Genetic Diversity in a Collection

[Krynn]

Nope,
not misleading at all. Every species behaves slightly differently,
genetics wise. Reptiles especially since they are not all that
closely related to mammals, which are our best model for why
inbreeding is bad. For example, all currently living cheetahs are
very interbred due to a natural bottleneck their species suffered
recently.

There are species who are resilient to inbreeding such as the naked mole rat. This has not been demonstrated for ball pythons. There has however, been many examples of inbreeding depression in both reptiles and amphibians. If you have have a good source that suggests otherwise, I would be very interested.

Not
true. A genetic mutation comes in three different forms, positive,
negative and NEUTRAL. Neutral mutations are slight differences in a
gene sequence that have absolutely no effect on the organism. These
happen more often than you might think.

Completely true. These are incredibly common, but I didnt think it was relevant to the explaination.

[Pythonfriend]

Originally Posted by Pythonfriend
i do believe reptiles to be somewhat more resilient when it comes to inbreeding. Resilient makes it sound like they have this super genome, they just on average have less gene that causes negative traits then more commonly bred things, like dogs and humans.

that doesnt mean that there wont be any negative consequences at all. also doesn't mean there won't be positive.

if a python has a diverse genome, its immune system will have more solutions to deal with disease. so the immune system is weakened by inbreeding. which means the BP looks completely fine, but the risks that it dies from an infection may be a bit elevated. which is something you dont notice at all, until its too late. Unless the homozygous is the solution or the heterozygous is the problem, you can't make a blanket statement like that.

another thing that happens is that fertility goes down, this is more obvious, and i have heared breeders confirm it. if you do a lot of inbreeding (lets say you are working on a triple recessive), after a while you can notice fertility in the project going down. add new blood and it goes back up. and ignore the breeders producing high fertility line bred animals or ignore the volta region ball pythons? Actually I think the volta region ball python are a great example for a few things said in this thread

so i think genetic health is a real issue. and while you can get away with ignoring it for a generation or two, you should not ignore it completely. You are assuming there are gene that produce negative traits in there. If there are none of those genes, how can there be any issues? It is quite simple, pay attention to your pairings, inbred or not. If there are negative traits, you shouldn't even be breeding the first generation, putting a generation number on it just seems silly.

so, you assume that inbreeding can have POSITIVE effects that outweigh the negative consequences, in spite of all the science that says the opposite? heterozygous: one gene can be broken, the individual is still fine. homozygous: either both are broken and you have a dead snake, or both are fine. either you roll two dice, and if you get a one on both, you lose. or you only roll one dice, and the second one is a copy of the first result, and if you get a one, you lose. whats better?

and you assume that having only one set of genes can be better than having two different sets of genes?

and you assume that the BP genome is somehow immune against ionizing radiation, carcinogens, and retroviruses? you must assume that if you want to believe that BPs dont have broken genes in their genome. if you accept that the genome of BPs is just as fragile as the genome of any other species, you have to let go of that false assumption.

and about the number of generations of inbreeding: it gets worse with each generation. and there is no possible project out there that would require more than one or two generations of inbreeding. so thats where i draw the line, 3 generations of inbreeding is excessive, because you can reach the same goal with less inbreeding.


all the assumptions you make, in order to arrive at the conclusion that inbreeding is perfectly fine no matter what, well, these assumptions contradict a lot of scientific knowledge. i could make a bunch of wild assumptions and then arrive at the conclusion that climate change is actually a good thing. i could make a bunch of wild assumptions to arrive at the conclusion that cigarettes are healthy.

i ignore cases where wildly inbred line-bred BPs are still doing fine, because when determining if smoking cigarettes is healthy or not, i also ignore cases of 105-year-old smokers. 105 year old smokers dont get that old because they smoke, and line-bred BPs that are doing fine are not doing fine because of inbreeding. they are the ones that got lucky, in spite of evidence that the risk of bad things happening is elevated, bad things didnt happen.

