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Palmetto question

The thing is that an ultramel corn snake would really be no more or less of a hybrid than any non ultra/ultramel corn snake descended, even distantly, from an ultra-containing corn. If the allele was truly not derived from corn snakes and instead came from a gray rat, then sequences from the gray rat will already be dispersed throughout much our captive population.
 
DuxorW said:
What would you even look for with a palmetto corn? A restriction fragment length polymorphism? It wouldn't be cheap or trivial to prove any polymorphism you saw was from hybridization. Maybe if the palmetto locus was actually cloned (a time consuming and expensive task), the sequence of the coding region or the introns of the palmetto allele (the sequence of introns changes more rapidly during evolution, so two related species would generally show more sequence divergence in the introns than the exons) of the palmetto allele could be informative as to whether it was derived from corn snakes. The morph is new and the hets look like regular corns, I suspect it is no more of a hybrid than a wild corn snake is.

As far as the ultra mutation, the group that identified the locus responsible for amelanism in corns are sequencing the ultra allele. Depending on how thorough their analysis is, they should be able to demonstrate if it arose from a mutation in the wt corn snake allele or if it is not derived from corns.
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I believe that the palmetto morph is actually a lucistic mutation that was crossed into the corn snake genome, similar to the recent addition of the scaleless mutation, if that is the case then I should be able use the corn snake DNA map that was recently created and contrast it with that of a palmetto corn. If they prove to be (as expected; the mutation will differ reguardles of where it came from) then I will compare it with sequences from other snake species that show similar mutations--the Calic Beauty Snake being a good example.

~Beau
 
Dragonling said:
I think the origin of ultra is more worth looking into. I tend to trust Don's opinion, particularly when he's put so much effort into the palmetto project. I mean he had $12,000 riding on it just being reproducible, so you know he did ever bit of homework he could.
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The Ultra gene is another I would be interested in looking into, but I feel that the answer to wether it is intra-species specific has already been answered to my satisfaction. Regardless, should I be able to answer definitively as to the origin of the palmetto, I would definitely be interested in also confirming the Ultra.

~Beau
 
BeauBoi said:
I believe that the palmetto morph is actually a lucistic mutation that was crossed into the corn snake genome, similar to the recent addition of the scaleless mutation, if that is the case then I should be able use the corn snake DNA map that was recently created and contrast it with that of a palmetto corn. If they prove to be (as expected; the mutation will differ reguardles of where it came from) then I will compare it with sequences from other snake species that show similar mutations--the Calic Beauty Snake being a good example.

~Beau
Click to expand...

You do realize it is not this easy, right? Even with the highly fragmented genome sequence published, in order to identify the palmetto locus you would have to spend thousands of dollars and use next generation sequencing. Any corn snake you sequence will differ from the draft sequence at a ton of nucleotides that are irrelevant. You would need to map the mutation to a candidate region either by sequencing pooled samples from siblings with and without the palmetto mutation and identifying the regions that segregate only with the palmetto corns (which merely narrows your list of candidate genes), or by doing some other form of linkage analysis. Both are time consuming and expensive. Look at all the effort this group had to go through, even after sequencing the corn snake genome, just to identify the locus containing the amel mutation. They did whole exome sequencing followed by linkage analysis. But what they generated will not be that useful to you, you would essentially have to repeat their strategy.
 
DuxorW said:
You do realize it is not this easy, right? Even with the highly fragmented genome sequence published, in order to identify the palmetto locus you would have to spend thousands of dollars and use next generation sequencing. Any corn snake you sequence will differ from the draft sequence at a ton of nucleotides that are irrelevant. You would need to map the mutation to a candidate region either by sequencing pooled samples from siblings with and without the palmetto mutation and identifying the regions that segregate only with the palmetto corns (which merely narrows your list of candidate genes), or by doing some other form of linkage analysis. Both are time consuming and expensive. Look at all the effort this group had to go through, even after sequencing the corn snake genome, just to identify the locus containing the amel mutation. They did whole exome sequencing followed by linkage analysis. But what they generated will not be that useful to you, you would essentially have to repeat their strategy.
Click to expand...

