Reptile & Amphibian Forums

It was brought to my attention that as of right now, Patherophis has been lumped with Pituophis. That means the Black Ratsnake is now the Western Ratsnake genus Pituophis Obsoletus! They must have some great DNA data on that. I was told that SSAR will come out with a new Taxonomy list early in 2009. Just curious what others know about this?

-Mike Thalman

>>It was brought to my attention that as of right now, Patherophis has been lumped with Pituophis.

Hmmmm...I'm sure this was a proposal in a journal? Taxonomic changes don't just happen overnight. Proposals usually don't mean anything until the majority of other herp systematists agree with the proposal and accept the changes (and this is demonstrated by making the name changes in their own museum collections, zoos, published papers, etc.).

If the other systematists don't make the changes, then the proposal sort of just fades away into oblivion and is forgotten of. For example, it was once proposed that Trans-Pecos Ratsnakes be called Elaphe sclerotica (which was called Elaphe subocularis back then)...nothing really ever happened with that, and the proposed species name sclerotica didn't stick.

I'm no systematist or taxonomist, but I believe that the fastest changes occur when a proposed name is "validated under the plenary powers" by the International Commission on Zoological Nomenclature and subsequently published in the Bulletin of Zoological Nomenclature. Though names validated by the ICZM may promote faster acceptance of a proposal, the validations are not irrefutable, and not every scientist will agree.

The problem that hobbyists often create for themselves is that, since they're not usually taxonomists, they often see a proposal as a bonafide change, and this just isn't so. You then usually start to see taxonomic "changes" in pet industry's books/magazines, for example, before you start to see changes in the peer-reviewed publications and specimen catalogue labels of the actual taxonomists, which is where the changes should occur first.

Soooo, I've ranted enough, but I hope that helps some people understand the name changing process a bit more clearly...no doubt, many on this forum already know this stuff.

Dusty Rhoads

Suboc.com

n/p
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"Better to be silent and thought a fool, than to open mouth and remove any doubt!"

Pantherophis itself is by no means universally accepted by herpetologists as of yet! At the moment there is great controversy between those who think DNA evidence should be the "be all and end all", those who support a traditional morphometric approach, and those who take a middle ground somewhere in between. It appears that, although this Pituophis proposal has some strong support, the jury is not in by any means....
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Brad Chambers
WWW.HCU-TX.ORG

The Avalanche has already started-it is too late for the pebbles to vote....

>>Pantherophis itself is by no means universally accepted by herpetologists as of yet! At the moment there is great controversy between those who think DNA evidence should be the "be all and end all", those who support a traditional morphometric approach, and those who take a middle ground somewhere in between.>>

Pantherophis was resurrected by a group of researchers who used primarily mtDNA or mitochondrial DNA in their analysis. These researchers, although they used hemipenial morphology as part of their analysis, did not identify any morphological differences among the dozen or so genera they resurrected.

As for DNA evidence being the "be all and end all", that is not the point. DNA evidence is very powerful evidence that can reveal the branching order of a group of species. But that information alone is not enough to classify organisms satisfactorily. Knowing, for example, that species A shares a more recent common ancestor with species B than either of them does with species C does not tell us how to classify these 3 species, for example. Should A and B be placed in a genus of its own, or should A, B and C be placed in the same genus? Or should all 3 be placed in their own separate genus? This question cannot be answered by DNA evidence alone. What we need to know is how different the 3 species are from each other morphologically. For example, if A and B are birds, and C is a reptile, then of course A and B should be placed in the same taxon and C into its own taxon. This is something most biologists would probably agree, except those who for their own philosophical reasons lump birds and reptiles in the same taxon. However, what if A and C are both reptiles but B is a bird? Should A and B (a reptile and a bird) be put in the same taxon with C in its own taxon, or should A and C be put in the same taxon and B in its own taxon? Or should they all be put into the same taxon? DNA evidence alone cannot answer the questions above.