[Pythonfriend]

I'm not trying to spam this thread, but my second question still stands. How do keepers keep track of their snake's lineages? Do you assign a number to a particular snake and then keep track of all its offspring, assigning numbers to them too?

you need to keep the data in such a way that anything you can know about the ancestry of each individual is in the system and can be found. so, yes, giving each breeder in your collection a name, or a code that makes it unique, is useful. and then, for each breeder, you compile all the data about ancestry that you have. and now for each egg / hatchling, you just need to know what the parents are, and that gives you all the relevant data.

for an individual horse, it can look like this, and the data reveals, this horse has an inbreeding coefficient of zero:




and when you breed, you just combine the pedigrees of both parents.

[CryHavoc17]

I'm not trying to spam this thread, but my second question still stands. How do keepers keep track of their snake's lineages? Do you assign a number to a particular snake and then keep track of all its offspring, assigning numbers to them too?

Sorry for not answering your question. Typically most breeders assign a combination of letters and numbers unique to each individual snake, which will allow them to immediately identify that snake. For example a code may be lp.f.11.5 which would tell me "This is a lesser platinum morph, female, hatched in 2011 out of my 5th clutch of that year". This is just an example, everyone has their own system. would then easily be able to look at your records and identify the lineage of that snake for however many generations have been produced by you.

As far as what kind of information you get from breeders/sellers, it varies a lot. Some breeders sell their snakes with no information at all other then sex, morph, and approximate age. My minimum requirements for any seller I buy from is: accurate sex, accurate genetics, hatch date, feeding and shed data, and pairing that produced the animal. Most people selling any kind of recessive het will also provide some kind of "genetics guarantee" that may include pictures of the parent snakes.

Accurate lineages going back multiple generations is not something that most sellers typically provide in ball pythons, but some other breeders will. Usually ts a fairly high value, rare snake that is also being repersented as a locality specific animal. For example diamond pythons. They have been intergraded with other carpet pythons so much that anyone who truely has pure diamond pythons also has lineages dating back to the locality of the founding stock, and anyone willing to drop the couple grand pure diamonds cost is going to require that lineage be provided


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[sorraia]

so, you assume that inbreeding can have POSITIVE effects that outweigh the negative consequences, in spite of all the science that says the opposite? heterozygous: one gene can be broken, the individual is still fine. homozygous: either both are broken and you have a dead snake, or both are fine. either you roll two dice, and if you get a one on both, you lose. or you only roll one dice, and the second one is a copy of the first result, and if you get a one, you lose. whats better?

I'm not sure which is the case, but you are either using incorrect terminology, or you don't fully understand how genetics work.

You can't have one gene that is "broken" and another gene takes its place. Genes code for specific functions (proteins, hormones, processes, etc). If a gene is "broken", that function is not met. Another gene doesn't take over and make that function work, it just isn't done. For example, if a gene codes for the production of red blood cells, and that gene is "broken", then red blood cells won't be produced (the organism dies if those red blood cells are necessary for life). That doesn't mean there can't be two genes that code for the same function (in this example, if a second gene ALSO codes for the production of red blood cells, then the organism can live, though there could be another affect of having one of those two genes "broken", maybe a lower production of red blood cells instead of no production), but those genes would arise independently, and not to replace one another.

I think what you might be referring to are alleles. In diploid organisms, each gene has 2 alleles. HOWEVER, your terminology is still wrong. There aren't 2 alleles in case one is "broken", there are 2 alleles because there are 2 chromosomes, and those alleles interact with one another depending on whether those alleles are recessive, dominant, incomplete dominant, co-dominant, sex-linked, sex-influenced, etc. You can't have a "broken" one where the other simply takes over the function. That's not how genes, alleles, and organisms work. If something is "broken", then it isn't working the way it is supposed to.

Also, your assumption that heterozygosity is "good" and homozygosity is "bad" is incorrect. It really depends on what gene is involved, what alleles are present, and how those genes and alleles interact with each other and other genes and alleles.

