Your opinion on inbreeding

I've heard a variety of opinions regarding inbreeding corn snakes. I've heard some say that it's totally fine and won't result in any deformities whatsoever, while others say that you can only cross daughter to father & son to mother (not siblings). This topic has been bugging me for the past couple of days so I decided to ask about it here. What do you think?

Lisa

A lot of people inbreed. If you buy 1.1 of a morph chances are you are getting 2 siblings unless the pair is specifically labeled 'unrelated'. If you have a new snake morph pop up the usual way to prove if its genetic is to inbreed back to a parent. Or if you are working on a certain look, like I am with stripe and silver queen, you want to cross the siblings that have the look you want I am keeping a couple of pairs of siblings to experiment with this combination.
If there were no inbreeding we wouldn't have these terms like 'F2' . I think if you inbreed or line breed you do need to outcross every so often, by narrowing the pool you are also increasing the chances of recombining 'bad' genes. The inbreeding itself isn't what causes the deformities, I think its the fact the odds of the mutation showing up if its recessive increase. The mutation can be 'good' as in a new color or pattern. But it could be bad as well, so adding new bloodlines is a good way to help keep the strain robust. I don't know if this made sense or not but I hope that it helps.

My comments don't pertain to corn snakes specifically, but rather to inbreeding in general.

In the short term, inbreeding may very likely not produce any noticable problems. However, inbreeding increases homozygosity over time. This means the odds of creating offspring that are homozygous for deleterious alleles increases, because family members tend to carry the same alleles.

I don't really know what the basis is for saying it's okay to mate father->daughter or mother->son but not brother->sister as it relates to deformities. Parents are related to their offspring to the same degree that a full brother and sister are related to one another. In other words, parents share 1/2 their genes with their offspring, and full sibs (brother and sister) share 1/2 their genes. From that stand point, there is no difference in any of those crosses because they are all equally related.

A very good breeder friend of mine told me that she has inbred without seeing any ill-effects to the offspring (referring to breeding siblings to each other and father to daughter, mother to son etc)

But she did say that problems start cropping up with 4th generation inbreeding... (something like you can have kids with your cousins without ill effects but you run into problems when having kids with your parent's cousins/second cousins...?!?!?! Or something along those lines... :crazy02:

I am certainly not an expert by any stretch of the imagination so waiting to hear from those "in the know" as well! :grin01:

The inbreeding itself isn't what causes the deformities, I think its the fact the odds of the mutation showing up if its recessive increase. The mutation can be 'good' as in a new color or pattern. But it could be bad as well, so adding new bloodlines is a good way to help keep the strain robust. I don't know if this made sense or not but I hope that it helps.

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Mutations are very rare though - they happen so infrequently that it's not worth worrying about, what is worth worrying about are deleterious genes that your initial stock may carry already. By nature of the beast, genetic problems tend to be genetic (there are dominant genetic problems, but it is very easy to eliminate a dominant problem in one generation, and also animals displaying the type of genetic problems you would want to eliminate don't tend to be able to breed)

There are two main schools of thought - the first one is outcross, don't inbreed, to narrow the chances of recessive defects rearing their heads. The second way of doing things is to inbreed to make sure your animals don't carry any deleterious mutants - if they do, you can stop the line or fashion a test mating program to clear your lines of the "bad gene". The problem with just outcrossing is that in a finite world, outcrossing every generation forever is just not possible, and also, if you were breeding a line with a recessive defect in it, then by outcrossing you're producing loads of unidentified potential hets, which could end up being a problem way down the line.

Inbreeding doesn't cause genetic illness, and if you inbreed and get mutants and monsters then your original breeding stock had all those genes to cause the problems you're seeing now.

The only problem that is really caused by inbreeding is termed inbreeding depression. Once a population reaches a certain point of relatedness (I think it's due to the levels of homozygosity in the mating) then fertility decreases, clutch sizes will decrease, and the overall size of the animals can also decrease. It's impossible to say that X number of generations of inbreeding will cause inbreeding depression, and especially difficult when matings are not always brother x sister, but looser inbreedings such as aunt x nephew can skew the overall inbreeding percentage.