I am quite aware of the processes involved. Nothing worth doing is ever "easy", however the sense of satisfaction one gains from finally answering a burning question makes it all worth while! :)

I expect that it will take years to accomplish.

~Beaux
 
DuxorW said:
You do realize it is not this easy, right? Even with the highly fragmented genome sequence published, in order to identify the palmetto locus you would have to spend thousands of dollars and use next generation sequencing. Any corn snake you sequence will differ from the draft sequence at a ton of nucleotides that are irrelevant. You would need to map the mutation to a candidate region either by sequencing pooled samples from siblings with and without the palmetto mutation and identifying the regions that segregate only with the palmetto corns (which merely narrows your list of candidate genes), or by doing some other form of linkage analysis. Both are time consuming and expensive. Look at all the effort this group had to go through, even after sequencing the corn snake genome, just to identify the locus containing the amel mutation. They did whole exome sequencing followed by linkage analysis. But what they generated will not be that useful to you, you would essentially have to repeat their strategy.
Click to expand...

Well, I did not realize it would be so complicated! I grew up reading Steven J. Gould, Biology was the only subject I cared about in HS, and I can have a basic idea about the double helix. I guess, I figured that if a hundred bucks can get you an ethnic history from "23 And Me," and about the same amount of cash will verify the dog's pedigree...

Good to know.
Thanks.
 
Distaff said:
Well, I did not realize it would be so complicated! I grew up reading Steven J. Gould, Biology was the only subject I cared about in HS, and I can have a basic idea about the double helix. I guess, I figured that if a hundred bucks can get you an ethnic history from "23 And Me," and about the same amount of cash will verify the dog's pedigree...

Good to know.
Thanks.
Click to expand...

Yeah, the human genome is very well annotated and many single nucleotide polymorphisms (SNPs) have been found that correlate with specific traits or diseases. That is what they test for with 23 and Me, they use something called a SNP array. But this required a ton of prior knowledge that we just don't have yet with the corn snake. Generating that knowledge is the expensive and time consuming part. :(
 
BeauBoi said:
I am quite aware of the processes involved. Nothing worth doing is ever "easy", however the sense of satisfaction one gains from finally answering a burning question makes it all worth while! :)

I expect that it will take years to accomplish.

~Beaux
Click to expand...

Sorry, the way you framed approaching the question made me think you didn't (I have a PhD in molecular genetics). I remain skeptical that anyone outside the field of reptile genetics/genomics will carry out such a task given the resources required and the huge financial/time commitment. Plus you are likely to be proven wrong about the palmetto mutation.
 
DuxorW said:
Sorry, the way you framed approaching the question made me think you didn't (I have a PhD in molecular genetics). I remain skeptical that anyone outside the field of reptile genetics/genomics will carry out such a task given the resources required and the huge financial/time commitment. Plus you are likely to be proven wrong about the palmetto mutation.
Click to expand...

You don't necessarily start out with hybridization probes (although, even if you did, all you are really taking about is a centrifuge and and spectrometer w/ a camera; yes equipment is expensive, if you buy it, same with computer time but that's the great thing about being a research student...).
Now that the genome has been mapped, we can start with spastical analysis of palmetto DNA samples against the mapped genome, and then work our way up from there.

I'm no molecular biologist. I am just an environmental engineer who decided to return to college after 20 years working in fossil fuel industry and agriculture R&D, but reverse-engineering is kinda what I do.

~Beau
 
But the corn snake genome is not really mapped or annotated. There are like 300,000 scaffolds. If you want to identify the palmetto locus you will have to use a next-gen sequencing and mapping approach. That is simply how spontaneous mutations must be cloned in species with poor genome assemblies.
 
Distaff said:
It is my understanding that the first Palmetto was just discovered one day in someone's yard. Aside from the distinctive stark white ground and confetti sprinkles, the feature I find most striking about this morph is the light grey iris.

