Reptile & Amphibian Forums

There is a link at the bottom of this post, which will lead to a web page containing an abstract of a paper published in 2002. Following is a short excerpt from the abstract:

Within the 13 species of the Colubridae, there are two major clades, the Rhabdophis and Sinonatrix clade, and the Zaocys, Ptyas, Dinodon and Elaphe clade, with bootstrap values of 99 and 98 respectively. In the second clade, seven species of Elaphe form a common branch before they cluster with other genera, contrary to Dessauer's assumption of the polyphyletic origin of this genus. [Acta Zoologica Sinica 48(4):494-500, 2002]
Phylogenetic relationships of 20 snake species based on partial sequences of 12S rRNA gene

The abstract you link to is for a study that simply doesn't have the data to test the polyphyly of Elaphe. There are only 13 colubrids in the study, and seven of those are members of Elaphe--a much larger sample is needed to get any idea of the phylogenetic relationships of Elaphe to other genera. And, without knowing what seven Elaphe he chose (unfortunately the biology library here at IU doesn't carry Acta Zoologica Sinica), he may well have chosen taxa that are all within one of the subsections of Elaphe split off by Utiger et al.

Patrick Alexander

Since you cited Utiger et al., you should be familiar with their tree. Their findings show that all species formerly classified in Elaphe, together with the Lampropeltini, form a clade with Ptyas as the outgroup. How can a clade be polyphyletic? Where is the evidence of polyphyly? Why are you so sure that Elaphe is polyphyletic if there is no evidence of it?

Below is a simplified version of Utiger et al.'s weighted MP tree (fig. 3). It illustrates the fact that New World Elaphe and the Lampropeltini is very much nested within Old World Elaphe. Elaphe is not polyphyletic. It is however, paraphyletic. Removing the Lampropeltine snakes from Elaphe is similar to removing birds from Reptilia. The cladists do not like it, but it is perfectly acceptable to the Darwinians or traditionalists to accept a paraphyletic Reptilia (minus the birds and mammals) and a paraphyletic Elaphe (minus Lampropeltis, Arizona, Pituophis among others). There are two courses of action available to the cladists: dumping species classified in Pituophhis, Arizona and Lampropeltis et al. back into Elaphe, or splintering Elaphe into many different genera that are not morphologically distinguishable from one another. The Darwinians have a better alternative not available to the cladists: Keep Elaphe paraphyletic and recognize Pituophis, Lampropeltis, Arizona et al.

`Below is a simplified version of Utiger et al.'s weighted MP tree (fig. 3). It illustrates the fact that New World Elaphe and the Lampropeltini is very much nested within Old World Elaphe. Elaphe is not polyphyletic. It is however, paraphyletic.'

Unfortunately, though, the simplified version is too simplified to demonstrate anything.

` Removing the Lampropeltine snakes from Elaphe is similar to removing birds from Reptilia. The cladists do not like it, but it is perfectly acceptable to the Darwinians or traditionalists to accept a paraphyletic Reptilia (minus the birds and mammals) and a paraphyletic Elaphe (minus Lampropeltis, Arizona, Pituophis among others). There are two courses of action available to the cladists: dumping species classified in Pituophhis, Arizona and Lampropeltis et al. back into Elaphe, or splintering Elaphe into many different genera that are not morphologically distinguishable from one another. The Darwinians have a better alternative not available to the cladists: Keep Elaphe paraphyletic and recognize Pituophis, Lampropeltis, Arizona et al.'

You appear to be under the impression that Utiger et al. split Elaphe in order to adhere with cladist methodology. This is another instance in which having read the paper is useful. In reference to the possibility that Pituophis arose from within Pantherophis, something suggested by other authors and by one of the phylogenies generated with their data, they write that paraphyletic taxa are `an inevitable result of evolution.' Helfenberger, one of the coauthors of the study, also created the genus Rhinechis for what was Elaphe scalaris even though the data he presented at the time showed that Rhinechis was nested within European Elaphe. The option of creating paraphyletic taxa clearly was open to Utiger et al.

I also disagree that the genera created are `morphologically indistinguishable.'

Patrick Alexander

You wrote:
Unfortunately, though, the simplified version is too simplified to demonstrate anything.

My response:
Does it not demonstrate that Elaphe is paraphyletic?

You wrote:
You appear to be under the impression that Utiger et al. split Elaphe in order to adhere with cladist methodology.

My response:
That is not just an impression. It is a fact.

You wrote:
This is another instance in which having read the paper is useful. In reference to the possibility that Pituophis arose from within Pantherophis, something suggested by other authors and by one of the phylogenies generated with their data, they write that paraphyletic taxa are `an inevitable result of evolution.'

My response:
Did you really read the paper? If so, you should see that an intolerance of paraphyly is the reason they split Elaphe. I cannot find a single paraphyletic taxon in their strict consensus tree except perhaps Pantherophis. It does look like they have left Pantherophis paraphyletic. May be it is a compromise among the authors. Often authors with different ideologies have to combine their studies and disagreements do arise. If all of the authors subscribe to this philosophy, they would have left paraphyletic Elaphe untouched. But they do not. Elaphe is indeed splintered by Utiger et al. because it is paraphyletic.

You wrote:
I also disagree that the genera created are `morphologically indistinguishable.'

My response:
The authors do not provide a key for distinguishing the many genera they recognize. The only diagnoses they provide are the two new genera they propose. In the diagnosis of Orthriophis, they state: "subocular usually present (often absent in hodgsonii, sometimes also in cantoris and taeniurus)..." That sort of definition for a new genus does not inspire confidence since one of the diagnostic characters for the genus is variable within the genus. If you disagree, then perhaps you can tell us how one can distinguish,say, Zamensis from Orthriophis and Elaphe from Coronella. I simply can't find anything that would allow me to do that in this paper. In sum, even the authors themselves disagree on the acceptability of paraphyletic taxa, but apparently the cladists among the authors win. They do throw a bone of concession to the Darwinians by recognizing a single paraphyletic genus: Pantherophis. But I am afraid that this bone is tied to a rope and that it can be withdrawn any time. Who is going to stop someone else from splintering the paraphyletic Pantherophis in the future? I am not going to accept the splintering of Elaphe simply because Pantherophis is left paraphyletic. Paraphyletic taxa are indeed the inevitable result of the process of evolution. There is therefore no scientifically tenable reason for not recognizing paraphyletic taxa such as Elaphe.

`Does it not demonstrate that Elaphe is paraphyletic?'

As mentioned, it doesn't accurately depict the situation. See the attached .jpg, figure 4 from the Utiger et al. paper. I put a line down along the taxa that were included in Elaphe prior to this paper. Rhinechis and Oocatochus, as mentioned elsewhere, were split from Elaphe by Helfenberger. Coelognathus, the other genus split by Helfenberger, doesn't appear here. All taxa included are more closely related to each other than they are to Ptyas, and Euprepriophis forms the outgroup (though poorly supported) to the remaining taxa. No well-supported relationships exist between the groups within Elaphe sensu lato that Utiger et al. split into seperate genera and, consequently, neither monophyly nor paraphyly are supported for Elaphe sensu lato.

`Did you really read the paper? If so, you should see that an intolerance of paraphyly is the reason they split Elaphe. I cannot find a single paraphyletic taxon in their strict consensus tree except perhaps Pantherophis. It does look like they have left Pantherophis paraphyletic.'

First, that an author has not created paraphyletic taxa does not imply that the author is intolerant of paraphyletic taxa. In this case, there simply are no well-supported paraphyletic taxa that could have been created within Elaphe, and the authors clearly voice their support for the existence of paraphyletic taxa.
Second, if they had left Pantherophis paraphyletic this also would have proven that the authors were not committed to the avoidance of paraphyletic taxa. However, their results did not show Pantherophis to be paraphyletic (on p. 113-`Pantherophis and Pituophis are sister taxa (bootstrap support 92%, Figs. 3-4) and the monophyly of the former is well supported by a bootstrap value of 74% (see footnote 6).'--footnote 6 referring to new calculations done after submission that include Rhinechis which slightly change the bootstrap percentages). One of several phylogenies they constructed suggested that this was the case, but this phylogeny was rejected by the authors, and was not published. LInked below for clarity are the sentences in which Utiger et al. address the issue.

`The authors do not provide a key for distinguishing the many genera they recognize.'

I don't believe this is necessary for the taxa to be morphologically distinguishable.

`The only diagnoses they provide are the two new genera they propose.'

And diagnoses for the other genera already exist.

`In the diagnosis of Orthriophis, they state: "subocular usually present (often absent in hodgsonii, sometimes also in cantoris and taeniurus)..." That sort of definition for a new genus does not inspire confidence since one of the diagnostic characters for the genus is variable within the genus.'

OTOH, other characters are given that adequately allow the genera to be distinguished.

` If you disagree, then perhaps you can tell us how one can distinguish,say, Zamensis from Orthriophis and Elaphe from Coronella. I simply can't find anything that would allow me to do that in this paper.'

I don't happen to have copies of the papers in which Elaphe, Coronella, and Zamensis are described, so I can't give you the various characters involved for them. I suggest you consult those sources.

If your wish were simply to be able to identify them, this would be quite simple given any familiarity with the taxa involved based simply on color patterning and the like.

` In sum, even the authors themselves disagree on the acceptability of paraphyletic taxa, but apparently the cladists among the authors win. They do throw a bone of concession to the Darwinians by recognizing a single paraphyletic genus: Pantherophis. But I am afraid that this bone is tied to a rope and that it can be withdrawn any time.'

This appears to be simply speculation on your part, and the paraphyly of Pantherophis is not supported by the authors.

`Who is going to stop someone else from splintering the paraphyletic Pantherophis in the future?'

Any taxonomist who cared to present compelling reasons for rejoining them, supposing data demonstrating the paraphyly of Pantherophis were presented and the split made, would be free to do so.

`Paraphyletic taxa are indeed the inevitable result of the process of evolution. There is therefore no scientifically tenable reason for not recognizing paraphyletic taxa such as Elaphe.'

It is far from certain that Elaphe sensu lato is paraphyletic (the evidence I'm aware of appears to argue strongly against it), and, of course, even if one accepts paraphyletic taxa in principle, it doesn't follow that all paraphyletic taxa should be recognized or that scientifically tenable reasons for rejecting certain paraphyletic taxa don't exist.

Patrick Alexander

Image

You wrote:
No well-supported relationships exist between the groups within Elaphe sensu lato that Utiger et al. split into seperate genera and, consequently, neither monophyly nor paraphyly are supported for Elaphe sensu lato.

My response:
Your "Elaphe sensu lato" is a narrower definition of Elaphe than most people accept. Regardless, this group does not form a polyphyletic group. They all share a common ancestor with Elaphe mandarina. You have not shown evidence of polyphyly.

You wrote:
First, that an author has not created paraphyletic taxa does not imply that the author is intolerant of paraphyletic taxa.

My response:
Their destruction of paraphyletic Elaphe is certainly evidence of that.

`The authors do not provide a key for distinguishing the many genera they recognize.'

You wrote:
I don't believe this is necessary for the taxa to be morphologically distinguishable.

My response:
They simply do not provide any information to distinguish any of the genera they resurrect. Without such information, there is no evidence that they use morphological disparity in their classification. They also do not provide evidence that Elaphe is polyphyletic. Hence the only conclusion one can draw from their paper is that they split Elaphe because of paraphyly. The destruction of paraphyletic taxa is of course scientifically untenable since paraphyletic taxa are the inevitable consequence of the process of evolution. The authors themselves even admit that, although it has not stopped them from splintering Elaphe because it is paraphyletic.

`Your "Elaphe sensu lato" is a narrower definition of Elaphe than most people accept.'

Nonetheless, it is the state of Elaphe prior to the publication of Utiger et al.'s paper. If Helfenberger's changes are not yet widely accepted, this is probably due to their recent publication.

`Regardless, this group does not form a polyphyletic group. They all share a common ancestor with Elaphe mandarina. You have not shown evidence of polyphyly.'

As mentioned, there are no well-supported relationships demonstrated between the members of Elaphe sensu lato. As a result, paraphyly is not supported and polyphyly is suggested. And, of course, there are the four other studies mentioned, which you have apparently rejected without evaluation.

`Their destruction of paraphyletic Elaphe is certainly evidence of that.'

The paraphyly of Elaphe remains unsupported.

`They simply do not provide any information to distinguish any of the genera they resurrect. Without such information, there is no evidence that they use morphological disparity in their classification.'

The morphological disparity on which these taxa are based is presented elsewhere, as mentioned in my other response in this thread today.

`They also do not provide evidence that Elaphe is polyphyletic. Hence the only conclusion one can draw from their paper is that they split Elaphe because of paraphyly.'

This conclusion relies on unsupported rejection of the statements of Utiger et al.

`The destruction of paraphyletic taxa is of course scientifically untenable since paraphyletic taxa are the inevitable consequence of the process of evolution.'

As mentioned in my previous response, the validity of all paraphyletic taxa does not follow from the inevitability of the existence of some paraphyletic taxa.

`The authors themselves even admit that, although it has not stopped them from splintering Elaphe because it is paraphyletic.'

No, Utiger et al. do not admit that `the destruction of paraphyletic taxa is of course scientifically untenable since paraphyletic taxa are the inevitable consequence of the process of evolution'. If this is a mistake, I suggest you be more careful. If not, it is simply intentional misrepresentation.

Patrick Alexander

You wrote:
As mentioned, there are no well-supported relationships demonstrated between the members of Elaphe sensu lato. As a result, paraphyly is not supported and polyphyly is suggested. And, of course, there are the four other studies mentioned, which you have apparently rejected without evaluation.

My response:
Not at all, Utiger et al. demonstrate that all species of Elaphe are part of a clade that also include the Lampropeltini. The branching order among these species may not be well supported, but the fact that they share a common ancestor is well supported by Utiger et al.'s study.

You wrote:
The paraphyly of Elaphe remains unsupported.

My response:
It is supported by morphological evidence. The N. American species of Elaphe are morphologically similar to Old World Elaphe. It is also supported by molecular evidence. Both Lopez and Maxson (1995) and Utiger et al. find that New World Elaphe is part of the Elaphe clade. They have both shown that New World Elaphe is not merely convergently similar to Old World Elaphe but that their similarities are almost certainly due to common ancestry. Since genera such as Pituophis and Lampropeltis are derived from a species of New World Elaphe, Elaphe is paraphyletic because it excludes Lampropeltis and Pituophis.

You wrote:
The morphological disparity on which these taxa are based is presented elsewhere, as mentioned in my other response in this thread today.

My response:
Yes it is found elsewhere since Utiger et al. do not rely on morphological disparity to delimit their taxa. It is plainly obvious that they delimit their taxa according to their consensus tree, which is of course poorly supported as you point out. Therefore their splitting of Elaphe is based on poor evidence on branching order and no evidence from morphological disparity. As such, their taxa are poorly delimited and therefore these taxa should be rejected.

You wrote:
No, Utiger et al. do not admit that `the destruction of paraphyletic taxa is of course scientifically untenable since paraphyletic taxa are the inevitable consequence of the process of evolution'. If this is a mistake, I suggest you be more careful. If not, it is simply intentional misrepresentation.

My response:
The authors of course admit that paraphyletic taxa is the inevitable result of the process of evolution, but it has not stopped them from destroying paraphyletic taxa. I hope it is clear to all what I meant.

`Not at all, Utiger et al. demonstrate that all species of Elaphe are part of a clade that also include the Lampropeltini. The branching order among these species may not be well supported, but the fact that they share a common ancestor is well supported by Utiger et al.'s study.'

Nope, the grouping of Euprepriophis with the other taxa studied rather than Ptyas is poorly supported. And Ptyas is the outgroup--it's supposed to be distantly related to all of the taxa involved, so a poor support for its outgroup status is particularly damning.

`It is supported by morphological evidence. The N. American species of Elaphe are morphologically similar to Old World Elaphe.'

According to... ? Remember, Pantherophis was sufficiently distinct to be placed in a different tribe from the rest of Elaphe sensu lato long before Utiger's work.