Unfortunately this is difficult to track in snakes as, over here at least, pedigree documents showing heritage seem to be non-existant. Just to show a comparison, in my rats I keep full family tree documents going back as many generations as possible (normally between 15-25 generations), and I have noticed that once you work out inbreeding calculations for a decent number of generations, a mating between brother and sister can actually be a lesser inbreed than a mating between two animals where there are no common names in the first three generations of the pedigree. So when you buy "unrelated pairs" of snakes - how unrelated are they really? You may find in some cases a brother-sister pair might be more genetically diverse

I'd say in the wild that chances are snakes at least will have some inbreeding as their territories are not as huge as many mammals. Rattlesnakes for instance return to the same dens to give birth and hibernate. I'm certain related animals are at some point breeding. Snake breeders use inbreeding to establish colors and morphs too and I think if used moderately, it shouldn't be a problem.

I posted this response in the Reptilescanada forum when you asked there - but thought I would repeat myself here - even if it does repeat several points made above.

I think inbreeding is of great value in a breeding program when used to achieve a goal - especially with selectively bred traits - like candycane or reverse okeetee morphs - even more than with single gene recessives that are easy to select for.

In general, inbreeding will increase homozygosity in your stock - increase the percentage of genes (both desirable and undesirable genes) that are homozygous. Uncovering these undesirable genes allows you to identify and cull them from your line. The homozygosity also means that a highly inbred line will tend to produce offspring that are more uniform in appearance than an outcrossed line. This is a real advantage if you want to produce a particular 'look' to your snakes - so people can know by looking at the parents what the offspring will grow up to look like. Close inbreeding (between siblings) for many generations is used in livestock to result in very uniform lines of stock that give consistent growth rates, carcass composition and quality - they have culled out the weak genes from these lines and only produce highest quality at this point and they are extremely genetically consistent. This is also used in developing lines of laboratory animals.

Along with increased homozygosity comes the disadvantage of what is usually termed 'inbreeding depression' - the genetics associated with things that affect general viability - feeding response, general vigor, maternal functions - all tend to get worse when overall homozygosity is increased. This is in addition to uncovering undesirable genes. This 'inbreeding depression' effect is why intermittant outcrosses are desirable to maintain vigor in the population and why you need to monitor the vigor of your stock closely if you plan to inbreed.

In my opinion, the best circumstance is to begin a breeding program with genetically diverse stock - to breed your high value single recessive genes (male) into several genetically distinct line females (all of which have the vigor, growth and other general characteristics that you want)- and then combine those lines to recover your recessive gene morph animals. These morph animals can then be combined - either morph to morph or better yet by morph to het - to get morph animals that have a very wide scope of genetic material. This genetic diversity within a group of morphs gives you a great deal of foundation material to inbreed within. You can develop one or ideally a couple lines that can then be strictly culled to achieve the 'look' you are after and as you inbreed these you will achieve greater consistency and retain the ability to outcross between your lines, without having to bring in outside 'unselected' lines - and be able to counteract the decline in vigor that comes with inbreeding.

Check back with me in another 5 years or so and I will let you know how it is progressing!! Reality doesn't always align with theory.


mary v.

A couple of obvious points:

All modern animal husbandry is based on inbreeding. Basically all the food sources we have all heavily inbred. That's why we have turkeys so heavy they can't fly and cattle that are nearly twice the bulk of their ancestors. It's a good thing. But food animals are not bred for longevity. Hopefully pet animals are.

By definition developing new morphs requires inbreeding. What I haven't seen discussed here is "Hybrid Vigor" or the tendency that multi generation inbreeding results in smaller, weaker, less healthy specimens. I bred dogs, cats, birds, and fish before acquiring the snakes. All of those species showed the negative effects of inbreeding after five generations.

It's kinda three steps forward, two steps back thing. You inbreed to establish desired traits and then outcross to get rid of the bad stuff that shows up.

My family and I like it just fine thank you.

jzal8 said:

My family and I like it just fine thank you.

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:eek1:

bill38112 said:

A couple of obvious points:

All modern animal husbandry is based on inbreeding. Basically all the food sources we have all heavily inbred. That's why we have turkeys so heavy they can't fly and cattle that are nearly twice the bulk of their ancestors.

