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Just got Utiger et al.'s paper (Russian Journal of Herpetology, Vol. 9, no. 2, pp. 105-124) from the library. Looking at page 115, their fig. 4, strict consensus tree. I find no evidence that the ratsnakes are polyphyletic. All of the species they studied form an unresolved polytomy, with the exception of the North American species of ratsnakes, kingsnakes, gopher snakes and glossy snakes. This node has low bootstrap value; it is poorly supported. Therefore it appears that all of the species they studied are simply part of an unresolved polytomy. In other words, their analysis largely failed to tell us anything about the branching order of the many genera they recognize. To splinter Elaphe on the basis of such a poorly resolved phylogeny is simply scientifically untenable. Arnold Kluge, when he was faced with a similarly unresolved polytomy in his erycine paper, dumped all of the species in the polytomy into the same genus, Eryx. I criticized him for doing that and said that he should have maintained the taxonomic status quo. Utiger et al., too, should have maintained the status quo. Instead, they named 2 new genera and resurrected a number of old ones, thus creating taxonomic chaos by the truckload. All of the name changes they propose, including the proposed transfer of the North American species of Elaphe into Pantherophis and Pseudelaphe, are unnecessary, destructive and scientifically untenable.

RS:

I have been waiting for someone on this forum with whom to discuss this article. I follow your discussion of Figure 4 (strict consensus tree) and see what you are saying about the low bootstrap values for determining the branching of the covered species but am also interested in your view of the specific groupings that do have higher confidence levels.

Specifically conspicillatus and mandarinus have high values and seem morphologically and ecologically similar.

I'm not as knowledgeable about the similarities for cantoris, moellendorfi and hodgsoni but I wouldn't disagree with it on a superfical basis.

Now what bootstrap values would you expect to see for high confidence of the branching shown. Is the 50% reasonable or too low?

And finally since I can't pass up a pun, do you see the irony in a researcher who arbitrarily clumps species together being named Kluge? Just kidding, just kidding, no offense meant.

John

I'd love to see a link to this paper. Not many on this forum have the opportunity to see it, or the training to make an analysis. I'd offer my opinion on the paper, but it would be strictly based on working with certain Asian species and general herp knowledge.

In one opinion of the snakes, if anyone cares, I think the Eurasian Elaphe, including quatuorlineata, schrencki, anomala, dione, and bimaculata (and possibly others), are allied with taeniura, and possibly moellendorffi. I also think, from working with them, that mandarina and conspicillata are closely allied, but not typical ratsnakes, and possibly in a different phylogenetic branch (which probably should include a couple others too). Therefore, I am grateful for a new genus name for mandarina and conspicillata.

>>Just got Utiger et al.'s paper (Russian Journal of Herpetology, Vol. 9, no. 2, pp. 105-124) from the library. Looking at page 115, their fig. 4, strict consensus tree. I find no evidence that the ratsnakes are polyphyletic. All of the species they studied form an unresolved polytomy, with the exception of the North American species of ratsnakes, kingsnakes, gopher snakes and glossy snakes. This node has low bootstrap value; it is poorly supported. Therefore it appears that all of the species they studied are simply part of an unresolved polytomy. In other words, their analysis largely failed to tell us anything about the branching order of the many genera they recognize. To splinter Elaphe on the basis of such a poorly resolved phylogeny is simply scientifically untenable. Arnold Kluge, when he was faced with a similarly unresolved polytomy in his erycine paper, dumped all of the species in the polytomy into the same genus, Eryx. I criticized him for doing that and said that he should have maintained the taxonomic status quo. Utiger et al., too, should have maintained the status quo. Instead, they named 2 new genera and resurrected a number of old ones, thus creating taxonomic chaos by the truckload. All of the name changes they propose, including the proposed transfer of the North American species of Elaphe into Pantherophis and Pseudelaphe, are unnecessary, destructive and scientifically untenable.

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I have this as a PDF from Utiger, if anyone wants it they can e-mail alex_wspcr[@]hotmail.com

My favourite is the wheel o' species with hemipene morphology

I think part of the problem is he's got far more specimens of asian species than he does of N.A. species.

Alex

>>I have this as a PDF from Utiger, if anyone wants it they can e-mail alex_wspcr[@]hotmail.com
>>
>>My favourite is the wheel o' species with hemipene morphology
>>
>>I think part of the problem is he's got far more specimens of asian species than he does of N.A. species.

???? That's because there are a lot more Asian/European species than N. American - as far as I can see, he has pretty much all of the latter represented. Whatever criticisms of this study you may wish to make, inadequate taxon sampling within Elaphe is not one of them! I would have liked a few more more other colubrids/colubrines chucked in as outgroups, though, rather than relying on Ptyas alone.

Let's also establish right here that this mtDNA study is a follow-on from an earlier study by Helfenberger, where he used a variety of morphological and data to come to similar conclusions. The DNA paper is not on its own!

Reference:
Helfenberger, Notker. 2001. Phylogenetic relationships of Old World ratsnakes based on visceral organ topography, Osteology, and allozyme variation. Russian Journal of Herpetology. 8(supplement):1-62.