` It is also supported by molecular evidence. Both Lopez and Maxson (1995) and Utiger et al. find that New World Elaphe is part of the Elaphe clade. They have both shown that New World Elaphe is not merely convergently similar to Old World Elaphe but that their similarities are almost certainly due to common ancestry. Since genera such as Pituophis and Lampropeltis are derived from a species of New World Elaphe, Elaphe is paraphyletic because it excludes Lampropeltis and Pituophis.'

This has already been addressed.

`Yes it is found elsewhere since Utiger et al. do not rely on morphological disparity to delimit their taxa. It is plainly obvious that they delimit their taxa according to their consensus tree, which is of course poorly supported as you point out. Therefore their splitting of Elaphe is based on poor evidence on branching order and no evidence from morphological disparity. As such, their taxa are poorly delimited and therefore these taxa should be rejected.'

This, also, has already been addressed.

`The authors of course admit that paraphyletic taxa is the inevitable result of the process of evolution, but it has not stopped them from destroying paraphyletic taxa. I hope it is clear to all what I meant.'

It's certainly clearer than it was. However, until you present a compelling reason to believe that Utiger et al. believe Elaphe sensu lato to be paraphyletic, there is no support for the claim that their split of Elaphe sensu lato represents a rejection on their part of paraphyletic taxa.

Patrick Alexander

You wrote:
Nope, the grouping of Euprepriophis with the other taxa studied rather than Ptyas is poorly supported.

My response:
If so, then their resurrection of Euprepriophis appears unwarranted. Splitting Elaphe mandarina from Elaphe on the basis of poorly supported evidence is scientifically untenable.

You wrote:
And Ptyas is the outgroup--it's supposed to be distantly related to all of the taxa involved, so a poor support for its outgroup status is particularly damning.

My response:
The outgroup is chosen arbitrarily. If one is not careful, one can choose a member of the ingroup as the outgroup. Damning? Ptyas is indeed an outgroup to Old World plus New World Elaphe according to Lopez and Maxson's mtDNA data. If there is poor support for its outgroup status, it is indeed damning evidence that Utiger et al.'s hypothesis is poorly supported.

You wrote:
until you present a compelling reason to believe that Utiger et al. believe Elaphe sensu lato to be paraphyletic, there is no support for the claim that their split of Elaphe sensu lato represents a rejection on their part of paraphyletic taxa.

My response:
Since there is no evidence that Elaphe is polyphyletic, and since there is no evidence that Utiger et al. split Elaphe on the basis of morphological disparity, the only reason I can think of is an ideological intolerance of paraphyletic taxa. If you can think of another reason for their splintering of Elaphe, please let us know what it may be.

BTW, Tong et al. (2002 Acta Zoological Sinica) include at least 2 racers among their colubrids, namely Zaocys and Ptyas. Both of these species are also sequenced by Lopez and Maxson (1995). Tong et al. and Lopez and Maxson both find that the ratsnakes (Elaphe) are more closely related to each other than they are to either Ptyas or Zaocys. Ptyas is clearly the outgroup to all of the species in Utiger et al.'s study. If their data only support this outgroup status weakly, then there is something wrong with their data.

`Ptyas is clearly the outgroup to all of the species in Utiger et al.'s study. If their data only support this outgroup status weakly, then there is something wrong with their data.'

Utiger et al. also include many taxa not included in Lopez and Maxson's study, or any other studies I've seen of colubrine phylogeny, such as the members of Euprepriophis and Othriophis. If Elaphe sensu lato is mono- or paraphyletic, inclusion of these taxa shouldn't result in reduced support for the outgroup status of Ptyas. Yet their inclusion does reduce this support. I know what my conclusion is.

Patrick Alexander

You wrote:
Utiger et al. also include many taxa not included in Lopez and Maxson's study, or any other studies I've seen of colubrine phylogeny, such as the members of Euprepriophis and Othriophis. If Elaphe sensu lato is mono- or paraphyletic, inclusion of these taxa shouldn't result in reduced support for the outgroup status of Ptyas. Yet their inclusion does reduce this support. I know what my conclusion is.

My response:
They do include more species of Elaphe than Lopez and Maxson, but their finding is the same as that of Lopez and Maxson: Elaphe is not a polyphyletic group. If it were, I would support dismantling it. Since it is not, I disagree with Utiger et al.'s splintering of Elaphe based on the Hennigian intolerance of paraphyletic taxa. As for the systematic status of Ptyas in reference to Elaphe, there is little doubt that Ptyas is an outgroup. Lopez and Maxson's study shows that it is closer to Coluber constrictor and Masticophis than to any species of Elaphe, New World or Old World. And I finally found a copy of Tong et al.'s paper in Acta Zoologica Sinica. They find a bootstrap value of 98 for the split between Ptyas and Elaphe, including the most basal member of Elaphe in Utiger et al.'s finding--Elaphe mandarina. See the "photo" below of part of their tree. They also found that Viperidae is sister taxon to Colubridae plus Elapidae, which is the same result that Wilcox et al. (2002, Molecular Phylogenetics and Evolution 25: 361-371) obtain. That shows Tong et al.'s data is corroborated by another independent study. Tong et al. also find E. mandarina to be the most basal member of Elaphe, corroborating Utiger et al. Tong et al. thus corroborate Lopez and Maxson, and both corroborate Utiger et al. All three studies strongly suggest Elaphe is not polyphyletic and that Ptyas is an outgroup to Elaphe. If your conclusion is that Ptyas is not an outgroup with respect to Elaphe, then I am afraid that your conclusion is independent of evidence.

`The outgroup is chosen arbitrarily. If one is not careful, one can choose a member of the ingroup as the outgroup. Damning? Ptyas is indeed an outgroup to Old World plus New World Elaphe according to Lopez and Maxson's mtDNA data'.

Data which represents only a small fraction of the taxa within Elaphe sensu lato...

`If there is poor support for its outgroup status, it is indeed damning evidence that Utiger et al.'s hypothesis is poorly supported.'

And yet poorer support for the outgroup status of Ptyas is exactly what is to be expected on the inclusion of larger numbers of taxa within Elaphe sensu lato if Elaphe sensu lato is polyphyletic.

`Since there is no evidence that Elaphe is polyphyletic, and since there is no evidence that Utiger et al. split Elaphe on the basis of morphological disparity, the only reason I can think of is an ideological intolerance of paraphyletic taxa. If you can think of another reason for their splintering of Elaphe, please let us know what it may be.'

Again, this has already been addressed.

Patrick Alexander

I will consolidate my replies to both of your posts, in the interest of taxonomic discussion efficiency.

You wrote:
Utiger et al. also include many taxa not included in Lopez and Maxson's study, or any other studies I've seen of colubrine phylogeny, such as the members of Euprepriophis and Othriophis.

My response:
These are Elaphe according to most taxonomists. Yes Utiger et al. include more ratsnakes (all of which are members of the genus Elaphe according to most taxonomists) in their study than most authors, but it does not change anything. All of the members of Elaphe share a more recent common ancestor with each other than any of them does with any racer, including Ptyas, in Lopez and Maxson (1995). The same is true in Utiger et al. All members of Elaphe (including E. mandarina and E. conspicillata) share a more recent common ancestor with each other than any of them does with Ptyas. There simply is no evidence that any of the large number of ratsnake species in Utiger et al.'s study is more closely related to the racers than to each other. In other words, there simply is no evidence to support the oft-repeated claim that Elaphe is polyphyletic.

You worte:
If Elaphe sensu lato is mono- or paraphyletic, inclusion of these taxa shouldn't result in reduced support for the outgroup status of Ptyas. Yet their inclusion does reduce this support. I know what my conclusion is.

My response:
I don't know what your conclusion is but I do know that there is no evidence Elaphe is polyphyletic.

`Since there is no evidence that Elaphe is polyphyletic, and since there is no evidence that Utiger et al. split Elaphe on the basis of morphological disparity, the only reason I can think of is an ideological intolerance of paraphyletic taxa. If you can think of another reason for their splintering of Elaphe, please let us know what it may be.'

You wrote:
Again, this has already been addressed.

Patrick Alexander

My response:
You have denied that they splinter Elaphe because of an ideological intolerance of paraphyly. But you cannot provide evidence Elaphe is polyphyletic and you cannot provide evidence that Elaphe is a morphologically disparate group. If there is a fourth reason why they splinter Elaphe, I don't know what it may be. Therefore I will maintain that they splinter Elaphe because of their scientifically untenable intolerance of paraphyletic taxa.

`These are Elaphe according to most taxonomists. Yes Utiger et al. include more ratsnakes (all of which are members of the genus Elaphe according to most taxonomists)'

I hate to nitpick, but Coronella, Lampropeltis, Arizona, Pituophis, Bogertophis, and Senticolis are all called `ratsnakes' in informal terminology (Lopez and Maxson call all members of Lampropeltini `ratsnakes' for instance) but these obviously are not Elaphe.

`in their study than most authors, but it does not change anything. All of the members of Elaphe share a more recent common ancestor with each other than any of them does with any racer, including Ptyas, in Lopez and Maxson (1995).'

No. Only four species of Elaphe (five if you wanted to include Rhinechis scalaris--a taxon created explicitly on the basis of morphological disparity, for what it's worth) share a more recent common ancestor than the other taxa in Lopez and Maxson's study. Without data about all of the members of Elaphe sensu lato, no conclusions can be reached about all of the members of Elaphe sensu lato.

`The same is true in Utiger et al. All members of Elaphe (including E. mandarina and E. conspicillata) share a more recent common ancestor with each other than any of them does with Ptyas. There simply is no evidence that any of the large number of ratsnake species in Utiger et al.'s study is more closely related to the racers than to each other. In other words, there simply is no evidence to support the oft-repeated claim that Elaphe is polyphyletic.'

This, again, has already been addressed. Mono- or paraphyly cannot be supported in the absence of any well-supported relationships among the taxa of Elaphe sensu lato.

`I don't know what your conclusion is'

My conclusion (which I had thought was obvious) is that the difference in outgroup support for Ptyas between Lopez and Maxson and Utiger et al.'s studies supports polyphyly of Elaphe sensu lato. Your conclusion, apparently, is that they suggest flaws with Utiger et al.'s data.

`but I do know that there is no evidence Elaphe is polyphyletic.'

In the face of multiple independent studies concluding that Elaphe sensu lato is polyphyletic? Even if you don't think it's -good- evidence, there clearly is evidence.

`You have denied that they splinter Elaphe because of an ideological intolerance of paraphyly. But you cannot provide evidence Elaphe is polyphyletic and you cannot provide evidence that Elaphe is a morphologically disparate group.'

I have already provided citations of several studies supporting both polyphyly and morphological disparity.

`If there is a fourth reason why they splinter Elaphe, I don't know what it may be. Therefore I will maintain that they splinter Elaphe because of their scientifically untenable intolerance of paraphyletic taxa.'

And, predictably enough, I'll continue to disagree.

Patrick Alexander

You wrote:
I hate to nitpick, but Coronella, Lampropeltis, Arizona, Pituophis, Bogertophis, and Senticolis are all called `ratsnakes' in informal terminology (Lopez and Maxson call all members of Lampropeltini `ratsnakes' for instance) but these obviously are not Elaphe.

My response:
The common name of the species classified in Ptyas is also ratsnake. Lopez and Maxson is calling Ptyas a racer. All of the racers in Lopez and Maxson's paper falls outside of the "ratsnake" clade, including Gonyosoma, which is another racer that has the common name of "ratsnake." The important thing to remember is that all species of Elaphe recognized by most taxonomists form a clade with the Lampropeltini. Lopez and Maxson call this clade ratsnakes. I have no problem with it. After all the Lampropeltini includes species that are not in Lampropeltis.

You wrote:
No. Only four species of Elaphe (five if you wanted to include Rhinechis scalaris--a taxon created explicitly on the basis of morphological disparity, for what it's worth) share a more recent common ancestor than the other taxa in Lopez and Maxson's study. Without data about all of the members of Elaphe sensu lato, no conclusions can be reached about all of the members of Elaphe sensu lato.

My response:
The claim that Utiger et al. delimited Elaphe on the basis of morphological disparity is unsupported. I am not sure what you mean, but as I said, all of the species of Elaphe in Lopez and Maxson are more closely related to each other than they are to Ptyas or any other racer. Similarly, all of the species that other folks have classified in Elaphe (but which Utiger splinter into many different genera) are also more closely related to each other than any of them is to Ptyas. That is strong evidence that Elaphe is not polyphyletic, and Tong et al. (Acta Zoological Sinica) independently verify this fact in their study.

You wrote:
"My conclusion (which I had thought was obvious) is that the difference in outgroup support for Ptyas between Lopez and Maxson and Utiger et al.'s studies supports polyphyly of Elaphe sensu lato. Your conclusion, apparently, is that they suggest flaws with Utiger et al.'s data.

My response:
You are suggesting that a difference in the amount of statistical support for Ptyas as an outgroup between the two studies is evidence of polyphyly of Elaphe? That is an unsupported interpretation of the available data. The only way Elaphe can be polyphyletic is if some of them form a clade with Ptyas to the exclusion of other species of Elaphe. Neither Lopez and Maxson nor Utiger et al.'s data shows that. Tong et al.'s study also include Ptyas. Like the other two studies, theirs also show Ptyas outside of the Elaphe clade. "Your conclusion" is simply unscientific.

You wrote:
In the face of multiple independent studies concluding that Elaphe sensu lato is polyphyletic? Even if you don't think it's -good- evidence, there clearly is evidence.

My response:
You are obviously influenced by Utiger et al.'s single sentence on page 105, in which they claim that several authors "...concluded that Elaphe auct. as presently understood represents a large polyphyletic group." One of the papers they cite is that of Dowling et al. (1983). Dowling et al. do not include any of the Old World Elaphe species in their study. Therefore they have no data to show that Elaphe is polyphyletic; they are merely speculating. Tong et al. (2002) also conclude that Dessauer (another paper cited by Utiger et al.) assumes that Elaphe is polyphyletic. Further, Utiger et al. fail to cite Lopez and Maxson (1995), which clearly shows that Elaphe is a monophyletic group (paraphyletic if the Lampropeltini is excluded). It appears that Utiger is including studies that speculate on the polyphyly of Elaphe and at the same time overlooking those that refutes polyphyly. If that is the source of your "multiple independent studies concluding that Elaphe...is polyphyletic," then you have been misled by Utiger et al.

You wrote:
And, predictably enough, I'll continue to disagree.

My response:
You may disagree all you want, but if your disagreement is unsupported by scientific evidence, then it is a meaningless disagreement.

`The common name of the species classified in Ptyas is also ratsnake.'

Indeed. Another taxon that causes your previous statement to be inaccurate.

` Lopez and Maxson is calling Ptyas a racer. All of the racers in Lopez and Maxson's paper falls outside of the "ratsnake" clade, including Gonyosoma, which is another racer that has the common name of "ratsnake." The important thing to remember is that all species of Elaphe recognized by most taxonomists form a clade with the Lampropeltini. Lopez and Maxson call this clade ratsnakes. I have no problem with it. After all the Lampropeltini includes species that are not in Lampropeltis.'

Fine with me. It just indicates a (fairly minor) error on your part.

`The claim that Utiger et al. delimited Elaphe on the basis of morphological disparity is unsupported.'

Weakly supported, I'd say, but either way, the claim that the taxa they created are `morphologically indistinguishable' is also unsupported.

`I am not sure what you mean, but as I said, all of the species of Elaphe in Lopez and Maxson are more closely related to each other than they are to Ptyas or any other racer.'

Agreed. The problem, as I mentioned, is that they have very few species of Elaphe sensu lato to work with, and can't draw any conclusions about Elaphe sensu lato as a whole.

`Similarly, all of the species that other folks have classified in Elaphe (but which Utiger splinter into many different genera) are also more closely related to each other than any of them is to Ptyas. That is strong evidence that Elaphe is not polyphyletic,'

I disagree, because, as already discussed, there are no well-supported relationships among the genera split from Elaphe sensu lato.

`and Tong et al. (Acta Zoological Sinica) independently verify this fact in their study.'

Which neither of us has read, and which contains very few taxa.

`You are suggesting that a difference in the amount of statistical support for Ptyas as an outgroup between the two studies is evidence of polyphyly of Elaphe?'

