>>CK,
>>Need to be educated. What precisely in the definition of 'paraphyletic taxa' and what is or are the alternatives that the cladists embrace?>>

A paraphyletic group is a monophyletic taxon (as traditionally defined) which does not include all the derived ex-groups. ---Mayr and Ashlock 1991

Hi, Richard. The term paraphyletic is an important one because a vast majority of the taxonomic proposals above the species rank we are seeing nowadays are based on the rejection of paraphyletic taxa by the German scientist Willi Hennig and his many followers, who are often known as cladists or “phylogenetic systematists.” There are other schools of systematists, namely the pheneticists (who claim that the order of descent is unknowable), and the Darwinians or traditional systematists. Pheneticism is on the decline because very few people still maintain that branching order or evolutionary history is unknowable. MtDNA and other molecular techniques, not to mention traditional morphological and paleontological (stratigraphic) evidence show that historical branching order can be estimated and in many cases with a great degree of certainty.

Today, we have basically two major schools of taxonomy: the Darwinians and the cladists. Perhaps the main difference between these 2 schools is their treatment of paraphyletic taxa. Darwinians accept paraphyletic taxa as valid but the cladists in general do not. There are a few cladists that do tolerate paraphyletic taxa but they are regarded with suspicion by the more orthodox cladists. Basically cladists will only recognize taxa that consist of a single ancestor and all of the descendant species of this ancestor. For example, cladists would not recognize the chimps, gorillas, orangutan, and gibbons as members of the family Pongidae, because this groupd excludes all of the bipedal primates including the australopithecines and the genus Homo. Some cladists have proposed including the chimps and gorillas in the family Hominidae, while other, even more radical cladistic proposals lump the chimps, gorillas and humans into the genus Homo.

What precisely are paraphyletic taxa? Ever since Darwin, biologists have accepted evolution as a basic fact and Darwin’s idea that all life on earth shares a single common ancestor. Thus all life on earth is monophyletic. “Monophyletic…was a term that was coined by Haeckel in 1866 in support of Darwin’s theory of common descent….Haeckel applied the term monophyletic to all the taxa recognized in his time—for instance, Reptilia, Aves, and Mammalia—each of which he thought consisted of descendants of a nearest common ancestor” (Mayr and Ashlock 1991, Principles of Systematic Zoology).

Then, in 1950, the German scientist Willi Hennig redefined the term “monophyletic.” “For him, a taxon is monophyletic only when it consists of the totality of the descendants of the ancestral stem species” (Mayr and Ashlock 1991). According to Hennig, a taxon like Reptilia, which consists of a group of species descended from a single ancestral species but not all of the descendants of that ancestral species, is not monophyletic. To Hennig and the cladists, Reptilia is “paraphyletic” because this taxon does not include birds and mammals, which are also descended from the ancestor of the Reptilia. Another taxon that is considered paraphyletic is Prokaryota. The classic distinction between Eukaryota and Prokaryota makes Prokaryota a paraphyletic taxon, because the eukaryotes are descended from a prokaryote, but the eukaryotes are excluded from Prokaryota. Hennig’s redefinition of monophyletic was largely ignored because his book was written in German and his ideas were unknown to most biologists around the world. Later, in 1966, his book was translated into English. His ideas gained popularity in the 1970’s and these ideas became more widely accepted in the 1980’s and 1990’s.

Arnold Kluge is a famous cladist who wrote many articles in the journal Cladistics concerning cladistic theory and practice. Practically all of Kluge’s taxonomic proposals (for example his proposal to classify Chondropython viridis as a member of Morelia) are based on the cladistic principle that paraphyletic taxa ought not be recognized. Since Morelia, according to his data, would become paraphyletic if Chondropython is recognized, he transferred C. viridis to Morelia. It does not matter to him or a vast majority of cladists whether C. viridis is morphologically disparate from Morelia. They are only concerned with eliminating paraphyletic taxa. Reptilia, as mentioned earlier, is paraphyletic. In an attempt to make Reptilia “monophyletic” sensu cladism, some cladists redefine Reptilia as all amniotes except the mammals and the therapsid and synapsid reptiles which are basal to the mammalian branch of the tree. The cladistic Reptilia also includes birds; Aves is therefore a part of cladistic Reptilia. Most scientists and laymen continue to recognize Reptilia as valid and monophyletic, and they continue to recognize Aves as a taxon equal in taxonomic rank to Reptlia. In fact, the cladists' taxonomic practice has largely been ignored by the rest of the scientific community. Even some cladists said they dislike the cladistic redefinition of Reptilia, but they nevertheless have to accept it because it adheres to the cladistic principle of intolerance of paraphyletic taxa and because disobedience to this principle can have undesirable consequences.