Cheers,

Wolfgang
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That is excellent. Utiger et al.'s tree shows Elaphe mandarina and Elaphe conspicillata to be sister species, with strong statistical support (bootstrap values of 100% and 99% using maximum parsimony and neighboring joining methods respectively). They have these species being basal to all other ratsnakes but this part of the tree is poorly supported, with bootstrap values of 47% and 30% using the different methods. Because of the poor statistical support for the base of their tree, their partitioning of the genus Elaphe is weakly supported and unjustifiable. It is almost certain that a future study with differ in tree topography. Therefore it is better to not recognize any of their new and resurrected genera and simply continue to retain all species of Elaphe in Elaphe.

You wrote:

"All of the name changes they propose, including the proposed transfer of the North American species of Elaphe into Pantherophis and Pseudelaphe, are unnecessary, destructive and scientifically untenable."

I'm absolutely unqualified to comment on the scientific tenability of the renaming of North American genera. Speaking from a hobbyist's viewpoint, I must say that I'm very pleased to see the North American "Elaphe" no longer lumped together with Eurasian species. It is very evident that North American "Elaphe" are more closely related to Lampropeltis, Pituophis, and other North American snakes, than they are to any of the Eurasians. My basis for drawing this conclusion, is that we see numerous hybridizations between the North American genera, but we never see any of the (to my mind misnamed) North American Elaphe hybidizing with any of the Eurasians.

I welcome the recent reversion to the old genus name, Pantherophis.
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tricia

You wrote:

It is very evident that North American "Elaphe" are more closely related to Lampropeltis, Pituophis, and other North American snakes, than they are to any of the Eurasians.

My response:

Scientific evidence does show that a number of North American snakes, including those in the genera Pituophis, Arizona, Cemophora, Lampropeltis and of course Elaphe, are descended from a Eurasian species of snake (most likely a species of Elaphe) that migrated to the New World in the Miocene. Some of these New World species have been classfied in several different genera because they have changed morphologically and differ from their Elaphe ancestor. Those species that have not changed morphologically are currently retained in Elaphe. There are some scientists who "assume" that Elaphe is polyphyletic, meaning that the species currently classified in this genus are only similar due to convergent evolution. Utiger et al. (2002), as well as a number of other papers, including one that Utiger et al. ignored (Lopez and Maxson 1995) clearly show that Elaphe is NOT polyphyletic. That means the similarities between Old World and New World Elaphe are due to common ancestry, not convergent evolution. Many scientists would argue that New World Elaphe is more closely related to Old World Elaphe because they share more similarities with each other than New World Elaphe does with Lampropeltis, Arizona and Pituophis. To codify this view, they have retained E. guttata, E. obseleta et al. in Elaphe. Utiger et al. have a different idea of what related means. They therefore propose a transfer of New World Elaphe to Pantherophis and "Psuedelaphe." Not all scientists subscribe to Utiger et al.'s ideology. I predict they will reject the resurrection of Pantherophhis and the new genus Pseudelaphe. There is nothing "pseudo" about the morphological similarity between Old World and New World Elaphe; their similarity is due to common ancestry. There are many scientists who, unlike Utiger et al., would never erect a new genus (or resurrect an old genus) for species that have not changed from the parental genus. These scientists would probably reject Utiger et al.'s destructive and scientifically untenable taxonomic proposal.

Looking at the weighted MP tree of Utiger et al. (fig. 3), New World Elaphe and other Lampropeltine species such as Lampropeltis ruthveni and Pituophis melanoleucus are nested deeply within Old World Elaphe. Some of the Old World Elaphe species (e.g. E. longissima, E. taeniurus, E. situla, E. mandarina) are basal to New World Elaphe and the group containing E. carinata, E. climacophora, E. sauromates and E. quatuorlineata. This tree contradicts the assumption that Old World Elaphe and New World Elaphe form a polyphyletic group. It shows that Elaphe is in fact paraphyletic. The ideological intolerance of paraphyly among Hennigian taxonomists is the real reason for their attempt to splinter Elaphe. The oft-repeated proclamation that Elaphe is an artificial or polyphyletic group is in reality a red herring.

>>Looking at the weighted MP tree of Utiger et al. (fig. 3), New World Elaphe and other Lampropeltine species such as Lampropeltis ruthveni and Pituophis melanoleucus are nested deeply within Old World Elaphe. Some of the Old World Elaphe species (e.g. E. longissima, E. taeniurus, E. situla, E. mandarina) are basal to New World Elaphe and the group containing E. carinata, E. climacophora, E. sauromates and E. quatuorlineata. This tree contradicts the assumption that Old World Elaphe and New World Elaphe form a polyphyletic group. It shows that Elaphe is in fact paraphyletic. The ideological intolerance of paraphyly among Hennigian taxonomists is the real reason for their attempt to splinter Elaphe. The oft-repeated proclamation that Elaphe is an artificial or polyphyletic group is in reality a red herring.

Paraphyletic groups ARE artificial: you are taking a radiaiton of animals and artificialy and subjectively pruning off a few more differentiated taxa 'cos you don't like'em there.

Nature produces paraphyletic groups no more than a real (botanical) tree produces branches with twigs lopped off.

Cheers,

Wolfgang
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Wolfgang wrote:
Paraphyletic groups ARE artificial: you are taking a radiaiton of animals and artificialy and subjectively pruning off a few more differentiated taxa 'cos you don't like'em there.