I'll use two examples in humans: sickle cell anemia and blood typing. In the case of sickle cell anemia, it is a recessive gene. If a person inherits 2 sickle cell genes, they have sickle cell anemia, which is a negative trait. HOWEVER heterozygotes for this trait (one sickle cell gene, and one normal gene) are not completely normal, because the trait is not completely recessive. Those heterozygotes still have some sickle cells. This would normally be considered a negative trait (not completely healthy), EXCEPT that's not entirely true. In areas where malaria is common, that sickle cell trait is actually advantageous, thus that negative trait is not truly negative, but can be considered neither, it depends on the environment that individual lives in. The dominant homozygous individuals do not have any sickle cell traits. In this case homozygosity is neither negative nor positive (unless you consider the sickle cell trait negative in all cases, which as I pointed out with malaria is not exactly true), it is a neutral. Homozygous for the dominant allele in this specific example, simply means the person does not have any sickle cells (positive in that the person doesn't have sickle cell anemia, but potentially negative in that they are more susceptible to malaria IF they live in an area where malaria is present, if they don't live in an area where malaria is present, then it doesn't matter).

Now with blood type, there are 3 alleles for the gene coding blood type. One allele, "A" codes for "anti-B" antibodies in the plasma. Another allele, "B" codes for "anti-A" antibodies in the plasma. The third allele, designated "O" codes for both "anti-A" and "anti-B" antibodies in the plasma. The alleles that are inherited determine the individual's blood type. Blood type is neither positive nor negative, and no blood type is more fit than another in a natural world. The only time blood type matters is where a blood transfusion is necessary, and that only matters because you need to transfer the correct type of blood or the person can die (this is a medical procedure separate from the natural world and does not determine any strength or weakness that would matter in the nature). In this case, homozygosity and heterozygosity simply do not matter. These alleles don't code for negative or positive traits, they are neutral.

and you assume that having only one set of genes can be better than having two different sets of genes?

All diploid organisms have 2 chromosomes, and each chromosome has a single allele for each gene. All together that means each gene has 2 alleles. Diploid organisms do not have single "sets" of genes, nor multiple "sets" of genes. Each gene is it's own entity. Alleles are the "sets". You can have a single allele (2 alleles are the same), or you can have two different alleles (2 alleles are different). Two identical alleles (homozygous) are not worse off than two different alleles (heterozygous), neither are two different alleles better than two identical alleles. It depends on the trait in question. In some cases homozygosity is positive, in other cases it is negative, and sometimes it is neutral. In some cases heterozygosity is positive, in other cases it is negative, and sometimes it is neutral. You can't make sweeping blanket statements that homozygosity is always bad and heterozygosity is always good.

and you assume that the BP genome is somehow immune against ionizing radiation, carcinogens, and retroviruses? you must assume that if you want to believe that BPs dont have broken genes in their genome. if you accept that the genome of BPs is just as fragile as the genome of any other species, you have to let go of that false assumption.[/quote]

These types of mutations are not necessarily inheritable. If they are not inheritable, then inbreeding is irrelevant. It depends on whether these mutations occur in the germ cells or the somatic cells. If they occur in the somatic cells (in the case of UV radiation, the somatic cells are those most likely to be affected because they are those cells most likely to be exposed to the UV radiation from the sun), they are not inheritable traits. No matter how much inbreeding occurs, those somatic mutations will NEVER be passed on to the offspring. If the mutations occur in the germ cells (as may occur if you aimed a radiation gun at the gonads), then the trait is inheritable and inbreeding can potentially concentrate that mutation such that most or all individuals inherit it.

But again, mutations are not necessarily negative. Some mutations are positive. It all depends on exactly what mutation occurs and how it affects the organism.

all the assumptions you make, in order to arrive at the conclusion that inbreeding is perfectly fine no matter what, well, these assumptions contradict a lot of scientific knowledge. i could make a bunch of wild assumptions and then arrive at the conclusion that climate change is actually a good thing. i could make a bunch of wild assumptions to arrive at the conclusion that cigarettes are healthy.

Science doesn't determine inbreeding is good or bad, science determines what happens during inbreeding: genes are concentrated and homozygosity occurs. In WILD populations this is generally considered negative, because homozygosity makes it less likely a species can adapt to a new environment, new predator, new food source, or new pathogen. This is why heterozygosity is considered good in wild populations: more variety means more chance at survival. (By the way, survival is ONLY important to the species, survival of the individual is meaningless.) In captive populations this isn't important, because captive populations are not exposed to the same challenges as wild populations. This does mean a single pathogen can wipe out an entire captive population, but that's why we are also (or should be) careful about quarantine: to prevent the introduction of pathogens. Yes, introduction of a pathogen can still occur, but that doesn't mean more heterozygous captive populations are going to be better off. Depends on what the pathogen is and how susceptible the population is to that pathogen. A single pathogen can wipe out the majority of a captive population regardless how little inbreeding occurred.