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There is a degree of accuracy here in that one could argue that animal husbandry (more specifically, animal domestication beginning thousands of years ago) is based on inbreeding to some degree. Additionally, many plant species are highly inbred.
However, turkeys so fat they can't fly aren't necessarily the result of inbreeding. It's important to make the distinction between artificial selection/selective breeding and inbreeding.

bill38112 said:

What I haven't seen discussed here is "Hybrid Vigor" or the tendency that multi generation inbreeding results in smaller, weaker, less healthy specimens. I bred dogs, cats, birds, and fish before acquiring the snakes. All of those species showed the negative effects of inbreeding after five generations.

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This may be a valid observation and I'm not discounting that you observed it, but it does depend on at least a few factors. The species in question, individual's relatedness, and the initial frequency of homozygotes all can change how soon you will notice things. A group of animals that have high heterozygosity to begin with are going to take longer to show inbreeding depression. Some populations will take less time depending on their initial size. :eek1:

bill38112 said:

All modern animal husbandry is based on inbreeding. Basically all the food sources we have all heavily inbred. That's why we have turkeys so heavy they can't fly and cattle that are nearly twice the bulk of their ancestors. It's a good thing. But food animals are not bred for longevity. Hopefully pet animals are.

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The examples you cite are not because of inbreeding - they're because of human selection, and one of the methods of selective breeding is inbreeding. A nit-picky distinction, but an important one all the same. Careful inbreeding can also be used to extend lifespan though - it all depends what you're selecting for.

bill38112 said:

By definition developing new morphs requires inbreeding. What I haven't seen discussed here is "Hybrid Vigor" or the tendency that multi generation inbreeding results in smaller, weaker, less healthy specimens. I bred dogs, cats, birds, and fish before acquiring the snakes. All of those species showed the negative effects of inbreeding after five generations.

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Hybrid vigor is the absolute opposite of inbreeding depression (which is what you describe), and inbreeding depression has been mentioned in this thread already. I disagree that after five generations you necessarily can see the negative aspects of inbreeding - do you mean five generations brother x sister, or looser breedings than that - and if the matings are not as close as bro-sis then how can you decide it definitely causes problems after five generations?

I don't really know what the basis is for saying it's okay to mate father->daughter or mother->son but not brother->sister as it relates to deformities. Parents are related to their offspring to the same degree that a full brother and sister are related to one another. In other words, parents share 1/2 their genes with their offspring, and full sibs (brother and sister) share 1/2 their genes. From that stand point, there is no difference in any of those crosses because they are all equally related.

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Not quite.
Because of the way genes mix up in gametes, an offspring always has 1/2 of its genes from its parent, but may have MORE than 1/2 of its genes in common with a sibling. To take an extreme example, identical twins share 100% of their DNA with eachother, but only 50% with mom or dad. You have anywhere from 0%* to 100% of your DNA in common with your sibling, though on average it will be somewhere in the middle.

That's why it's sometimes preferrable to pair an offspring with a parent, rather than a sibling. Let's take the example of a parent carrying a recessive gene X, which by itself is harmless. Let's say there's another gene, Y, which also by itself is harmless. But when X and Y are homozygous in the same animal, the offspring dies in the egg. Parent A is XXYy (het for y), Parent B is XxYY (het for x). The offspring will be a mix of XXYY, XxYY, XXYy, and XxYy. Obviously the XXYY's are fully healthy and will never produce deformed offspring. The XxYY and XXYy snakes are likewise fine, because their offspring will never produce the double-homozygous form needed for offspring death. It's only the XxYy snakes that have a potential for disaster. But if the XxYy snake gets bred to either parent, the offspring will all still be healthy. If the XxYy snake gets bred to an XXYY, XxYY, or XXYy sibling, all the offspring will also be healthy. But if the XxYy snake gets bred to another XxYy snake by accident, you will get some dead offspring. (This is a ficticious example designed to illustrate the theory, for those who are wondering.)

Conversely, if x and y were amel and anery, you'd want to breed siblings if you wanted snows out of the mix. It's simply the same theory in reverse.