Not just a difference, but, specifically, the correlation between increased in-group represenation and decreased support for the out-group's position.

`That is an unsupported interpretation of the available data. '

It's just common sense. Low outgroup support implies differences in relatedness between the out-group and different members of the in-group. If your in-group members are all closely related, out-group support should be high. If out-group support is low, probably the outgroup is either very closely related to all of the in-group taxa (which is argued against by the much higher outgroup support of Lopez and Maxson's study) or your in-group contains fairly divergent taxa, some of which are fairly closely related to the outgroup, and some of which aren't. It's not great evidence of polyphyly, but my main reason for mentioning it was that it's a more plausible explanation for the differences in out-group support than your offhand conclusion that it must indicate some problem with Utiger et al.'s data. Which, by the way, seems to be an `unsupported interpretation'.

`The only way Elaphe can be polyphyletic is if some of them form a clade with Ptyas to the exclusion of other species of Elaphe. he only way Elaphe can be polyphyletic is if some of them form a clade with Ptyas to the exclusion of other species of Elaphe. Neither Lopez and Maxson nor Utiger et al.'s data shows that. Tong et al.'s study also include Ptyas. Like the other two studies, theirs also show Ptyas outside of the Elaphe clade.'

This has already been addressed.

`You are obviously influenced by Utiger et al.'s single sentence on page 105, in which they claim that several authors "...concluded that Elaphe auct. as presently understood represents a large polyphyletic group." One of the papers they cite is that of Dowling et al. (1983). Dowling et al. do not include any of the Old World Elaphe species in their study. Therefore they have no data to show that Elaphe is polyphyletic; they are merely speculating'

Very good. So if you're willing to make the argument that an insufficient number of taxa can prevent conclusions about a genus as a whole here, why do you reject it in reference to Tong et al.'s and Lopez and Maxson's studies?

And I think that leaves us still with four papers concluding that Elaphe sensu lato is polyphyletic.

`Tong et al. (2002) also conclude that Dessauer (another paper cited by Utiger et al.) assumes that Elaphe is polyphyletic.'

Correct me if I'm wrong, but as far as I know we still don't know either what Tong et al.'s reasons for coming to this conclusion are, or even if Utiger et al. and Tong et al. are referring to the same paper.

` Further, Utiger et al. fail to cite Lopez and Maxson (1995), which clearly shows that Elaphe is a monophyletic group (paraphyletic if the Lampropeltini is excluded).'

This has already been addressed.

`It appears that Utiger is including studies that speculate on the polyphyly of Elaphe and at the same time overlooking those that refutes polyphyly. If that is the source of your "multiple independent studies concluding that Elaphe...is polyphyletic," then you have been misled by Utiger et al.'

Interestingly, Utiger et al. also cite Lenk et al. (mentioned elsewhere in this thread) but do not mention that Lenk et al. conclude that Elaphe sensu lato is polyphyletic. There doesn't appear to be a bias in regards to their citation on the matter.
Furthermore, which papers they've chosen to cite doesn't influence the validity of the papers they've cited. There are indeed multiple independent studies concluding that Elaphe sensu lato is polyphyletic, whether Utiger et al. may have failed to cite other studies (whether they support the opposite conclusion or not) or not.

`You may disagree all you want, but if your disagreement is unsupported by scientific evidence, then it is a meaningless disagreement.'

If we'll accept the converse implication, it would appear my disagreement is not meaningless.

Patrick Alexander

I wrote:
`The claim that Utiger et al. delimited Elaphe on the basis of morphological disparity is unsupported.'

You wrote:
Weakly supported, I'd say, but either way, the claim that the taxa they created are `morphologically indistinguishable' is also unsupported.

My response:
You seem to be contradicting yourself. Your words "also unsupported" seem to be an acknowledgement that your claim is unsupported and that my claim is also similar to your unsupported claim. But you also claim that it is "weakly supported." Either it is unsupported or supported (albeit weakly). It cannot be both weakly supported and unsupported.

I wrote:
`I am not sure what you mean, but as I said, all of the species of Elaphe in Lopez and Maxson are more closely related to each other than they are to Ptyas or any other racer.'

Your response:
Agreed. The problem, as I mentioned, is that they have very few species of Elaphe sensu lato to work with, and can't draw any conclusions about Elaphe sensu lato as a whole.

My response:
It is true that they do not have all species of Elaphe in their study. It is a weakness they themselves acknowledge. But their study does include both New World and Old World species of Elaphe. Both groups are more closely related to each other than either one is to Ptyas in Lopez and Maxson's study. Utiger et al. find the same thing. Utiger et al. also find Elaphe mandarina (along with E. conspicillata) to be the most basal lineage within Elaphe. Tong et al. (Acta Zoologica Sinica) find the same things Utiger et al. do: E. mandarina is the most basal member of Elaphe and Ptyas is an outgroup. Tong et al. also finds a bootstrap value of 98 for the split between Ptyas and Elaphe.

I wrote:
`You are suggesting that a difference in the amount of statistical support for Ptyas as an outgroup between the two studies is evidence of polyphyly of Elaphe?'

Your response:
Not just a difference, but, specifically, the correlation between increased in-group represenation and decreased support for the out-group's position.

My response:
I suggested that there may be something wrong with Utiger et al.'s data. You disagreed.

I wrote:
`That is an unsupported interpretation of the available data. '

You wrote:
It's just common sense. Low outgroup support implies differences in relatedness between the out-group and different members of the in-group. If your in-group members are all closely related, out-group support should be high. If out-group support is low, probably the outgroup is either very closely related to all of the in-group taxa (which is argued against by the much higher outgroup support of Lopez and Maxson's study) or your in-group contains fairly divergent taxa, some of which are fairly closely related to the outgroup, and some of which aren't. It's not great evidence of polyphyly, but my main reason for mentioning it was that it's a more plausible explanation for the
differences in out-group support than your offhand conclusion that it must indicate some problem with Utiger et al.'s data. Which, by the way, seems to be an `unsupported interpretation'.

My response:
It is not common sense. Low outgroup support could also mean that there is adaptive radiation at that node, which could result in an unresolved polytomy. Unresolved polytomies can also be the result of uninformative characters. As you admit, Lopez and Maxson's findings clearly shows that Ptyas is an outgroup. So does Utiger et al.'s tree. Now Tong et al. (Acta Zoologica Sinica) have shown that Ptyas is an outgroup to all of the species of Elaphe they study, including the most basal member (E. mandarina), there can be little doubt that Elaphe is not polyphyletic (Darwinians will wonder why I choose to say "not polyphyletic" instead of "monophyletic." I do so because I want to obviate the typical Hennigian tactic of erecting a red herring argument by engaging in semantic arguments about the meaning of monophyletic, a term that they hijacked from the Darwinians).

I wrote:
`The only way Elaphe can be polyphyletic is if some of them form a clade with Ptyas to the exclusion of other species of Elaphe. Neither Lopez and Maxson nor Utiger et al.'s data shows that. Tong et al.'s study also include Ptyas. Like the other two studies, theirs also show Ptyas outside of the Elaphe clade.'

Your response:
This has already been addressed.

My response:
That is a weak response. Your slim hope that Utiger et al.'s data somehow suggest that Elaphe is polyphyletic has been dashed by Tong et al.'s bootstrap value of 98 for the Ptyas-Elaphe split.

I wrote:
`You are obviously influenced by Utiger et al.'s single sentence on page 105, in which they claim that several authors "...concluded that Elaphe auct. as presently understood represents a large polyphyletic group." One of the papers they cite is that of Dowling et al. (1983). Dowling et al. do not include any of the Old World Elaphe species in their study. Therefore they have no data to show that Elaphe is polyphyletic; they are merely speculating'

Your response:
Very good. So if you're willing to make the argument that an insufficient number of taxa can prevent conclusions about a genus as a whole here, why do you reject it in reference to Tong et al.'s and
Lopez and Maxson's studies?

My response:
No, I am not making that argument. I am arguing that Dowling et al. do not include any species of Old World Elaphe in their study and therefore they have no evidence to support the speculation that Old World and New World Elaphe form a polyphyletic group. They have to include at least one species from each group to demonstrate that. This is clearly not the case with Lopez and Maxson's study, who includes several species of Old World and several species of New World Elaphe. They find that Old World and New World Elaphe are part of a monophyletic group that excludes Ptyas. Further, they find that New World Elaphe is a derived group and that Old World Elaphe is basal. Utiger et al. rectify the shortcomings of Lopez and Maxson and includes a lot more species. They, too, find that Old World and New World Elaphe are part of a monophyletic group and that New World Elaphe is derived and Old World Elaphe is basal. Tong et al. do not include any New World species of Elaphe, but they show that Ptyas is an outgroup of Old World Elaphe, including the most basal member E. mandarina. These 3 studies conclusively show that Ptyas is an outgroup to Elaphe.

You wrote:
And I think that leaves us still with four papers concluding that Elaphe sensu lato is polyphyletic.

My response:
Then it is up to you to dig them out to prove that Elaphe is polyphyletic.

I wrote:
`Tong et al. (2002) also conclude that Dessauer (another paper cited by Utiger et al.) assumes that Elaphe is polyphyletic.'

You wrote:
Correct me if I'm wrong, but as far as I know we still don't know either what Tong et al.'s reasons for coming to this conclusion are, or even if Utiger et al. and Tong et al. are referring to the same paper.

My response:
Both Utiger et al. and Tong et al. cite Dessauer et al. 1987. "Patterns of snake evolution suggested by their proteins," Field. Zool. New Ser. 34:1-34

As for the reason Tong et al. claim that Dessauer [et al.] is assuming that Elaphe is polyphyletic, it is obvious that if one has no evidence, then one is merely making an assumption.

I wrote:
` Further, Utiger et al. fail to cite Lopez and Maxson (1995), which clearly shows that Elaphe is a monophyletic group (paraphyletic if the Lampropeltini is excluded).'

Your response:
This has already been addressed.

My response:
That is not much of a response. A weak response but still a response.

I wrote:
`It appears that Utiger is including studies that speculate on the polyphyly of Elaphe and at the same time overlooking those that refutes polyphyly. If that is the source of your "multiple independent
studies concluding that Elaphe...is polyphyletic," then you have been misled by Utiger et al.'

Your response:
Interestingly, Utiger et al. also cite Lenk et al. (mentioned elsewhere in this thread) but do not mention that Lenk et al. conclude that Elaphe sensu lato is polyphyletic. There doesn't appear to be a bias in regards to their citation on the matter. Furthermore, which papers they've chosen to cite doesn't influence the validity of the papers they've cited. There are indeed multiple independent studies concluding that Elaphe sensu lato is polyphyletic, whether Utiger et al. may have failed to cite other studies (whether they support the opposite conclusion or not) or not.

My response:
Utiger et al. cite 4 papers. One of these (Dowling et al.), as I point out, cannot possibly make that conclusion since it does not include a single species of Old World Elaphe in it. A second paper (Dessauer et al. 1987) is claimed by Tong et al. to have made an assumption for Elaphe polyphyly. A third study (Dessauer 1983) predates the 1987 assumption (interestingly, Utiger et al. neglect to give the full citation for this paper). So the only unrefuted (by me) study that Utiger et al. cites for Elaphe polyphyly is Minton (1976, Serological relationships among some congeneric North American and Eurasian colubrid snakes. Copeia 1976:672-678)

You are on thin ice indeed if Minton's 1976 paper is your only unread evidence of a polyphyletic Elaphe, especially since Utiger et al.'s own study (as well as that of Lopez and Maxson and Tong et al.) refutes Elaphe polyphyly.

I wrote:
`You may disagree all you want, but if your disagreement is unsupported by scientific evidence, then it is a meaningless disagreement.'

Your response:
If we'll accept the converse implication, it would appear my disagreement is not meaningless.

Patrick Alexander

My response:
To give it meaning, you must submit evidence for a polyphyletic Elaphe. So far the best you can do is your assumption that the four papers cited by Utiger et al. prove that, and your weak argument that the low bootstrap value for Ptyas as outgroup in Utiger et al. suggest possible polyphyly. That is skating on very thin ice indeed. Or perhaps you are actually skating on the surface tension of the water molecules.

It has been more than a quarter of a century since Minton published his paper. If there is actual evidence of a polyphyletic Elaphe within it or within any of the papers cited by Utiger et al., Elaphe would have been dismantled a long time ago. Dowling, who is one of the leading authorities on this genus, would not have tolerated polyphyletic taxa, and neither would Dessauer or Minton or for that matter any self-respecting systematist of any school. The fact that Elaphe has survived as a valid genus is itself prima facie evidence that the studies cited by Utiger et al. do not contain scientific evidence that Elaphe is polyphyletic.

Just found Dessauer et al. (1987, Fieldiana Zoology), which is supposedly one of the four papers cited by Utiger et al., suggesting that Elaphe is polyphyletic. I had noted that one of the four papers (Dowling et al. 1983) does not contain any Old World species of Elaphe, and therefore the authors have no data to show whether Elaphe is polyphyletic or not. The present paper tested mostly New World species of Elaphe and the Lampropeltine snakes. Dessauer et al. find that snakes now classified in the genera Arizona, Lampropeltis, Rhinocheilus, Bogertophis, Cemophora, Pituophis, Senticolis and Elaphe (obsoleta, vulpina, bairdi, and guttata) are closely related to each other. Elaphe quatuorlineata is the outgroup to this American assemblage. Dessauer et al.'s (1987) data therefore shows that an Eurasian species of Elaphe is ancestral to the North American species of Elaphe and the genera listed above. This is not evidence that Elaphe is polyphyletic at all! This is in fact evidence that all of these American species of snakes are descended from a single species of Eurasian Elaphe.

Dessauer et al. do make the following conclusion on page 28: "Comparative biochemical studies suggest that several widespread colubrid genera are not monophyletic (e.g. Natrix sensu Malnate, 1960; Elaphe; Coluber; Rhadinaea)."

This conclusion can only be reached if the common ancestor of North American Elaphe and Lampropeltis, Arizona, Senticolis, Bogertophis, Pituophis, Stilosoma, Cemophora and Rhinocheilus is not a member of Eurasian Elaphe. But this is unlikely since Elaphe quatuorlineata is basal to this group of American snakes. Since Dessauer (1983) is the third of four papers cited by Utiger et al. as studies suggesting Elaphe is a polyphyletic genus, and it predates this one, the only remaining paper that suggests Elaphe is polyphyletic is that of Minton (1976). It appears that those who are convinced that Elaphe is polyphyletic is left with but one paper as their support.

`You seem to be contradicting yourself. Your words "also unsupported" seem to be an acknowledgement that your claim is unsupported and that my claim is also similar to your unsupported claim.'

That's simply an error on my part in writing that sentence. Feel free to disregard the word `also', as it shouldn't have been there.

`It is true that they do not have all species of Elaphe in their study. It is a weakness they themselves acknowledge. But their study does include both New World and Old World species of Elaphe.'

But, IIRC, all the Old World `Elaphe' Lopez and Maxson use are in Elaphe sensu stricto. Most of the problematic members of Elaphe sensu lato are not in Elaphe sensu stricto, so this isn't a good test.

`I suggested that there may be something wrong with Utiger et al.'s data. You disagreed.'

Indeed. Your point?

`It is not common sense. Low outgroup support could also mean that there is adaptive radiation at that node, which could result in an unresolved polytomy.'

Could you be more explicit, here? Adaptive radiation, of itself, doesn't have any consequences for resolution of a genetically-based phylogeny.

`Unresolved polytomies can also be the result of uninformative characters.'

Ok. So, can this be used to explain the low outgroup support for Ptyas, and the concordance of this low outgroup support with increased ingroup representation as compared to other studies of colubrine phylogeny?

`As you admit, Lopez and Maxson's findings clearly shows that Ptyas is an outgroup. So does Utiger et al.'s tree.'

Nope. I'd rather you didn't misrepresent what I've written, and the problems with outgroup support for Ptyas on both the Lopez and Maxson and Utiger et al. papers have had to be mentioned too many times already.

