johnscanlon wrote:
(1-2) What advantage does paraphyly have here? It always obscures actual relationships when these are known, and it is purely arbitrary what parts of the clade are excluded.

Me:
Traditional taxa are not defined arbitrarily. They are recognized on the basis of both morphological disparity and phylogenetic relationships. Contrast this with recent taxonomic proposals by the likes of Utiger et al., who split the morphologically conservative genus Elaphe into nearly a dozen genera on the basis of mtDNA data. Their taxa are arbitrarily delimited since none of the genera they recognize can be morphologically distinguished from one another or from Elaphe. The reason they split Elaphe is because a number of morphologically distinct genera (e.g. Pituophis, Lampropeltis, Cemophora et al.) have budded off of Elaphe, rendering it paraphyletic.

The advantages of paraphyletic taxa are obvious:
1. There is no need to recognize contrived taxa due to excessive splitting
2. There is no need to lump taxa excessively, which is the only other alternative available to the cladists
3. Paraphyletic taxa can be more morphologically homogeneous than holophyletic taxa.

johnscanlon:
(3) I try to avoid groups with unwieldy numbers of species per genus, but the Australian skink genera Ctenotus and Lerista are examples where a species-group classification has been used including various monotypic 'groups' (e.g. in work by Storr where phylogeny was not a consideration).

Me:
If a group of species closely resemble each other and their common ancestor morphologically, then it is not wise to split it into many different genera, even if distinct lineages can be discerned (e.g. using mtDNA) and even though such a group may be paraphyletic. The resultant mess is far worse because there would then be many contrived genera that are morphologically indistinguishable from one another. Because they are placed in different genera, their close relationship is also obscured. The cladistic alternative, which is excessive lumping, creates an unwieldly large genus, which is also morphologically heterogeneous.

Johnscanlon:
(4) Cladistics IS a comprehensible hierarchical naming system; or what part of monophyly don't you comprehend? Recognising paraphyletic taxa involves arbitrarily and subjectively jacking up subgroups of a clade to a higher rank, adding 'information' of dubious value and deleting true information about their genealogical relationships. Just because it has been done by default since before Darwin was born, doesn't mean it makes any sense, or is intuitively more satisfying than monophyly. You may find it so, but I don't.

Me:
I am sure Patrick comprehends “monophyly”. In reality, the destruction of paraphyletic taxa involves arbitrarily and subjectively jacking up subgroups of a clade to a higher rank. Species which are classified by most systematists in the paraphyletic genus Elaphe are being subjectively and arbitrarily elevated into new genera by cladists who cannot tell us the difference between the genera they recognize. Splitting Elaphe into a number of morphologically indistinguishable genera such as Euprepiophis, Pseudelaphe and Pantherophis actually deletes information about the genealogical relationships among them and adds no new information whatsoever. Darwin, who understands evolution perhaps better than Hennig and most cladists, fully recognizes the utility of paraphyletic groups, for he recognizes that different lineages may have evolved morphologically at vastly different rates, and it would be impossible to codify these different rates of evolutionary change without recognizing paraphyletic groups.

Darwin wrote:
“I believe that the arrangement of the groups within each class, in due subordination and relation to the other groups, must be strictly genealogical in order to be natural; but that the amount of difference in the several branches or groups, though allied in the same degree in blood to their common progenitor, may differ greatly, being due to the different degrees of modification which they have undergone; and this is expressed by the forms being ranked under different genera, families, sections, or orders.

Darwin elaborated further:
“The forms descended from A, now broken up into two or three families, constitute a distinct order from those descended from I, also broken up into two families. Nor can the existing species, descended from A, be ranked in the same genus with the parent A; or those from I, with the parent I. But the existing genus F14 may be supposed to have been but slightly modified; and it will then rank with the parent-genus F; just as some few still living organic beings belong to Silurian genera.”

Me:
Darwin thus shows us that in order to codify the morphological changes the descendants of A have accumulated, these descendants should be removed from the same genus, and even the same family, as A. On the other hand, since the descendant of F has not changed, it should be classified in the same family and genus as its ancestor F. Paraphyletic groups are therefore not arbitrarily defined; paraphyletic taxa are the result of the need to codify evolutionary change. If there is no evolutionary change, then there is nothing to codify and evolutionary biologists do not have to recognize anything but holophyletic groups. But a world in which no evolutionary changes occur is an uninteresting one for biologists, and of course systematics would not even exist. Neither would human beings. In a world in which nothing ever changes evolutionarily, all we would find are blue-green bacteria.

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