular data for allopolyploids and hybrids echo these concerns, especially with the use of rDNA or other genes that typically undergo homogenization. Just as McDade’s results caution against the use of putative hybrids in phylogenetic analyses based on morphology, we similarly advise that our data join a wealth of already available data indicating that caution be employed in analyses involving ITS and ETS sequence data of diploid or allopolyploid hybrids."

The changes are never gradual, but abrupt, because the descendants either are adaptable or not, not existing middle term.It happens multiple structural divergences in the descendants, and not isolated divergences.

Evidences in this sense: adaptive radiation, rapid changes caused by abrupt niche shifts lead to speciation (see Levin, D. A. 2005. Systematic Botany 30(1):9-15).

Evolution is much more complex than the point of view of Cladistics!

Critic of the Cladistic Method

Moreover, this method is highly distortional, the distortions can be:

• resolution: as it has to be objective, it doesn't ponder (weighting) the characters, it means that vegetative characters that have minor phylogenetic importance are equivalent (have same weight) to the sexual characters (actually, much more important phylogeneticly) and this is a great error; it needs of many characters and will look for them in genic polymorphisms, but from allogenome (that is, prokaryote DNA), and again a great error!
• There is also the serious problem of heterobathmy, described by Takhtajan 1997: "the more strongly heterobathmy is expressed, the more contradictory is the taxonomic information provided by different sets of characters, and the more difficult it is to pass from the evolutionary series of separate characters to the phyletic sequences of the organisms themselves".
• "Transitional groups" or strongly anagenetics "break" the cladogram, this is characterized by polytomy and low resolution (weak support).
• "Bridge" taxon as Henriqueziaceae should not be considered neither Bignoniaceae, nor Rubiaceae, this is an example of bad application of the taxonomic category. (see discussion at: George King Rogers. (1984). Gleasonia, Henriquezia, and Platycarpum (Rubiaceae). Flora Neotropica, 39, p.3)
• The cladistic analysis should be as the named Total Evidence, or be, a combined analysis of several data sets (mainly: morphological, from nuclear genome and including fossils).
• The cladogenesis analysis can be (preferentially) refined by the insert in the space context (through phylogeography) and time context (through calibration by molecular clocks).
• polarity: according to the choice of outgroup, cladograms will vary, becoming the system very contingent (amplifying the subjectivity degree).
• parsimony analysis made by beta softwares (that is, with bugs).
• "configuration" (topologies): according to the elements (the "ingroup") that will be analyzed, the configuration of the cladogram could change completely. Now, do we know that the fossils have a primordial importance in the explanation of the phylogeny, and however I almost do not see analysis of fossils in the cladograms, how is that possible? Fossils should be used much more to build phylogenetic trees (not only as molecular clocks). Example:Jacques, Frédéric M.B.; Gallut, Cyril; Vignes-Lebbe, Régine; Zaragüeta i Bagils, René (2007):Resolving phylogenetic reconstruction in Menispermaceae(Ranunculales) using fossils and a novel statistical test. Taxon 56(2):379-392.

About fossils, "megatrees", ...:"Recent reviews of the construction of large phylogenies have focused on supertree methods that involve separate analyses of data sets and subsequent integration of the resulting trees. Here, we consider the alternative method of analyzing all character data simultaneously. Such ‘supermatrix’ analyses use information from each character directly and enable straightforward incorporation of diverse kinds of data, including characters from fossils." De Queiroz, A. & J. Gatesy (2007):The supermatrix approach to systematics.Trends in Ecology & Evolution 22(1):34-41. And from the same source:"Molecular databases such as GenBank (http://www.ncbi.nih.gov/GenBank/) are a crucial resource for assembling supermatrices. However, to gain a more complete view of phylogeny, morphological characters must also be included."

