# Exciting genetics



## intravenous (Dec 20, 2006)

Do any snake species have exciting genetics :razz:...beyond recessive, dominant or co-dominant. I.e. are there any X or Y linked genes that effect phenotype? Or any transposable elements?


Edit: I realise reptiles don't have X and Y the way we do but you get the idea...


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## intravenous (Dec 20, 2006)

Or even linked genes?


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## paulh (Sep 19, 2007)

The brindle black rat snake shows sexual dimorphism, with the female being darker than the male. (That's the way it looks in pictures; I have not seen a brindle black rat snake in the flesh.) It is possible that this is caused by sexlinkage. Female colubrids have a large Z sex chromosome and a smaller W sex chromosome, while males have two Z sex chromosome. It is possible that the two doses of brindle mutant gene in the male lightens it more than the one dose of brindle mutant gene in the females. This is what seems to happen in the autosexing pilgrim goose and autosexing faded pigeon.

I have been told that for quite a while efforts to combine Tremper albino and patternless failed, though the effort ultimately succeeded. This could be really bad luck, or it could be that the two loci are linked.

Both of these ideas need to be tested. They are guesses that I have made from things people have told me or that I have seen on the internet. If either is true, it would be a first in lizards and snakes, as far as I know.


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## intravenous (Dec 20, 2006)

paulh said:


> The brindle black rat snake shows sexual dimorphism, with the female being darker than the male. (That's the way it looks in pictures; I have not seen a brindle black rat snake in the flesh.) It is possible that this is caused by sexlinkage. Female colubrids have a large Z sex chromosome and a smaller W sex chromosome, while males have two Z sex chromosome. It is possible that the two doses of brindle mutant gene in the male lightens it more than the one dose of brindle mutant gene in the females. This is what seems to happen in the autosexing pilgrim goose and autosexing faded pigeon.
> 
> I have been told that for quite a while efforts to combine Tremper albino and patternless failed, though the effort ultimately succeeded. This could be really bad luck, or it could be that the two loci are linked.
> 
> Both of these ideas need to be tested. They are guesses that I have made from things people have told me or that I have seen on the internet. If either is true, it would be a first in lizards and snakes, as far as I know.


If snakes are anything like mammals then having something on the Z chromosome shouldn't have a double dosage effect...I guess it might be different from mammals though.

But tremper x paternless leapoard geckos? That's interesting :smile:.

Thanks for the information!


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## paulh (Sep 19, 2007)

intravenous said:


> If snakes are anything like mammals then having something on the Z chromosome shouldn't have a double dosage effect...I guess it might be different from mammals though.


Birds and colubrid snakes have sex chromosomes the reverse of mammals. Female mammals have two large X sex chromosomes. Male mammals have one large X and a smaller Y sex chromosomes.

A female colubrid snake has one large Z sex chromosome and a smaller W sex chromosome. One brindle mutant gene on the Z and none of the W chromosome makes a single dose. Male colubrid snakes have two Z chromosomes. A brindle mutant gene on each Z makes two brindle mutant genes, a double dose. As far as I know, a snake with a brindle mutant paired with a normal allele looks normal.

I'm not sure how common autosexing is in the animal kingdom. A lot rarer than ordinary sexlinkage, from what little I do know.


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## intravenous (Dec 20, 2006)

paulh said:


> Birds and colubrid snakes have sex chromosomes the reverse of mammals. Female mammals have two large X sex chromosomes. Male mammals have one large X and a smaller Y sex chromosomes.
> 
> A female colubrid snake has one large Z sex chromosome and a smaller W sex chromosome. One brindle mutant gene on the Z and none of the W chromosome makes a single dose. Male colubrid snakes have two Z chromosomes. A brindle mutant gene on each Z makes two brindle mutant genes, a double dose. As far as I know, a snake with a brindle mutant paired with a normal allele looks normal.
> 
> I'm not sure how common autosexing is in the animal kingdom. A lot rarer than ordinary sexlinkage, from what little I do know.


No, what I meant is that in mammals, when they carry two copies of the same sex chromsome (XX) one is turned off and isn't expressed. So I wondered if in snakes if would be the same (but for males instead, i.e. ZZ). If that were the case then brindle couldn't be a case of "double dose = darker".


