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RE: canebrakes
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by creep77 on May 28, 2003
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The darker snakes overheat easily but also heat up easily. SO, they can survive just a little further north than the others.
I agree with the reasoning behind the first pasted sentence. However, how do you explain an approximate 50/50 ratio of yellow to black phase timbers in the northern most reaches of their distribution? Are you implying that yellow rattlesnakes are not being selected for in terms of a not-so-stable ESS?
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Taxonomic housecleaning...
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by Buzztail1 on May 28, 2003
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:This canebreak/timber controversy is a perfect example of historical problems with taxonomy. Far too much importance has been placed on colour and pattern. It actually takes remarkably little genetic difference to accomplish a change in one, the other, or both. Does C. horridus look different across its range? Yes It it continous and clinal? Yes Is there a sharp or appreciable difference in the genetics? No Is it all one species with no subspecies across the range? Yes.
Very simplified, indeed. Colour, pattern, adult size and venom composition differences should account for something. I think maybe Chris Harper has a good point in comparing this to the various breeds of dogs. A Great Dane is obviously not a Yorkshire Terrier and yet they are both Canis lupus familiarus. The current trend in taxonomy seems to indicate that we should discard what we can actually observe in the field and rely SOLELY on mtDNA which can't be observed in the field. Not a refutation of the above paragraph, merely an observation.
:Of course, the situation can easily go the other way. What we are seeing now is a big clean up of taxonomy. So many historical assumptions and oversights has created a total cluster f*k.
Actually, I believe we are just seeing the penduluim swing the other way. Instead of fixing all of the taxonomic problems by incorporating newly available data, we are creating new problems which will have to be cleaned up by the next generation.
:For example, whatever wasn't an elapid or viper was a colubrid. Elaphe became a dumping ground for anything that superficially resembed a ratsnake. This of course extended to various ratsnake species being dumping grounds for snakes that upon close scruiteny were so not the same snake.
While Colubridae did become the "If not this or this, then it must be Colubridae" dumping ground, that classification was facilitated by poor definition of family.
So we ended up with a situation where things as diverse as Leioheterodon, Psammophis, Rhabdophis and Dispholidus are all 'colubrids' . This is evee though Leioheterodon (and all other Madagascar 'colubrids') and Psammophis are actually elapids, if a choice had to be made between elapids and colubrids. They are sister group to each other, then sister group to Atractaspidae, then sister group to Elapidae, then and only then do you run into other 'colubrids'.. However there are several true families there. Enhydris and Cerberus for example are nowhere near at all to the Colubrinae such as Elaphe. Rhabdophis is distinct from Colubridae as well.
I believe that the snakes you have listed became "colubrids" because they did not meet the current definition to be "elapids". For instance, it appears that one of the defining characteristics of "elapids" is "a more or less enlarged, canaliculate tooth, which is held permanently in an erect position and fits into a pocket in the gum tissue on the outside of the mandible but inside the lip when the jaw is closed." (Introduction to Herpetology, Goin & Goin, 1962, W. H. Freeman and Company) Since that definition, we have learned to work with mtDNA and look deeper than tooth structure. Do Leioheterodon, Psammophis, Rhabdophis and Dispholidus meet the tooth structure definitions of Elapidae? Probably not. So that means that we will be changing the definition of Elapidae based on mtDNA instead of observable physiology?
:So the Colubridae as a family does not exist. There are several true families in there that are in some case more genetically distinct from each other than from an elapid.
Colubridae as a family probably DOES exist. The defining principles just need to be revisited.
:If you thought the mess at the family level was impressive, keep extending it to genus level, fractioning genera like Elaphe into the true genetic diversity. The American Elaphe are more like Pituophis and Lampropeltis then they are to the Asian Elaphe. Same sort of situation is going on with the species.
Restructuring and separating American and Asian/European Elaphe is admittedly long overdue. Combining that process with mtDNA research on individually previously recognized subspecies and broadhandedly saying such things as "There is no such thing as a Yellow Rat Snake, it is just a southern phase of the Eastern Black Rat Snake." is foolishness. The snake is still yellow! That is the entire point of "COMMON names"!
:We have historically placed far far too much importance on pattern and colour. Nature however is much more clever than that. The cleverness lies in its inherent simplicity. With every clutch, there is variation. Variation that seems significant but is actually coded for by far little genetic information than we really though. So with minimal genetic changes you can have a pretty wide range of patterns and colours.