Morphometric evidence can also be used to work out the evolutionary relationships among these species. In many cases (for example when dealing with fossils), this is the only evidence since DNA evidence cannot be retrieved from fossils that are millions of years old. However, after the branching order has been determined, we still need to consider morphological disparity in classifying organisms. At least that is the classical way of classifying organisms. A more recent approach, mainly championed by the cladists, is to ignore morphological disparity and simply split or lump at will, as long as the resulting taxa are not paraphyletic.

Besides the fact that we have different methods (morphometrics and DNA) for working out evolutionary or branching relationships, we also have different philosophies of classifying organisms. These different methods and philosophies are the sources of many of the taxonomic controversies we see today.

>It appears that, although this Pituophis proposal has some strong support, the jury is not in by any means....
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>>Brad Chambers
>>WWW.HCU-TX.ORG

I haven't seen the evidence for this proposal yet, but I doubt that it is "strong." The mtDNA data of Rodriguez Robles does not support a "Pantherophis-Pituophis" group, since the lampropeltine snakes appeared to have undergone adaptive radiation once it migrated to the New World from Eurasia. Because of this radiation, relationships among the many New World lampropeltine snake genera are difficult to resolve. Lumping Pantherophis and Pituophis also make little sense since these species form two morphologically disparate groups.

http://faculty.unlv.edu/jrodriguez/20.pdf

and people say I worry about things too much!

954564
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Diego

Here's a link to the paper: http://www.cnah.org/pdf_files/687.pdf

The researchers' taxonomic tree placed Pituophis melanoleucus within the Pantherophis clade, rendering Pantherophis paraphyletic. They chose to resolve the problem by combining the two genera into one, and the name "Pituophis" is older, so it has priority. Whether this change will be accepted remains to be seen.

The newest SSAR common names list uses Pantherophis for the ratsnakes, cornsnakes, and fox snakes. It discusses Burbrink and Lawson's paper, but "we retain the use of Pantherophis until further data are gathered and analyzed."

>>Here's a link to the paper: http://www.cnah.org/pdf_files/687.pdf >>

Thank you very much for the link.

>>The researchers' taxonomic tree placed Pituophis melanoleucus within the Pantherophis clade, rendering Pantherophis paraphyletic.>>

Just as I thought. This proposal is based in part on the cladistic intolerance of paraphyletic taxa.

It is also based in part on unreliable data. Their tree shows Senticolis triaspis to be a close relative of the New World Elaphe and Pituophis. Dowling studied Senticolis for many years and could not figure out to which genus Senticolis is most closely related. Senticolis does not even have the interpulmonary bronchus that defines the Lampropeltini, which of course includes the New World ratsnakes. Behaviorally, Senticolis acts more like a racer than a ratsnake (personal observation). 2 of the 3 trees in Rodriguez-Robles' mtDNA data also shows Senticolis to be outside of the Lampropeltini. The one tree that shows Senticolis inside of the Lampropeltini also shows it more closely related to Arizona than Arizona is to Pituophis, which is rather anomalous given the obvious close relationship between Pituophis and Arizona.

>>They chose to resolve the problem by combining the two genera into one, and the name "Pituophis" is older, so it has priority. >>

There is no problem really. Paraphyletic taxa have been and are continued to be in use. It has been known for decades that Elaphe is paraphyletic and it remained a valid taxon until the cladists figure it is time to dismantle it on the basis of their dogma. Splitting Elaphe into a dozen or so morphologically indistinguishable genera is apparently not enough for the cladists. Now they have decided to lump two morphologically disparate taxa like Pituophis and "Pantherophis" or New world Elaphe. Pituophis is the only snake in the world that has vocal cords. That fact alone should mean that it is deserving of a new genus, separate from Elaphe or "Pantherophis." It is tragic what the cladists are doing to the existing taxonomy. It would be comical if it wasn't so destructive.