My response:
Only Hennigians believe that paraphyletic groups are artificial. According to scientific research, the most common form of speciation is peripatric speciation. That means when a new species evolves from an old one, the old one continues to live. Hennig himself assumes otherwise. He assumes that when speciation occurs, two new species appear and the old one becomes extinct. Even Hennig himself admits that his assumption is incorrect. If the old one does not become extinct, it becomes paraphyletic since the new species must be given a new name. If the new species does not have a new name, how can one tell it apart from the old species? Similarly, when a new genus evolves, it must be given a new name to distinguish it from the old genus. The old genus is now paraphyletic because it does not include its descendant the old genus. It is thus obvious that whenever evolution occurs, paraphyletic taxa result. Unless you consider evolution to be unnatural, you cannot consider paraphyletic taxa unnatural, unless of course you are a Hennigian. That is why Darwinians consider the Hennigians' intolerance of paraphyletic taxa scientifically untenable.

Your argument about speciation is a red herring and irrelevant to the question of paraphyletic genera.

Cheers,

Wolfgang
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Wolfgang wrote:
Your argument about speciation is a red herring and irrelevant to the question of paraphyletic genera.

My response:
All new taxa, including higher taxa, originate by the process of speciation. Higher taxa do not originate from higher taxa. A novel species may arise from one of many species within a higher taxon. This new species may be so different that it deserves recognition as a different genus (for example, Lampropeltis warrants recognition because one population of one species of Elaphe evolved into a distinct species classifiable in this new genus while other populations of this species of Elaphe remain unchanged). In most cases this new species arise through the process of peripatric speciation (or even sympatric speciation), in which the parental species continues to live, unchanged by the speciation process, alongside the new species. The parental species is now paraphyletic. If this new species is classifiable in a different higher taxon, then the parental higher taxon, though unchanged, is also paraphyletic. Hence peripatric speciation can create paraphyletic higher taxa, not just paraphyletic species. Darwin and Darwinians like Ernst Mayr both recognize the central role of speciation in the evolution of higher taxa. If the Hennigians fail to see the same connection, then it is no wonder they are on a crusade to destroy the inevitable result of the process of evolution: paraphyletic taxa. It is no wonder that the opponents of the Hennigians are the Darwinians. The Hennigians do not understand evolution because they do not understand speciation. Darwin did not title his book "The Origin of Species" for nothing.

Looking back at my previous replies to your post, I realized that I was more focused on the scientific evidence for a close relationship between Eurasian and American species of Elaphe than directly addressing your arguments. I did not address some of the points you brought up. So I will do so in this post:

You wrote:
I must say that I'm very pleased to see the North American "Elaphe" no longer lumped together with Eurasian species. It is very evident that North American "Elaphe" are more closely related to Lampropeltis, Pituophis, and other North American snakes, than they are to any of the Eurasians.

My response:
That is one view point for measuring relationship. You are arguing that American ratsnakes are closer to their cousins (Lampropeltis, Pituophis et al.) than to their uncles (Old World Elaphe such as Elaphe scalaris). Using the same guidelines you have proposed, one would be arguing that the chimpanzees are closer to Homo sapiens than it is to the gorilla. And indeed there are scientists who would agree with that view point. Other scientists, however, would argue that the chimpanzee and the gorilla are more closely related to each other than they are to Homo sapiens. They would classify gorilla and chimpanzee in the same family (Pongidae) and support the recognition of a different family (Hominidae) for Homo sapiens. They do that because most of the evolutionary changes occured in the lineages leading to Homo sapiens. The chimpanzee has changed little from its ancestor, and therefore it is classifiable in its ancestral family. The same is true of New World Elaphe. Species such as Elaphe obsoleta, E. vulpina and E. guttata have changed little from their Eurasian Elaphe "uncles." Species like Lampropeltis and Cemophora, who are cousins of American species of Elaphe, have undergone most of the evolutionary changes and they are therefore classified in several different genera. If a classification is to reflect evolutionary history, shouldn't new species that have changed a lot be classified in their own genus and those that have not changed much be retained in the old genus? It is for this reason that Darwinians are classifying E. obsoleta, E. guttata and E. vulpina in Elaphe. It is for the lack of evolutionary changes in the American species of Elaphe that I oppose resurrecting Pantherophis and the creation of the new genus Pseudelaphe for the American species previously placed in Elaphe. Why invent new names for old taxa that have not changed?

You wrote:
My basis for drawing this conclusion, is that we see numerous hybridizations between the North American genera, but we never see any of the (to my mind misnamed) North American Elaphe hybidizing with any of the Eurasians.

My response:
Hybridization experiments can be helpful in evaluating relationships but it is an imprecise one. For example, if A, B, and C can hybridize freely with each other, is A more closely related to B than it is to C? Or is B and C more closely related to each other than either of them is to A? We can never know unless we look elsewhere for additional evidence. A more precise measure of relationship is available in the form of molecular data. Molecular data has shown that Old World Elaphe is ancestral to New World Elaphe, and New World Elaphe is ancestral to Lampropeltis, Pituophis, Arizona et al. That brings us back to the question of how we are to determine closeness of relationship. Are the American species of Elaphe closer to the relatives of their ancestor in the Old World or are they closer to their descendants such as Lampropeltis et al.? Of course I believe that American species of Elaphe are closer to the Old World species of Elaphe because they have not changed much from their ancestral form since migrating to the New World from the Old. Other scientists may have a different opinion. They are entitled to it. I believe that my preferred classification is more consistent with evolution, and it is no wonder that the sort of classification that retains American species of Elaphe in the same genus as Eurasian species of Elaphe is called "evolutionary taxonomy" or "Darwinian taxonomy." One of the alternatives to evolutionary taxonomy is Utiger et al.'s classification, which is in my view chaotic and not useful. Utiger et al.'s classification does not take into account evolutionary changes. Hence they have resurrected or erected nearly a dozen genera for the species of Elaphe that have not changed much since the Miocene. New names for taxa that do not change? There are many who may prefer that sort of classification but I do not.