As for climate change... that's a strawman argument, but as a conservation wildlife biologist, I'll entertain it for a minute. Climate change is neither negative nor positive to the natural world. To individual species it can be negative, if those species are unable to adapt to the change. It can also be positive, if the species is adapted for the change actually finds an advantage over other species. For example... As the climate gets warmer, polar bears and penguins might die out if they are unable to adapt to the warmer climate. However, other species such as some reptiles may actually thrive because they are adapted and actually do better with a warmer climate. You see... you can't make sweeping generalizations.

i ignore cases where wildly inbred line-bred BPs are still doing fine, because when determining if smoking cigarettes is healthy or not, i also ignore cases of 105-year-old smokers. 105 year old smokers dont get that old because they smoke, and line-bred BPs that are doing fine are not doing fine because of inbreeding. they are the ones that got lucky, in spite of evidence that the risk of bad things happening is elevated, bad things didnt happen.

Another strawman argument. Comparing smoking cigarettes and inbreeding or line-breeding ball pythons is like comparing apples to lichens.

[Pythonfriend]

i would say when species go extinct, thats negative. science doesnt tell us its negative, i say it is. science is neutral. its up to is to determine if its better when species go extinct, or if its better when species survive. climate change will cause mass extinction, and a conservation biologist should think thats bad.

science doesnt care if more or fewer sick and deformed snakes among the offspring is good or bad. but i say its better to have healthy hatchlings. and then science tells me that inbreeding is bad. when you think getting weakened snakes with a higher chance of genetic defects is perfectly alright, then inbreeding is perfectly alright.

BTW, the homozygous form of sicke cell anemia is lethal, the heterozygous form has the advantage of making the individual resilient against malaria, but it has the disadvantage of shortened life expectancy, a higher chance of blood vessels getting blocked, and lower oxygen transport. but if you only have one copy, at least you are not dead, because you still have one healthy copy of the gene that makes red blood cells.

and no matter how you want to put it, we generally have two healthy copies of each gene. or you could say we generally have each gene two times in two locations, which is the same, at least according to 1 + 1 = 2. if you have two copies of a gene, one can be broken and the other one can be fine. and thats generally fine, well, not in the case of sickle cell anemia, that one sucks even in the heterozygous form. im not following the semantic contortions here. the key point is that it adds redundancy, it allows individuals to survive with one broken copy of a vital gene, because one broken copy leaves them with one copy that is intact. as in 2 - 1 = 1. if each gene is its own entity, it means i have two of each, because the genes sit on the chromosomes, and i have two of each of these. basically you are trying to tell me that 2 = 1, and therefore 2 - 1 can be equal to zero. nope, not buying it.

[sorraia]

i would say when species go extinct, thats negative. science doesnt tell us its negative, i say it is. science is neutral. its up to is to determine if its better when species go extinct, or if its better when species survive. climate change will cause mass extinction, and a conservation biologist should think thats bad.

Well good thing you aren't the authority!

I haven't given my opinion on the matter one way or the other, but I will say in general conservation biologists have the opinion of whether it is good or bad depending on the organism and where it happens. The extinction of the HIV virus would generally be considered a good thing to any one, no matter who you asked (Unless there was some sick individual who thought HIV infection was a good thing...). The local extinction of the Burmese python in Florida would be considered a good thing by conservation biologists, because Burmese pythons aren't native to Florida and are considered an invasive pest. Mass extinction across the globe is generally thought by the general populations to be a bad thing, but if you start asking individual scientists, you might get different answers. Extinction of one species is what allows other species to thrive. What matters more, in terms of ecology and conservation, is how quickly and how widespread the extinction is occurring, not whether it is occurring at all. Believe it or not, there ARE conservation biologists who believe all of our human efforts to preserve some species are meaningless if that species is unable to adapt to its changing world. Allowing that species to go extinct could mean another species is able to take over that niche, and new species may evolve as a result. In the natural world, these changes occur all the time. What conservation biologists are most concerned about is the affect human activity is having on the natural world, not those processes that naturally occur. Oh and by the way, scientists by and large can't even agree on whether the current climate change is man-made, natural, or natural influenced by human activity. But that's a whole different debate in and of itself.