Cladists often find vociferous and widespread opposition to their incessant taxonomic proposals to lump and split taxa on the basis of their intolerance of paraphyletic taxa. Hence, even in their own writings, many of them have wisely chosen not to use the term paraphyletic. They instead use the more ambiguous term “non-monophyletic” or “not monopyletic.” Of course such a practice is dishonest because “not monophyletic”, to most people including the cladists, may also mean polyphyletic. In fact, to many Darwinians, the term paraphyletic makes no sense, because they consider paraphyletic taxa monophyletic. Therefore, many people who are not familiar with the cladists’ intolerance of paraphyletic taxa often do not know that a new taxonomic proposal is made by a cladist (because cladists often do not brand themselves as cladists in their own scientific papers). By avoiding the use of the term paraphyletic, many cladists also attempt to conceal the fact that they are splitting or lumping taxa on the basis of cladistic intolerance of paraphyletic taxa. Many scientists and laymen are instead misled into thinking that the “non-monophyletic” or “not monophyletic” taxa being disqualified by the cladists may be polyphyletic, because to them, that is what "not monophyletic" means. To most biologists, the term "not monophyletic" means polyphyletic. Therefore the cladists are using dishonest practices in order to gain wider acceptance to their taxonomic proposals.

>>Secondly, you sort of lost me when you begin my mentioning that the southern and northern subclades are the same age. But then later indicate that the northern subclade likely budded off of the southern subclade which in turn would indicate that the northern subclade is younger than the parent southern subclade. >>

The northern and southern subclades of the rubber boa are both descended from their common ancestor. Therefore they are the same age. However, I also pointed out that this common ancestor is almost certainly a dwarf morph boa that is morphologically indistinguishable from the southern subclade. Therefore one can consider the southern subclade to in fact be the lineage that dates all the way back to the founding population of the species Charina bottae. Hence, it is with this broader definition of the southern subclade that I claimed that the northern subclade had budded off the southern subclade. I would also include the Kern county dwarf boas as part of the southern subclade since they appeared to be morphologically indistinguishable from the common ancestor of the southern California boas and their common ancestor and their lineage is also basal to the large morphs (both northwestern and Sierra Nevada large morphs). Perhaps I should have made that more clear. My definition of the Sierra Nevada subclade would therefore exclude the Kern County dwarf morph boas and the southern Rubber boa would be a paraphyletic group. I was switching between my own definitions of subclades and Rodriguez-Robles et al.’s definitions without making it more clear. That may have confused you and I apologize.

>>I thought I mentioned the following once before. I took a couple of side trips to view the habitat in all directions of Mt. Lassen and to make some searches. I confirmed that there is no break in suitable boa habitat anywhere in that region. Secondly, I collected two specimens northwest of Mt. Lassen in Shasta county near the junction of highways 89 and 299 near Burney, one specimen northeast of Mt. Lassen in western Lassen county along hwy 44, and two specimens southeast of Mt. Lassen near Deer Creek along hwy 36 in extreme northeastern Tehama county. Shortly thereafter, in my communication with Chris Feldman, I learned that he and another grad student at Utah St. U. had collected a number of other boas in the vicinity of Mt. Lassen in Plumas and Lassen counties and perhaps also in Shasta Co. that were for the CAS collection. >>

Perhaps I wasn’t paying close enough attention to what you wrote. I apologize if that is the case.

>>Thus about 2 years ago, I urged the current researcher to have all of those samples tested which he has done. It is from those specimens plus some others that were deposited at CAS from yet a forth county that have produced results that conflict with Javier's hypothesis that a break occurs in the distribution of the species and that the Northwestern and Sierra Nevada subclades are thus allopatric in distribution. As I have mentioned some time ago, biologically such a scenario makes no sense given the fact that suitable boa habitat occurs throughout that region.
>>
>>Richard F. Hoyer

At the time of Rodriguez-Robles et al.’s paper, there was indeed a break in the distribution of the rubber boa in the vicinity of Lassen National Park. Depending on the mtDNA haplotypes of these additional specimens, Rodriguez-Robles et al.’s claim of allopatry may or may not be disproven. I am curious as to the phylogenetic affinity of these boas, but I will await publication of the results.

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