`Now Tong et al. (Acta Zoologica Sinica) have shown that Ptyas is an outgroup to all of the species of Elaphe they study, including the most basal member (E. mandarina), there can be little doubt that Elaphe is not polyphyletic'

Would you mind listing all of the species studied by Tong et al.? I've already mentioned (quite a few times) that they appear to have far too few species to make any effective test of the monophyly of Elaphe sensu lato. So what makes you think their study is a good test?

`That is a weak response.'

When I say `this has already been addressed' it means that I have already rebutted the point you have raised, and that rebutting it again would require me to repeat myself excessively. In such a case, I suggest you either address the points I have already raised, or present a new argument.

` Your slim hope that Utiger et al.'s data somehow suggest that Elaphe is polyphyletic has been dashed by Tong et al.'s bootstrap value of 98 for the Ptyas-Elaphe split.'

This has already been addressed.

Hint: look about a dozen lines up. : )

`No, I am not making that argument. I am arguing that Dowling et al. do not include any species of Old World Elaphe in their study and therefore they have no evidence to support the speculation that Old World and New World Elaphe form a polyphyletic group. They have to include at least one species from each group to demonstrate that. This is clearly not the case with Lopez and Maxson's study, who includes several species of Old World and several species of New World Elaphe.'

The relationship of Old World taxa to New World taxa to each other is not the issue. The relationships to each other of all members of Elaphe sensu lato, whether they happen to be New or Old World, is the issue. As a result, your argument above, which is predicated on the sole importance of New vs. Old World taxa, doesn't apply.

`Then it is up to you to dig them out to prove that Elaphe is polyphyletic.'

I've already dug up a few of them. See elsewhere in the thread.

`Both Utiger et al. and Tong et al. cite Dessauer et al. 1987. "Patterns of snake evolution suggested by their proteins," Field. Zool. New Ser. 34:1-34'

Ok.

`As for the reason Tong et al. claim that Dessauer [et al.] is assuming that Elaphe is polyphyletic, it is obvious that if one has no evidence, then one is merely making an assumption.'

That's not an answer to the question.

`Utiger et al. cite 4 papers. One of these (Dowling et al.), as I point out, cannot possibly make that conclusion since it does not include a single species of Old World Elaphe in it.'

Ok. But what if they thought that New World members of Elaphe sensu lato formed a polyphyletic group?

`A second paper (Dessauer et al. 1987) is claimed by Tong et al. to have made an assumption for Elaphe polyphyly.'

So why should we take their word for it?

`A third study (Dessauer 1983) predates the 1987 assumption (interestingly, Utiger et al. neglect to give the full citation for this paper). So the only unrefuted (by me) study that Utiger et al. cites for Elaphe polyphyly is Minton (1976, Serological relationships among some congeneric North American and Eurasian colubrid snakes. Copeia 1976:672-678)'

So you claim to have refuted two papers by Dessauer that you haven't even read?

`You are on thin ice indeed if Minton's 1976 paper is your only unread evidence of a polyphyletic Elaphe, especially since Utiger et al.'s own study (as well as that of Lopez and Maxson and Tong et al.) refutes Elaphe polyphyly.'

This has already been addressed.

You're also forgetting another paper I mentioned. I don't recall the citation offhand, but it's in the thread somewhere.

`To give it meaning, you must submit evidence for a polyphyletic Elaphe.'

This has already been addressed.

`It has been more than a quarter of a century since Minton published his paper. If there is actual evidence of a polyphyletic Elaphe within it or within any of the papers cited by Utiger et al., Elaphe would have been dismantled a long time ago. Dowling, who is one of the leading authorities on this genus, would not have tolerated polyphyletic taxa, and neither would Dessauer or Minton or for that matter any self-respecting systematist of any school.'

Now this is an interesting argument. You appear to be saying that, since Dowling, Minton, and Dessauer would have dismantled Elaphe sensu lato if they believed it to be polyphyletic, Elaphe must be either mono- or paraphyletic. However, we already know that these authors have stated that they believe Elaphe sensu lato is polyphyletic, and we already know that they didn't dismantle it. So the premise of your argument is clearly false...

Apart from that, a taxon's long-term recognition is very poor evidence of mono- or paraphyly.

`Dessauer et al. find that snakes now classified in the genera Arizona, Lampropeltis, Rhinocheilus, Bogertophis, Cemophora, Pituophis, Senticolis and Elaphe (obsoleta, vulpina, bairdi, and guttata) are closely related to each other. Elaphe quatuorlineata is the outgroup to this American assemblage. Dessauer et al.'s (1987) data therefore shows that an Eurasian species of Elaphe is ancestral to the North American species of Elaphe and the genera listed above. This is not evidence that Elaphe is polyphyletic at all! This is in fact evidence that all of these American species of snakes are descended from a single species of Eurasian Elaphe.'

`Basal to' does not mean `ancestral to'. If Dessauer's results are as you suggest, they mean that the Lampropeltinines and Elaphe quatuorlineata form sister taxa among the taxa studied by Dessauer, i.e., that they share a more recent common ancestor than either does with any taxa. It doesn't say anything about what that common ancestor was.

Patrick Alexander

`So you claim to have refuted two papers by Dessauer that you haven't even read?'

That should read `one' rather than `two'. Forgot to go back and correct for your responses to yourself.

BTW, any particular reason for the month-long absence?

Patrick Alexander

You wrote:
But, IIRC, all the Old World `Elaphe' Lopez and Maxson use are in Elaphe sensu stricto. Most of the problematic members of Elaphe sensu lato are not in Elaphe sensu stricto, so this isn't a good test.

My response:
Not so. Elaphe scalaris, which is one of the species analyzed by Lopez and Maxson is considered a member of the monotypic "Rhinechis" by Utiger et al.

You wrote:
Adaptive radiation, of itself, doesn't have any consequences for
resolution of a genetically-based phylogeny.

My response:
If several species evolve from a single species so quickly that there is no time for the mtDNA to evolve into more than 1 lineage, then all of the species will have identical ancestral mtDNA markers, with subsequent autapomorphic changes appearing in each descendant species but no common markers to link any species pair more closely to each other than to other species. The result is an unresolved polytomy involving multiple species, such as the kind seen in Rodriguez-Robles et al.'s analysis of the Lampropeltini. Adaptive radiation can result in polytomies. This is something that competent systematists know.

I wrote:
'Your slim hope that Utiger et al.'s data somehow suggest that Elaphe is polyphyletic has been dashed by Tong et al.'s bootstrap value of 98 for the Ptyas-Elaphe split.'

You wrote:
This has already been addressed.

My response:
That is not possible. This is the first time I brought up Tong et al's bootstrap value for this node.

You wrote:
The relationship of Old World taxa to New World taxa to each other is not the issue. The relationships to each other of all members of Elaphe sensu lato, whether they happen to be New or
Old World, is the issue. As a result, your argument above, which is predicated on the sole importance of New vs. Old World taxa, doesn't apply.

My response:
Tong et al. show that all of the Old World species of Elaphe, including the most basal member, Elaphe mandarina, form a monophyletic group with Ptyas as the outgroup. Lopez and Maxson show that all species of New World Elaphe (along with their descendants in the Lampropeltini) form a monophyletic group with the Old World species they study basal to the New World clade. Ptyas is the outgroup. Utiger et al. find that New World Elaphe plus the Lampropeltini form a clade with the Old World species of Elaphe basal to the New World clade and Ptyas as the outgroup. The similarities in their findings suggest that Old World Elaphe is paraphyletic with respect to New World Elaphe and New World Elaphe is paraphyeltic with respect to the Lampropeltini. All of these species (Old World Elaphe plus New World Elaphe plus the Lampropeltini) form a clade with Ptyas as an outgroup. Conversely, there isn't any study that demonstrate polyphyly in Elaphe. Hence Elaphe is not polyphyletic.

I wrote:
`Utiger et al. cite 4 papers. One of these (Dowling et al.), as I point out, cannot possibly make that conclusion since it does not include a single species of Old World Elaphe in it.'

You wrote:
Ok. But what if they thought that New World members of Elaphe sensu lato formed a polyphyletic group?

My response:
That is not possible. Their data shows that New World members of Elaphe are all part of a monophyletic group they call "Elaphini." As I said, they have a hunch that Old World Elaphe and New World Elaphe may form a polyphyletic group, but they have no data to show one way or another. Utiger et al., nevertheless, cites this paper for evidence that some authors have concluded that Elaphe is polyphyletic. Dowling et al. are merely speculating about this possibility since their data cannot answer that question one way or the other.

I wrote:
`A second paper (Dessauer et al. 1987) is claimed by Tong et al. to have made an assumption for Elaphe polyphyly.'

You wrote:
So why should we take their word for it?

My response:
If any author had convincingly demonstrated that Elaphe is polyphyletic, it would not have survived the past decade and a half intact. It is quite obvious that Dessauer et al. are speculating based on that fact alone.

You wrote:
So you claim to have refuted two papers by Dessauer that you haven't even read?

My response:
I might not have read it, but Tong et al. did. I have since read it, and there is nothing in there that shows Elaphe is polyphyletic. Dessauer et al. find that Elaphe quatorlineata is basal to New World Elaphe and the Lampropeltine species. That is consistent with the results from the newer papers that refute Elaphe polyphyly.

You wrote:
You're also forgetting another paper I mentioned. I don't recall the citation offhand, but it's in the thread somewhere.

My response:
I do not remember any such paper. Please refresh my memory.

You wrote:
Now this is an interesting argument. You appear to be saying that, since Dowling, Minton, and Dessauer would have dismantled Elaphe sensu lato if they believed it to be polyphyletic, Elaphe
must be either mono- or paraphyletic. However, we already know that these authors have stated that they believe Elaphe sensu lato is polyphyletic, and we already know that they didn't dismantle it. So the premise of your argument is clearly false...

My response:
They would have dismantled Elaphe if they had proof that it is polyphyletic. Absolutely! They have no proof that Elaphe is polyphyletic. That is why they do not dismantle it. Nothing wrong with my argument, especially since I have shown that Dowling et al. and Dessauer have no data to prove that Elaphe is polyphyletic. I still haven't read Minton but I am confident that he has no data to show that either.

You wrote:
Apart from that, a taxon's long-term recognition is very poor evidence of mono- or paraphyly.

My response:
Do you have any evidence that a polyphyletic taxon, any polyphyletic taxon, has continued to be recognized despite its polyphyletic status? Let me guess: Elaphe!

You wrote:
`Basal to' does not mean `ancestral to'.

My response:
True. But a lineage that is basal to another can indeed be ancestral to it.

You wrote:
If Dessauer's results are as you suggest, they mean that the Lampropeltinines and Elaphe quatuorlineata form sister taxa among the taxa studied by Dessauer, i.e., that they share a more recent common ancestor than either does with any taxa. It doesn't say anything about what that common ancestor was.

My response:
If New World Elaphe and E. quatorlineata share a recent common ancestor, then there are two possibilities. Their common ancestor is a species of Elaphe or they are only convergently similar, meaning that their common ancestor is not like Elaphe and that the New World species of Elaphe are only convergently similar to E. quatorlineata. The second alternative is certainly possible, but not as parsimonious. Most systematists would agree that New World Elaphe is descended from an Old World species of Elaphe. Most systematists would agree that Elaphe is not polyphyletic.

`Not so. Elaphe scalaris, which is one of the species analyzed by Lopez and Maxson is considered a member of the monotypic "Rhinechis" by Utiger et al.'

Ah yeah, I'd forgotten that they included Rhinechis. Rhinechis'd already been split off before Utiger et al.'s study, though, and, given the large amounts of both morphological and genetic disparity involved, I don't think there's much reason to doubt that the split was warranted. And, since some of that morphological disparity is in nice and obvious features of scalation and head shape, even you should approve. : )

`If several species evolve from a single species so quickly that there is no time for the mtDNA to evolve into more than 1 lineage, then all of the species will have identical ancestral mtDNA markers, with subsequent autapomorphic changes appearing in each descendant species but no common markers to link any species pair more closely to each other than to other species. The result is an unresolved polytomy involving multiple species, such as the kind seen in Rodriguez-Robles et al.'s analysis of the Lampropeltini. Adaptive radiation can result in polytomies. This is something that competent systematists know.'

Ok. I'd guessed that rapid lineage divergence and the resulting `shallow' phylogeny was what you were referring to, but since this isn't inherent in adaptive radiation, and can result from other processes such as sudden range expansion, I wasn't sure.

So, is there any reason to suspect that this is the case in Elaphe sensu lato? I seem to recall Utiger et al. discussing phylogeography at the end of their paper, but don't have the paper with me...

`That is not possible. This is the first time I brought up Tong et al's bootstrap value for this node.'

The bootstrap value isn't the problem. The taxon representation is the problem.

`Tong et al. show that all of the Old World species of Elaphe, including the most basal member, Elaphe mandarina, form a monophyletic group with Ptyas as the outgroup.'

They can't show that, because they didn't study all Old World members of Elaphe sensu lato. Outgroup representation would also need to be much higher for this to be compelling.

`Lopez and Maxson show that all species of New World Elaphe (along with their descendants in the Lampropeltini) form a monophyletic group with the Old World species they study basal to the New World clade. Ptyas is the outgroup.'

Lopez and Maxson don't study all New World species that were in Elaphe at the time of their publication, so they don't demonstrate anything about all of them. Furthermore, all studies of lampropeltinine phylogeny I've seen show Pantherophis to be one of the more derived clades within Lampropeltini. Though lacking sufficient taxa to provide good support for this, Lopez and Maxson's results are also consistent with a derived status for Pantherophis within Lampropeltini.

It's also worth mentioning that Ptyas is not the taxon most closely related to Elaphe sensu lato in Lopez and Maxson's study, so is not `the' outgroup.

`That is not possible. Their data shows that New World members of Elaphe are all part of a monophyletic group they call "Elaphini." As I said, they have a hunch that Old World Elaphe and New World Elaphe may form a polyphyletic group, but they have no data to show one way or another. Utiger et al., nevertheless, cites this paper for evidence that some authors have concluded that Elaphe is polyphyletic. Dowling et al. are merely speculating about this possibility since their data cannot answer that question one way or the other.'

Ok.

Did Dowling et al. conclude that Elaphe sensu lato is polyphyletic, BTW? I ask because, if they did, then whether or not this conclusion was speculative is irrelevant to their having been cited as having concluded that Elaphe sensu lato is polyphyletic--your wording above suggests that you think Utiger et al. cite him for this erroneously, and I'm curious as to whether or not this is the case.

`If any author had convincingly demonstrated that Elaphe is polyphyletic, it would not have survived the past decade and a half intact. It is quite obvious that Dessauer et al. are speculating based on that fact alone.'

There's a large gulf between `convincingly demonstrated' and `speculated'. My guess is that Dessauer et al. fall into this gulf.

`I might not have read it, but Tong et al. did. I have since read it, and there is nothing in there that shows Elaphe is polyphyletic. Dessauer et al. find that Elaphe quatorlineata is basal to New World Elaphe and the Lampropeltine species.`

Which paper are you referring to, here? I'm guessing you're referring to the 1987 paper. As per my corrective post, the 1983 paper was what I was referring to.

`That is consistent with the results from the newer papers that refute Elaphe polyphyly.'

I do wish you'd quit begging the question like that...

`I do not remember any such paper. Please refresh my memory.'

See the link.

`They would have dismantled Elaphe if they had proof that it is polyphyletic. Absolutely! They have no proof that Elaphe is polyphyletic. That is why they do not dismantle it. Nothing wrong with my argument, especially since I have shown that Dowling et al. and Dessauer have no data to prove that Elaphe is polyphyletic. I still haven't read Minton but I am confident that he has no data to show that either.'

I suggest you re-read what I wrote. Note that I was phrasing this in terms of
belief rather than proof. There's a pretty wide gulf between the two, and I put it in those terms because that's what I thought was implied in your post. AFAIK, it is the case that Dessauer, Minton, and Dowling believed that Elaphe sensu lato is polyphetic. They didn't dismantle the genus, however. My guess is that they thought that a revision of the genus should await more comprehensive and definitive studies.

I said:
`Apart from that, a taxon's long-term recognition is very poor evidence of mono- or paraphyly.'

