“In considering this view of classification, it should be borne in mind that the element of descent has been universally used in ranking together the sexes, ages, dimorphic forms, and acknowledged varieties of the same species, however much they may differ from each other in structure. If we extend the use of this element of descent – the one certainly known cause of similarity in organic beings, - we shall understand what is meant by the Natural System: it is genealogical in its attempted arrangement, with the grades of acquired difference marked by the terms, varieties, species, genera, families, orders, and classes.”

Very interesting quote from Darwin. He realizes that the species category is not typological. Species concepts that rely on typology, for example, the phylogenetic species concept on which many cladists rely, are thus scientifically untenable. Darwin advocates that classification be "genealogical." He also advocates that paraphyletic taxa be recognized by ranking an ancestor in a different genus as its descendants if the amount of morphological disparity between ancestor and descendant justifies it. Therefore paraphyletic taxa is not anathema to his genealogy-based classification. Conversely, strictly holophyletic taxa, such as those advocated by Hennig and his followers, do contradict Darwin's natural system, since ranking different genera according to their degrees of modification is not possible if only holophyletic taxa are recognized.

As I said, ever since Haeckel coined the term monophyletic in 1866, and ever since Darwin's theory gained widespread acceptance, all taxa that are recognized have been tested for monophyly. Hence the decades old 'grade vs. clade' debate is not a 'polyphyletic vs. monophyletic' debate. It is instead a monophyletic vs. holophyletic debate. To recognize grades in classification, it is therefore necessary to recognize paraphyletic groups. Hence it would be inaccurate to suggest that some biologists (including those who are called 'gradists') are advocating the recognition of polyphyletic taxa. It is true that some taxa recognized on the basis of morphological similarities are polyphyletic but then again many cladistically delimited taxa have also been shown to be polyphyletic. For example, some cladists consider the hooked fifth metatarsal to be a synapomorphy and they claim that turtles are diapsids. Other evidence suggest instead that turtles are anaspids. Hence, if the hooked fifth metatarsal is indeed a homoplasy, as Michael Lee has advocated, the group that consists of turtles diapsid would be polyphyletic, even if it is a cladistically delimited group.

“Since Darwin’s day, users of classifications (for example, those designing comparisons and experiments to test evolutionary theory and particular patterns and processes) expect members of the same taxon to be ‘related’ to each other more closely than to those of other taxa at the same rank. Much of the time, accepted classification has failed to do what was expected, and much experimental effort has been wasted as a result. An example, probably typical: which species of Python should be compared serologically with Australian and New Guinea pythonines to test the systematic ideas of McDowell 1975? Schwaner and Dessauer 1981 picked the wrong one (P. regius) to test, recisely because McDowell had a paraphyletic concept of the genus but they assumed he meant it to be a clade.”

Since most taxa have traditionally been classified phenetically, it is thus no surprise that sometimes these taxa fail to inform us of branching order. Picking the incorrect outgroup is unfortunately a fairly common error in systematic analysis. In one recent study, for example, Lampropeltis (which is descended from a species of Elaphe which migrated to the Old World from the New) was picked as an “outgroup” in a mtDNA analysis of European species of Elaphe. That is analogous to picking Homo sapiens as the outgroup when analyzing the relationship among Gorilla, Pan and Pongo! One certainly cannot blame the classification for that mistake. The researcher is to blame in these cases. Even if were to adopt a holophyletic arrangement, the same mistake can still be made. Recognizing the dozen or so contrived taxa proposed by Utiger et al. to accommodate the pieces of the genus Elaphe, for example, will not prevent someone from mistakenly using Lampropeltis as an outgroup in an analysis of relationships among the European ratsnakes.

“Once the artificial and misleading features of paraphyletic taxa are recognized and we adopt a monophyletic arrangement instead, actually practicing systematics on real organisms (in contrast to bombinating in a vacuum ) will show the impracticality of ranks.”

Actually it is well known for decades to taxonomists that holophyletic groups are impractical, hence the grade vs. clade debate. In order to recognize Lampropeltis and other derived genera, the basal genus Elaphe, which is paraphyletic, had to be splintered into a dozen or so contrived genera that cannot be defined or diagnosed under Utiger et al.’s proposal. The alternative is excessive lumping. Lampropeltis, Pituophis, Arizona, Bogertophis, Rhinocheilus, Stilosoma, and Cemophora have to be transferred back to Elaphe. Neither alternative is tenable as both require wholesale taxonomic changes. If Utiger et al.’s data is contradicted by a newer study, more wholesale reshuffling is necessary. Scientific communications may grind to a screeching halt, if the cladists’ ideological distaste for paraphyletic taxa must be accommodated. The better alternative is for the cladists to lose their religion, as some cladists have done, and accept paraphyletic taxa. Recently even Frost and Etheridge have not objected to the recognition of the paraphyletic Agamidae as their proposal to lump Chameleonidae and Agamidae was never fully accepted and it has been reversed by fellow cladists.

“If we know (as we think we do) that snakes are varanoid, anguimorph, scleroglossan squamates, and only one of numerous independently evolved groups of limbless lizards, why ‘promote’ them to the same rank as ‘other lizards’? There is no imaginable justification apart from claiming ignorance of actual relationships – an interim solution at best, now requiring heroic effort to ignore the accumulated evidence.”

Although I agree with you that snakes are most likely the descendants of a derived, varanoid lizard, some scientists nevertheless still believe that snakes and lizards are possibly sister taxa. Whether snakes should continue to be classified as a suborder under Squamata would require a certain amount of scientific discussion. The current arrangement of Squamata is certainly a good idea, vs. the older arrangement of separate orders for snakes and lizards. Order Squamata is certainly a genalogical arrangement. It is thus a Darwinian taxon that should be retained.

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