>>Just got Utiger et al.'s paper (Russian Journal of Herpetology, Vol. 9, no. 2, pp. 105-124) from the library. Looking at page 115, their fig. 4, strict consensus tree. I find no evidence that the ratsnakes are polyphyletic. All of the species they studied form an unresolved polytomy, with the exception of the North American species of ratsnakes, kingsnakes, gopher snakes and glossy snakes.

Correction: a number of species groups are highly supported. The relationships *between* these species groups are unsupported and unresolved.

> This node has low bootstrap value; it is poorly supported. Therefore it appears that all of the species they studied are simply part of an unresolved polytomy.

Correction: the often highly supported *species groups* emanate from a largely unresolved polytomy.

> In other words, their analysis largely failed to tell us anything about the branching order of the many genera they recognize. To splinter Elaphe on the basis of such a poorly resolved phylogeny is simply scientifically untenable. Arnold Kluge, when he was faced with a similarly unresolved polytomy in his erycine paper, dumped all of the species in the polytomy into the same genus, Eryx. I criticized him for doing that and said that he should have maintained the taxonomic status quo. Utiger et al., too, should have maintained the status quo. Instead, they named 2 new genera and resurrected a number of old ones, thus creating taxonomic chaos by the truckload.

Taxonomic chaos by the truckload? Hardly. History suggests that after a few years of readjustment, these changes get absorbed fairly easily. Who, today, still uses Bothrops schlegelii or Bothrops nasutus instead of Bothriechis schlegelii and Porthidium nasutum?

> All of the name changes they propose, including the proposed transfer of the North American species of Elaphe into Pantherophis and Pseudelaphe, are unnecessary, destructive and scientifically untenable.

Correction: the node supporting the monophyly of Pituophis and Pantherophis is strongly supported. If you don't like Pantherophis, you can always consider Pantherophis Fitzinger, 1843 as a junior synonym of Pituophis Holbrook, 1842. Welcome Pituophis guttatus, obsoletus, bairdi and vulpinus! But then again, Lirpa 1, Cal King, RS Newton, or whoever you are, you seem to be the born again anti-cladist, so nothing will ever convince you that classification should follow phylogeny.

Cheers,

Wolfgang
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Wolfgang wrote:
Correction: a number of species groups are highly supported. The relationships *between* these species groups are unsupported and unresolved.

My response:
May be it does not bother you that the base of their tree is unresolved. It bothers me. It shows that phylogenetic relationships within the genus Elaphe is far from resolved. Kluge, when he found a similar situation in his study of the Erycine boids, dumped all species of the polytomy into the same genus--Eryx. Utiger et al. adopt the opposite taxonomic extreme. They split Elaphe into 10 different genera, none of which can be adequately distinguished from the remaining. That shows that one can simply flip a coin in such a situation since the decision between 1 genus and 10 genera is totally arbitrary. I demand that Utiger et al. flip their coin a second time, because it may result in a completely different outcome: a single genus instead of 10 genera.

Wofgang wrote:
Taxonomic chaos by the truckload? Hardly. History suggests that after a few years of readjustment, these changes get absorbed fairly easily. Who, today, still uses Bothrops schlegelii or Bothrops nasutus instead of Bothriechis schlegelii and Porthidium nasutum?

My response:
Yes, people do get used to new names but why inconvenience ourselves with unncessary name changes? I simply question the need for any of the new names. None of these genera is morphologically distinct enough to warrant recognition. Sure, taxa can and should be split if they are polyphyletic. But there is no evidence that Elaphe is polyphyletic. In the absence of evidence for polyphyly and for morphological distinctness, the proposed taxonomic changes are indeed scientifically untenable.

Wolfgang wrote:
nothing will ever convince you that classification should follow phylogeny.

My response:
Classification should indeed follow phylogeny. It is just that we have different interpretations of what phylogeny means. The genus Elaphe is not polyphyletic. A single genus is consistent with Utiger's phylogeny. In fact, it is a better fit for Utiger's unresolved phylogeny. If the Lampropeltini never evolved, then the cladists would not have sent the genus Elaphe to the chopping block. But why should a morphologically conservative genus such as Elaphe be splintered because one species crossed a land bridge and evolved into a number of different disparate taxa in the New World? What happened in the New World did not change Old World Elaphe in any way. So, why should new genera be proposed in a group in which there have been no recognizable evolutionary changes?

I criticized Kluge for dumping all of the species in his polytomy into the single genus Eryx, and said that he should have maintained the status quo. The same prudent course of action could have been followed by Utiger et al. They could have maintained the status quo (which would result in the classification of most species in the polytomy within the single genus Elaphe), instead of the destructive new arrangement of 10 different genera for a group of snakes that are closely related to each other and that are morphologically very similar.