science doesnt care if more or fewer sick and deformed snakes among the offspring is good or bad. but i say its better to have healthy hatchlings. and then science tells me that inbreeding is bad. when you think getting weakened snakes with a higher chance of genetic defects is perfectly alright, then inbreeding is perfectly alright.

Except science doesn't say inbreeding is bad. If healthier animals is better and inbreeding can actually produce healthier animals by eliminating deleterious traits, how can you say inbreeding is always bad? Inbreeding in and of itself doesn't cause illness and weakness, inbreeding simply concentrates those genes already in existence. If there is a deleterious gene in the population, that gene should be eliminated in order to produce stronger individuals. Constant outcrossing doesn't eliminate it, but actually keeps it in the populations by potentially spreading it throughout the population. Now you don't know which animals carry that gene and which ones don't, and it is only a matter of time before the right animals are paired and that trait comes out. By inbreeding, you can concentrate that gene within your population, identify which animals carry the gene, and eliminate them from your population. You then take the healthy surviving animals, continue to breed them to relatives (not necessarily close relatives), and again eliminate those animals carrying the gene. Continue until you have essentially eliminated that deleterious trait, and now you have a healthy line of linebred or inbred animals.

BTW, the homozygous form of sicke cell anemia is lethal, the heterozygous form has the advantage of making the individual resilient against malaria, but it has the disadvantage of shortened life expectancy, a higher chance of blood vessels getting blocked, and lower oxygen transport. but if you only have one copy, at least you are not dead, because you still have one healthy copy of the gene that makes red blood cells.

Having that sickle cell trait is better than being dead, but it is also not completely healthy, even though it makes the individual less susceptible to malaria. My point is, you are claiming heterozygosity is better than homozygosity, but in this case it is not.

and no matter how you want to put it, we generally have two healthy copies of each gene.

HOw do you know we generally have two "healthy" alleles (I'm assuming you mean allele when you say "copy") for each gene? Have you done genetic typing of all individuals? That is in fact false. There are a myriad of diseases, deformities, syndromes, defects, and weaknesses in the human population, due to the fact we DO carry so many deleterious genes. The same occurs in many captive bred animals who have not been specifically selected to eliminate those deleterious traits.

or you could say we generally have each gene two times in two locations, which is the same, at least according to 1 + 1 = 2. if you have two copies of a gene, one can be broken and the other one can be fine. and thats generally fine, well, not in the case of sickle cell anemia, that one sucks even in the heterozygous form. im not following the semantic contortions here. the key point is that it adds redundancy, it allows individuals to survive with one broken copy of a vital gene, because one broken copy leaves them with one copy that is intact. as in 2 - 1 = 1. if each gene is its own entity, it means i have two of each, because the genes sit on the chromosomes, and i have two of each of these. basically you are trying to tell me that 2 = 1, and therefore 2 - 1 can be equal to zero. nope, not buying it.

Actually, no. Diploid organisms have 2 of each chromosome. In humans, that's 23 chromosome pairs, or 46 chromosomes total. Each chromosome has a single allele for a single gene. That means we have 2 alleles for each gene. We don't have 2 copies of the gene, we have 2 alleles for that gene. If we had 2 copies of the gene, that would mean we had 4 chromosomes with 4 alleles. There are no "broken" gene copies. The ONLY exception to this rule is the case of sex chromosomes, where female mammals have 2 X chromosomes and male mammals only have 1 X chromosome and 1 Y chromosome. In this case, one of the 2 X chromosomes in females is deactivated, called the "Barr body". That deactivation is random though, and if a deleterious traits is coded for on one of those two X chromosomes, it can still be expressed. (I presume there is a similar mechanism in other diploid organisms, though I have not specifically researched it.) There are no second copies of genes to take over in case one gene is "broken" as you call it.