• cladogram is not the same as phylogenetic tree. See Potter, Daniel & John V. Freudenstein. 2005. Taxon 54:1033–1035. "Since we never can know the true underlying phylogeny of a group of organisms, the only phylogenetic trees we can draw are hypothetical ones in which the ancestors depicted as giving rise to real (i.e., observable) taxa are based on speculation. Such phylogenetic trees are generally derived from cladograms, but there is a distinction between the two, and it is the latter that are derived directly from phylogenetic analysis of character state distributions, i.e., via the formulation and testing of hypotheses. Thus, cladograms fall strictly under the realm of science while hypothetical phylogenetic trees do not, and only the former should be used as the basis for constructing and revising classifications." But Hörandl, Elvira in Taxon 55:567 says: "So far the theory; now to the practice of classification. I do not agree with Potter & Freudenstein (2005) that 'we can never know the true underlying phylogeny of relationships' but I would rather say that usage of tree-building methods alone will fail to give insights in the underlying phylogenies. Admittedly, only at lower (species and generic) levels we may have a realistic chance to get insights into the kind of evolutionary processes..."
• cladogram also is not the same as true tree, it is an inferred tree, likewise, true phylogeny is not the same as inferred phylogeny.
• cladogram, its graphic representation, induces to evaluation error. When you look at a cladogram, you don't notice clearly that many branches are not simply supported (not even indicated the support percentage, a lot of times inferior to 50%).It should be represented in a clear way the ramification pattern that is supported by the robustness indexes (= support, in percentage) of the phylogenetic tree: Bootstrap or Jackknife or NNI (= Nearest-neighbour-interchange) swapping > 90%.
• cladogram, its treelike model is a bad simplification of the evolutionary complexity, see Vriesendorp, Bastiaantje & Freek T. Bakker. 2005.Reconstructing patterns of reticulate evolution in angiosperms: what can we do? Taxon 54:593–604. "Hybridization is thought to be an important phenomenon in angiosperm evolution, and it has been suggested that a majority of all plant species may be derived from past hybridization events (e.g., Stebbins, 1959; Raven, 1976; Grant, 1981; Arnold, 1997).In addition to species-level hybridization, other (genome-level or molecular) evolutionary processes such as recombination, gene conversion or horizontal gene transfer can confound the phylogenetic signal in the data to such an extent that it may become non-treelike, and phylogenetic methods are not appropriate for analysis. It is best to check prior to phylogenetic analysis whether this applies, and if so, then use network methods to represent it (Bryant & Moulton, 2004)."
• dichotomous branching patterns (= "each inner node is ideally binary"), E. Hörandl analyzed five speciation patterns, concluded that the cladogram, reflects well the underlying phylogeny in only one (cladogenetic speciation) with strictly dichotomous branching pattern, see E. Hörandl (2006) for more details.
• completely complex methodology ("esoteric"): heuristic searches, parameters, algorithms, ...
• statistical artefacts such as long-branch attraction.
• serious problems with samples: misidentification, low representativeness.
• counter-intuitive results: birds regarded as reptiles, cactus as portulacaceous, frankly!
  • Are the birds feathered-crocodiles or crocodiles birds-scaly? Could be answered that they would be like Archosauria, but this idea is a chimerical monster, it adds nothing to true Science. Would not it be better simply to admit that there are genes that are turned on or turned off, depending on environmental factors, example epigenetics?

Conclusions

Hörandl, Elvira. 2006.Taxon 55(3):569."Considering these different aspects, I suggest that clades retrieved by phylogenetic analyses should be not used solely as a basis for classification, but should be regarded primarily just as information for a better understanding of relationships. If there is any indication that phylogenies are not dichotomous, researchers should refrain from quick taxonomic conclusions and try first to understand better evolutionary processes leading to such tree topologies, whereby a broad array of analytical methods and datasets, including external evidence,should be used."

As the monophyly (its basic premise) doesn't exist, then Cladistics should be reformulated ab initio. Cladograms are not valid to represent reality (they are false).

Synthesis: several (poly) elements (= divergent lineages) suffering the influence of several speciation mechanisms evolve for several new elements (= new species), not existing place for monophyly.