>>I criticized Kluge for dumping all of the species in his polytomy into the single genus Eryx, and said that he should have maintained the status quo. The same prudent course of action could have been followed by Utiger et al. They could have maintained the status quo (which would result in the classification of most species in the polytomy within the single genus Elaphe), instead of the destructive new arrangement of 10 different genera for a group of snakes that are closely related to each other and that are morphologically very similar.

You clearly have very little experience with the diversity of Asian Elaphe. Many of these differ just as much from Pantherophis, or indeed from "real" Elaphe, as do Lampropeltis or Pituophis.

Your taxonomic philosophy clearly differs from that of Utiger and from most praticing taxonomists. No problem, but you wqill have to accept that you are in a minority, and the rest of us have moved on.

Cheers,

Wolfgang
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Wolfgang wrote:
You clearly have very little experience with the diversity of Asian Elaphe. Many of these differ just as much from Pantherophis, or indeed from "real" Elaphe, as do Lampropeltis or Pituophis.

My response:
If that is the case, I welcome any study that would attempt to justify transferring species of Elaphe to other genera on the ground of morphological disparity. Utiger et al.'s study deals not with morphological disparity but with branching order. They clearly delimit their taxa only on the basis of branching order, not morphological disparity. Phylogeny means both morphological disparity and branching order. Utiger et al. ignore morphological disparity and their study fails to resolve branching order. Their taxonomy is therefore based on neither component of phylogeny. So, how can one claim that Utiger et al.'s new arrangement is based on "phylogeny."

Wolfgang wrote:
Your taxonomic philosophy clearly differs from that of Utiger and from most praticing taxonomists. No problem, but you wqill have to accept that you are in a minority, and the rest of us have moved on.

My response:
My taxonomic philosophy is indeed clearly different from that of Utiger et al. and from yours. But my taxonomic philosophy is clearly the same as that of H.G. Dowling, C.M. Bogert, Ernst Mayr, and Charles Darwin himself, not to mention a large number of veteran herpetologists who find no use for classifications that take into account only one of the components of phylogeny, namely branching order, while ignoring the other component: morphological disparity.

Science is not a popularity contest.

>>If that is the case, I welcome any study that would attempt to justify transferring species of Elaphe to other genera on the ground of morphological disparity. Utiger et al.'s study deals not with morphological disparity but with branching order. They clearly delimit their taxa only on the basis of branching order, not morphological disparity. Phylogeny means both morphological disparity and branching order.

Absolute nonsense. "Phylogeny" means branching order, nothing more and nothing less. You may not like classification based on branching order only - fine, you are of course fully entitled to your views, but using your own unique, idiosuncratic redefinitions of commonly used scientific terms does not help your case.

>> Utiger et al. ignore morphological disparity

Quite rightly, since similarity due to shared primitive characters provides no evidence of common ancestry.

>>Wolfgang wrote:
>>Your taxonomic philosophy clearly differs from that of Utiger and from most praticing taxonomists. No problem, but you wqill have to accept that you are in a minority, and the rest of us have moved on.
>>
>>My response:
>>My taxonomic philosophy is indeed clearly different from that of Utiger et al. and from yours. But my taxonomic philosophy is clearly the same as that of H.G. Dowling, C.M. Bogert, Ernst Mayr, and Charles Darwin himself, not to mention a large number of veteran herpetologists who find no use for classifications that take into account only one of the components of phylogeny, namely branching order, while ignoring the other component: morphological disparity.

Note that the people you mention are either dead, or at least long past their systematic heyday. With all due respect to some truly great biologists, for whom I have huge respect, the direction of the discipline is determined by those who are leading the field now, not by those who led it 40 years ago. Our understanding of evolution and our conceptual framework of taxonomy have moved on. Stay behind if you want, but don't complain about others catching the train.

>>Science is not a popularity contest.

Neither is it an immutable fossil that must never change - quite the contrary.

Cheers,

Wolfgang
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Wolfgang:
Although I agree that the study in question is addressing a valid problem in the taxonomy of the Elaphe species, I think you have to question whether some of the branching shown will be the last word. As I stated in an earlier thread, some of the groupings with high bootstrap values (such as the new genus Euprepiohis) seem pretty well supported even on morphological and ecological grounds. But the higher order divisions have much lower values that will probably require additional work to confirm or refute. What I'm wondering is whether the current technologies will allow a more definitive study any time soon, or whether these questions will have to wait a generation for the next advance.
John

New and better characters are being discovered all the time. These will shed more light on the branching order of this group. Besides, there are equally valid alternatives to classify organisms even if one only takes into account branching order. Kluge, for example, states that he could have recognized one, two or three genera in classifying Calabaria, Charina and Lichanura. All three alternatives are equally valid according to his hypothesis of branching order. The decision to pick any particular one is thus totally arbitrary. Unfortunately Kluge picks the arrangement that is the most disruptive; so do Utiger et al. Even if some of the ratsnakes are more closely related to each other than to other ratsnakes, species groups or subgenera can be used instead of resurrecting old genera and naming new ones. The goal for a taxonomist should be minimal taxonomic destruction, but it appears that some Hennigians are aiming for the maximum number of disruptive changes, even if they do not have a hypothesis of branching order. An unresolved polytomy is not a hypthesis of branching order. Other Hennigians appear obligated to support whatever taxonomic decision fellow Hennigians make. Scientists who are not Hennigians need not follow their need.