While I agree that there is quite a bit of diversity within each snake clutch, I would like to see a pair of (previously named) Yellow Rat Snakes produce a Black Rat Snake or vice versa (and I truthfully don't care how many generations the experiment goes on).
People who are touting mtDNA evidence as the end-all, be-all are overlooking that there just might be something in the clinal differences that truly makes a snake different. Perhaps it is something which will not show up in our scientific abilities until 50 years from now when we discover that mtDNA is like looking up Chin in a Chinese phone book (ie just the tip of the identification iceberg).
:What this does is gaurantee that in every clutch, at least one of the snakes has the right combination for a particular environment. So, for example, in each clutch some snakes are lighter or darker than others. The darker snakes overheat easily but also heat up easily. SO, they can survive just a little further north than the others. Over time, the snakes could extend a long way and get entirely black. Not difficult to do at all. Also, from external appearances, black = black. Lets say there are two southern snakes, totally different lines but in same genus. They both over time extend North. Same basic pressures. Over time they may occupy similar habitats (give or take a bit) and both be black at similar latitudes (assuming same general size and build). Oila. Two different species. One black snake.
Perhaps, but the point is that they are both black - not one yellow and one black.
:This is all greatly simplified of course but it should illustrate the general point. Why is alll this coming out? Because molecular biology and computing have finally met in a very useable way. Time to clean house.
Time to clean house - yes. Time to completely level and build a new neighborhood - I sincerely hope not.
Cheers
Dr. Bryan Grieg Fry
Australian Venom Research Unit
University of Melbourne.
Cheers
Karl H. Betz
Just speaking for l'il ol' me
PS It is good to see you here sharing your expertise with us, Bryan. Thanks for trying to enlighten us even in the face of such backwards beliefs as a yellow snake MUST be different than a black one. ;-) KHB
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RE: Taxonomic housecleaning...
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by BGF on May 28, 2003
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Glad to see we are all enjoying the discussion.
>I agree with the reasoning behind the first pasted sentence. However, how do you explain an approximate 50/50 ratio of yellow to black phase timbers in the northern most reaches of their distribution? Are you implying that yellow rattlesnakes are not being selected for in terms of a not-so-stable ESS?
That statement was more in reference to the parallel debate about the validity of a ratsnake species being ablee to be both yellow and black. There are of course other factors at work (such as randomness in gene recombination as well as essential items such as camoflauge). I don't know the answer to that very relevant question.
>Very simplified, indeed.
LOL
>Colour, pattern, adult size and venom composition differences should account for something.
Actually, they should account for less than we give them credit for. Colour and pattern account for little of the total DNA yet are given disproportionate weight. Obviously this is because we can see them with our own eyes. However, at the end of the day, that does not concern me. I am more interested in how similar/different the animals are. If they are easy to distinguish, bonus. If not, this does not change the fact that they are different animals. Similarly, even if regional variations in colour/pattern are evident, if the animals are genetically the same and fullfill the criterion of being a single species, then so be it. Its pretty hard to argue with the DNA. Is it more accurate? Certainly. Does it make things easier? Not necessarily. Should making things easier for field work be necessarily important to the determination of the true natural grouping? Nope.
Venom is a different story entirely. Venom evolves at a different rate and under different selection pressures from the rest of the animal. So, we can just as easily end up with a wide ranging species with significant variation in venom across its range as we can end up with two very genetically distinct species having remarkably similar venoms.
>I think maybe Chris Harper has a good point in comparing this to the various breeds of dogs. A Great Dane is obviously not a Yorkshire Terrier and yet they are both Canis lupus familiarus.
or the million bloody variants of the corn snake as well.
>The current trend in taxonomy seems to indicate that we should discard what we can actually observe in the field and rely SOLELY on mtDNA which can't be observed in the field. Not a refutation of the above paragraph, merely an observation.
When we are talking about true species then yes, we should rely on the empirical evidence rather than shallow and often arbitrary divisions based upon colour and pattern. Simply put, if the DNA work helps in the field, bloody excellent. If it doesn't, well... tough. However, often times there are other more subtle physical characteristics other than colour which help distinguish a species.