I think the problem here is you don't understand basic genetics. There are no "broken" genes, we don't have 4 chromosomes and 2 of every gene. We have 2 chromosomes, each pair of chromosomes has an area for 1 of each gene containing 2 alleles for each gene. In total, that gives us 1 of every gene, and 2 alleles for every gene. The only exception to this rule are where mistakes happen and an organisms inherits the wrong number of chromosomes (in some cases that organisms doesn't survive).

Here's a website with the basics that might be helpful: http://history.nih.gov/exhibits/genetics/sect1a.htm

[sorraia]

and no matter how you want to put it, we generally have two healthy copies of each gene. or you could say we generally have each gene two times in two locations, which is the same, at least according to 1 + 1 = 2. if you have two copies of a gene, one can be broken and the other one can be fine. and thats generally fine, well, not in the case of sickle cell anemia, that one sucks even in the heterozygous form. im not following the semantic contortions here. the key point is that it adds redundancy, it allows individuals to survive with one broken copy of a vital gene, because one broken copy leaves them with one copy that is intact. as in 2 - 1 = 1. if each gene is its own entity, it means i have two of each, because the genes sit on the chromosomes, and i have two of each of these. basically you are trying to tell me that 2 = 1, and therefore 2 - 1 can be equal to zero. nope, not buying it.

I'm really trying to understand what you are describing without using the proper terminology. If in fact by "genes" you are referring to "alleles", you are still in correct. We don't have two alleles in two locations, we have one allele in two locations, giving two alleles total for each gene. Your math is still wrong, by saying we have each gene "two times in two locations". Two times in two locations isn't 1 + 1 = 2, that's in fact 2 + 2 = 4. We don't have four copies of each gene (or four alleles for each gene), we only have two alleles of each gene.

That said, you are are still incorrect in your assumption that the "good" allele will make up for the "broken" allele. Which by the way I hate the term "broken", because "broken" means it isn't working. A broken allele isn't working. An allele coding for a deleterious trait is still working, it isn't "broken", it just codes for something that isn't good for the organism. That being said, the "healthy" allele isn't necessarily going to be able to make up for the deleterious allele, as is the case with sickle cell anemia. That's only one example, there are hundreds of examples. The only time that deleterious allele would be unable to express itself is if it is a simple complete recessive allele (which although the sickle cell trait is recessive, it is not completely recessive, it is in fact what we can call "incompletely recessive" where it still expresses partially when paired with the dominant allele) paired with a simple complete dominant allele. In which case, the heterozygote would be as healthy as the dominant homozygote (thus homozygosity in and of itself is not "negative" or deleterious, it depends on which version of homozygosity you are looking at). In this case, inbreeding can actually be advantageous by selecting for that dominant homozygote, in which case the deleterious recessive allele would be eliminated from the population.

Here's a simplified example:

Allele Z is a complete dominant and codes for "healthy". Allele z is a complete recessive and codes for "unhealthy".
ZZ = healthy, Zz = healthy carrying the unhealthy trait, zz = unhealthy.

You have 5 unrelated animals in your population. ZZ (#1), Zz (#2), Zz (#3), Zz (#4), and zz (#5). #5 ends up being unhealthy so you eliminate it leaving you with 4 unrelated animals which you can breed together. Each pairing results in only 4 offspring.

#1 x #2 = ZZ (#6), ZZ (#7), Zz (#8), Zz (#9)
#3 x #4 = ZZ (#10), Zz (#11), Zz (#12), zz (#13)

#13 ends up being unhealthy, so you eliminate it. Now realizing you have the deleterious allele in your population, you decide to try some inbreeding to determine which animals carry that trait, and eliminate them from your population, while selecting those individuals who do not produce that trait.

You breed an offspring back to each parent, and breed two siblings together, resulting in the following pairs and resulting offspring:

#6 x #1 (offspring back to parent) = ZZ (#14), ZZ (#15), ZZ (#16), ZZ (#17) -> All healthy. Since you can't see genotypes of these animals, you don't know for sure none of them are carriers of the deleterious trait, but you can continue to work with these animals to determine if they are healthy.