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## Ssthisto (Aug 31, 2006)

Are you sure about that, Intravenous? I know that in order for a female cat to be visually "orange" she must carry a copy of orange on BOTH X chromosomes - if she carries black on one and orange on the other, she comes out tortoiseshell. Obviously there the colour genetics from each chromosome are being expressed....

The thing with Tremper Albino is not just with patternless, either - it's more difficult to get Blazing Blizzards (Tremper Albino + Blizzard) from a pair of hets from a first-generation cross than the 1:16 odds would imply. In practice, the odds are more like 1:256 - but if you have a related pair of hets who have a Blazing Blizzard ancestor, it seems to follow the normal 1:16 rule.


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## toyah (Aug 24, 2006)

Ssthisto said:


> Are you sure about that, Intravenous? I know that in order for a female cat to be visually "orange" she must carry a copy of orange on BOTH X chromosomes - if she carries black on one and orange on the other, she comes out tortoiseshell. Obviously there the colour genetics from each chromosome are being expressed....


In each cell of the female cat, only one gene on the X chromosome is active (have a look for x chromosome inactivation). This is why female tortie cats have patches of black and orange, as each cell is only expressing one of the two possibilities on the X chromosome.



Ssthisto said:


> The thing with Tremper Albino is not just with patternless, either - it's more difficult to get Blazing Blizzards (Tremper Albino + Blizzard) from a pair of hets from a first-generation cross than the 1:16 odds would imply. In practice, the odds are more like 1:256 - but if you have a related pair of hets who have a Blazing Blizzard ancestor, it seems to follow the normal 1:16 rule.


If Tremper is linked to both patternless and blizzard (which I am assuming are recessives?), then patternless should also show some linkage to blizzard. Is this true?


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## Ssthisto (Aug 31, 2006)

toyah said:


> In each cell of the female cat, only one gene on the X chromosome is active (have a look for x chromosome inactivation). This is why female tortie cats have patches of black and orange, as each cell is only expressing one of the two possibilities on the X chromosome.


Fair enough  I hadn't realised that that was why they expressed the colour as patches... now what I want to know is why adding the white spotting genes tends to make the patches on a Calico BIGGER rather than staying the scattered hairs/splotches on a Tortoiseshell.

Still remains that the animal _as a whole_ is expressing both X chromosomes - it'sindividual cells or structures that aren't.



> If Tremper is linked to both patternless and blizzard (which I am assuming are recessives?), then patternless should also show some linkage to blizzard. Is this true?


Well, I do know there are very few if any proven Banana Blizzard (homozygous patternless and blizzard)... lots of yellow blizzards, but I don't know how many have proven out to be homozygous for both genes via breeding trials. Certainly, again, a lot less than the 1/16 ratio for a pair of unrelated hets would imply. 

It's a shame I don't have a female Patternless to test my very yellow blizzard male against.


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## toyah (Aug 24, 2006)

Ssthisto said:


> Fair enough  I hadn't realised that that was why they expressed the colour as patches... now what I want to know is why adding the white spotting genes tends to make the patches on a Calico BIGGER rather than staying the scattered hairs/splotches on a Tortoiseshell.


The theory I read, if I remember it correctly, states that white spotting on cats (and indeed all animals) is a failure of the neural crest to properly produce the cells that produce pigmentation, so there's fewer pigment cells to start with. The fewer pigment cells there are, the less you will see the effects of x-chromosome inactivation, as there are fewer patches to "compete". X-chromosome inactivation happens near the beginning of embryonic formation, though it can occur somewhat later (producing bigger patches of pigment), or sooner (producing properly brindled tortoiseshells).



Ssthisto said:


> Still remains that the animal _as a whole_ is expressing both X chromosomes - it'sindividual cells or structures that aren't.


Quite, but there's no cumulative effect, I think was my point. I forget, I just find the whole thing quite interesting. 


Sex chromosomes in colubrids do not vary wildly in size - according to Graves and Shetty (2001) they are distinguishable only by the location of the centromere. That suggests there's not that much space for loci to exist in one sex that do not exist in the other sex.

While many colours and patterns do seem to be affected by the sex of the animal (the best example in corns - lavenders), I feel this is more likely to be due to hormonal or other factors than something as simple as sex linked genes.