>>Wolfgang:
>>Although I agree that the study in question is addressing a valid problem in the taxonomy of the Elaphe species, I think you have to question whether some of the branching shown will be the last word. As I stated in an earlier thread, some of the groupings with high bootstrap values (such as the new genus Euprepiohis) seem pretty well supported even on morphological and ecological grounds. But the higher order divisions have much lower values that will probably require additional work to confirm or refute. What I'm wondering is whether the current technologies will allow a more definitive study any time soon, or whether these questions will have to wait a generation for the next advance.

Hi John,

Current technology is certainly no obstacle, and since the authors of the study have the tissue samples, getting more data should be easy, subject to funding. I would certainly like to see them sequence more mtDNA genes, simply to make their tree more robust. Low bootstrap support is certainly a problem in that database. Another thing that is unusual is their choice of genes - COI is rarely used, most people use cytochrome b and ND4 as well as 12S and 16S. One consequence of the authors' choice of genes is that their sequences are now very difficult to integrate into existing sequence datasets. This is something that has bedevilled the history of snake phylogenies from mtDNA for a long time: everybody sequences different genes for different species, so if you look through GenBank to see what genes are available for what species, and biuld a spreadsheet with the relevant boxes ticked, what you end up with looks like a Swiss cheese. Obviously, I have no knowledge of the history of teh Utiger et al. study, what led to their choice of methods, and what the funding and employment situation of the participants is/was - it is always easy to criticise from a distance.

Another future direction they could and should take will be to sequence some nuclear genes - some nuclear introns should be perfect for that taxonomic level, and would provide an independent assessment of relationship, which different mtDNA genes cannot do.

Of course, in the real world, getting this sort of thing funded is difficult, and many good projects are terminated long before they have yielded their full potential, simply because the participants are unable to get the study funded, or becuase their employment contract expires and they are forced to move elsewhere. Few people working outside academia realise the extent to which these constraints influence the direction peoples' work takes.

As to the future of the Utiger et al. classification - I suspect many of the genera will stand more or less as at present, but doubtless, new data willproduce some new changes and discoveries. even then, let's not forget that the taxonomic conclusions of Utiger et al. are also based on the preious study by Helfenberger, not JUST on the mtDNA data. While one can always see how more could be done, I am happy to accept what Utiger et al. have done, simply because the evidence they have provided is considerably more convincing than the evidence for teh status quo. If new, more convincing evidence contradicts any part of their study, then that will have to be taken into account when it happens.

Cheers,

Wolfgang
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Wolfgang wrote:
As to the future of the Utiger et al. classification - I suspect many of the genera will stand more or less as at present, but doubtless, new data willproduce some new changes and discoveries. even
then, let's not forget that the taxonomic conclusions of Utiger et al. are also based on the preious study by Helfenberger, not JUST on the mtDNA data. While one can always see how more could
be done, I am happy to accept what Utiger et al. have done, simply because the evidence they have provided is considerably more convincing than the evidence for teh status quo. If new, more
convincing evidence contradicts any part of their study, then that will have to be taken into account when it happens.

My response:
I pointed out that they do not have to split Elaphe into little chunks given their unresolved phylogeny. They could have left Elaphe intact and even reverse some recent attempts to splinter it, just as Kluge had done with Eryx. I am not saying Kluge was correct for dumping all those species in the polytomy in the genus Eryx, just that it is an alternative course of action available to the cladist. Of course they did not leave Elaphe unscathed. It is as though they are hellbent on chopping it up. The only evidence that justifies the wholesale destruction of Elaphe is polyphyly. There is no data to support the oft-repeated but unproven claim that Elaphe is "artificial", "polyphyletic" and "in need of revision." What their data have shown is that Elaphe is not polyphyletic and it is not artificial. It is not monophyletic sensu Hennig, but it is monophyletic sensu Darwin and Mayr-Simpson. And that is a good enough reason to maintain the status quo. Hennig simply has a scientifically untenable view of how new species originate. His classificatory philosophy is based on the erroneous assumption that a parental species becomes extinct as soon as 2, and only 2 daughter species evolve. Half a century of research into the process of speciation have shown that Hennig's assumption is disproven. The rest of the scientific community do not have to make the same mistake the Henngians make everyday by adopting Hennig's scientifically untenable classificatory philosophy.

Wolfgang claims that Eurasian species of Elaphe are as morphologically disparate from each other as N. American Elaphe is from Lampropeltis and Pituophis. If that is the case, then systematists should justify their splitting of Elaphe on morphological grounds. Unfortunately, Wolfgang no longer wishes to elaborate on this claim and he has retreated to the position that morphology should not be taken into consideration in classification. And he also claims that those systematists who take morphological disparity into account in their classifications are either dead or past their prime. That is nonsense indeed.

I submit that Einstein and Darwin are both dead. Yet their theories are very much alive. Scientific theories and valid ideas are independent of the life span of their proponents. Besides, Willi Hennig is also dead. So, what makes Hennig's taxonomic philosophy any better than those of Darwin's? I submit that Darwin and Mayr know a whole lot more about evolution than Hennig, who has to retreat from his assumption that a species becomes extinct when two, and only two, new daughter species evolve. Since peripatric speciation is the most common form of speciation, an old species can continue to exist when one or more species arise from peripheral populations. Hennig's classification can only work if his assumption about speciation is correct. Since Hennig is incorrect, his classification does not work. Ideas that do not work may be popular for a short time, but eventually Hennigian classifications will suffer the same fate as Lamarckism.

