User:Berton/Cladistics

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Contents 1 Cladistics as method not compatible with Linnaean Taxonomy 1.1 Phylogenetic Concepts 1.1.1 Monophyly 1.1.2 Paraphyly 1.1.3 Polyphyly 1.2 Evolution Concepts 1.3 Critic of the Method 1.4 Debate Cladism X Taxonomy (references) 1.5 Conclusions

[edit] 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 live 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 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.

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

[edit] 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.

"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. Darwin didn't also use the terms evolution (previously used by the preformationists), nor speciation.

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 (only) applicable to humans.

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).

[edit] 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.

See: 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."

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

[edit] 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. Berton 13:19, 5 October 2006 (UTC)

[edit] Polyphyly

Then only it remains the polyphyly of taxa. Berton 13:26, 5 October 2006 (UTC)

[edit] 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.

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.

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 transfer, infections for retrovirus: important mutation vectors, transposons and retrotransposons, etc) besides interferences of environment (hybridization, etc). See also Horizontal gene transfer#Evolutionary theory.

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).

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". Berton 16:09, 5 October 2006 (UTC)

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). See also rapid modes of evolution.

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

[edit] Critic of the Method

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

• resolution: as it has to be objective, it doesn't ponder 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!
• polarity: according to the choice of outgroup, cladograms will vary, becoming the system very contingent.
• 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?
• 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, ...
• counter-intuitive results: birds regarded as reptiles, cactus as portulacaceous, frankly!

[edit] Debate Cladism X Taxonomy (references)

• 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.
• 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." Berton 18:17, 4 October 2006 (UTC)

[edit] 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.

Concludingly, Cladistics as systematic approach is erroneous method leading to erroneous conclusions...

P.S.:Wow! I have just known that the turtles are our close relatives! see polyphyly