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## intravenous (Dec 20, 2006)

toyah said:


> The theory I read, if I remember it correctly, states that white spotting on cats (and indeed all animals) is a failure of the neural crest to properly produce the cells that produce pigmentation, so there's fewer pigment cells to start with. The fewer pigment cells there are, the less you will see the effects of x-chromosome inactivation, as there are fewer patches to "compete". X-chromosome inactivation happens near the beginning of embryonic formation, though it can occur somewhat later (producing bigger patches of pigment), or sooner (producing properly brindled tortoiseshells).


All I know is that the orange and black are alleles of the same gene and the white patches are controlled by a different gene...II didn't know where it was or what it did so that could well be the case :razz:.



> Quite, but there's no cumulative effect, I think was my point. I forget, I just find the whole thing quite interesting.


That's what I was getting at when I said that if brindle in snakes is sex linked and if their sex chromosomes behaved the same as mammals then darker brindle wouldn't be due to sex linkage (seeing as two copies does not equal double the dose...for each patch only one dose is being expressed).


Those leopard gecko morphs sound interesting though .


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## paulh (Sep 19, 2007)

intravenous said:


> No, what I meant is that in mammals, when they carry two copies of the same sex chromsome (XX) one is turned off and isn't expressed. So I wondered if in snakes if would be the same (but for males instead, i.e. ZZ). If that were the case then brindle couldn't be a case of "double dose = darker".


  Sorry, I misunderstood. 

My understanding is that in birds, both sex chromosomes are active. So a ZZ male is lighter (not darker) than a ZW female. That's the way it works in faded pigeons and pilgrim geese. I do not know (and possibly nobody knows) whether it works the same way in colubrids. If brindle does turn out to be sexlinked, it could throw some light on the sex chromosome activation question in snakes, too.

BTW, inactivation of one of the X chromosomes in female mammals does not occur in the zygote. It happens considerably later. So one cell line has one X inactivated and a different cell line could have the other X inactivated. Which gives rise to the patchy effect in calico and tortoiseshell cats. My family has been raising calico cats for decades. Contrary to what you see in many text books, black is NOT an allele of orange. The scientific works have had it right for a long time, but many of the textbooks have not caught up.


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## intravenous (Dec 20, 2006)

paulh said:


> Sorry, I misunderstood.
> 
> My understanding is that in birds, both sex chromosomes are active. So a ZZ male is lighter (not darker) than a ZW female. That's the way it works in faded pigeons and pilgrim geese. I do not know (and possibly nobody knows) whether it works the same way in colubrids. If brindle does turn out to be sexlinked, it could throw some light on the sex chromosome activation question in snakes, too.


I don't think there are any published journals on sex chromosome inactivation in snakes...its a pity though.



> BTW, inactivation of one of the X chromosomes in female mammals does not occur in the zygote. It happens considerably later. So one cell line has one X inactivated and a different cell line could have the other X inactivated. Which gives rise to the patchy effect in calico and tortoiseshell cats. My family has been raising calico cats for decades. Contrary to what you see in many text books, black is NOT an allele of orange. The scientific works have had it right for a long time, but many of the textbooks have not caught up.


I'm not sure how much later on after fertilisation X-inactivation occurs...its obviously not at the very beginning or you would only get one X being expressed in the whole animal (which isnt the case) but I don't think its that long after fertilisation? Well before its ever considered a feotus anyway. If they aren't alleles of each other then what happens when black and orange are present on the same chromosome?


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## toyah (Aug 24, 2006)

intravenous said:


> I'm not sure how much later on after fertilisation X-inactivation occurs...its obviously not at the very beginning or you would only get one X being expressed in the whole animal (which isnt the case) but I don't think its that long after fertilisation? Well before its ever considered a feotus anyway. If they aren't alleles of each other then what happens when black and orange are present on the same chromosome?


It's a semantics thing. Preferably, the alleles on the O locus should be called something along the lines of "orange" and "non-orange" - it's just for ease of use we call them black and orange.

A dilute cat with orange and non-orange genes at the O locus will not be black and orange ... it will be blue and cream ... the non-orange gene does not produce black pigmentation, it just allows the production of melanin which can then be modified by any other number of pigmentation genes expressed in the animal.