You said:
`Do you have any evidence that a polyphyletic taxon, any polyphyletic taxon, has continued to be recognized despite its polyphyletic status?'

Many taxa now known to be polyphyletic have been recognized. A couple examples that come to mind are Natrix, when it included Nerodia, and Coluber. The problems of Coluber still haven't been comprehensively addressed, though Schatti and Utiger (Revue Suisse de Zoologie, 2001; 108 (4): 919-948) have begun to sort it out.

`True. But a lineage that is basal to another can indeed be ancestral to it.'

If two groups form sister taxa (as you say Elaphe quatuorlineata and Lampropeltini do in Dessauer et al. (1987)), one by definition cannot be ancestral to the other. So, according to this phylogeny, Elaphe quatuorlineata cannot be ancestral to Lampropeltini.

`If New World Elaphe and E. quatorlineata share a recent common ancestor, then there are two possibilities. Their common ancestor is a species of Elaphe or they are only convergently similar, meaning that their common ancestor is not like Elaphe and that the New World species of Elaphe are only convergently similar to E. quatorlineata. The second alternative is certainly possible, but not as parsimonious.'

That is incorrect. If we take Lampropeltini and Elaphe quatuorlineata to form a monophyletic clade, then if Pantherophis and Elaphe quatuorlineata share similarities not found in a common ancestor, their similarities evolved once in an ancestor of Pantherophis and once in an ancestor of Elaphe quatuorlineata. Because Pantherophis is a derived taxon within Lampropeltini, if Pantherophis and Elaphe quatuorlineata share similarities present in a common ancestor their similarities arose once in a common ancestor, were lost in an ancestor to Lampropeltini, and arose again in an ancestor to Pantherophis. So you've got two state changes vs. three.

`Most systematists would agree that New World Elaphe is descended from an Old World species of Elaphe. Most systematists would agree that Elaphe is not polyphyletic.'

Have you asked them?

Patrick Alexander
Link

You wrote:
Rhinechis'd already been split off before Utiger et al.'s study, though, and, given the large amounts of both morphological and genetic disparity involved, I don't think there's much reason to doubt that the split was warranted.

My response:
Tong et al.'s analysis includes Elaphe mandarina, which is the basal most member of Elaphe. They find Ptyas, Zaocys et al. outside of the cluster of Elaphe species included in their study. Since E. mandarina is more basal than E. scalaris and E. scalaris is more basal than the New World species of Elaphe in both Utiger et al. and Lopez and Maxson, Tong et al. thus demonstrate that all species of Elaphe are more closely related to each other than any of them is to any of the racers.

According to you every taxonomic change that results in the removal of species from Elaphe is warranted. I have not seen one single change that you say is unwarranted. If one is going to blindly accept taxonomic changes, that is fine. Many people do it, including among them professional herpetologists.

You wrote:
So, is there any reason to suspect that this is the case in Elaphe sensu lato?

My response:
The unresolved polytomy only occurs in their consensus tree. The MP tree is better resolved. That shows there is something wrong with their data since the MP tree does not suggest adaptive radiation.

You wrote:
They can't show that, because they didn't study all Old World members of Elaphe sensu lato. Outgroup representation would also need to be much higher for this to be compelling.

My response:
The unusally high bar you have raised for Tong et al.'s data, which contradicts your preconception, is in sharp contrast with the blind faith you show on the other authors' taxonomic proposals splitting Elaphe.

You wrote:
Lopez and Maxson don't study all New World species that were in Elaphe at the time of their publication, so they don't demonstrate anything about all of them.

My response:
They demonstrate that Elaphe scalaris is basal to the North American species of Elaphe. That is one important finding. Utiger et al. sure included them all and they show that Elaphe is part of the monophyletic group, with E. mandarina the basal most member. They corroborate each other. Have you forgotten about Utiger et al.'s paper?

You wrote:
Furthermore, all studies of lampropeltinine phylogeny I've seen show Pantherophis to be one of the more derived clades within Lampropeltini.

My response:
Are you suggesting that Elaphe obsoleta is a descendant of Lampropeltis or Pituophis and that it is only convergently similar to Elaphe scalaris? Fact is, all species of Elaphe share similarities with each other and with Lampropeltis in hemipenial structure. Pituophis is more derived in this respect. If Elaphe obsoleta is descended from Pituophis and not vice versa, then Elaphe obsoleta would have to re-evolve the hemipenial structure that its Pituophis ancestor had lost. If Elaphe obsoleta is descended from Lampropeltis, then it would have to re-evolve the keeled dorsal scale that its Lampropeltis ancestor had lost. Part of the problem may be the studies you read, part of the problem may be your inability to infer relationships from the tree.

You wrote:
It's also worth mentioning that Ptyas is not the taxon most closely related to Elaphe sensu lato in Lopez and Maxson's study, so is not `the' outgroup.

My response:
Lopez and Maxson show that Ptyas is not even close to Elaphe. Utiger et al. also find that Ptyas is not closer to any Elaphe than other species of Elaphe. Tong et al. find the same thing. Unless you know of some other species that would make Elaphe polyhyletic, your slim hope that Ptyas would do that has evaporated.

You wrote:
Did Dowling et al. conclude that Elaphe sensu lato is polyphyletic

My response:
They cannot make that conclusion because they have no data to do it. They are merely speculating.

You wrote:
There's a large gulf between `convincingly demonstrated' and `speculated'. My guess is that Dessauer et al. fall into this gulf.

My response:
You guess. Dessauer et al. assume. Neither of you have the data to show that Elaphe is polyphyletic.

You wrote:
Which paper are you referring to, here? I'm guessing you're referring to the 1987 paper. As per my corrective post, the 1983 paper was what I was referring to.

My response:
Utiger et al. do not give the full citation for this paper so how can you be referring to this paper? Besides, the 1987 paper merely cite data from the 1983 paper. So, you are just hoping that the 1983 paper will deliver what the 1987 paper fails to. No dice.

You wrote:
AFAIK, it is the case that Dessauer, Minton, and Dowling believed that Elaphe sensu lato is polyphetic. They didn't dismantle the genus, however. My guess is that they thought that a revision of the genus should await more comprehensive and definitive studies.

My response:
Those studies are now available, and they show that, contrary to their speculation, Elaphe is in fact not polyphyletic.

You wrote:
Many taxa now known to be polyphyletic have been recognized. A couple examples that come to mind are Natrix, when it included Nerodia, and Coluber. The problems of Coluber still haven't been comprehensively addressed, though Schatti and Utiger (Revue Suisse de Zoologie, 2001; 108 (4): 919-948) have begun to sort it out.

My response:
That is not the question. The question was "Do you have any evidence that a polyphyletic taxon, any polyphyletic taxon, has continued to be recognized despite its polyphyletic status?"

You wrote:
If two groups form sister taxa (as you say Elaphe quatuorlineata and Lampropeltini do in Dessauer et al. (1987)), one by definition cannot be ancestral to the other. So, according to this phylogeny, Elaphe quatuorlineata cannot be ancestral to Lampropeltini.

My response:
Elaphe quatuorlineata is basal to New World Elaphe and Lampropeltis, Pituophis et al. in Dessauer et al. (1987).

You wrote:
If we take Lampropeltini and Elaphe quatuorlineata to form a monophyletic clade, then if Pantherophis and Elaphe quatuorlineata share similarities not found in a common ancestor, their similarities evolved once in an ancestor of Pantherophis and once in an ancestor of Elaphe quatuorlineata. Because Pantherophis is a derived taxon within Lampropeltini, if Pantherophis and Elaphe quatuorlineata share similarities present in a common ancestor their similarities arose once in a common ancestor, were lost in an ancestor to Lampropeltini, and arose again in an ancestor to Pantherophis. So you've got two state changes vs. three.

My response:
Which similarity is shared by Elaphe obsoleta and Elaphe quatorlineata but not found in their common ancestor? I cannot think of any. All of their similarities appear to be shared among all species of Elaphe, which means they probably originated in the common ancestor of all species of Elaphe.

I wrote:
`Most systematists would agree that New World Elaphe is descended from an Old World species of Elaphe. Most systematists would agree that Elaphe is not polyphyletic.'

You wrote:
Have you asked them?

My response:
Do I have to? Utiger et al., Lopez and Maxson and Tong et al. all show that Elaphe is not polyphyletic. There also does not exist any paper that shows otherwise, why wouldn't most systematists agree that Elaphe is not polyphyletic? Are most systematists as dogmatic as you?

`According to you every taxonomic change that results in the removal of species from Elaphe is warranted. I have not seen one single change that you say is unwarranted. If one is going to blindly accept taxonomic changes, that is fine. Many people do it, including among them professional herpetologists.'

LOL! There are plenty of taxonomic changes I've already mentioned in this thread (some of which even involve Pantherophis) that I disagree with. That's blind acceptance of taxonomic changes?

`The unresolved polytomy only occurs in their consensus tree. The MP tree is better resolved. That shows there is something wrong with their data since the MP tree does not suggest adaptive radiation.'

Different methods of phylogenetic reconstruction give different phylogenies... that's not a problem with data, that's just how phylogenies work. And you seem to be ditching the adaptive radiation hypothesis...

`The unusally high bar you have raised for Tong et al.'s data, which contradicts your preconception, is in sharp contrast with the blind faith you show on the other authors' taxonomic proposals splitting Elaphe.'

Yeah, yeah, more invective. I think Utiger et al. can tell us more about Elaphe sensu lato because they include a whole lot more species of it. Simple as that. I'd rather Utiger et al. had more outgroup representation, too, but, hey, it's still the best we've got.

`They demonstrate that Elaphe scalaris is basal to the North American species of Elaphe. That is one important finding. Utiger et al. sure included them all and they show that Elaphe is part of the monophyletic group, with E. mandarina the basal most member. They corroborate each other. Have you forgotten about Utiger et al.'s paper?'

I don't think this has anything to do with the comment of mine to which you were referring, though.

`Are you suggesting that Elaphe obsoleta is a descendant of Lampropeltis or Pituophis and that it is only convergently similar to Elaphe scalaris?'

I suggested that Pantherophis is a derived clade within Lampropeltini. Rhinechis and Pantherophis really aren't that similar, though. In basic external morphology and habits, Rhinechis is more similar to Pituophis.

`Part of the problem may be the studies you read, part of the problem may be your inability to infer relationships from the tree.'

If you care to back that up, feel free to point out any error that I've made in either regard.

`Lopez and Maxson show that Ptyas is not even close to Elaphe. Utiger et al. also find that Ptyas is not closer to any Elaphe than other species of Elaphe. Tong et al. find the same thing. Unless you know of some other species that would make Elaphe polyhyletic, your slim hope that Ptyas would do that has evaporated.'

I've never thought, or claimed, that Ptyas would make Elaphe sensu lato polyphyletic. And I already have mentioned other species that appear to be more closely related to Elaphe sensu lato and would thus be more likely to be grouped with it.

`Utiger et al. do not give the full citation for this paper so how can you be referring to this paper? Besides, the 1987 paper merely cite data from the 1983 paper. So, you are just hoping that the 1983 paper will deliver what the 1987 paper fails to. No dice.'

You claimed to have refuted this paper. That's what I was asking about. Keep it straight.

`That is not the question. The question was "Do you have any evidence that a polyphyletic taxon, any polyphyletic taxon, has continued to be recognized despite its polyphyletic status?"'

And I said that polyphyletic taxa have been recognized, and gave examples. No problem there.

Hint: a taxon is polyphyletic (or not) whether we know it or not. If you want to talk about our knowledge of polyphyly, do so. I wasn't talking about our knowledge of polyphyly, though, so you'd just be talking past me.

`Which similarity is shared by Elaphe obsoleta and Elaphe quatorlineata but not found in their common ancestor? I cannot think of any. All of their similarities appear to be shared among all species of Elaphe, which means they probably originated in the common ancestor of all species of Elaphe.'

What similarities would those be, exactly? And what do you know of the morphology of their common ancestor?

`Do I have to?'

If you're going to tell me what most systematicists think, yes, you're going to need to've asked (or have access to some other source that asked, etc) them.

Anyways, as over in the discussion over on that other forum, this isn't going anywhere. So I'm out unless it starts to look like it might go somewhere.

Patrick Alexander

You wrote:
LOL! There are plenty of taxonomic changes I've already mentioned in this thread (some of which even involve Pantherophis) that I disagree with. That's blind acceptance of taxonomic changes?

My response:
Such as?

You wrote:
And you seem to be ditching the adaptive radiation hypothesis...

My response:
The MP tree does not support it.

You wrote:
I think Utiger et al. can tell us more about Elaphe sensu lato because they include a whole lot more species of it. Simple as that.

My repsonse:
They tell us, for example, that Elaphe is not polyphyletic as a group. But you seem to reject that information because there are 4 papers cited by Utiger et al., in which the authors speculated that Elaphe is polyphyletic. You even claimed that they outnumber Utiger four to one, in spite of the fact that you never read these 4 papers. I have read two of them and neither show any data to support polyphyletic Elaphe.

You wrote:
I suggested that Pantherophis is a derived clade within Lampropeltini. Rhinechis and Pantherophis really aren't that similar, though. In basic external morphology and habits, Rhinechis is more similar to Pituophis.

My response:
Pituophis is a descendant of the ancient paraphyletic species Elaphe obsoleta (or sister taxon if you prefer) according to immunological data. Elaphe scalaris is morphologically similar to Pituophis. Does that suggest Elaphe obsoleta and E. scalaris are only convergently similar?

You wrote:
If you care to back that up, feel free to point out any error that I've made in either regard.

My response:
The fact that you think E. obsoleta (your “Pantherophis”) is a derived taxon shows that you do not know how to read the trees. This sort of phylogenetic relationship requires Elaphe obsoleta to lose the ancestral Elaphe characters it shares with Old World Elaphe (e.g. hemipenial structure) and then re-evolve very similar ones from a more derived condition such as that in Pituophis. Although Pituophis may seem to be similar to E. scalaris, its hemipenis does not look like those of Old World Elaphe. See for yourself by grabbing a hold of Dowling and Fries (1987, Herpetologica 43:200-207). All of the hemipenes of Elaphe, whether Old World or New World, are strikingly similar and thus indicative of a close relationship, especially in view of other similarities they share. Pituophis, though sharing some of the characteristics of Elaphe hemipenis, is clearly more derived, and it shares these derived similarities with its close relative Arizona, which has been described as a faded gopher snake. Clearly E. obsoleta is basal to Pituophis and Old World Elaphe is basal to New World Elaphe. Otherwise it would require 2 reversals for every similarity E. obsoleta shares with Old World Elaphe, if these similarities are only convergent. No change is definitely more parsimonious than 2 reversals.

You wrote:
I've never thought, or claimed, that Ptyas would make Elaphe sensu lato polyphyletic. And I already have mentioned other species that appear to be more closely related to Elaphe sensu lato and would thus be more likely to be grouped with it.

My response:
Denial again. You claim that the weakened statistical support for Ptyas as outgroup in Utiger et al. may mean that Elaphe is polyphyletic. I suggest instead that there may be something wrong with Utiger et al.'s data. Regardless, you never named a single species of racer that is more closely related to Elaphe than the species of Elaphe are to each other, which would in fact render Elaphe polyphyletic.

You wrote:
And I said that polyphyletic taxa have been recognized, and gave examples. No problem there.

Hint: a taxon is polyphyletic (or not) whether we know it or not.

My response:
That is not the point. I claim that no systematist will knowingly recognize polyphyletic taxa. Therefore the fact that Elaphe has survived intact for decades is prima facie evidence that it is not polyphyletic. You disagree but can cite no example of known polyphyletic taxa that continue to be recognized.

You wrote:
What similarities would those be, exactly? And what do you know of the morphology of their common ancestor?

My response:
I was asking you since you mentioned them. I take it that you do not know what similarity is shared by Elaphe obsoleta and Elaphe quatorlineata but not found in their common ancestor. Therefore you do not know which characters are supposedly convergent between these two species of Elaphe. If no one knows of the existence of such convergent characters, then the similarities between them is more likely than not shared derived characters. Molecular data also support this conclusion. They all show that Elaphe is not polyphyletic.