>>Whether this change will be accepted remains to be seen.>>
>>The newest SSAR common names list uses Pantherophis for the ratsnakes, cornsnakes, and fox snakes. It discusses Burbrink and Lawson's paper, but "we retain the use of Pantherophis until further data are gathered and analyzed."

Unfortunately, the SSAR is controlled by the cladists, and they almost always rubber stamp taxonomic proposals made by fellow cladists. As much as I dislike the current taxonomic proposal because it is neither well supported nor necessary, it will probably be blindly followed by many.

>>>>It was brought to my attention that as of right now, Patherophis has been lumped with Pituophis. >>

Says who?

>>Hmmmm...I'm sure this was a proposal in a journal? Taxonomic changes don't just happen overnight. Proposals usually don't mean anything until the majority of other herp systematists agree with the proposal and accept the changes (and this is demonstrated by making the name changes in their own museum collections, zoos, published papers, etc.).>>

Or it could just be a totally unfounded rumor.

>>If the other systematists don't make the changes, then the proposal sort of just fades away into oblivion and is forgotten of. For example, it was once proposed that Trans-Pecos Ratsnakes be called Elaphe sclerotica (which was called Elaphe subocularis back then)...nothing really ever happened with that, and the proposed species name sclerotica didn't stick.>>

Correct. No one has the authority to make any taxonomic proposal stick.

>>I'm no systematist or taxonomist, but I believe that the fastest changes occur when a proposed name is "validated under the plenary powers" by the International Commission on Zoological Nomenclature and subsequently published in the Bulletin of Zoological Nomenclature. Though names validated by the ICZM may promote faster acceptance of a proposal, the validations are not irrefutable, and not every scientist will agree.>>

These changes by the ICZN do not deal with the scientific merits of a name. They usually deal with disputes that can be resolved by applying the rules or by deliberately not to apply a rule if a name has been well established.

>>The problem that hobbyists often create for themselves is that, since they're not usually taxonomists, they often see a proposal as a bonafide change, and this just isn't so. You then usually start to see taxonomic "changes" in pet industry's books/magazines, for example, before you start to see changes in the peer-reviewed publications and specimen catalogue labels of the actual taxonomists, which is where the changes should occur first. >>

Hobbyists are in many cases more informed of taxonomic proposals than many working biologists. Hobbyists like to be current on the usage so that if they sell their animals, they are assured of using the most "correct" name. Of course, many hobbyists are not trained in the fine points of taxonomy or systematics, so they are often incapable of judging from themselves why a taxnomic change has been proposed and whether such a proposal should be accepted or rejected.

>>Soooo, I've ranted enough, but I hope that helps some people understand the name changing process a bit more clearly...no doubt, many on this forum already know this stuff.
>>
>>Dusty Rhoads
>>
>>
>>Suboc.com

Surprisingly, even many biologists are not well trained enough to judge for themselves as to whether changes should be accepted. Those who are qualified to judge often disagree because they adhere to different schools of classification. Many taxonomic proposals nowadays are made because of a change in philosophy, rather than the result of new data invalidating an earlier classification. In many cases new data confirms the old classification, but the old classification is dismantled merely because they were made by people who have a different philosophy of classifying organisms. For example, many of the old school systematists accept paraphyletic taxa (such as Elaphe) as valid. Elaphe is paraphyletic because the species contained within in does not include all of the descendants of its common ancestor. Some of these descendant species have been removed from Elaphe and placed in Pituophis, Lampropeltis, Arizona, Cemophora and Stilosoma, for example, because of their morphological differences they evolved. A new school of taxonomy, called the cladists, reject paraphyletic taxa. And they would split Elaphe into many different genera even though the species within Elaphe differ little from one another.

Another option for the cladists is to lump taxa so that they can eliminate paraphyletic taxa. Elaphe can be made a non-paraphyletic taxon if Pituophis, Elaphe, Arizona, Cemophora and Stilosoma et al. are lumped back into Elaphe. Lumping Pituophis alone back into Elaphe would not make Elaphe "non-paraphyletic." Hence I do not believe the rumor of the proposed taxonomic change. If there is data to support such a change, I would love to look at it. But based on past studies, the probability of such data being reliable is low.