Enough digression. Although Wolfgang claims that Utiger et al.'s classification is based on "phylogeny" or actually branching order without regard to morphological disparity, Utiger et al.'s inability to resolve branching order makes their classification invalid according to Wolfgang's own definition of "phylogeny." If branching order is the only component of "phylogeny" then Utiger et al. has no phylogeny. They therefore have no classification based on phylogeny. They do have a classification based on ideology. I submit that Wolfgang is championing Utiger et al.'s classification because of ideology, not phylogeny.

>>Wolfgang claims that Eurasian species of Elaphe are as morphologically disparate from each other as N. American Elaphe is from Lampropeltis and Pituophis. If that is the case, then systematists should justify their splitting of Elaphe on morphological grounds.

Splitting needs to me justified on PHYLOGENETIC grounds - what data were used the generate the phylogeny does not matter, and there is no need to invoke morphology (although, in the long run, studies based on a maximum of evidence are likely to yield the most robust phylogenies.

>Unfortunately, Wolfgang no longer wishes to elaborate on this claim and he has retreated to the position that morphology should not be taken into consideration in classification.

Please do not put words into my mouth, I have said no such thing. Morphology is a perfectly good indicator of phylogeny IF PROPERLY ANALYSED. The latter means a PHYLOGENETIC analysis based on a substantial selection of characters, not hanging everything onto one supposed "key" character, or some "gut feeling" perception of similarity.

In other words, morphological *characters* are a perfectly good source of data, morphological *disparity* is not.

>>
>>I submit that Einstein and Darwin are both dead. Yet their theories are very much alive.

... but have been substantially developed. That's why we use new evolution textbooks in our classes, not simply Darwin's Origin. That does not diminish Darwin's achievements, it simply shows that theories move on and are developed with time. That's why evolutionary biology is a thriving and developing science, not an exercise of stamp collecting and curation. I dare say Darwin himself would be rather disappointed if nobody had developed his ideas further since his death.

>> Ideas that do not work may be popular for a short time, but eventually Hennigian classifications will suffer the same fate as Lamarckism.

The cladistic approach has gone from strength to strength over the last 40 years, from being a subversive tendency in the late 60s and 70s to being the overwhelmingly dominant approach to the study of phylogeny and classification around. Deal with it.

>> I submit that Wolfgang is championing Utiger et al.'s classification because of ideology, not phylogeny.

I am hardly a hard-core ideological cladist when it comes to taxonomy, and am in fact far more concerned about stability of the nomenclature than many of my colleagues. I even agree with some of your comments re Kluge's reclassifications of erycines and Boa/Sanzinia/Acrantophis (which were in all other respects excellent studies at the forefront of the subject), but not, for instance, with your views re Chondropython, which was quite rightly sunk into Morelia by Kluge in another one of his excellent studies.

Cheers,

Wolfgang
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Wolfgang wrote:
Splitting needs to me justified on PHYLOGENETIC grounds - what data were used the generate the phylogeny does not matter, and there is no need to invoke morphology (although, in the long run, studies based on a maximum of evidence are likely to yield the most robust phylogenies.

My response:
I do agree that taxonomy should be based on phylogeny. We simply disagree on the definition of phylogeny. Utiger et al. do take into account morphological disparity, otherwise they would be unable to tell whether two terminal nodes on their cladogram really represent two populations of the same species or two different species. If morphology cannot be taken into account, then every one of their terminal nodes can be treated as a distinct species or even genus. Hence it is blatantly disingenuous to claim that cladists do not rely on morphological distance. They do rely on it, but their reliance is inconsistent. If they truly ignore morphological disparity, then they may have to rely on Hennig's rule that sister taxa be given equal rank. Utiger et al. seem to be following that rule for most of their tree, but they abruptly depart from that practice in the Lampropeltini part of that tree. If they follow their rule, they should have given equal rank to Euprepiophis and its sister taxon. If Utiger were relying only on "phylogeny" then there should only be two genera: Euprepiophis and Elaphe. The alternative is 76 genera, one for each terminal node in their cladogram. Obviously, cladists cannot completely ignore morphological distance. They just have to selectively ignore it in order to classify organisms according to Hennig's scientifically untenable classificatory philosophy.

Wolfgang wrote:
In other words, morphological *characters* are a perfectly good source of data, morphological *disparity* is not.

My response:
Morphological disparity cannot be ignored in taxonomy. I have shown that cladists cannot completely ignore it. You are suggesting that morphological disparity cannot be used in ascertaining branching order. That I do agree with since the rate of morphological evolution is different within and among different lineages. However, once branching order is ascertained, morphological distance can indeed be taken into account in delimiting taxa and ranking taxa. Cladists prohibit such practice but they do have to ignore their own prohibitions. Otherwise, they cannot possibly distinguish two populations of the same species from 2 different species.

Wolfgang wrote:
I dare say Darwin himself would be rather disappointed if nobody had developed his ideas further since his death.