You wrote:
If you're going to tell me what most systematicists think, yes, you're going to need to've asked (or have access to some other source that asked, etc) them.

My response:
Why would any systematist claim that Elaphe is polyphyletic if there are three recent mtDNA analyses that refute this hypothesis and there is zero evidence that supports it? Systematists are scientists, and scientists rely on evidence (at least they are supposed to). If systemtists do what they are supposed to do, then most of them would indeed conclude that Elaphe is not polyphyletic. I do not have to ask them.

Patrick wrote:

"Nope, the grouping of Euprepriophis with the other taxa studied rather than Ptyas is poorly supported. And Ptyas is the outgroup--it's supposed to be distantly related to all of the taxa involved, so a poor support for its outgroup status is particularly damning."

Tong et al. find strong statistical support both for Ptyas as an outgroup to Elaphe and for Elaphe mandarina as the basal most member of the Elaphe clade. Lopez and Maxson have a similar finding regarding Ptyas as the outgroup. Neither Tong et al. nor Lopez and Maxson included Senticolis in their analysis. The fact that Utiger et al. included Senticolis in their analysis may have weakened the statistical support for their tree near the base, since Senticolis may very well be a racer and an outgroup to Ptyas plus Elaphe. Senticolis plus Elaphe may well be a polyphyletic group. But since Senticolis triaspis has already been shown to be morphologically and genetically distant from any known species of Elaphe, there is no reason to transfer it back to Elaphe. Elaphe (sans Senticolis) is not polyphyletic. If Utiger et al. redo their analysis without Senticolis, they may find much better statistical support for their tree.

Utiger et al. apparently had the preconception that Senticolis is part of the American ratsnake clade and they chose a cladogram that reflects such a relationship accordingly, resulting in poorer support for Ptyas as the outgroup than in other studies of colubrid relationships, such as those of Tong et al. and Lopez and Maxson.

You wrotie:
First, that an author has not created paraphyletic taxa does not imply that the author is intolerant of paraphyletic taxa. In this case, there simply are no well-supported paraphyletic taxa that could have been created within Elaphe, and the authors clearly voice their support for the existence of paraphyletic taxa.

My response:
Since Elaphe mandarina is basal to all other species of Elaphe in their trees, Elaphe is clearly a paraphyletic taxon. The fact that Utiger et al. splintered Elaphe is evidence that they do not tolerate paraphyletic taxa, nothwithstanding their "support" for paraphyletic taxa.

Patrick wrote:

"It is far from certain that Elaphe sensu lato is paraphyletic (the evidence I'm aware of appears to argue strongly against it), and, of course, even if one accepts paraphyletic taxa in principle, it doesn't follow that all paraphyletic taxa should be recognized or that scientifically tenable reasons for rejecting certain paraphyletic taxa don't exist."

It is in fact a foregone conclusion that Elaphe is paraphyletic. Old World Elaphe is ancestral to New World Elaphe according to both Lopez and Maxson and Utiger et al.'s mtDNA data. New World Elaphe and the lampropeltine genera (such as Pituophis, Lampropeltis and Arizona) form a subclade within the Elaphe clade. The New World ratsnakes are derived taxa according to both studies. Removing derived genera such as Lampropeltis, Pituophis and Arizona leaves Elaphe (Old World plus New World) paraphyletic. The inclusion of Senticolis in Utiger et al.'s study and their preference for a tree which nests Senticolis within the Elaphe clade (albeit with dismal statistical support for that particular node) may have weakened their hypothesis of the phylogenetic relationships among the ratsnakes. Their study would have been better if they had an open mind concerning the systematic status of Senticolis. If they choose a tree with the best statistical support for the position of Senticolis, they may find that Senticolis may be basal to all of the ratsnakes they studied, including Elaphe mandarina and E. conspicillata. It may even be basal to Ptyas plus Elaphe.

`Since you cited Utiger et al., you should be familiar with their tree. Their findings show that all species formerly classified in Elaphe, together with the Lampropeltini, form a clade with Ptyas as the outgroup. How can a clade be polyphyletic?'

The clade isn't the group in question, Elaphe is.

`Where is the evidence of polyphyly?'

FWIW, Utiger et al. also cite Minton (1976), Lawson and Dessauer (1981), Dowling et al., and Dessauer et al. (1987) as having concluded that Elaphe is polyphyletic. I can give you the complete citations, if you want.

Patrick Alexander

The whole group (minus the Lampropeltini and Senticolis) is Elaphe. The group is not polyphyletic; Elaphe is not polyphyletic.

"FWIW, Utiger et al. also cite Minton (1976), Lawson and Dessauer (1981), Dowling et al., and Dessauer et al. (1987) as having concluded that Elaphe is polyphyletic. I can give you the complete citations, if you want."

These authors are obviously wrong. Utiger et al. show that all species they study form a clade. Besides, Utiger et al. fail to cite Lopez and Maxson (1995), who show that Old World Elaphe and New World Elaphe form a clade with the Lampropeltini.

`The whole group (minus the Lampropeltini and Senticolis) is Elaphe.'

There's also Rhinechis, Oocatochus, and Coronella. Rhinechis and Oocatochus being splits made by Helfenberger--I'd guess offhand that you disapprove of them, but I don't recall you mentioning it.

` The group is not polyphyletic; Elaphe is not polyphyletic.'

I await new data suggesting that this is the case.

`These authors are obviously wrong.'

That's one hell of a conclusion to jump to. Have you read the papers in question?

`Utiger et al. show that all species they study form a clade.'

No, they don't. See my other post in this thread for today.

`Besides, Utiger et al. fail to cite Lopez and Maxson (1995), who show that Old World Elaphe and New World Elaphe form a clade with the Lampropeltini.'

Well, so far it seems the non-Utiger papers are 4 to 1 in favor of Elaphe having been polyphyletic. Until I've either read the papers in question or have some other good reason to choose between them, I think I have to stick with the democratic result.

Patrick Alexander

NP

` The group is not polyphyletic; Elaphe is not polyphyletic.'

You wrote:
I await new data suggesting that this is the case.

My response:
Before such new data becomes available, it is premature to assert that Elaphe is polyphyletic. If it is not polyphyletic, then it ought not be splintered unless the members of this genus form a morphologically disparate group. Utiger et al. show no evidence that they use morphological disparity to splinter Elaphe. Hence their destruction of Elaphe is untenable.

`Besides, Utiger et al. fail to cite Lopez and Maxson (1995), who show that Old World Elaphe and
New World Elaphe form a clade with the Lampropeltini.'

You wrote:
Well, so far it seems the non-Utiger papers are 4 to 1 in favor of Elaphe having been polyphyletic. Until I've either read the papers in question or have some other good reason to choose between them, I think I have to stick with the democratic result.

My response:
Both Utiger et al. and Lopez and Maxson find that Elaphe is not polyphyletic. Their findings are supported by a third paper recently published in Acta Zoologica Sinica. That is three independent studies proving that Elaphe is not polyphyletic. There may well be new data suggesting otherwise, but until they are available, there simply is no evidence of polyphyly. You certainly cannot cite any such evidence, notwithstanding your belief to the contrary.

` The group is not polyphyletic; Elaphe is not polyphyletic.'

I wrote:
I await new data suggesting that this is the case.

Your response:
Before such new data becomes available, it is premature to assert that Elaphe is polyphyletic.

You're saying that it's premature to assert that Elaphe is polyphyletic until we have data demonstrating that Elaphe is not polyphyletic? This amounts to an a priori rejection of the possibility of polyphyly.

`If it is not polyphyletic, then it ought not be splintered unless the members of this genus form a morphologically disparate group. Utiger et al. show no evidence that they use morphological disparity to splinter Elaphe. Hence their destruction of Elaphe is untenable.'

Utiger et al. do, however, cite other works which demonstrate that Elaphe sensu lato is a morphologically disparate group. See, for instance, Helfenberger, N. `Phylogenetic Relationships of Old World Ratsnakes Based on Visceral Organ Topography, Osteology, and Allozyme Variation', Russian Journal of Herpetology 8 (Suppl.) 1-64.

`Both Utiger et al. and Lopez and Maxson find that Elaphe is not polyphyletic.'

Your assessment of their results differs with theirs. For the Utiger et al., see other discussion in this thread. Out of curiosity I got hold of the Lopez et al. (Lopez, Maxson, and Dowling) paper, and found the following:

First, they do not have the data to adequately test the phylogenetic relationships within Elaphe sensu lato (albumin distances for were only found between Pantherophis obsoletus and each of four species of Elaphe sensu stricto and Pantherophis guttatus). Given that the purpose of the paper was the determination of the intergeneric relationships between Dasypeltis and other colubrine genera, this is not surprising.

Second, the conclusion to which they come regarding phylogenetic relationships within Elaphe sensu lato is that: `From these tests we conclude only that the Eurasian ratsnakes are roughly equidistant from the Nearctic ratsnakes and the racers.'

`Their findings are supported by a third paper recently published in Acta Zoologica Sinica.'

The inadequacies of this study have already been mentioned.

`That is three independent studies proving that Elaphe is not polyphyletic. There may well be new data suggesting otherwise, but until they are available, there simply is no evidence of polyphyly.'

Your assessment of two of those studies disagrees with that of their authors. Including the other papers cited by Utiger et al. and mentioned elsewhere in the thread demonstrating polyphyly of Elaphe sensu lato, this gives a total of 5 independent studies demonstrating polyphyly of Elaphe sensu lato and 1 disagreeing.

Patrick Alexander

You wrote:
You're saying that it's premature to assert that Elaphe is polyphyletic until we have data demonstrating that Elaphe is not polyphyletic? This amounts to an a priori rejection of the possibility of polyphyly.

My response:
I do not reject the possibility that Elaphe is polyphyletic. I reject your assumption that Elaphe is polyphyletic. You are assuming polyphyly since you have no evidence of polyphyly. There are three independent studies showing that Elaphe is not polyphyletic. That is strong evidence against your assumption of polyphyly.

You wrote:
Utiger et al. do, however, cite other works which demonstrate that Elaphe sensu lato is a morphologically disparate group. See, for instance, Helfenberger, N. `Phylogenetic Relationships of Old World Ratsnakes Based on Visceral Organ Topography, Osteology, and Allozyme Variation', Russian Journal of Herpetology 8 (Suppl.) 1-64.

My response:
There is no evidence that they rely on these types of evidence in delimiting their taxa. They delimit their taxa strictly according to their consensus tree, which is poorly supported by your own admission. Their taxa are therefore poorly supported.

You wrote:
Out of curiosity I got hold of the Lopez et al. (Lopez, Maxson, and Dowling) paper, and found the following:

My response:
You have the wrong paper. The correct one is Lopez and Maxson's 1995 study comparing mitochondrial DNA among ratsnakes and racers. They compared the mtDNA of N. American and Eurasian Elaphe with those of a large number of racers. All of the racer species are basal to Elaphe in their tree. Since racers are the sister taxa of the ratsnakes, this is a good test to see if different species of Elaphe are in fact only convergently similar. If Elaphe is polyphyletic, some species should be closer to some of the racers than they are to each other. This is clearly not the case. All species of Elaphe form a clade along with Cemophora, Lampropeltis and Pituophis.

You wrote:
Your assessment of two of those studies disagrees with that of their authors. Including the other papers cited by Utiger et al. and mentioned elsewhere in the thread demonstrating polyphyly of Elaphe sensu lato, this gives a total of 5 independent studies demonstrating polyphyly of Elaphe sensu lato and 1 disagreeing.

My response:
In some of these papers, the authors merely assume that Elaphe is polyphyletic. You are placing too much weight on these papers that you have not read. Whatever weakness the Acta Zoologica Sinica paper may have is adequately addressed by the paper of Lopez and Maxson. They include a large number of racers and find that none of the species of Elaphe cluster more closely to any of the racers than they do to each other. This is clear evidence that Elaphe is descended from a single species of racer; the ratsnakes are monophyletic. The morphological similarities among all species of ratsnakes are therefore shared derived characters, not convergences. Elaphe is paraphyletic according to the cladists because some of its descendants, such as Lampropeltis and Pituophis, have been removed from Elaphe on the grounds of morphological disparity. Paraphyly is the reason Utiger et al. are applying their machete to Elaphe, not because Elaphe is polyphyletic, since there is no evidence of polyphyly in their paper. Utiger et al. concede that paraphyletic taxa is the inevitable result of evolution, but it has not stopped them from splintering Elaphe because it is paraphyletic. Darwinians, on the other hand, insist that disqualifying or splintering paraphyletic taxa is scientifically untenable. I concur.

The full citation to the paper by Lopez and Maxson is:

Lopez, T.J. and L.R. Maxson 1995.
Mitochondrial DNA Sequence Variation and Genetic Differentiation Among Colubrine Snakes (Reptilia, Colubridae, Colubrinae). Biochemical Systematics And Ecology 23(5):487-505

This paper clearly shows that the ratsnakes cluster more closely with each other than they do to any of the large number of ratsnakes they sequence. They clearly show that N. American and Eurasian ratsnakes form a clade with Lampropeltis, Pituophis and Cemophora. Utiger et al. ignore or overlook this important paper.

`You have the wrong paper.'

Ah. Sorry about that. I'll go look at the right paper, then, and get back to you. : )

`In some of these papers, the authors merely assume that Elaphe is polyphyletic.'

Which papers? And on what grounds do you conclude that it is merely assumption?

`You are placing too much weight on these papers that you have not read.'

Have you read them?

`Whatever weakness the Acta Zoologica Sinica paper may have is adequately addressed by the paper of Lopez and Maxson.'

Which suggests that we should just ignore the Acta Zoologica Sinica paper and only worry about the Lopez and Maxson paper.

`They include a large number of racers and find that none of the species of Elaphe cluster more closely to any of the racers than they do to each other. This is clear evidence that Elaphe is descended from a single species of racer; the ratsnakes are monophyletic. The morphological similarities among all species of ratsnakes are therefore shared derived characters, not convergences.'

BTW, to what morphological similarities are you referring?

`Paraphyly is the reason Utiger et al. are applying their machete to Elaphe, not because Elaphe is polyphyletic, since there is no evidence of polyphyly in their paper. Utiger et al. concede that paraphyletic taxa is the inevitable result of evolution, but it has not stopped them from splintering Elaphe because it is paraphyletic.'

Along with some of the unquoted material in your post, this has already been addressed. Feel free to rebut my rebuttals, but, until then, my simply repeating them here wouldn't accomplish much.

`Darwinians, on the other hand, insist that disqualifying or splintering paraphyletic taxa is scientifically untenable. I concur.'

I'd be interested in seeing any works you could cite in which taxonomists express this view. Though I'm well aware that some taxonomists (with which I happen to agree) view paraphyletic taxa as acceptable, I haven't ever seen the idea that all paraphyletic taxa are inherently valid and cannot be modified put forth.

Patrick Alexander

"`In some of these papers, the authors merely assume that Elaphe is polyphyletic.'

You wrote:
Which papers? And on what grounds do you conclude that it is merely assumption?

My response:
Tong et al. (2002, Acta Zoological Sinica) write in their abstract: "seven species of Elaphe form a common branch before they cluster with other genera, contrary to Dessauer's assumption of the polyphyletic origin of this genus"
I have not read Dessauer's paper, but Tong et al. have. They claim that Dessauer only assumed that Elaphe is polyphyletic. I have read Dowling's paper. He also presents no evidence that Elaphe is polyphyletic but thinks that it may be.

You wrote:
Which suggests that we should just ignore the Acta Zoologica Sinica paper and only worry about the Lopez and Maxson paper.

My response:
Since your library does not subscribe to this journal, you would probably have to ignore it. I have not been able to find this paper even though the library has it; it is missing from the shelf. I will not ignore it. It is an independent study that corroborates both Lopez and Maxson and Utiger et al.

You wrote:
BTW, to what morphological similarities are you referring?

My response:
Similarities in scalation, in body proportions, in hemipenial morphology and in microdermatoglyphics of the dorsal scales.

You wrote:
I haven't ever seen the idea that all paraphyletic taxa are inherently valid and cannot be modified put forth.