#8 x #2 (offspring back to other parent) = ZZ (#18), Zz (#19), Zz (#20), zz (#21) -> You produced an unhealthy animal which you can eliminate from your population, and you have determined #2 is a carrier of that deleterious trait. You can now eliminate #2 from your population. To be safe, you eliminate all of these offspring and #8 (who must have also been a carrier to produce an unhealthy animal) from your program.

#7 x #9 (full sibling pair) = ZZ (#22), ZZ (#23), Zz (#24), Zz (#25) -> All healthy. Again you can't see the genotype so you don't know which ones are carriers, but since all animals are healthy you can continue working with them.

#10 x #3 (offspring back to parent) = ZZ (#26), ZZ (#27), Zz (#28), Zz (#29) -> All healthy. Again you can't see the genotype so you don't know which ones are carriers, but since all animals are healthy you can continue working with them.

#12 x #4 (offspring back to other parent) = ZZ (#30), Zz (#31), Zz (#32), zz (#33) -> You produced an unhealthy animal which you can eliminate from your population, and you have determined #2 is a carrier of that deleterious trait. You can now eliminate #2 from your population. To be safe, you eliminate all of these offspring and #12 (who must have also been a carrier to produce an unhealthy animal) from your program.

Now you have the following animals to continue working with:
Related Group #1: #1 (ZZ), #6 (ZZ), #7 (ZZ), #9 (Zz), #14(ZZ), #15 (ZZ), #16 (ZZ), #17 (ZZ), #22 (ZZ), #23 (ZZ), #24 (Zz), #25 (Zz)

Related Group #2: #3 (Zz), #10 (ZZ), #26 (ZZ), #27 (ZZ), #28 (Zz), #29 (Zz)

You randomly select 2 pairs from each group to breed back together for another inbred group:

#22 (ZZ) x #14 (ZZ) = #34 (ZZ), #35 (ZZ), #36 (ZZ), #37 (ZZ) -> All healthy. Again you can't see the genotype so you don't know which ones are carriers, but since all animals are healthy you can continue working with them.

#7 (ZZ) x #17 (ZZ) = #38 (ZZ), #39 (ZZ), #40 (ZZ), #41 (ZZ) -> All healthy. Again you can't see the genotype so you don't know which ones are carriers, but since all animals are healthy you can continue working with them.

#28 (Zz) x #3 (Zz) = #42 (ZZ), #43 (Zz), #44 (Zz), #45 (zz) -> You produced an unhealthy animal which you can eliminate from your population, and since #3 is one of your founding animals, you can safely presume that was one of your original carriers of the deleterious trait and eliminate it from your breeding program. To be safe, you can also eliminate all offspring in this group.

#26 (ZZ) x #10 (ZZ) = #46 (ZZ), #47 (ZZ), #48 (ZZ), #49 (ZZ) -> All healthy. Since both parents of this pairing are offspring of your founding carrier, #3, you either just got lucky and had all healthy animals, OR you managed to eliminate the deleterious trait through inbreeding. You can choose to continue working with this group, breeding offspring back to parents and siblings together to try to weed out that deleterious trait. If that deleterious trait doesn't come out, you can safely say you've eliminated it, and have at least 2 safe animals to work with, #26 and #10. You can now outcross this line to bring in other genes, then work with more linebreeding and inbreeding to eliminate any deleterious traits you might introduce in the process of outcrossing.

In this simplified example, you can see how the deleterious trait z was very effectively and quickly eliminated through very close inbreeding. Real life examples are a lot more simple because you are not getting perfect statistical ratios of genotypes, and you are working with multiple traits and polygenic traits, not single traits and single genes. However the application is similar even in real life examples. Through carefully recorded inbreeding and linebreeding, and very strict and careful selection, you can very quickly and effectively isolate and eliminate those deleterious traits from your population. You can also tease out mutations, whether desirable or undesirable, and isolate and eliminate them (if undesirable) from your population or isolate and propogate them (if desirable) in the population. This doesn't mean inbreeding and linebreeding are your only tools to work with when breeding an animal, but they are useful when used properly. You can use a machete to hack off your own arm, or you can use that machete to hack a trail through the forest to a fresh water source in order to survive.