My response:
Darwin would definitely be disappointed because the Hennigians are simply ignoring his ideas. That has led to a split among taxonomists: one school following Hennig and calling themselves cladists and another school following Darwin, and calling themselves Darwinians or the evolutionary school. The Hennigians have not developed Darwin's ideas. The Hennigians are simply reverting to pre-Darwinian taxonomic practice. The cladists are as far apart from Darwinism as are the Lamarckians.

Wolfgang wrote:
I am hardly a hard-core ideological cladist when it comes to taxonomy, and am in fact far more concerned about stability of the nomenclature than many of my colleagues. I even agree with of your comments re Kluge's reclassifications of erycines and Boa/Sanzinia/Acrantophis (which were in all other respects excellent studies at the forefront of the subject), but not, for instance, with your views re Chondropython, which was quite rightly sunk into Morelia by Kluge in another one of his excellent studies.

My response:
Your philosophy seems to be pretty ideological since you ignore the large amount of morphological disparity between Chondropython and Morelia and you support the splintering of Elaphe even though these snakes form a rather homogeneous group in terms of morphology. I agree that you may not be as "hard core" as some of the hard line cladists, because they themselves would have rejected Utiger et al.'s classification. As I said, Kluge dumped all species of his polytomy into Eryx. He would probably have done the same with Elaphe, given his similar dumping of Chondropython into Morelia. Utgier et al. depart from established cladistic practice of equal rank for sister taxa, but their classification is also not Darwinian because they also ignore morphological disparity for the most part. Utiger et al.'s taxonomic arrangement is therefore both scientifically AND cladistically untenable.

Utiger et al. and even Kluge do not lead the field of herpetology. Most of the leaders are not Hennigians. Some of those who are using the cladistic method are beginning to pay more attention to character homology, unlike the self-proclaimed "leaders" of herpetology.

>>Utiger et al. and even Kluge do not lead the field of herpetology. Most of the leaders are not Hennigians. Some of those who are using the cladistic method are beginning to pay more attention to character homology, unlike the self-proclaimed "leaders" of herpetology.

Just shows how little you know.

Character homology is *central* to the Hennigian approach. The better cladistic studies contain abundant discussions of character states and homology.

As to self-proclaimed leaders... - they are not self-proclaimed, they lead through producing the most influential papers that the most people cite, and are recognised for that. And, at the moment, they happen to be people like Arnold Kluge, Michael Lee, Olivier Rieppel, Kevin de Queiroz, Jacques Gauthier, and others, all of them cladists, not the greats of the 1950s and 1960s (who led then by being the best at the time, and brilliant they were, too), and whose word you seem to regard as final on everything. Deal with it.

Cheers,

Wolfgang
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Wolfgang wrote:
Character homology is *central* to the Hennigian approach. The better cladistic studies contain abundant discussions of character states and homology.

My response:
I agree that homology is central to systematics, not just to the Hennigian approach. All systematists should be concerned with homology, not just the "better cladistic studies."

Wolfgang wrote:
As to self-proclaimed leaders... - they are not self-proclaimed, they lead through producing the most influential papers that the most people cite, and are recognised for that. And, at the moment, they happen to be people like Arnold Kluge, Michael Lee, Olivier Rieppel, Kevin de Queiroz, Jacques Gauthier, and others, all of them cladists, not the greats of the 1950s and 1960s (who led then by being the best at the time, and brilliant they were, too), and whose word you seem to regard as final on everything. Deal with it.

My response:
Kluge writes in his paper on Calabaria and Erycine snake phylogeny: "Homology is dealt with only indirectly by character congruence, the ultimate arbiter of character history." That means Kluge did not analyze his characters.

Michael Lee has written a paper arguing that one of Olivier Rieppel's taxonomic characters, the hooked fifth metatarsal, is a convergence. At least Lee is analyzing his characters.

As for Jacques Gauthier, he himself admits that he did not analyze his characters in his paper on the origin of birds.

de Queiroz himself has been criticized for selecting diet as a character in his analysis of the iguanian lizards.

In sum, most of the people you cite as being leaders in the field of herpetology do not analyze their characters. They are therefore more likely to rely on convergent characters than on homologies. It appears that these people are not true to the Hennigian approach nor can their studies be classified as "better cladistic studies" by your own definition.

I don't have time to spend all day arguing with you, and wil thus confine myself to noting that you have not seen fit to propose alternative suggestions for leaders in the field of reptile taxonomy, and certainly not any non-cladists.

Cheers,

Wolfgang
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There are no leaders. Taxonomy is in a state of chaos. Many Darwinians have stopped criticizing the cladists since their criticism have been openly ignored. The cladists will continue to crusade against paraphyletic taxa while the Darwinians will simply ignore these unnecessary and destructive taxonomic proposals. Those who wish to be "current" or up to date will simply follow the latest proposals regardless of merit.

I would simply like to add that a previous paper published in 'The Russian Journal of Herpetology' looked at visceral organ topography as one way of separating the overblown Elaphe genus into several different new genera. That paper laid some of the groundwork for what appeared in the Utiger paper. Decent arguements were made in both papers and I support the splitting of the genus as Utiger has proposed it. Cladistics is a very fluid study. As new techniques become available our knowledge of various species relations to each other becomes more well known and through that, some of these relationships naturally have to be re-evaluated.

Matt Campbell