My response:
As I said, paraphyletic taxa may be splintered if some members of such taxa can be shown to be morphologically disparate. For example, I am open to the idea that some species may be removed from the paraphyletic Elaphe on morphological grounds. So far you have provided no evidence that Utiger et al. resurrected numerous old names on the basis of morphological disparity.

`Tong et al. (2002, Acta Zoological Sinica) write in their abstract: "seven species of Elaphe form a common branch before they cluster with other genera, contrary to Dessauer's assumption of the polyphyletic origin of this genus"
I have not read Dessauer's paper, but Tong et al. have. They claim that Dessauer only assumed that Elaphe is polyphyletic.'

Dessauer's written a number of papers, as I'm sure you're aware. To which paper do Tong et al. refer? And, of course, what are their reasons to characterizing his claim of a polyphyletic Elaphe as `assumption'?

` I have read Dowling's paper. He also presents no evidence that Elaphe is polyphyletic but thinks that it may be.'

I may have to go find that paper just to check. In any case, I was hoping for something more specific than `he presents no evidence'.

`Since your library does not subscribe to this journal, you would probably have to ignore it. I have not been able to find this paper even though the library has it; it is missing from the shelf. I will not ignore it.'

We'll both have to ignore it until we know what it says. But the small number of taxa alone argues against any adequate test of the phylogenetic relationships within Elaphe sensu lato.

`Similarities in scalation, in body proportions, in hemipenial morphology and in microdermatoglyphics of the dorsal scales.'

What characters specifically? From K. Dieter-Schulz's monograph on Elaphe:
`The only existing complete work on Ratsnakes so far was undertaken by Boulenger (1894b) and was based exclusively on morphological characteristics. His definition however does not permit a separation of the genus from other colubrids, e.g. the genus Coluber.' K. Dieter-Schulz doesn't present a workable definition (it isn't his aim), which apparently leaves us without any morphological definition for the species that has been based on a comprehensive study of the genus. On scalation in particular it's worth mentioning that Lenk et al. state that groups corresponding to Rhinechis, Elaphe sensu stricto, and Zamensis were recognized prior to Boulenger's work on the basis of differences in pholidosis. On hemipenes, K. Dieter-Schulz writes that `the male copulatory organs of members of this genus are extremely variable' (p. 21).

`As I said, paraphyletic taxa may be splintered if some members of such taxa can be shown to be morphologically disparate. For example, I am open to the idea that some species may be removed from the paraphyletic Elaphe on morphological grounds.'

Then why have you stated repeatedly that splitting paraphyletic taxa is `scientifically untenable'?

`So far you have provided no evidence that Utiger et al. resurrected numerous old names on the basis of morphological disparity.'

OTOH, I have provided reference to a paper demonstrating morphological disparity among the Old World members of Elaphe sensu lato (namely, Helfenberger's 2001 paper)/ K. Dieter-Schulz is another good source. So long as the taxa are morphologically disparate, why be so concerned withi whether or not this morphological disparity was explicitly stated as the reason for the splits? Is your objection to the validity of the taxa themselves, or simply that Utiger et al. didn't make what you feel to be the appropriate nods to morphology?

Patrick Alexander

`As I said, paraphyletic taxa may be splintered if some members of such taxa can be shown to be morphologically disparate. For example, I am open to the idea that some species may be removed from the paraphyletic Elaphe on morphological grounds.'

You wrote:
Then why have you stated repeatedly that splitting paraphyletic taxa is `scientifically untenable'?

My response:
Very good question. Darwinians do not distinguish between paraphyletic taxa and monophyletic (sensu Hennig) taxa. All paraphyletic taxa are monophyletic according to the Darwinians since both types of taxa share a single common ancestor. Since Darwinians find it scientifically tenable to splinter monophyletic (sensu Hennig) taxa on the basis of morphological disparity, it is therefore scientifically tenable to splinter paraphyletic taxa on the same basis. On the other hand, splintering monophyletic (sensu Hennig) or paraphyletic taxa without a valid reason is scientifically untenable.

`So far you have provided no evidence that Utiger et al. resurrected numerous old names on the basis of morphological disparity.'

You wrote:
OTOH, I have provided reference to a paper demonstrating morphological disparity among the Old World members of Elaphe sensu lato (namely, Helfenberger's 2001 paper)/ K. Dieter-Schulz is another good source. So long as the taxa are morphologically disparate, why be so concerned withi whether or not this morphological disparity was explicitly stated as the reason for the splits? Is your objection to the validity of the taxa themselves, or simply that Utiger et al. didn't make what you feel to be the appropriate nods to morphology?

Patrick Alexander

My response:
Any two species, unless they are diploid-polyploid species pairs, are morphologically disparate. So it is not hard to find morphological disparity between closely related species most authors classify in the same genus. The question is whether the amount of morphological disparity rises to genus level. Utiger et al. simply do not provide any data on morphological disparity to justify their taxonomic proposal to remove a large number of species from Elaphe and place them in other genera. Since they also provide no evidence to support a polyphyletic Elaphe, they have provided no scientifically tenable reason to justify their highly destructive taxonomic proposal.

`Very good question. Darwinians do not distinguish between paraphyletic taxa and monophyletic (sensu Hennig) taxa. All paraphyletic taxa are monophyletic according to the Darwinians since both types of taxa share a single common ancestor. Since Darwinians find it scientifically tenable to splinter monophyletic (sensu Hennig) taxa on the basis of morphological disparity, it is therefore scientifically tenable to splinter paraphyletic taxa on the same basis. On the other hand, splintering monophyletic (sensu Hennig) or paraphyletic taxa without a valid reason is scientifically untenable.'

Morphological data aren't the only valid data, though. Evidence of genetic disparity is, these days, generally considered to be of greater importance and utility in taxonomy, though only the hardcore cladists (Burbrink comes to mind) are willing to use it to split a taxon into morphologically indistinguishable taxa.

I'd guess that Utiger et al. don't explicitly mention morphology for some of their taxa simply because the morphological disparity among the members of Elaphe sensu lato is so conspicuous and has been previously reported often enough that they figure their readers are already well aware of it.

`Any two species, unless they are diploid-polyploid species pairs, are morphologically disparate. So it is not hard to find morphological disparity between closely related species most authors classify in the same genus. The question is whether the amount of morphological disparity rises to genus level.'

And that question is simply a judgment call--they could provide all the data on morphological disparity they wanted, and still have no objective means of demonstrating that the disparity is `enough'. I think most people familiar with Elaphe sensu lato will agree, though, that the disparity is indeed enough for generic distinction to be appropriate.

`Utiger et al. simply do not provide any data on morphological disparity to justify their taxonomic proposal to remove a large number of species from Elaphe and place them in other genera.'

See above and previous discussion. The data had already been presented by other authors.

`Since they also provide no evidence to support a polyphyletic Elaphe, they have provided no scientifically tenable reason to justify their highly destructive taxonomic proposal.'

I continue to disagree with your assessment of the data as regards polyphyly. I suppose that's not a shock at this point...
And anyways, what good's it do anyone to have all these different taxa lumped in together in Elaphe sensu lato? It keeps the generic name from conveying any useful information.

Patrick Alexander

You wrote:
Morphological data aren't the only valid data, though. Evidence of genetic disparity is, these days, generally considered to be of greater importance and utility in taxonomy, though only the hardcore cladists (Burbrink comes to mind) are willing to use it to split a taxon into morphologically indistinguishable taxa.

My response:
Molecular data of all sorts have indeed proven more useful than morphological similarities in elucidating branching order. However, it is cladistic dogma to ignore morphological disparity in classification, since Hennig rejects its use. The way Burbrink split Elaphe guttata is no different than the way Utiger et al. have splintered Elaphe; they both ignore morphological disparity and only rely on branching order only.

You wrote:
I'd guess that Utiger et al. don't explicitly mention morphology for some of their taxa simply because the morphological disparity among the members of Elaphe sensu lato is so conspicuous and has been previously reported often enough that they figure their readers are already well aware of it.

My response:
My interpretation is different. As one can see by the two new genera they coin, there isn't any good morphological character to distinguish one genus from another since these characters are variable intragenerically or even intraspecifically. On the other hand, the taxa they recognize clearly are delimited from their consensus cladogram. Each major branch in that cladogram is classified as a different genus. That is no different than Burbrink, who classifies each major branch in his analysis as a different species.

You wrote:
And that question is simply a judgment call--they could provide all the data on morphological disparity they wanted, and still have no objective means of demonstrating that the disparity is `enough'. I think most people familiar with Elaphe sensu lato will agree, though, that the disparity is indeed enough for generic distinction to be appropriate

My response:
It is true that there is no objective measure of morphological disparity. Darwinian taxa are indeed subjectively delimited. The alternative is far worse. The cladists, who have no guideline for delimiting taxa other than equal rank for sister taxa, are far more subjective. Kluge, for example, states that he can either recognize one, two or three genera given the particular topology of his cladogram. He finally decides that, for the sake of taxonomic efficiency, he will recognize but one genus for Charina bottae, Lichanura trivirgata and Calabaria reinhardtii. I submit that taxonomic efficiency is not an objective method for classifying organisms. In fact, it is far more subjective than if one relies on morphological disparity. Below I have two trees with very similar topologies to illustrate my point. The top one is from Kluge's study of erycine relationships. The bottom one is a hominoid tree that is accepted by most scientists. If one totally ignores morphological disparity, then a cladist may choose either one, two or three genera to classify the bottom set of taxa. The first alternative of lumping all three into the same genus results in a morphologically heterogeneous taxon. The second alternative is to recognize three genera, meaning that Pan paniscus and Pan troglodytes would be classified in different genera, not very satisfactory. The third alternative is to recognize Pan and Homo as valid genera, the nearly universally accepted classification. Without any guidelines, the cladist is free to choose among any of these three equally valid alternatives. The Darwinians, however, are far more likely than not to choose the third alternative of recognizing 2 genera since they take morphological disparity into account.

Finally, as Kluge demonstrates, it is equally valid for the cladist to lump all taxa sharing a single ancestor into one genus as it is to recognize each terminal node as a different genus. Hence Utiger et al. do not have to splinter Elaphe. They can lump all species of Elaphe into a single genus. Doing so, however, would mean that they would have to transfer all species in the Lampropeltini back into Elaphe. Neither alternative is satisfactory since the taxa that result are too heterogeneous. The best alternative unfortunately, is one that is not available to the Hennigians, who are intolerant of paraphyletic taxa. The Darwinians, since they have no ideological aversion to paraphyly, can maintain the status quo and recognize a paraphyletic Elaphe and all of the genera currently assigned to the species within the Lampropeltini, which include Pituophis, Lampropeltis, Arizona, Cemophora and Stilosoma.

`Molecular data of all sorts have indeed proven more useful than morphological similarities in elucidating branching order. However, it is cladistic dogma to ignore morphological disparity in classification, since Hennig rejects its use.'

I disagree. Both Kluge and Burbrink paid quite a bit of attention to morphology.

` The way Burbrink split Elaphe guttata is no different than the way Utiger et al. have splintered Elaphe; they both ignore morphological disparity and only rely on branching order only.'

Actually, Burbrink takes morphological disparity into account, and demonstrates its existence among the taxa he creates, in the splits of both guttata and obsoleta. He's just willing to accept very low amounts of morphological disparity if they agree with the cladogram.
Utiger et al. has already been addressed in this matter.

`My interpretation is different. As one can see by the two new genera they coin, there isn't any good morphological character to distinguish one genus from another since these characters are variable intragenerically or even intraspecifically.'

This is incorrect. Two characters are given that unambiguously differentiate Orthriophis and Oreophis from each other, specifically:
precaudal vertebrae 193 in Oreophis, 222-272 in Orthriophis (yes, variable intragenerically, but there is no overlap, and thus no ambiguity in the differentiation of the genera)
hemipenis cylindrical and with a basal hook for Oreophis, hemipenis biolobed and without a basal hook for Orthriophis.

`On the other hand, the taxa they recognize clearly are delimited from their consensus cladogram. Each major branch in that cladogram is classified as a different genus. That is no different than Burbrink, who classifies each major branch in his analysis as a different species.'

This is also incorrect. Though the weighted MP tree shows Zamensis as monophyletic, the consensus tree shows a polyphyletic Zamensis, with Zamensis persicus apparently unrelated to the remaining Zamensis. Apart from the very close morphological resemblance between Zamensis persicus and other Zamensis (particularly Z. lineatus and Z. longissimus, with which it was formerly considered conspecific), there doesn't appear to be a compelling reason to conclude that these taxa should be congeneric. Yet Utiger et al. conclude they are congeneric.

`It is true that there is no objective measure of morphological disparity. Darwinian taxa are indeed subjectively delimited. The alternative is far worse. The cladists, who have no guideline for delimiting taxa other than equal rank for sister taxa, are far more subjective. Kluge, for example, states that he can either recognize one, two or three genera given the particular topology of his cladogram. He finally decides that, for the sake of taxonomic efficiency, he will recognize but one genus for Charina bottae, Lichanura trivirgata and Calabaria reinhardtii. I submit that taxonomic efficiency is not an objective method for classifying organisms.'

Any taxonomist could have recognized one, two, or three genera based on the available data. It's hardly a particular fault of cladism that it allows this.

I agree, though, that `taxonomic efficiency' is a very poor justification for any classification, particularly, in this case, because no greater efficiency is gained.

`In fact, it is far more subjective than if one relies on morphological disparity.'

Kluge based his reassessment of the New World erycines entirely on morphology, though. He simply decided that the level of morphological disparity he found between Charina, Lichanaura, and Calabaria wasn't great enough to require a generic distinction. A Darwinian could have done the same.

`The first alternative of lumping all three into the same genus results in a morphologically heterogeneous taxon. The second alternative is to recognize three genera, meaning that Pan paniscus and Pan troglodytes would be classified in different genera, not very satisfactory. The third alternative is to recognize Pan and Homo as valid genera, the nearly universally accepted classification. Without any guidelines, the cladist is free to choose among any of these three equally valid alternatives. The Darwinians, however, are far more likely than not to choose the third alternative of recognizing 2 genera since they take morphological disparity into account.'

All three options are open to all taxonomists, though. I suspect that most cladists would be likely to recognize two genera, as well. I think the primary problem with Kluge's taxonomy isn't that it's cladistic, it's that it isn't very well done.

`The best alternative unfortunately, is one that is not available to the Hennigians, who are intolerant of paraphyletic taxa.'

And yet, as already discussed, an option that was available to Utiger et al. But, of course, that would've resulted in perpetuating a morphologically heterogeneous taxon.

Patrick Alexander

Kluge based his analysis on morphological characters; he has no alternative but to pay attention to morphological characters. Burbrink is only using morphology as an afterthought, to justify the splitting of his taxa on the basis of mtDNA data. The number of precaudal vertebrae in and of itself is not a diagnostic character for anything.

Yes, any taxonomist could have recognized one, two or three genera given Kluge's tree. But the cladists have no guideline other than "one ancestor and all descendants" in delimiting their taxa. They are forbidden by their methodology to recognize paraphyletic taxa even though such taxa may be morphologically homogeneous.

You claim that "Kluge based his reassessment of the New World erycines entirely on morphology, though. He simply decided that the level of morphological disparity he found between Charina, Lichanaura, and Calabaria wasn't great enough to require a generic distinction. A Darwinian could have done the same."

That is not true at all. Kluge made no comments on morphological disparity among these three genera, and based his decision of a single genus for all three on "taxonomic efficiency."

Finally you claimed that recognizing a paraphyletic Elaphe would have resulted in "in perpetuating a morphologically heterogeneous taxon." That is not true at all, since Elaphe was delimited on the basis of morphological similarity by systematists and this genus is thus rather homoegeneous morphologically. The fact that it has proven to be a natural group (monophyletic sensu Darwin) is icing on the cake. There is no scientifically tenable reason to splinter a natural group such as Elaphe, which is also morphologically homogeneous.

If you want further evidence that cladism and reliance on genetic data aren't responsible for poorly done taxonomy, just go look at Hoser's new species. If you don't like Utiger et al., you should absolutely despise him. : )

Patrick Alexander

You wrote:
Actually, Burbrink takes morphological disparity into account, and demonstrates its existence among the taxa he creates, in the splits of both guttata and obsoleta. He's just willing to accept very low amounts of morphological disparity if they agree with the cladogram.
Utiger et al. has already been addressed in this matter.