-Kat

*I'm referring to the areas of DNA which differ between individuals in a species. There's a large percentage of DNA which is identical between members of the same species, so the percentage of total DNA that differs between siblings will actually be quite small... but for the part we care about, the explaination holds.

Kat said:

Not quite.
Because of the way genes mix up in gametes, an offspring always has 1/2 of its genes from its parent, but may have MORE than 1/2 of its genes in common with a sibling. To take an extreme example, identical twins share 100% of their DNA with eachother, but only 50% with mom or dad. You have anywhere from 0%* to 100% of your DNA in common with your sibling, though on average it will be somewhere in the middle.



*I'm referring to the areas of DNA which differ between individuals in a species. There's a large percentage of DNA which is identical between members of the same species, so the percentage of total DNA that differs between siblings will actually be quite small... but for the part we care about, the explaination holds.

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I was exlcuding identical twins. There is always the chance that sibs don't fit the .5 average, but unless we know the genetic makeup of the individuals our best estimate is r=.5. In any equations or calculations one would never randomly assume r to be equal to .325 or .768. I just feel like the average is more useful to illustrate the point.
A parent may have exactly 50% in common with it's offspring, but statistically, a brother or sister has 50% in common as well. I don't know if I'm making sense or not. I'm just saying that deviations from .5 for full sibs is not the norm, and the best value we can use in everyday talk about relatedness is the average or .5.

Zach, my point is it's the fact that it CAN differ that causes the difference (however slight it may be) between offspring to parent and sibling to sibling pairings.

It's like the difference between .00001 and 0. Sure, .00001 is pretty close to 0, and for most applications it doesn't matter which one you use, but if someone asks you what the difference between .0001 and 0 is, responding that "They're both the same." is wrong. And more importantly, it's not a useful answer.

-Kat

Kat said:

Zach, my point is it's the fact that it CAN differ that causes the difference (however slight it may be) between offspring to parent and sibling to sibling pairings.

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Agreed.

It's like the difference between .00001 and 0. Sure, .00001 is pretty close to 0, and for most applications it doesn't matter which one you use, but if someone asks you what the difference between .0001 and 0 is, responding that "They're both the same." is wrong. And more importantly, it's not a useful answer.

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I just feel like you're analogy is misleading. I'm really not just trying to be difficult or argumentative. Using a value of r=.5 to describe full sibs is not the same as what you are suggsting. Using such a value is certainly more proper than just picking an arbitrary value between 0 and 1. Of course, this method may be based on a certain assumption, but how many theories/calculations/etc in biology are based on assumptions but still widely used because they generally hold true under a wide range of circumstances. Hardy-Weinberg takes making many assumptions that could change the numerical outcome, but it is still is a very useful tool for making inferences (even when some of those assumptions are violated).

I agree that we should always use the correct/absolute values when we know them. My point is that, when we don't know the specific relatedness of two full sibs, they are typically designated as being .5 because that is the most accurate estimation we can use. It's true that the value may actually deviate from the mean, but we don't know that for sure and so we don't just randomly assign some value as the relatedness.

My point is that, when we don't know the specific relatedness of two full sibs, they are typically designated as being .5 because that is the most accurate estimation we can use.

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My point is that the original question was what the difference between parent->offspring and sibling->sibling was. In this case, using the approximation of .5 for sibling relatedness is incorrect, because it doesn't show the difference. For MOST applications you can use .5 because it simplifies things. But in this case, you cannot. It is not useful to say that parent->offspring and sibling->sibling pairings are identical, because they are NOT identical. For parent->offspring comparisons, the percentage of genes related is ALWAYS .5. For sibling->sibling comparisons, the percentage of genes related is ALMOST NEVER EXACTLY .5, but more than likely something close to that number.

