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I normally get a lot of questions regarding native U.S. identification, and I like to be as thorough as possible. But this whole mess has got me at a stand still. Which genus is most commonly accepted now for North American Ratsnakes?

Has the DNA really proven the Pituophis placement?

Hi,

>Has the DNA really proven the Pituophis placement?

well, yes..., but the evidence from the statistical methods used to build the tree (bootstrap, bayes etc.) presented is quite weak. So there should be some more research done on this topic until we have to remember the new names...

Cheers,
Wulf
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>>Hi,
>>
>>>Has the DNA really proven the Pituophis placement?
>>
>>well, yes...,>>

Actually no. It has not been proven.

>> but the evidence from the statistical methods used to build the tree (bootstrap, bayes etc.) presented is quite weak.>>

If the evidence is weak, then it is not proven. In fact, it is so weak as to be unreliable. Senticolis does not even have the interpulmonary bronchus that is characteristic of the Lampropeltini, and yet the DNA data of Burbrink and Lawson shows that it is within this tribe. That is evidence of unreliable evidence to me.

>> So there should be some more research done on this topic until we have to remember the new names...
>>
>>Cheers,
>>Wulf

Yes and no. Yes, there should be more research done. No, we shouldn't accept the lumping of Pituophis and "Pantherophis" even if the data is reliable. The data does not logically lead to lumping these taxa. The data is consistent with recognizing a paraphyletic Elaphe, without lumping it with Pituophis, as long as one does not find paraphyletic taxa objectionable. Therefore the problem is not just the data, but the dogma of those who insist on dismantling paraphyletic taxa.

"I normally get a lot of questions regarding native U.S. identification, and I like to be as thorough as possible. But this whole mess has got me at a stand still. Which genus is most commonly accepted now for North American Ratsnakes?"

"Most commonly accepted" is a difficult thing to evaluate. IMO, it's clear that Pantherophis is the right name, though, and that retention of Elaphe tends to obscure present knowledge.

"Has the DNA really proven the Pituophis placement?"

Unequivocally no. Different analyses (i.e., maximum parsimony, maximum likelihood, and Bayesian) of the same data give different results (as evident for MP & ML in the publication by Burbrink & Lawson, although they do not discuss this at all), and no analyses give strong support. Neither monophyly of either genus nor relationship of each to other members of tribe Lampropeltini is resolved at this point.

I've got a very brief submission to Molecular Phylogenetics & Evolution (the same journal that published Burbrink & Lawson's study) on this point. I should hear soon whether or not it has been accepted for publication.

>>"Most commonly accepted" is a difficult thing to evaluate. IMO, it's clear that Pantherophis is the right name, though, and that retention of Elaphe tends to obscure present knowledge.

Pantherophis has been used informally by Dowling when he discusses the North American species of Elaphe, but he did not formally propose the name for the North American Elaphe. Rather than obscuring present knowledge, the retention of Elaphe actually informs us of the relationship between North American forms of this genus and the Eurasian species. Elaphe ought not be broken up unless it is polyphyletic. It has been known for decades that Elaphe is paraphyletic (since it has been known that Pituophis, Lammpropeltis and Stilosoma et al. form a clade with N. American Elaphe), but no one bothered to break it up on that basis.

>>"Has the DNA really proven the Pituophis placement?"
>>
>>Unequivocally no. Different analyses (i.e., maximum parsimony, maximum likelihood, and Bayesian) of the same data give different results (as evident for MP & ML in the publication by Burbrink & Lawson, although they do not discuss this at all), and no analyses give strong support. Neither monophyly of either genus nor relationship of each to other members of tribe Lampropeltini is resolved at this point.

As I said, Elaphe is a well known paraphyletic taxon. It is also well known (and supported by immunological data) that Arizona is closely related to Pituophis. It is therefore also likely that recognition of Arizona elegans will make Pituophis paraphyletic. I presume that you use the term "monophyly" sensu Hennig. It would be tragic if Pituophis is broken up into several genera should it be found not to be "monophyletic" when it is indeed monophyletic sensu Darwin, Simpson and Mayr.

>>I've got a very brief submission to Molecular Phylogenetics & Evolution (the same journal that published Burbrink & Lawson's study) on this point. I should hear soon whether or not it has been accepted for publication.

I hope it gets published. I will keep it in mind next time I am in the library and see if I can find the article.

>>I normally get a lot of questions regarding native U.S. identification, and I like to be as thorough as possible. But this whole mess has got me at a stand still. Which genus is most commonly accepted now for North American Ratsnakes?
>>
>>Has the DNA really proven the Pituophis placement?

The North American species of ratsnakes have traditionally been classified in the genus Elaphe, the same genus as the ratsnakes of Eurasia. There have been a recent attempt to split this genus by a group of researchers who, on the basis of mtDNA evidence and hemipenis morphology, resurrected a large number of genera from the synonymy of Elaphe. One of the problems with this study is its reliability, if the placement of Senticolis triaspis (the green ratsnake) is any indication. Another problem is that these authors fail to provide any definition for the genera they recognize, so it is impossible to know what the differences exist between one genus and another, if any. The main reason for dividing the genus Elaphe appear to be philosophical. There is no evidence that the genus Elaphe is an unnatural polyphyletic assemblage of species, but there is evidence (in fact it has been well known for decades) that the genus Elaphe is paraphyletic. The proposal to split the genus Elaphe is apparently a philosophical intolerance of paraphyletic taxa.

The distinction between paraphyletic and polyphyletic is important. A polyphyletic taxon is unnatural because it consists of species that are descended from two or more recent common ancestors. No taxomist will knowingly recognize polyphyletic taxa, although it has been pointed out that cladists are more likely to recognize polyphyletic taxa because of their uncritical choice of taxonomic characters and the likelihood that the characters they use are convergent similarities, which are not evidence of common ancestry but which can lead to the recognition of polyphyletic taxa. A paraphyletic taxon, on the other hand, is descended from a single recent common ancestor. For centuries, paraphyletic taxa (e.g. Reptilia) have been recognized by taxnomists as valid. However, about a half a century ago, the German scientist Willi Hennig proposed that paraphyletic taxa should not be recognized. His proposal was largely ignored for decades. Recently, a group of taxonomists known as the cladists adopted Hennig's classification and began dismantling paraphyletic taxa.

Traditionally, taxonomists recognize only monophyletic taxa. To them, paraphyletic taxa is a term that did not exist, since paraphyletic taxa are considered monophyletic. Hennig, however, redefined monophyletic as a group that consists of all of the descendants of a common ancestor, and excluded paraphyletic groups (which consists of the descendants of a common ancestor but not all of the descendants) from the definition of monophyletic. The traditional Reptilia is a paraphyletic taxon, since the birds and mammals are descended from the same ancestor that gave rise to the reptiles, but the birds and mammals are excluded from Reptilia. To the cladists, the taxon Reptilia is paraphyletic and therefore it is "non-monophyletic". As such it is not valid. To the traditionalists, the taxon Reptila is in fact monophyletc. This hair-splitting difference between the philosophies of two schools of taxonomists is the source of a great deal of taxonomic controversy which exists today.

The group of researchers who propose to split Elaphe do so because Elaphe is paraphyletic or "non-monophyletic." The traditionalists would disagree with this distinction, because paraphyletic taxa are indeed monophyletic. It is a well known fact for decades that Elaphe is paraphyletic by the definition of Hennig, and yet nobody bothered to split Elaphe on that basis. The proposal to split Elaphe is therefore unnecessary and it will only lead to taxanomic chaos.