Once upon a time, in a galaxy far, far away, scientific names were touted as better than common names since they were more accurate and consistent, and did not change all the damn time.....
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Lloyd Heilbrunn

Palm Beach Gardens, Fl.

Man!,....that's EXACTLY what I think, If I just recently got into snakes, I guess it wouldn't be such a big deal, because all the names would be strange, and foreign to me anyway, and I wouldn't have much memorized either, but dang it,....I've been heavy into snakes for 41 years now, and it sort of irks me that taxononomic nomenclature seems to be changing at the rate I change underwear!,.........I used to have just about every type of snake that was generally kept in captivity, and then some, down to the scientific Latin name, including the subspecific level!,.....now I seem to stumble all over myself when I try to rethink what all the updated names to everything actually are on any given day!........geeeesh!

And what's REALLY funny, is like you mentioned earlier, scientific names were started to give an exacting, precise name so there would be NO confusion, no matter where you were in the world, it would be "universal"....................I guess now everyone in the universe is confused..LOL!

~Doug





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"Better to be silent and thought a fool, than to open mouth and remove any doubt!"

That's been the trend since the DNA revolution-reviewing traditionally agreed-upon philogenetics with genetic tests. It bothers us, but it has lead to a much better understanding of the relationship between organisms. For example, did you know that you are more closely related to an earthworm than you are to the mitochondria inside your own cells?
Anyway, the genus Pantherophis hasn't been universally accepted yet, and from what I've heard some of the controversy stems from the fact that the basis of the taxonomic change is mRNA, or the RNA of the mitochondria. This is often used to establish philogenetic trees, but some scientists protest that it isn't the same as testing the DNA of the organism itself. I'm sure there's more to it than that, but I make no claim to be in on all the details...

So I looked it up, and the russian study used mitochondrial DNA, not nuclear DNA. Nuclear DNA is found in the nucleus of the snake's cells, whereas mitochondrial DNA is found in the mitochondria of their cells. I do know that mitochondrial DNA is often used for these studies because it is believed that you can determine how long ago different philogenetic paths diverged based on the similarity of their mitochondrial DNA. Mitochondria are more or less bacterial in nature, so their DNA changes much more rapidly than that of eukaryotes. Due to that fact, mitochondrial DNA can be used to determine how long ago two populations became isolated.

>>So I looked it up, and the russian study used mitochondrial DNA, not nuclear DNA. Nuclear DNA is found in the nucleus of the snake's cells, whereas mitochondrial DNA is found in the mitochondria of their cells.>>

That is correct. mtDNA is also matrilineal, that means all snakes, regardless of female or male, inherited their mtDNA from their mother. Any mtDNA mutation occurring in a male will not be passed on to future generations.

>>I do know that mitochondrial DNA is often used for these studies because it is believed that you can determine how long ago different philogenetic paths diverged based on the similarity of their mitochondrial DNA.>>

mtDNA is not the only molecule that can be used for molecular clocks. Basically any molecule which undergoes neutral mutations through time can be used for such purposes. Serum albumin, a protein found in blood, was used to determine how long ago organisms last shared ancestors by the late Allan Wilson and his students at UC Berkeley beginning way back in the 1970's. Non-neutral mutations often change much less frequently. Sometimes changes to important molecules (such as chlorophyll) are so detrimental to an organism that these molecules change very little over vast expanses of time.

>>Mitochondria are more or less bacterial in nature, so their DNA changes much more rapidly than that of eukaryotes.>>

The rate a molecule changes and the rate the changes are passed on to the next generation depend a great deal on whether the molecule is adaptive and on whether the changes are neutral or not.