[Krynn]

Sorraia,

Yes, sometimes populations can benefit from inbreeding. Naked mole rats are a species like this, and they can in fact suffer from outbreeding depression. This is certainly not a common strategy however.

By inbreeding, you can concentrate that gene within your population, identify which animals carry the gene, and eliminate them from your population. You then take the healthy surviving animals, continue to breed them to relatives (not necessarily close relatives), and again eliminate those animals carrying the gene. Continue until you have essentially eliminated that deleterious trait, and now you have a healthy line of linebred or inbred animals.

Do you really think that this describes captive ball pythons? I certainly hope not. Nonetheless, im sure you are aware of all of the problems that have come up in most (although I agree, not all) line bred animals.

[sorraia]

Sorraia,

Yes, sometimes populations can benefit from inbreeding. Naked mole rats are a species like this, and they can in fact suffer from outbreeding depression. This is certainly not a common strategy however.



Do you really think that this describes captive ball pythons? I certainly hope not. Nonetheless, im sure you are aware of all of the problems that have come up in most (although I agree, not all) line bred animals.

It depends entirely on the population in question, the breeder in question, their record keeping, their selections, etc. I can't speak for all captive ball pythons, I don't know about the health of all captive ball pythons. Within my own personal population of ball pythons, I have only received pedigrees for 2. Pedigrees were not offered for any of my other snakes. That leads me to believe that ball python breeders (at least those I have dealt with) either don't keep these records, or don't share these records. If these records aren't kept or aren't shared, then we really don't know about the status of the captive ball python population in terms of inbreeding, linebreeding, or outcrossing. The animals in question could be any of those, we simply don't know, it is a huge unknown.

I also don't know what kind of health selections ball python breeders make when choosing their pairs. So far the vast majority of discussion I have seen is almost entirely about color morphs and patterns. When talking to breeders, that's almost the only thing talked about. This leads me to believe ball python breeders really aren't that interested in health, but are more interested in color and pattern. I could be wrong, this is only my conclusion based on the discussions I have seen and been involved in. This is also based on the fact written pedigrees are not provided, pedigrees which could provide familial health information if records had been kept and included on those pedigrees. Since no such records have been provided to me, I can only conclude that at least in the animals I have acquired or considered acquiring, breeding for health is not a priority compared to breeding for color and pattern.

That being said, I have a lot of experience when it comes to breeding rats for health and selecting desired traits, and I can speak from my own personal experience and that of others I have worked with that inbreeding and linebreeding are VERY useful tools. In just a few short generations I was able to eliminate many health problems in my population of pet rat, as well as increase their natural life expectancy. Those breeders I worked with who chose to avoid linebreeding and inbreeding had "average" health in their rats. Some would be healthy, some would be very unhealthy, they'd have a few good litters, then suddenly have disaster. It was random, no pattern, none at all. In my rats, because I was able to achieve some homozygosity and consistency through selective and carefully recorded linebreeding and inbreeding, I not only could give reasonable guarantees on my animals, but I also knew what to expect when I made certain pairings.

Will this translate the same way in snakes? I can't say. I don't breed snakes. I don't have experience breeding snakes, and I have not been able to extensively study genetics in snakes. However if what's being said here is true, and snakes are generally more resilient to inbreeding than mammals, then I would feel comfortable saying if rats can be successful inbred and linebreed, then so too could ball pythons.

Also about those problems that have come up within inbred/linebred animals - how many of those problems were already in the population and simply concentrated BECAUSE of the inbreeding/linebreeding? That inbreeding/linebreeding didn't create those problems, it revealed them. The population had issues to begin with that were only brought out by concentrating those genes through breeding close relatives. This doesn't mean linebreeding/inbreeding should always be used for all species, or should be used to great extent, but it CAN be a very helpful tool in selection for or against certain traits.

It is very interesting to me that in these kinds of topics inbreeding/linebreeding seems to only be viewed as helpful to select for specific color mutations. Why is that its only useful application? Why can it not also be used to eliminate undesirable traits, such as poor health? That is exactly how I used it in my rats. I did not use it to select for colors (because the colors i was working with were either so common or were dominant such that I had no need to inbreed in order to produce them), I used it to eliminate undesirable traits, such as poor health.