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## intravenous (Dec 20, 2006)

toyah said:


> It's a semantics thing. Preferably, the alleles on the O locus should be called something along the lines of "orange" and "non-orange" - it's just for ease of use we call them black and orange.
> 
> A dilute cat with orange and non-orange genes at the O locus will not be black and orange ... it will be blue and cream ... the non-orange gene does not produce black pigmentation, it just allows the production of melanin which can then be modified by any other number of pigmentation genes expressed in the animal.


Ah ok :razz:, we were only taught about calico cats as an example of X-inactivation...other than that I don't actually know anything about cat genetics.


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## paulh (Sep 19, 2007)

toyah said:


> It's a semantics thing. Preferably, the alleles on the O locus should be called something along the lines of "orange" and "non-orange" - it's just for ease of use we call them black and orange.


"Wild type" or "normal" are preferable to "non-orange". Fewer characters to type, too.


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## toyah (Aug 24, 2006)

paulh said:


> "Wild type" or "normal" are preferable to "non-orange". Fewer characters to type, too.


Yes, and you can see why the general nomenclature used is orange and black - much simpler, easier, and clearer to understand!

PS the first paper my search brought up on JoH re: tortie cats (actually on fertile male tortoiseshell cats) referred to the alleles as O (orange) and o (nonorange:black).


... but back to the original question, the fact that colubrid sex chromosomes are not unequally sized (as in mammals) makes it unlikely that they have any sex linked genes. Elapids and Viperids I think have more differentiated sex chromosomes, so might be a better bet to look into?


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## intravenous (Dec 20, 2006)

toyah said:


> ... but back to the original question, the fact that colubrid sex chromosomes are not unequally sized (as in mammals) makes it unlikely that they have any sex linked genes. Elapids and Viperids I think have more differentiated sex chromosomes, so might be a better bet to look into?


Chromosome size doesn't necessarily have any bearing on gene number though...for example chromosome 19 of humans is very gene rich where as chromosome 18 has barely any and they are both roughly the same size. Genes are unevenly dispersed between chromosomes. I spoke to a member of the university who specialises in X-inactivation and she's done a lot of experiments on birds (which also have ZW) and they found that although there is some dosage compensation there isnt W-inactivation. Now I'm not sure how well a bird model could be used on reptiles but its likely that they give a more realistic view than humans?


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## toyah (Aug 24, 2006)

intravenous said:


> Chromosome size doesn't necessarily have any bearing on gene number though...for example chromosome 19 of humans is very gene rich where as chromosome 18 has barely any and they are both roughly the same size.


That is true, but sex linked genes tend to occur because the locus located on the X (or equivalent) has no homologous locus on the Y (or equivalent) chromosome - due to the uneven sizes of the chromosomes. This is not the case from what I have read in colubrids, both sex chromosomes are of equal size, so surely that means there is less scope for loci to exist on one chromosome and not the other?

Their overall size makes no difference, but the inequality is what allows us to have sex linked genes...


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## intravenous (Dec 20, 2006)

toyah said:


> That is true, but sex linked genes tend to occur because the locus located on the X (or equivalent) has no homologous locus on the Y (or equivalent) chromosome - due to the uneven sizes of the chromosomes. This is not the case from what I have read in colubrids, both sex chromosomes are of equal size, so surely that means there is less scope for loci to exist on one chromosome and not the other?
> 
> Their overall size makes no difference, but the inequality is what allows us to have sex linked genes...


Are there any genes that are homologous in the X and Y though? Or should X and Y be considered to be two completely separate chromosomes? If snake sex chromosomes behaved the same way then wouldn't that mean there would be more scope for sex linkage because there would be more non-homologous genes present to be able to mutate?


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## paulh (Sep 19, 2007)

I wasn't able to get on the web yesterday. 

My impression is that a lot of genes in the mammalian Y chromosome do not have a corresponding gene in the X chromosome. That impression came out of an article on the evolution of the Y chromosome that was printed in Scientific American within the last three years. As far as I know, sequencing would be needed to tell how similar the genomes in the Z and W chromosomes are.

By the way, pictures of chromosome preparations of king snakes and a number of other colubrids show Z and W chromosomes of different sizes. The W is large, but still smaller than the Z.


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