>>Due to that fact, mitochondrial DNA can be used to determine how long ago two populations became isolated.>>

Many other molecules can also be used. The molecular clock is not calibrated only with mtDNA. As I pointed out earlier, serum albumin can also be used. The mtDNA data of Utiger et al. can indeed be used to determine how long ago the ratsnakes diverged from one another. That fact alone does not tell us whether any species or groups of species of ratsnakes have evolved evolutionary novelties. For example, mtDNA does not tell us that Lampropeltis has evolved smooth skin and it does not tell us that Pituophis has evolved a vocal cord.

New taxa, such as a new genus, can only be justified by the appearance of new features, at least that is the way it works traditionally according to the Darwinians. Traditional or Darwinian taxonomists do not, for example, put the corn snake and the fox snake into different genera arbitrarily. Snakes of the genus Lampropeltis, OTOH, has been placed by Darwinian taxonomists in their own genus because of the morphological features that they have evolved which make them different from the genus Elaphe. Utiger et al. divided up the genus Elaphe and resurrected about a dozen names from the synonymy of Elaphe without demonstrating or explaining how these genera differ from each other morphologically. Utiger et al. are not Darwinian taxonomists. They are a new school called the cladists. Cladists differ from Darwinians in some very important ways philosophically. Cladists pay no attention to morphological disparity when classifying organisms. Cladists are also intolerant of paraphyletic taxa, whereas Darwinians accept paraphyletic taxa as the same as monophyletic taxa.

Utiger et al. therefore split up Elaphe without regard to any morphological disparity which may or may not exist. If there is no difference morphologically between, say, "Pantherophis" and Elaphe, then it does not bother the cladists or Utiger et al. The flip side of the coin is that they will also lump morphologically disparate species into the same genus. A good example is the proposal to lump Pituophis and New World Elaphe (or 'Pantherophis') into the same genus. The only thing Utiger et al., Burbrink and Lawson, and cladists in general care about is whether a taxon is paraphyletic or polyphyletic. Like the Darwinians, the cladists do not tolerate polyphyletic taxa. Unlike the Darwinians, cladists also do not tolerate paraphyletic taxa.

Just what exactly is paraphyletic taxa and why do the Darwinians tolerate it but the cladists don't? Paraphyletic taxa are taxa that consist of the descendants of a single recent common ancestor, but not all of the descendants. The term recent is important because all life on earth ultimately share a single common ancestor, and therefore any group of species can be called monophyletic. Paraphyletic taxa are therefore not polyphyletic, since polyphyletic groups are comprised of descendants of more than one recent common ancestor. Darwinians consider paraphyletic taxa monophyletic. Darwinians tolerate paraphyletic taxa because they realize that a useful classification can only be achieved if morphologically disparate species are removed from a taxon and placed in a taxon of its own, leaving the parental group paraphyletic. The cladists, OTOH, are following the leads of Willi Hennig, the German scientist who tells his followers that taxa should only consist of one ancestor and all of its descendant species.

If we follow Hennig's lead, then traditional taxa such as Reptilia would be invalid because it is paraphyletic. Indeed the Hennigians redefined Reptilia to include the birds, but to exclude the mammals, the extinct reptilian ancestors of mammals (called the synapsids and therapsids) and also the first organisms that laid amniotic eggs from the Reptilia. The cladists' "Reptilia" is therefore more heterogeneous than traditional Reptilia, and most biologists and lay people alike have ignored the cladists and continue to use Reptilia the traditional way.

So, we now know where the cladists are coming from philosophically. It is the intolerance of paraphyletic taxa which prompted Utiger et al. to split up Elaphe into a dozen or so morphologically indistinguishable genera. It is also the intolerance of paraphyletic taxa which motivated Burbrink and Lawson to propose lumping Pituophis and "Pantherophis" into the same genus. Both the scientific community and the general public should be informed of the motives of the cladists. Both the scientific community and the general public should reject the irrational intolerance of paraphyletic taxa that is unique to cladistic philosophy. The proposed merging of the genus Pituophis with the New World Elaphe should be rejected. The resurrection of the genus "Pantherophis" should also be rejected. There is precedence for such rejection, and the rejection of the cladistic redefinition of Reptilia is such a precedence. Both the scientific community and the general public do not accept the cladists' "Reptilia" (which regards birds as 'reptiles') and both should reject the more recent taxonomic proposals by the cladists on similar grounds.

