The term holophyletic has remained obscure perhaps because most cladists find it unnecessary, since they have already altered the meaning of the term monophyletic to fit their need. The traditionalists, on the other hand, simply continue to use the term monophyletic as they have always done so, and find no need to use the term holophyletic since they do not make a distinction between paraphyletic and holophyletic taxa.

“Well, Darwin was a great biologist – a revolutionary, saint and prophet of science indeed – but only came close, without ever explicitly stating or applying the principles of homology and synapomorphy that turned phylogenetics into a science. That all happened after his time....”

Darwin in reality pays close attention to homology and synapomorphy. He points out that taxonomically informative characters can often be found in the embryos and among atrophied or rudimentary organs, and that both of these types of characters are often of higher taxonomic value than vital organs. He therefore realized the possibility of convergent evolution producing superficial similarities and warned his readers about relying on these characters to group taxa. In fact, he and his contemporary systematists display far more insight than many modern systematists, such as the pheneticists and the cladists, who treat all characters equally. Darwin knows better; the Darwinians know better. Now it appears that some cladists have independently rediscovered the wisdom contained in Darwin’s book Origin. Some cladists have reinvented character weighting on their own! Darwin opens his chapter with the following statement:

“The existence of groups would have been of simple signification, if one group had been exclusively fitted to inhabit the land, and another the water; one to feed on flesh, another on vegetable matter, and so on; but the case is widely different in nature; for it is notorious how commonly members of even the same subgroup have different habits.”

Thus Darwin realizes that similarities in some characters (such as diet or habitat preference) may be uninformative of phylogenetic relationship because they are found in different groups. Contrast this insight with recent attempts by some cladists to use food habits as a taxonomic character (de Queiroz’s use of herbivory in analyzing the iguanian lizards and Rodriquez-Robles’ use of dietary preference in analyzing the lampropeltine snakes) and one should realize how unwise it is to ignore the wisdom of past great minds, as cladists have often been accused of doing.

Ernst Mayr writes: “Monophyletic: This term was coined by Haeckel in 1866 in support of Darwin’s theory of common descent. He was unalterably opposed to then current theories of Darwin’s opponents, who espoused numerous independent origins of living things. Haeckel termed such multiple origin theories polyphyletic.”

Johnscanlon:
“Hennig explicitly proposed that a natural classification should use only monophyletic taxa.”

Ever since Darwin’s theory of common descent became widely accepted, all of the then currently recognized taxa would have been subjected to the test of monophyly. By the time Hennig was practicing systematics, practically all known taxa were already considered monophyletic according to the best available data at the time. Hence Hennig did not advocate that only monophyletic taxa be recognized, he came along and mandated that only holophyletic taxa be recognized. If anyone should insist that taxa must be holophyletic to be acceptable, he/she is thus following the dictates of Hennig. He/she is thus a Hennigian in his/her classificatory philosophy.

Hennig, as Mayr points out, has considerable difficulty coming up with a workable ranking system. Mayr writes:
“His followers have abandoned both of Hennig's basic criteria (equal rank of sister groups and geological age) not only because they led to too great an imbalance between explosively evolving and slow groups (including living fossils) but also because strict coordination of sister groups led to a veritable explosion of categorical levels.”

Some (but not all) cladists who have not abandoned Hennig’s criteria are advocating the abandonment of the Linnaean ranks, since it cannot accommodate the explosion of categorical levels. Nevertheless, Linnaean ranks are useful for most biologists. Therefore most biologists will continue to use them.

johnscanlon:
"I can’t see any net advantage in abandoning genera; but I like them monophyletic, and this is always possible except in the case of species that are actual ancestors of two or more genera that it would be impractical to lump. Since actual ancestors are unlikely to be observed (even as fossils) but may be indistinguishable from some of their descendants (like F – F14 in Darwin’s diagram), nothing is lost by naming a monotypic genus for the ‘ancestral’ species in such a case."

I agree, there is no reason to abandon the rank of genus. Neither is there any reason to abandon the other Linnaean ranks. Forcing species into strictly holophyletic groups would simply lead to either excessive splitting (e.g. Utiger et al.’s split of Elaphe) or excessive lumping (Kluge’s lumping of Morelia and Chondropython) or both (Frost and Etheridge’s splitting of the Iguanidae and their lumping of the Chameleonidae and Agamidae). Not surprisingly these taxonomic proposals have been controversial. More than a decade later, Frost and Etheridge’s classification has been reversed and Kluge’s proposal has largely been ignored. Utiger et al.’s proposal will likely be ignored by most veteran herpetologists, since none of the genera they resurrect and erect is morphologically distinguishable from Elaphe, unlike Pituophis, Arizona, Lampropeltis, Cemophora, Stilosoma, Rhinocheilus and Bogertophis. There is no reason to splinter a slowly evolving genus such as Elaphe simply because one member migrated to North America and evolved rapidly to give rise to a number of divergent species, classifiable in different genera, thus rendering Elaphe paraphyletic. The parental genus Elaphe remains unaffected by the evolution of new taxa in the New World and it should not be sacrificed at the altar of the Hennigian's ideological distaste for paraphyletic taxa.

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