Since all taxa are polyphyletic (several divergent lineages derivative of several ancestors), that constant argument that certain taxa should be rejected for that reason, must be substituted for: this taxa is not similarly homologous, or be they are heterologous (divergent lineages that don't share ancestors in common) or they contain homoplasic characters (that demonstrate apparent affinity, but due to convergent evolution).

However, even if they are homologous, these taxa can still be highly heterogeneous.

Example

See Malvales.

Concludingly, Cladistics as systematic approach is erroneous leading to erroneous conclusions...but it may be useful as method to evaluate homology.

Summary

The formula for a perfect classification is:

• To join together the similar elements (homologous) into groups through a method as Cladistics. This could avoid the homoplasy.
• To evaluate the degree of homogeneity of those elements to separate them in minor homogeneous groups (taxa). This could avoid the tendency to merge taxa too much, named lumping.
• And to apply the correct taxonomic category (Family, Subfamily, Tribe, Genus, Subgenus, etc). This could avoid the tendency to divide taxa too much, named splitting.

The method to evaluate homogeneity could be named "Anagenistics" (from Anagenesis) and it would be inverse from Cladistics, analyzing divergent characters.

Debate Cladism versus Taxonomy (references)

Further reading

• Mayr, E. & Bock, W. J. 2002. Classifications and other ordering systems. J. Zool. Syst. Evol. Research 40: 169–194. for more details PDF file available here.
• Stebbins, G. L. 1959. The role of hybridization in evolution. Proc. Amer. Philos. Soc. 103: 231–251.
• Raven, P. H. 1976. Systematics and plant population biology. Syst. Bot. 1: 284–316.
• Grant, V. 1981. Plant Speciation, ed. 2. Columbia Univ. Press,New York.
• Arnold, M. L. 1997. Natural Hybridization and Evolution.Oxford Univ. Press, Oxford.
• Brummitt, R. K. (1997). Taxonomy versus cladonomy, a fundamental controversy in biological systematics. Taxon 46(4):723-734.
• Grant, Verne:INCONGRUENCE BETWEEN CLADISTIC AND TAXONOMIC SYSTEMS. American Journal of Botany 90(9):1263-1270. 2003.
• Sosef, M. S. M. 1997. Hierarchical models, reticulate evolution and the inevitability of paraphyletic supraspecific taxa. Taxon 46:75-85.
• Brummitt, R. K. (2002). How to chop up a tree. Taxon 51:31-41.
• Brummitt, R. K. (2003).Further dogged defense of paraphyletic taxa. Taxon 52:803-804.
• Brummitt, R. K. (2006), Am I a bony fish? Letter to the editor. Taxon 55(2):268-269.
• See also this very important initiative, like a manifest against PhyloCode and excesses of Cladistics: Taxon 54(1)(2005): 5-8 LETTERS TO THE EDITOR (Coordinated by: Nordal, I. & Stedje, B.): Paraphyletic taxa should be accepted. available online here (pdf file; page 18), including proposal, but without the 150 signatories, several notable botanists from world-wide, among them: Brumitt, R. K. (from Kew) and Sosef, Mark.

• Hörandl, Elvira. 2006:Paraphyletic versus monophyletic taxa—evolutionary versus cladistic classifications. Taxon 55(3):564–570.For updated information on the controversy "Cladism versus Taxonomy". Example: "Here I want to show that a strict application of monophyly for grouping of taxa is problematic, because the commonly used tree-building methods result in a too strong abstraction and a too simplified visualization of evolutionary processes."
• Hörandl, Elvira. 2007:Neglecting evolution is bad taxonomy. Taxon 56(1):1–5.
• Alves, R. J. Válka; Vianna Filho, M. D. Machado (2007).Is classical taxonomy obsolete? Taxon 56(2):287-288(2)."Computers can organize information with amazing speed, but they can not travel into the past, fill in current information gaps and produce true phylogenies. The Angiosperm Phylogeny Group (APG, 2006) website is a pioneer initiative taking the first steps toward the construction of a hypothetic phylogeny. But, no matter how elegant the results seem to be, the available data simply can not provide all the answers. No novel or miraculous solution has filled in the gaps since Hedberg (1995) so eloquently commented on this matter over a decade ago: “…cladistics, as currently practised in taxonomic botany, is no less subjective than ‘traditional evolutionary systematics’, although nowadays it generally attempts to avoid idiosyncratic reactions by delegating the combination of facts and assumptions and the construction of ‘phylogenetic trees’ to standardized computer programs.” In fact it is quite surprising that eleven years after Hedberg’s article, not much has changed in the way phylogenies are proposed."