This eye and the quality of the bright white, remind me a LOT of leucistic rat snakes. Now, I know that cornsnakes are ratsnakes, but the classification Pantheropis gutta (spell?) is specific to corns, and the Palmetto is marketed as a corn. Since no other cornsnake morphs look at all like the Palmetto, I am curious if that morph isn't actually a hybrid (or even a pure ratsnake?).

Does anyone have more info on this question?

Thanks.
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With the fact that Leucism is caused by a genetic mutation that prevents pigment (melanin) from being properly deposited, and it can/does happen in humans and animals, I do not think the Palemtto is a hybrid. I think it is a naturally occurring defect that was discovered (just like Albanism).

We have a herd of deer not too far from me that has a few leucistic ones in it.
 
MysticExotics said:
With the fact that Leucism is caused by a genetic mutation that prevents pigment (melanin) from being properly deposited, and it can/does happen in humans and animals, I do not think the Palemtto is a hybrid. I think it is a naturally occurring defect that was discovered (just like Albanism).

We have a herd of deer not too far from me that has a few leucistic ones in it.
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Plus I did look into it and leucism in the black rat is incomplete dominant. So that pretty much eliminates black rat as a source. I'm in agreement with you for multiple reasons.
 
DuxorW said:
Plus I did look into it and leucism in the black rat is incomplete dominant. So that pretty much eliminates black rat as a source. I'm in agreement with you for multiple reasons.
Click to expand...

Every time a new morph comes out "hybrid" is thrown around. LOL
 
MysticExotics said:
Every time a new morph comes out "hybrid" is thrown around. LOL
Click to expand...

Yep. The only only one I suspect (other than ultra, which we may actually have a definitive answer on soon) is tessera, for reasons already discussed. But it looks exactly like a corn and is so cool that I don't care if it is.
 
DuxorW said:
Yep. The only only one I suspect (other than ultra, which we may actually have a definitive answer on soon) is tessera, for reasons already discussed. But it looks exactly like a corn and is so cool that I don't care if it is.
Click to expand...

I agree. I don't think it is, but I would say Tessera is a hybrid before Palmetto.
 
DuxorW said:
Yep. The only only one I suspect (other than ultra, which we may actually have a definitive answer on soon) is tessera, for reasons already discussed. But it looks exactly like a corn and is so cool that I don't care if it is.
Click to expand...

I would be very interested to hear more about the study on "ultra". It would be nice to know if I had been lied to about them.
 
The group that identified the amel mutation is sequencing the ultra allele. Finding the locus is the hard part. After that it's relatively trivial to sequence the alleles. But it depends on what they find and if they even care about this question. The info that they publish may not be enough to resolve this question if they are not specifically addressing it. If there are polymorphisms in the allele that are present in gray rats but not in corns then that would be strong evidence. But if the differences from the corn locus are relatively minor and they don't go out of their way to look at the sequence in gray rats, then we still won't know for sure.
 
Rich Z said:
I would be very interested to hear more about the study on "ultra". It would be nice to know if I had been lied to about them.
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Rich I think you know this but for the rest of the class...Andy Barr produced the first "ultras" from his "Grey Snow" line, the line he used to promote as "frosted Cremes", Grey rat X Corn crosses...Whether or not the ultra came from the corn snake(s) used in these breedings, a grey rat(s), or it was just something that "popped up" initially in breedings has never been confirmed by him...As well as the story that there were two lines of ultra's, one pure corn, one corn/grey rat...It's plausible, but no proof has ever been forthcoming on it...I've had several conversations about them (ultras) with Mike Shivers. Andy's collection was full of "crossed" animals, per Mike. That Ultra and the Amel gene found in corns produces a visible het has always been interesting to myself. Don't know if this makes all Ultra based corns hybrids...Does make them suspect...but what isn't suspect in corn morphs anymore?...I kept "grey Snows" (aka Tequila Sunrises) for years...They were identical to "Frosted creams", but toned down some in their extreme "frosted" look...Kinda like you'd expect them to be with more corn genes than grey rat via outcrossing ;)

 
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