-Kat

The degree of relatedness, or shared genes is going to be an inexact quantity, given that you will never know the exact degree of relatedness of the original pair.
Inbreeding, whether parent to offspring or between siblings is going to increase the degree of shared genes over generations, this will increase the chance of desirable traits being reproduced, which is why it's such common practise in animal breeding. It will only increase the chances of genetic defects if those defects are present in the original stock.
Unfortunately the presence of 'bad genes' isn't something you'll know about until they are expressed, but it's seen as a chance worth taking to improve most domestic stock, be it poultry, cattle etc or pets

Kat said:

My point is that the original question was what the difference between parent->offspring and sibling->sibling was. In this case, using the approximation of .5 for sibling relatedness is incorrect, because it doesn't show the difference. For MOST applications you can use .5 because it simplifies things. But in this case, you cannot. It is not useful to say that parent->offspring and sibling->sibling pairings are identical, because they are NOT identical. For parent->offspring comparisons, the percentage of genes related is ALWAYS .5. For sibling->sibling comparisons, the percentage of genes related is ALMOST NEVER EXACTLY .5, but more than likely something close to that number.

-Kat

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Okay, now we're getting somewhere! Would you agree that any given full sib pair is just as likely to have r<.5 as they are likely to have r>.5? From that perspective, wouldn't it be inaccurate to say that a parent->offspring mating is necessarily "safer" than a full sib mating?

My, people do like to make things difficult. To clarify my previous remarks:

In breeding is a form of selective breeding and ALL animal Husbandry uses it. The Cat Fanciers Association is 100 years old this year; The American Kennel Club is 126 years old; As Bill Love's excellent documentary, REPTILEMANIA, points out, the domestication of snakes is in its infancy. There are almost no studies on snake genetics available. I am, therefore, relying on almost 40 years of my personal experience and research with other species.

As for the application of selective breeding and in breeding (and by in breeding I mean brother/sister and parent/offspring pairings. Less closely related pairings, I consider line breeding). In breeding specimens with the visible desired trains will produce the trait in off spring more reliably than when breeding unrelated specimens exhibiting the trait. I stand by the turkey and cattle example.

As for the discussion of hybrid vigor or "inbreeding depression" I suspect that there are very few of you out there who have five generations of your own breeding to test my theory. I am basing the five generation rule on a study done with birds by the San Diego Zoo in the 70's. I found that data to be reliable in dogs, cats, birds and fish, all of which I have bred to the fifth generation or more. As far as the hetero/homo-zygosity of your initial population, tell me, who has viability data on their snakes for even three generations? The five generation rule is based on the "probability" that fertility, viability issues OTHER THAN specific disease will manifest within five generations.

Bottomline, In breed to develop the traits you want, then line breed to maintain that trait, with an occasional outcross to maintain vigor.

bill38112 said:

As for the discussion of hybrid vigor or "inbreeding depression" I suspect that there are very few of you out there who have five generations of your own breeding to test my theory. I am basing the five generation rule on a study done with birds by the San Diego Zoo in the 70's. I found that data to be reliable in dogs, cats, birds and fish, all of which I have bred to the fifth generation or more. As far as the hetero/homo-zygosity of your initial population, tell me, who has viability data on their snakes for even three generations? The five generation rule is based on the "probability" that fertility, viability issues OTHER THAN specific disease will manifest within five generations.

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One study hardly makes it a rule. Personally, in all seriousness, I would love to read the findings of that study if you have a link or article title. 3 generations of viability data? Well, I'm sure there are lots of members who have stats of such things. Many members track how many fertile and infertile eggs they have, hatchling deaths, etc... Do they have the same degree of inbreeding as you are proposing? No, probably not quite as much. Changing the subject to viability does nothing to address the issue of intitial hetero and homozygosity. I believe it would have been more accurate to say "The five generation rule is based on the assumption that fertility, viability issues OTHER THAN specific disease will manifest within five generations." because a few limited observations just doesn't establish a "probability".

There's no precedent to warrant saying that "There is a probability that x or y issues will be present by generation 5." At least not based on such limited observations. Like I said before, I'm not discounting that you observed such things. It wouldn't make any sense for you to lie about it, especially if people like me are gonna give you a hard time It's just that when I feel like something is being misrepresented, I want to put my .02 in. I just felt that implying rules or probabilities based on limited info is premature.

And to go so far as to even give your own theory support...absence of evidence is not evidence of absence. There may well be some such thing as a 5 or 10 generation rule with certain species when it's applied to certain parameters such as some sort of viability or whatever. However, I still believe that it would be at least partly dependent on the species in questions and the intial population size and genetic structure.