• Farjon, Aljos (2007). "In defence of a conifer taxonomy which recognises evolution". Taxon 56(3):639-641. "It is time to start firmly rejecting “phylogenetic” classifications that violate evolutionary principles, such as the understanding that taxa must evolve from other taxa and that whether the ancestral taxa are extinct or not is irrelevant. “Paraphyly is evolution” joked Asterix and Obelix in a recent cartoon on a poster electronically distributed by R.M. Schmelz & T. Timm (December 2006). Good jokes are always serious. Hennig (1996) in his book Phylogenetic Systematics declared: “The task of the phylogenetic system is not to present the result of evolution, but only to present the phylogenetic relationships of species and species groups.” The task of evolutionary biologists is to argue, with support of evidence from morphology and the fossil record and even from other disciplines such as ecology and geology, that the broad basis on which a classification of organisms must rest is to reflect the results of evolution. Morphology also reflects genetics, although imperfectly, and with the development of “evo-devo” we may learn to understand both better. This broader approach of course includes consideration of a phylogenetic hypothesis based on DNA sequence data. The narrow alternative based on monophyly, as succinctly stated by Albach & al.(2004) is “to either lump some well recognized genera into a large genus Veronica or split Veronica into several genera that seem impossible to separate using morphological or structural characters.” The accumulating examples of this negation of several pathways of evolution, or even all evolution (the creationists are attentively looking on, thinking they are onto something) are indeed creating chaos, as Brummitt (2006) and others have argued. When users of classifications become familiar with the arguments over which taxonomists fight and begin to see the lack of logical argument behind these upheavals in their familiar groups of plants, they may well abandon the results of our research altogether and simply stick with what they have. Taxonomy should be a science that earns its respect from users as well as fellow scientists. If it insists on strict adherence to a spurious dictum, more appropriate to a religious sect than to science, it will loose that respect. It is hardly the time to risk being so treated."
• Zander, Richard H. (2007). Paraphyly and the species concept, a reply to Ebach & al. Taxon 56(3):642-644.
• van Wyk, Abraham E. (2007).The end justifies the means. Taxon 56(3):645-648.
• Arnold, M. L. (2007). Evolution through Genetic Exchange. Oxford University Press. ISBN 0-19922-903-1.
• Soltis, Douglas E.; Mavrodiev, Evgeny V.; Doyle, Jeff J.; Rauscher, Jason; Soltis, Pamela S. 2008. ITS and ETS Sequence Data and Phylogeny Reconstruction in Allopolyploids and Hybrids. Systematic Botany 33(1):7-20
• Stuessy, Tod F. & König, Christiane (2008). Patrocladistic classification. Taxon 57(2):594-601.
• Hörandl, Elvira (2010). Beyond cladistics: Extending evolutionary classifications into deeper time levels. Taxon 59(2):345-350.
• Stuessy, Tod F. 2010. Paraphyly and the origin and classification of angiosperms. Taxon 59(3): 689-693.
• Hörandl, Elvira; Stuessy, Tod F. (2010). Paraphyletic groups as natural units of biological classification. Taxon 59(6): 1641-1653. ["paraphyly is a natural transitional stage in the evolution of taxa"]
• Shapiro, James A. (2011). Evolution: A View from the 21st Century. FT Press Science. ISBN 978-0-13-278093-3