My response:
So, in your opinion, he will ignore morphological disparity if it does not jive with his cladogram? That is still ignoring morphological disparity to me.

I wrote:
`My interpretation is different. As one can see by the two new genera they coin, there isn't any good morphological character to distinguish
one genus from another since these characters are variable intragenerically or even intraspecifically.'

Your response:
This is incorrect. Two characters are given that unambiguously differentiate Orthriophis and Oreophis from each other, specifically:
precaudal vertebrae 193 in Oreophis, 222-272 in Orthriophis (yes, variable intragenerically, but there is no overlap, and thus no ambiguity in the differentiation of the genera) hemipenis cylindrical and with a basal hook for Oreophis, hemipenis biolobed and without a basal hook for Orthriophis.

My response:
Does the number of vertebrae distinguish Oreophis or Orthriophis from other species of Elaphe? Do the differences in hemipenial morphology, even if they are confirmed, justify the erecting (pun intended) of new genera?

I wrote:
`On the other hand, the taxa they recognize clearly are delimited from their consensus cladogram. Each major branch in that cladogram is
classified as a different genus. That is no different than Burbrink, who classifies each major branch in his analysis as a different species.'

Your response:
This is also incorrect. Though the weighted MP tree shows Zamensis as monophyletic, the consensus tree shows a polyphyletic Zamensis,
with Zamensis persicus apparently unrelated to the remaining Zamensis. Apart from the very close morphological resemblance between
Zamensis persicus and other Zamensis (particularly Z. lineatus and Z. longissimus, with which it was formerly considered conspecific), there
doesn't appear to be a compelling reason to conclude that these taxa should be congeneric. Yet Utiger et al. conclude they are congeneric.

My response:
You are correct about Zamensis not being a major branch in their consensus cladogram. You are incorrect that Zamensis is polyphyletic. All species of Zamensis do share a common ancestor, but this ancestor, at least according to the consensus cladogram, is also ancestral to all other genera they recognize, with the exception of "Euprepiophis." You have a very peculiar definitino of polyphyletic.

I wrote:
`It is true that there is no objective measure of morphological disparity. Darwinian taxa are indeed subjectively delimited. The alternative is far worse. The cladists, who have no guideline for delimiting taxa other than equal rank for sister taxa, are far more subjective. Kluge, for example, states that he can either recognize one, two or three genera given the particular topology of his cladogram. He finally decides that, for the sake of taxonomic efficiency, he will recognize but one genus for Charina bottae, Lichanura trivirgata and Calabaria reinhardtii. I submit that taxonomic efficiency is not an objective method for classifying organisms.'

Your response:
Any taxonomist could have recognized one, two, or three genera based on the available data. It's hardly a particular fault of cladism that it allows this.

My response:
That is not my point though.

You wrote:
I agree, though, that `taxonomic efficiency' is a very poor justification for any classification, particularly, in this case, because no greater efficiency is gained.

My response:
It can be a factor, especially if there is little morphological disparity among taxa within a monophyletic group. One can say that I support the recognition of a paraphyletic Elaphe partly because of taxonomic efficiency, but the primary reason remains the fact that there is no good reason in terms of morphological disparity to split it.

I wrote:
`In fact, it is far more subjective than if one relies on morphological disparity.'

Your response:
Kluge based his reassessment of the New World erycines entirely on morphology, though. He simply decided that the level of morphological disparity he found between Charina, Lichanaura, and Calabaria wasn't great enough to require a generic distinction. A Darwinian could have done the same.

My response:
There is no evidence that he ever considers morphological disparity in the classification of Charina, Lichanura and Calabaria. It is not present in his discussion. The only factor he considers is taxonomic efficiency. That is simply untenable.

I wrote:
`The first alternative of lumping all three into the same genus results in a morphologically heterogeneous taxon. The second alternative is to recognize three genera, meaning that Pan paniscus and Pan troglodytes would be classified in different genera, not very satisfactory. The third alternative is to recognize Pan and Homo as valid genera, the nearly universally accepted classification. Without any guidelines, the cladist is free to choose among any of these three equally valid alternatives. The Darwinians, however, are far more likely than not to choose the third alternative of recognizing 2 genera since they take morphological disparity into account.'

You wrote:
All three options are open to all taxonomists, though. I suspect that most cladists would be likely to recognize two genera, as well. I think the primary problem with Kluge's taxonomy isn't that it's cladistic, it's that it isn't very well done.

I wrote:
`The best alternative unfortunately, is one that is not available to the Hennigians, who are intolerant of paraphyletic taxa.'

You wrote:
And yet, as already discussed, an option that was available to Utiger et al. But, of course, that would've resulted in perpetuating a
morphologically heterogeneous taxon.

Patrick Alexander

My response:
If Elaphe is morphologically heterogeneous, then Utiger et al. have provided no evidence to support it. The fact that one has to look inside the lung to distinguish Old World Elaphe from New World Elaphe is stong evidence that your argument is baseless. The fact that Helfenberger, a junior author of Utiger et al., has to look inside the visceral organ for topographic differences among the species of Elaphe is further evidence that your claim of a heterogeneous Elaphe is also incorrect. There are some authors who, rightly or wrongly, argue that Bogertophis may not be morphologically disparate enough to warrant removal from Elaphe. That would contradict your unsupported assumption that Elaphe is a morphologically heterogeneous genus.

`So, in your opinion, he will ignore morphological disparity if it does not jive with his cladogram? That is still ignoring morphological disparity to me.'

Not at all. He appears to've gone to quite a bit of trouble to demonstrate that statistically significant morphological disparity exists between the taxa he created. It's just that the morphological disparity, statistically significant or not, is pretty minor. My impression (not being as familiar with genetic data as I'd like) is that the genetic data don't support his taxa all that well, either. His problem isn't that he bases his taxa on cladist ideology, it's that he's willing to split taxa based on minor differentiation, i.e., he's a splitter.

`Does the number of vertebrae distinguish Oreophis or Orthriophis from other species of Elaphe?'

We'd need a comprehensive and accurate generic description for the other members of Elaphe to know that, I think. We don't have one. Last I checked, we didn't even have such a description for Elaphe sensu lato.

`Do the differences in hemipenial morphology, even if they are confirmed, justify the erecting (pun intended) of new genera?'

In conjunction with the genetic data and generally poor morphological (and ecological, for that matter) unity of Elaphe sensu lato, yes. Alone? Probably not.

`You are correct about Zamensis not being a major branch in their consensus cladogram. You are incorrect that Zamensis is polyphyletic. All species of Zamensis do share a common ancestor, but this ancestor, at least according to the consensus cladogram, is also ancestral to all other genera they recognize, with the exception of "Euprepiophis." You have a very peculiar definitino of polyphyletic.'

All snakes, so far as we know, share a common ancestor. Does that make all arbitrary assemblages of snake species paraphyletic? Nope. Neither Utiger et al.'s data, nor any other data of which I'm aware, support the existence of a common ancestor for Zamensis that is more closely related and/or more morphologically similar to the members of Zamensis than to other members of Elaphe sensu lato. So neither paraphylys nor monphyly are supported.

If you think I'm using a definition of polyphyly with which you disagree, present your preferred definition and we can see how well that one works in this situation.

`That is not my point though.'

You said that a problem with cladism is that its guidelines for taxon distinctions are `more subjective' than those of other taxonomic philosophies. Your support for this position was the fact that Kluge, as a cladist, could have recognized one, two, or three genera within what he called `Charina'. I pointed out that any taxonomist could have done so. This removes your support for the argument that cladism is more subjective. If the relevance was unclear earlier, hopefully it is less so now...

`It can be a factor, especially if there is little morphological disparity among taxa within a monophyletic group.'

Certainly. But I think we agree that taxonomic efficiency should not be the only factor.

`One can say that I support the recognition of a paraphyletic Elaphe partly because of taxonomic efficiency,'

IMO, taxonomic efficiency decreases when taxon are created that are not very informative about their members. The large amount of variation within Elaphe sensu lato makes the generic name fairly uninformative about its members, so taxonomic efficiency is gained by splitting it into more morphologically, ecologically, behaviourally, and genetically comprehensible units.

`but the primary reason remains the fact that there is no good reason in terms of morphological disparity to split it.'

As mentioned previously, some of the genera involved were originally (back in the 19th century) considered distinct from Elaphe on the basis of morphology.
And, of course, morphological data are not the only data, nor necessarily the most important data.

`There is no evidence that he ever considers morphological disparity in the classification of Charina, Lichanura and Calabaria. It is not present in his discussion. The only factor he considers is taxonomic efficiency. That is simply untenable.'

The clade that he calls Charina is united by morphological disparity from the other erycine snakes. His genus is, therefore, explicitly based on morphological disparity. He also apparently doesn't consider the morphological disparity within Charina to be of taxonomic significance. We both disagree with him in that, but that doesn't seem to be the result of cladism.

`If Elaphe is morphologically heterogeneous, then Utiger et al. have provided no evidence to support it.'

OTOH, if Elaphe sensu lato is morphologically homogeneous (or at least sufficiently so to warrant generic identity) I'm aware of anyone who's provided evidence to support it.

`The fact that one has to look inside the lung to distinguish Old World Elaphe from New World Elaphe is stong evidence that your argument is baseless.'

? I don't know about you, but I don't have to look inside a snake's lung to know whether it belongs to Pantherophis or Elaphe sensu stricto.

`The fact that Helfenberger, a junior author of Utiger et al., has to look inside the visceral organ for topographic differences among the species of Elaphe is further evidence that your claim of a heterogeneous Elaphe is also incorrect.'

I'd be interested in your reason for thinking that internal anatomy is not of any use in generic distinctions. Or, if this is not what you're claiming here, you'll have to make your intent clearer and tell me why the data on internal anatomy gathered by Helfenberger is not of use.

Given that internal anatomy (including hemipenes) has been used extensively in taxonomy both in snakes and in vertebrates generally, I think you'll have a hard time supporting an argument against its validity in taxonomy.

`There are some authors who, rightly or wrongly, argue that Bogertophis may not be morphologically disparate enough to warrant removal from Elaphe. That would contradict your unsupported assumption that Elaphe is a morphologically heterogeneous genus.'

1) Who are the authors you refer to?
2) Many authors (Dieter-Schulz, Helfenberger, others that came up earlier in this thread, and more that I don't recall offhand in reference to Gonyosoma, Bogertophis, and Senticolis, which do not belong to Elaphe sensu lato as it was considered to exist prior to the splits of Utiger et al. and Helfenberger) have stated that Elaphe is morphologically heterogeneous. What authors have claimed otherwise?
3) Why should an author claiming that Bogertophis should be included in Elaphe (I'm assuming sensu lato) be taken to indicate that Elaphe sensu lato is homogeneous?

Patrick Alexander

BTW, I'm still curious to know what specific morphological characters unite Elaphe sensu lato.

Patrick Alexander

` The correct one is Lopez and Maxson's 1995 study comparing mitochondrial DNA among ratsnakes and racers. They compared the mtDNA of N. American and Eurasian Elaphe with those of a large number of racers. All of the racer species are basal to Elaphe in their tree. Since racers are the sister taxa of the ratsnakes, this is a good test to see if different species of Elaphe are in fact only convergently similar. If Elaphe is polyphyletic, some species should be closer to some of the racers than they are to each other. This is clearly not the case. All species of Elaphe form a clade along with Cemophora, Lampropeltis and Pituophis.'

I would add that Rhinechis is in this clade. That said, only four species of Elaphe sensu lato were included, and these belong to only two of the seven lineages within Elaphe sensu lato recognized by Utiger et al. There aren't enough taxa to support any conclusions about the phylogenetic relationships within Elaphe sensu lato, but even so, though the monophyly of the ratsnakes relative to the racers (whose monophyly is not supported) is supported, Lopez and Maxson's data support Utiger et al.'s conclusions that the relationship between Pantherophis and Elaphe is distant, and that Pantherophis is a derived taxon within Lampropeltini.

I can also add:
Lenk, Joger, and Wink, `Phylogenetic relationships among European ratsnakes of the genus Elaphe Fitzinger based on mitochondrial DNA sequence comparisons.' Amphibia-Reptilia, 22:329-339.
to the list of papers concluding that Elaphe sensu lato is polyphyletic. It's also worth mentioning that both Lenk et al. and Utiger et al. argue for East-Asian origins for the ratsnakes. Given that the taxa found by Lopez and Maxson to group most closely with the ratsnakes are European or Mediterranean (Coluber viridis, Coluber hippocrepis, and Spalerosophis diadema), this suggests that the closest relatives of the ratsnakes may not have been included in Lopez and Maxson's study.

Patrick Alexander

`The whole group (minus the Lampropeltini and Senticolis) is Elaphe.'

There's also Rhinechis, Oocatochus, and Coronella. Rhinechis and Oocatochus being splits made by Helfenberger--I'd guess offhand that you disapprove of them, but I don't recall you mentioning it.

` The group is not polyphyletic; Elaphe is not polyphyletic.'

I await new data suggesting that this is the case.

`These authors are obviously wrong.'

That's one hell of a conclusion to jump to. Have you read the papers in question?

`Utiger et al. show that all species they study form a clade.'

No, they don't. See my other post in this thread for today.

`Besides, Utiger et al. fail to cite Lopez and Maxson (1995), who show that Old World Elaphe and New World Elaphe form a clade with the Lampropeltini.'

Well, so far it seems the non-Utiger papers are 4 to 1 in favor of Elaphe having been polyphyletic. Until I've either read the papers in question or have some other good reason to choose between them, I think I have to stick with the democratic result.

Patrick Alexander

I wrote:
`Besides, Utiger et al. fail to cite Lopez and Maxson (1995), who show that Old World Elaphe and New World Elaphe form a clade with the Lampropeltini.'

You wrote:
Well, so far it seems the non-Utiger papers are 4 to 1 in favor of Elaphe having been polyphyletic. Until I've either read the papers in question or have some other good reason to choose between them, I think I have to stick with the democratic result.

Patrick Alexander

My response:
As I have said elsewhere in this thread, Dessauer et al. (1987) provide no data to support their assumption of a polyphyletic Elaphe. In fact, their exact words are "not monophyletic." That means different things to different people. A taxon that is "not monophyletic" can be paraphyletic to a cladist, whereas the same phrase means polyphyletic to a Darwinian.

As I have also said elsewhere, the other three papers are Minton (1976), Dowling et al. (1983) and Dessauer (1983). Dessauer (1983) is obviously a paper published by the same senior author as Dessauer et al. (1987). Whatever concludion in that paper would be superseded by the later paper. Dowling et al. (1983), as I pointed out, do not include any Palearctic species of Elaphe. It therefore has no data to inform us as to whether Elaphe is polyphyletic or not. That leaves you with a single paper by Minton (1976, Copeia) as your sole "support."

As I said elsewhere, Lopez and Maxson (1995) include both Palearctic and Nearctic species of Elaphe in their mtDNA analysis. They find that Palearctic species of Elaphe are basal to Nearctic species of Elaphe and that these two groups form a clade with such Lampropeltine snakes as Cemophora, Lampropeltis and Pituophis. They call this clade the "ratsnakes." Lopez and Maxson find that Ptyas and Zaocys are outgroups to the ratsnakes. Tong et al. (2002) find that the Palearctic species of Elaphe (which are of course basal to Nearctic Elaphe) form a clade and Ptyas and Zaocys are outgroup colubrines. Utiger et al. (2002) find that Palearctic Elaphe is basal to Nearctic Elaphe, and that Ptyas is outgroup to all of the species of Elaphe they study.

Therefore 3 independent studies using the latest molecular techniques have shown that Ptyas is an outgroup to all known species of Elaphe, including the most basal ones. They have thus demonstrated that Elaphe is not a polyphyletic genus. If you are going to argue for "democratic result", I have you outnumbered 3 to 1 for the time being. Once I have read Minton, I will show you that the score is 3:0 because, as I have said elsewhere, if Minton had demonstrated that Elaphe is polyphyletic back in 1976, this genus would have been dismantled by the Darwinians way back then.