Perhaps it may be a good idea to figure out if a future taxonomic proposal is made on the basis of the cladists' irrational intolerance of paraphyletic taxa. Simply ask the authors of a proposed taxonomic change whether they include the birds in Reptilia. If they are cladists, and if they are intolerant of paraphyletic taxa, then they would say that birds are reptiles. If they are not cladists but Darwinians, then their answer is that birds are not part of Reptilia. There is no good reason to include birds in Reptilia, and there is no good reason to lump Elaphe ('Pantherophis') with Pituophis. Following cladistic thinking blindly is not a good reason.

>>That's been the trend since the DNA revolution-reviewing traditionally agreed-upon philogenetics with genetic tests. >>

Don't blame DNA data. DNA data is not responsible for the current flood of taxonomic proposals. Blame, instead, the current flood on the cladists, who are following the lead of Willi Hennig, the German scientist who did not even work with DNA but who tells his followers not to recognize "paraphyletic taxa." Briefly, paraphyletic taxa are those that do not include all of the descendants of a common ancestors. For example, Reptilia is a paraphyletic taxon because the common ancestor of Reptilia is also ancestral to birds and mammals, but Reptilia excludes birds and mammals. TO Hennig and his followers, paraphyletic taxa like Reptilia must be dismantled. Indeed, the cladists have redefined Reptilia to include all birds, but to exclude mammals and the reptilian ancestors of mammals. To Charles Darwin and his followers, paraphyletic taxa are perfectly acceptable. Darwinians do not use Reptilia the way the Hennigians or cladists do. And Darwinians certainly do not find any reason to accept the resurrection of Pantherophis.

>> It bothers us, but it has lead to a much better understanding of the relationship between organisms. For example, did you know that you are more closely related to an earthworm than you are to the mitochondria inside your own cells?>>

DNA has indeed led to a better understanding of relationships, but it does not have to lead to taxonomic chaos. In fact, Hennig's followers, not DNA data, are responsible for the chaos. In fact, many taxonomic changes were made by the Hennigians even before the availability of DNA data. Frost and Etheridge (1989), for example, split the traditional Iguanidae into several different families and lumped the Chameleonidae and Agamidae into the family Chameleonidae! Frost and Etheridge did not even have any DNA data to support their proposal but they generated a huge controversy and a debate on the merits of cladistic methodology and Hennigian classifications.

>>Anyway, the genus Pantherophis hasn't been universally accepted yet, and from what I've heard some of the controversy stems from the fact that the basis of the taxonomic change is mRNA, or the RNA of the mitochondria.>>

Pantherophis was resurrected by Utiger et al. in the following paper

http://www.venomdoc.com/downloads/Utiger_Elaphe_Phylogeny.pdf

Their data is in part based on mtDNA, but they also used hemipenial morphology. Pantherophis, IMO, should not be accepted because it is not morphologically distinct from Elaphe and because the motivation to resurrect Pantherophis is simply an adherence to Hennigian dogma.

>>This is often used to establish philogenetic trees, but some scientists protest that it isn't the same as testing the DNA of the organism itself. I'm sure there's more to it than that, but I make no claim to be in on all the details...>>

Yes, mtDNA is a powerful tool that can be used to build phylogenetic trees. However, other molecules can also be used to build these trees. What some people object to is classification based only on one set of data. They do not want to accept Pantherophis because they want to await other trees based on other sorts of DNA data. What I object to is not mtDNA data, but the fact that the proposals are made on the basis of Hennigian dogma, to which I do not subscribe. I, as a Darwinian, find the Hennigian proposal to resurrect Pantherophis unnecessary and destructive. And I find the Hennigian proposal to lump Pantherophis with Pituophis unacceptable as well.