>Actually, I believe we are just seeing the penduluim swing the other way. Instead of fixing all of the taxonomic problems by incorporating newly available data, we are creating new problems which will have to be cleaned up by the next generation.
Such as?
>While Colubridae did become the "If not this or this, then it must be Colubridae" dumping ground, that classification was facilitated by poor definition of family.
Actually, there are several very very deep ancient splits that have been evolving independently ever since. It is only through the molecular data that this is finally being teased out.
>I believe that the snakes you have listed became "colubrids" because they did not meet the current definition to be "elapids". For instance, it appears that one of the defining characteristics of "elapids" is "a more or less enlarged, canaliculate tooth, which is held permanently in an erect position and fits into a pocket in the gum tissue on the outside of the mandible but inside the lip when the jaw is closed." (Introduction to Herpetology, Goin & Goin, 1962, W. H. Freeman and Company) Since that definition, we have learned to work with mtDNA and look deeper than tooth structure. Do Leioheterodon, Psammophis, Rhabdophis and
Dispholidus meet the tooth structure definitions of Elapidae? Probably not. So that means that we will be changing the definition of Elapidae based on mtDNA instead of observable physiology?
A little too much reliance has been put on dentition but as it is a much less plastic character than colour/size/pattern, it still has use. However those snakes are genetically distinct from Elapidae and thus are deserving of their own families (to which they have more or less been given names for).
>Colubridae as a family probably DOES exist. The defining principles just need to be revisited.
There are a number of distinct families in there, all with unique venoms (another long thread there.... basically that primative snakes such as pythons, boas, sunbeam snakes, file snakes, etc.) the other snakes (collectively called the 'Colubroidea' or 'advanced snakes' are inherently venomous. The venom gland has been secondarily lost in some (but not many) of the lineages (ie American genera such as Patherophis, Pituophis, Lampropeltis).
>Restructuring and separating American and Asian/European Elaphe is admittedly long overdue.
The results are quite shocking actually. It was revealed that things like the Asian snake Elaphe radiata and close relatives are not actually rat snakes all but are actually more closely genetically relasted to the some racers (Coluber being another one due for a major shakeup). This shows the problem of assigning snakes based on superficial characteristics like colour and pattern.
>Combining that process with mtDNA research on individuallypreviously recognized subspecies and broadhandedly saying such things as "There is no such thing as a Yellow Rat Snake, it is just a southern phase of the Eastern Black Rat Snake." is foolishness. The snake is still yellow! That is the entire point of "COMMON names"!
Call them what you want, it does not change the fact that they are the same animal. Why include colour in the common name? What about Eastern ratsnake, southern ratsnake, or something similar to reflect range ala the diamondbacks.
>While I agree that there is quite a bit of diversity within each snake clutch, I would like to see a pair of (previously named) Yellow Rat Snakes produce a Black Rat Snake or vice versa (and I truthfully don't care how many generations the experiment goes on).
How about green corn snakes? Striped burmese pythons? Any of this soundind familiar? Look on the Glades list for even more bizzare examples produced in only a few generations.
> People who are touting mtDNA evidence as the end-all, be-all are overlooking that there just might be something in the clinal differences that truly makes a
snake different. Perhaps it is something which will not show up in our scientific abilities until 50 years from now when we discover that mtDNA is like looking up Chin in a Chinese phone book (ie just the tip of the identification iceberg).
A proper study will of course look at more than just mitochondrial DNA. It will also look at nuclear DNA and also try to fit in morphological details as well. The study that split the American ratsnakes into the proper species also included morphological details that are more relevant to colouration but not as easily visible (but are still there if you look).
>Perhaps, but the point is that they are both black - not one yellow and one black.
But they are yellow in other parts of their range. Thats the point.
>Time to clean house - yes. Time to completely level and build a new neighborhood - I sincerely hope not.
Why not? Why continue with inaccuracies simply because of historical inertia?
>PS It is good to see you here sharing your expertise with us, Bryan. Thanks for trying to enlighten us even in the face of such backwards beliefs as a yellow snake MUST be different than a black one. ;-) KHB
LOL ;-) No worries mate. I don't claim to have all the answers. I can only claim to have a couple good questions. Wait till you see what we are doing to the entire concept of venomous snake ;-)
Cheers
B
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